outline - University of Edinburgh - Millard infinite campus

Title: Predicting the structure of soil communities from plant community taxonomy, phylogeny, and traitsShort running title: Associations between soil and plant communitiesAuthors: Jonathan W. Leff1,2, Richard D. Bardgett3, Anna Wilkinson3, Benjamin G. Jackson4, William J. Pritchard3, Jonathan R. De Long3, Simon Oakley5, Kelly E. Mason5, Nicholas J. Ostle6, David Johnson3, Elizabeth M. Baggs7, and Noah Fierer1,2*Affiliations:1Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA2Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA3School of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, UK.4School of Geosciences, Grant Institute, The King’s Buildings, James Hutton Road, Edinburgh, EH9 3FE, UK5Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, UK6Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK7The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG Buildings, UK*Corresponding author:Noah FiererUniversity of ColoradoCooperative Institute for Research in Environmental SciencesUCB 216, CIRES Bldg. Rm. 318Boulder, CO 80309-0216 USATelephone number: 303-492-5615E-mail: Noah.Fierer@colorado.eduSources of financial support: The UK Biotechnology and Biological Sciences Research Council and the U.S. National Science Foundation.Subject category: Microbial population and community ecologyConflicts of interest: The authors declare no conflict of interest.AbstractThere are numerous ways in which plants can influence the composition of soil communities. However, it remains unclear whether information on plant community attributes, including taxonomic, phylogenetic, or trait-based composition, can be used to predict the structure of soil communities. We tested, in both monocultures and field-grown mixed temperate grassland communities, whether plant attributes predict soil communities including taxonomic groups from across the tree of life (fungi, bacteria, protists, and metazoa). The composition of all soil community groups was affected by plant species identity, both in monocultures and in mixed communities. Moreover, plant community composition predicted additional variation in soil community composition beyond what could be predicted from soil abiotic characteristics. In addition, analysis of the field aboveground plant community composition and the composition of plant roots suggests that plant community attributes are better predictors of soil communities than root distributions. However, neither plant phylogeny nor plant traits were strong predictors of soil communities in either experiment. Our results demonstrate that grassland plant species form specific associations with soil community members and that information on plant species distributions can improve predictions of soil community composition. These results indicate that specific associations between plant species and complex soil communities are key determinants of biodiversity patterns in grassland soils.IntroductionThe interactions between plants and soil organisms can have important ramifications for ecosystem functioning and plant community dynamics, but the extent to which these interactions influence the spatial distributions of soil communities remains poorly understood. Knowing how plants control the spatial variation in belowground communities is important for building a predictive understanding of the heterogeneity in soil communities and contributing to pre-existing research that has identified how certain site and abiotic soil properties can influence the spatial variation in soil communities across large geographic scales ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/j.1461-0248.2009.01360.x", "ISBN" : "1461-0248 (Electronic)\\r1461-023X (Linking)", "ISSN" : "1461-0248", "PMID" : "19674041", "abstract" : "Although belowground ecosystems have been studied extensively and soil biota play integral roles in biogeochemical processes, surprisingly we have a limited understanding of global patterns in belowground biomass and community structure. To address this critical gap, we conducted a meta-analysis of published data (> 1300 datapoints) to compare belowground plant, microbial and faunal biomass across seven of the major biomes on Earth. We also assembled data to assess biome-level patterns in belowground microbial community composition. Our analysis suggests that variation in microbial biomass is predictable across biomes, with microbial biomass carbon representing 0.6-1.1% of soil organic carbon (r(2) = 0.91) and 1-20% of total plant biomass carbon (r(2) = 0.42). Approximately 50% of total animal biomass can be found belowground and soil faunal biomass represents < 4% of microbial biomass across all biomes. The structure of belowground microbial communities is also predictable: bacterial community composition and fungal : bacterial gene ratios can be predicted reasonably well from soil pH and soil C : N ratios respectively. Together these results identify robust patterns in the structure of belowground microbial and faunal communities at broad scales which may be explained by universal mechanisms that regulate belowground biota across biomes.", "author" : [ { "dropping-particle" : "", "family" : "Fierer", "given" : "Noah", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Strickland", "given" : "Michael S.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Liptzin", "given" : "Daniel", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bradford", "given" : "Mark a.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Cleveland", "given" : "Cory C.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Ecology Letters", "id" : "ITEM-1", "issue" : "11", "issued" : { "date-parts" : [ [ "2009", "11" ] ] }, "page" : "1238-1249", "title" : "Global patterns in belowground communities", "type" : "article-journal", "volume" : "12" }, "uris" : [ "" ] }, { "id" : "ITEM-2", "itemData" : { "DOI" : "10.1038/ismej.2012.147", "ISBN" : "1751-7362", "ISSN" : "1751-7362", "PMID" : "23235291", "abstract" : "Aim The biogeography and global distribution of protists has long been disputed, with two primary, opposing views. To test these two sets of views in greater detail, we have compiled the available data for marine benthic ciliates and assessed the general patterns of their diversity and distribution compared with Metazoa. Location World-wide. Methods A comprehensive database (1342 species, over 350 sources) was used to analyse the diversity, distribution, species occurrences and range size distribution of free-living ciliates that inhabit marine sediments in 17 geographical regions. Results Twenty-five per cent of the species have been found in a single region only, whereas 18% are widespread (they occur in more than half the regions covering both hemispheres). Only 5\u20137% of regional faunas are endemic, which is much lower than for macroorganisms. Regional diversity depends neither on total area nor on coastline length and does not show any obvious latitudinal trends, but correlates highly with the investigation effort expended in a region and (negatively) with the average salinity. A comparison of species composition reveals distinctions between the Arctic Area (the White, Barents and Kara seas), Laurasian Area (north Atlantic, north Pacific and European seas), Gondwanian Area (Southern Ocean) and the Antarctic. No clear geographical correlations are found for faunistic com-position at the genus or family levels. There is the tendency to narrow the latitudinal ranges for species found at high latitudes (reversal of Rapoport's rule). Main conclusions Undersampling and data insufficiency are the key factors affecting the observed diversity and distribution of microorganisms. Nevertheless, marine benthic ciliates demonstrate certain patterns that generally agree with the 'moderate endemicity' model (Foissner, 2004, 2008), but consistently contradict the regularities commonly observed for multicellular taxa. Thus, ciliates do have a biogeography, but their macroecological patterns may be different in some respects from that of macroorganisms.", "author" : [ { "dropping-particle" : "", "family" : "Bates", "given" : "Scott T", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Clemente", "given" : "Jose C", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Flores", "given" : "Gilberto E", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Walters", "given" : "William Anthony", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Parfrey", "given" : "Laura Wegener", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Knight", "given" : "Rob", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Fierer", "given" : "Noah", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "The ISME Journal", "id" : "ITEM-2", "issue" : "3", "issued" : { "date-parts" : [ [ "2013" ] ] }, "page" : "652-659", "title" : "Global biogeography of highly diverse protistan communities in soil", "type" : "article-journal", "volume" : "7" }, "uris" : [ "" ] }, { "id" : "ITEM-3", "itemData" : { "DOI" : "10.1126/science.1256688", "ISSN" : "0036-8075", "author" : [ { "dropping-particle" : "", "family" : "Tedersoo", "given" : "L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bahram", "given" : "M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Polme", "given" : "S.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Koljalg", "given" : "U.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Yorou", "given" : "N. 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Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management. Soil bacteria play an important role in biogeochemical cycles 1,2 . They control soil processes such as decompo-sition 3 and mineralization, including the associated release of greenhouse gases such as carbon dioxide (CO 2), nitrous oxide (N 2 O), and methane (CH 4) 4,5 into the atmosphere. Moreover, several soil bacteria promote plant growth and productivity 2,6 . As soil represents a highly dynamic and complex environment, bacterial communi-ties living in this ecosystem are influenced by a multitude of different biotic and abiotic factors. Previous studies showed that soil pH is a major driver of these communities 7\u20139 . Lauber and colleagues 8 observed that the overall bacterial community composition in different soils from across South and North America was significantly cor-related with soil pH. This was confirmed by a study of bacterial communities in German grassland and forest soils 9 . Other studies investigating the effect of edaphic parameters on soil bacteria found that these communities were influenced by the availability of nutrients such as carbon, nitrogen 10,11 , and soil moisture in grasslands 12 and forests 13 . In recent years, the impact of land use intensifica\u2026", "author" : [ { "dropping-particle" : "", "family" : "Kaiser", "given" : "Kristin", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Wemheuer", "given" : "Bernd", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Korolkow", "given" : "Vera", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Wemheuer", "given" : "Franziska", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Nacke", "given" : "Heiko", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Sch\u00f6ning", "given" : "Ingo", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Schrumpf", "given" : "Marion", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Daniel", "given" : "Rolf", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Scientific Reports", "id" : "ITEM-4", "issued" : { "date-parts" : [ [ "2016" ] ] }, "page" : "33696", "title" : "Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests", "type" : "article-journal", "volume" : "6" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Fierer et al., 2009; Bates et al., 2013; Tedersoo et al., 2014; Kaiser et al., 2016)", "plainTextFormattedCitation" : "(Fierer et al., 2009; Bates et al., 2013; Tedersoo et al., 2014; Kaiser et al., 2016)", "previouslyFormattedCitation" : "(Fierer et al., 2009; Bates et al., 2013; Tedersoo et al., 2014; Kaiser et al., 2016)" }, "properties" : { }, "schema" : "" }(Fierer et al., 2009; Bates et al., 2013; Tedersoo et al., 2014; Kaiser et al., 2016). Further, this information will aid our ability to probe the undescribed and likely diverse ways in which soil organisms interact with plants since comparatively few plant-microbe interactions are well understood ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/1365-2745.12054", "ISBN" : "1365-2745", "ISSN" : "00220477", "PMID" : "1021606268291538410", "abstract" : "Summary 1. Plant \u2013 soil feedbacks is becoming an important concept for explaining vegetation dynamics, the invasiveness of introduced exotic species in new habitats and how terrestrial ecosystems respond to global land use and climate change. 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Certain soil organisms are known to form close associations with particular plant species ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1126/science.1094875", "ISSN" : "1095-9203", "PMID" : "15192218", "abstract" : "All terrestrial ecosystems consist of aboveground and belowground components that interact to influence community- and ecosystem-level processes and properties. Here we show how these components are closely interlinked at the community level, reinforced by a greater degree of specificity between plants and soil organisms than has been previously supposed. As such, aboveground and belowground communities can be powerful mutual drivers, with both positive and negative feedbacks. A combined aboveground-belowground approach to community and ecosystem ecology is enhancing our understanding of the regulation and functional significance of biodiversity and of the environmental impacts of human-induced global change phenomena.", "author" : [ { "dropping-particle" : "", "family" : "Wardle", "given" : "David A", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Klironomos", "given" : "John N", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Set\u00e4l\u00e4", "given" : "Heikki", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Putten", "given" : "Wim H", "non-dropping-particle" : "van der", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Wall", "given" : "Diana H", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Science", "id" : "ITEM-1", "issue" : "5677", "issued" : { "date-parts" : [ [ "2004", "6", "11" ] ] }, "page" : "1629-33", "title" : "Ecological linkages between aboveground and belowground biota", "type" : "article-journal", "volume" : "304" }, "uris" : [ "" ] }, { "id" : "ITEM-2", "itemData" : { "author" : [ { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Wardle", "given" : "David A", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "id" : "ITEM-2", "issued" : { "date-parts" : [ [ "2010" ] ] }, "publisher" : "Oxford University Press Oxford", "publisher-place" : "New York, NY, USA", "title" : "Aboveground-belowground linkages: biotic interactions, ecosystem processes, and global change", "type" : "book" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Wardle et al., 2004; Bardgett and Wardle, 2010)", "plainTextFormattedCitation" : "(Wardle et al., 2004; Bardgett and Wardle, 2010)", "previouslyFormattedCitation" : "(Wardle et al., 2004; Bardgett and Wardle, 2010)" }, "properties" : { }, "schema" : "" }(Wardle et al., 2004; Bardgett and Wardle, 2010). Mycorrhizal relationships, for instance, involve a direct exchange of nutrients between plants and symbiotic soil fungi, and these relationships can influence plant-soil diversity linkages ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "author" : [ { "dropping-particle" : "", "family" : "Heijden", "given" : "Marcel G A", "non-dropping-particle" : "van der", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Klironomos", "given" : "John N", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Ursic", "given" : "Margot", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Moutoglis", "given" : "Peter", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Streitwolf-Engel", "given" : "Ruth", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Boller", "given" : "Thomas", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Wiemken", "given" : "Andres", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Sanders", "given" : "Ian R", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Nature", "id" : "ITEM-1", "issue" : "6706", "issued" : { "date-parts" : [ [ "1998" ] ] }, "page" : "69-72", "publisher" : "Nature Publishing Group", "title" : "Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity", "type" : "article-journal", "volume" : "396" }, "uris" : [ "" ] }, { "id" : "ITEM-2", "itemData" : { "DOI" : "10.1111/nph.12765", "ISBN" : "1469-8137", "ISSN" : "14698137", "PMID" : "24641509", "abstract" : "Although experiments show a positive association between vascular plant and arbuscular mycorrhizal fungal (AMF) species richness, evidence from natural ecosystems is scarce. Furthermore, there is little knowledge about how AMF richness varies with belowground plant richness and biomass. We examined relationships among AMF richness, above- and belowground plant richness, and plant root and shoot biomass in a native North American grassland. Root-colonizing AMF richness and belowground plant richness were detected from the same bulk root samples by 454-sequencing of the AMF SSU rRNA and plant trnL genes. In total we detected 63 AMF taxa. Plant richness was 1.5 times greater belowground than aboveground. AMF richness was significantly positively correlated with plant species richness, and more strongly with below- than aboveground plant richness. Belowground plant richness was positively correlated with belowground plant biomass and total plant biomass, whereas aboveground plant richness was positively correlated only with belowground plant biomass. By contrast, AMF richness was negatively correlated with belowground and total plant biomass. Our results indicate that AMF richness and plant belowground richness are more strongly related with each other and with plant community biomass than with the plant aboveground richness measures that have been almost exclusively considered to date.", "author" : [ { "dropping-particle" : "", "family" : "Hiiesalu", "given" : "Inga", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "P\u00e4rtel", "given" : "Meelis", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Davison", "given" : "John", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Gerhold", "given" : "Pille", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Metsis", "given" : "Madis", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Moora", "given" : "Mari", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "\u00d6pik", "given" : "Maarja", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Vasar", "given" : "Martti", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Zobel", "given" : "Martin", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Wilson", "given" : "Scott D.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "New Phytologist", "id" : "ITEM-2", "issue" : "1", "issued" : { "date-parts" : [ [ "2014" ] ] }, "page" : "233-244", "title" : "Species richness of arbuscular mycorrhizal fungi: Associations with grassland plant richness and biomass", "type" : "article-journal", "volume" : "203" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(van der Heijden et al., 1998; Hiiesalu et al., 2014)", "plainTextFormattedCitation" : "(van der Heijden et al., 1998; Hiiesalu et al., 2014)", "previouslyFormattedCitation" : "(van der Heijden et al., 1998; Hiiesalu et al., 2014)" }, "properties" : { }, "schema" : "" }(van der Heijden et al., 1998; Hiiesalu et al., 2014). Indirect mechanisms, such as the release of root exudates and microbial attraction to those exudates, can also drive associations between specific microbes and plant species ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1016/j.tim.2004.06.008", "ISSN" : "0966842X", "author" : [ { "dropping-particle" : "", "family" : "Singh", "given" : "Brajesh K.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Millard", "given" : "Peter", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Whiteley", "given" : "Andrew S.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Murrell", "given" : "J.Colin", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Trends in Microbiology", "id" : "ITEM-1", "issue" : "8", "issued" : { "date-parts" : [ [ "2004" ] ] }, "page" : "386-393", "title" : "Unravelling rhizosphere\u2013microbial interactions: opportunities and limitations", "type" : "article-journal", "volume" : "12" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Singh et al., 2004)", "plainTextFormattedCitation" : "(Singh et al., 2004)", "previouslyFormattedCitation" : "(Singh et al., 2004)" }, "properties" : { }, "schema" : "" }(Singh et al., 2004). However, these described interactions are likely only a small fraction of the numerous interactions among plants and soil organisms in a given ecosystem. Thus, it is uncertain whether the composition of soil communities as a whole is associated with plant community attributes under field conditions.It has long been known that individual plant species can exert a powerful influence on soil microbial communities ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "author" : [ { "dropping-particle" : "", "family" : "Grayston", "given" : "Susan J", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Wang", "given" : "Shenquiang", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Campbell", "given" : "Colin D", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Edwards", "given" : "Anthony C", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Soil Biology and Biochemistry", "id" : "ITEM-1", "issue" : "3", "issued" : { "date-parts" : [ [ "1998" ] ] }, "page" : "369-378", "title" : "Selective influence of plant species on microbial diversity in the rhizosphere", "type" : "article-journal", "volume" : "30" }, "uris" : [ "" ] }, { "id" : "ITEM-2", "itemData" : { "DOI" : "10.1111/j.1574-6941.2009.00654.x", "ISBN" : "0168-6496", "ISSN" : "01686496", "PMID" : "19243436", "abstract" : "The rhizosphere is of central importance not only for plant nutrition, health and quality but also for microorganism-driven carbon sequestration, ecosystem functioning and nutrient cycling in terrestrial ecosystems. A multitude of biotic and abiotic factors are assumed to influence the structural and functional diversity of microbial communities in the rhizosphere. In this review, recent studies on the influence of the two factors, plant species and soil type, on rhizosphere-associated microbial communities are discussed. Root exudates and the response of microorganisms to the latter as well as to root morphology were shown to shape rhizosphere microbial communities. All studies revealed that soil is the main reservoir for rhizosphere microorganisms. Many secrets of microbial life in the rhizosphere were recently uncovered due to the enormous progress in molecular and microscopic tools. Physiological and molecular data on the factors that drive selection processes in the rhizosphere are presented here. Furthermore, implications for agriculture, nature conservation and biotechnology will also be discussed.", "author" : [ { "dropping-particle" : "", "family" : "Berg", "given" : "Gabriele", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Smalla", "given" : "Kornelia", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "FEMS Microbiology Ecology", "id" : "ITEM-2", "issue" : "1", "issued" : { "date-parts" : [ [ "2009" ] ] }, "page" : "1-13", "title" : "Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere", "type" : "article-journal", "volume" : "68" }, "uris" : [ "" ] }, { "id" : "ITEM-3", "itemData" : { "DOI" : "10.1046/j.1365-2435.1999.00362.x", "ISBN" : "02698463", "ISSN" : "02698463", "PMID" : "128", "abstract" : "1. The aim was to assess the extent to which the microbial biomass and activity, and community structure of fertilized upland grasslands are directly related to changes in soil N availability or indirectly related to individual plant species effects caused by changes in plant species composition and dominance. We investigated the short-term interactive effects of dominant plant species (Lolium perenne, Agrostis capillaris, Holcus lanatus and Festuca rubra) and nitrogen (N) amendment using an N-limited upland grassland soil. 2. In soils planted with different grass species, soil microbial biomass, and to some extent microbial activity, were determined by temporal changes in plant productivity. Variations in the way that individual plants influenced soil microbial biomass and activity were highly inconsistent over time, and largely independent of N-additions and differences in plant productivity. At the final sample date, those grass species which co-dominate the total plant biomass of intermediate fertility (H. Lanatus) and semi-improved grasslands (A. Capillaris and f. Rubra) had a beneficial effect on the soil microbial biomass. In contrast, the dominant plant species of improved grasslands, L. Perenne, had zero or a negative effect on soil microbial biomass. Two plant species (A. Capillaris and H. Lanatus) increased the proportion of fungi relative to bacteria in the soil microbial community, relative to the unplanted control soil and the other plant species. Lolium perenne and A. Capillaris reduced the evenness of microbial PLFAs, suggesting negative effects of these plant species on the diversity of the soil microbial community. 3, The addition of N had no consistent effect on measures of soil microbial biomass or activity, but significantly altered the structure of the microbial community in favour of fungi. The lack of effects of N-addition on microbial biomass and activity were despite the finding that nitrogen addition reduced root biomass in all plant species and increased rhizosphere acidity. 4. The results suggest that in the short term, the abundance and activity of soil microorganisms in upland grasslands are regulated more by plant species traits than by a direct effect of nitrogen. These effects are likely to be related to variations amongst plant species in root exudation patterns and/or efficiency of nutrient aquisition. 5. Our study provides evidence that the functional characteristics of dominant plant species are important determinan\u2026", "author" : [ { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Mawdsley", "given" : "J.L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Edwards", "given" : "S.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Hobbs", "given" : "Philip J.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Rodwell", "given" : "J.S.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Davies", "given" : "W.J.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Functional Ecology", "id" : "ITEM-3", "issued" : { "date-parts" : [ [ "1999" ] ] }, "page" : "650-660", "title" : "Plant species and nitrogen effects on soil biological properties of temperate upland grasslands", "type" : "article-journal", "volume" : "13" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Grayston et al., 1998; Berg and Smalla, 2009; Bardgett et al., 1999)", "plainTextFormattedCitation" : "(Grayston et al., 1998; Berg and Smalla, 2009; Bardgett et al., 1999)", "previouslyFormattedCitation" : "(Grayston et al., 1998; Berg and Smalla, 2009; Bardgett et al., 1999)" }, "properties" : { }, "schema" : "" }(Grayston et al., 1998; Berg and Smalla, 2009; Bardgett et al., 1999), and there is evidence that divergence in soil bacterial and fungal communities is broadly linked to plant community composition at landscape ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/j.1461-0248.2012.01844.x", "ISSN" : "1461023X", "author" : [ { "dropping-particle" : "", "family" : "Vries", "given" : "Franciska T.", "non-dropping-particle" : "de", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Manning", "given" : "Pete", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Tallowin", "given" : "Jerry R. 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Soil microbial biomass (Cmic), activity (respiration and potential carbon utilisation) and community structure (phospholipid fatty acid (PLFA) analysis, culturing and community level physiological profiles (CLPP) (Biolog\u00ae)) were measured across a gradient of three upland grassland types; Festuca-Agrostis-Galium grassland (unimproved grassland, National Vegetation Classification (NVC) - U4a); Festuca-Agrostis-Galium grassland, Holcus -Trifolium sub-community (semi-improved grassland, NVC - U4b); Lolium - Cynosurus grassland (improved grassland, NVC - MG6) at three sites in different biogeographic areas of the UK over a period of 1 year. Variation in Cmic was mainly due to grassland type and site (accounting for 55% variance, v, in the data). Cmic was significantly (P < 0.001) high in the unimproved grassland at Torridon (237.4 g C m-2 cf. 81.2 g C m-2 in semi- and 63.8 g C m-2 in improved grasslands) and Sourhope (114.6 g C m-2 cf. in 44.8 g C m-2 semi- and 68.3 g C m-2 in improved grasslands) and semi-improved grassland at Abergwyngregyn (76.0 g C m-2 cf. 41.7 g C m-2 in un- and 58.3 g C m-2 in improved grasslands). Cmic showed little temporal variation (\u03bd = 3.7%). Soil microbial activity, measured as basal respiration was also mainly affected by grassland type and site (n = 32%). In contrast to Cmic, respiration was significantly (P < 0.001) high in the improved grassland at Sourhope (263.41 h-1m-2 cf. 79.61 h-1m-2 in semi- and 203.91 h-1m-2 unimproved grasslands) and Abergwyngregyn (198.81 h-1m-2 cf. 173.71 h-1m-2 in semi- and 88.21 h-1m-2 unimproved grasslands). Microbial activity, measured as potential carbon utilisation, agreed with the respiration measurements and was significantly (P < 0.001) high in the improved grassland at all three sites (A590 0.14 cf. 0.09 in semi- and 0.07 in unimproved grassland). However, date of sampling also had a significant (P < 0.001) impact on C utilisation potential (\u03bd = 24.7%) with samples from April 1997 having highest activity at all three sites. Variation in microbial community structure was due, predominantly, to grassland type (average \u03bd = 23.6% for bacterial and fungal numbers and PLFA) and date of sampling (average \u03bd = 39.7% for bacterial and fungal numbers and PLFA). Numbers of culturable bacteria and bacterial PLFA were significantly (P < 0.001) high in the \u2026", "author" : [ { "dropping-particle" : "", "family" : "Grayston", "given" : "S. J.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Griffith", "given" : "G. 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Additionally, correlational analyses have revealed associations between individual plant species and soil fungal ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1016/j.funeco.2016.05.012", "ISSN" : "17545048", "abstract" : "Plant species can influence communities of arbuscular mycorrhizal fungi (AMF) by hosting different AMF taxon identities and/or richness. We used presence/absence data from a recent global survey of AMF communities to assess how often AMF communities differ among plant species, and to explore whether differences result from dissimilarities in AMF taxon identity or richness. We found that AMF communities clustered among plant species in 24% of sites, and that plant species were more likely to differ in AMF taxon richness (23% of sites) than the particular taxa with which they associate (5% of sites). Overall though, the variation in both AMF richness and identity was often as great within as between plant species, suggesting that plant species identity may be less important for structuring local AMF communities than other factors, such as environmental conditions, fungal interactions or even stochastic distributions of AMF. This has implications for how we should view plant-AMF interactions and community patterns.", "author" : [ { "dropping-particle" : "", "family" : "Lekberg", "given" : "Ylva", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Waller", "given" : "Lauren P.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Fungal Ecology", "id" : "ITEM-1", "issued" : { "date-parts" : [ [ "2016" ] ] }, "page" : "10-13", "title" : "What drives differences in arbuscular mycorrhizal fungal communities among plant species?", "type" : "article-journal" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Lekberg and Waller, 2016)", "plainTextFormattedCitation" : "(Lekberg and Waller, 2016)", "previouslyFormattedCitation" : "(Lekberg and Waller, 2016)" }, "properties" : { }, "schema" : "" }(Lekberg and Waller, 2016), bacterial ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1007/s00253-009-2092-7", "ISBN" : "0175-7598", "ISSN" : "01757598", "PMID" : "19568745", "abstract" : "Plant-associated microorganisms fulfill important functions for plant growth and health. Direct plant growth promotion by microbes is based on improved nutrient acquisition and hormonal stimulation. Diverse mechanisms are involved in the suppression of plant pathogens, which is often indirectly connected with plant growth. Whereas members of the bacterial genera Azospirillum and Rhizobium are well-studied examples for plant growth promotion, Bacillus, Pseudomonas, Serratia, Stenotrophomonas, and Streptomyces and the fungal genera Ampelomyces, Coniothyrium, and Trichoderma are model organisms to demonstrate influence on plant health. Based on these beneficial plant-microbe interactions, it is possible to develop microbial inoculants for use in agricultural biotechnology. Dependent on their mode of action and effects, these products can be used as biofertilizers, plant strengtheners, phytostimulators, and biopesticides. There is a strong growing market for microbial inoculants worldwide with an annual growth rate of approximately 10%. The use of genomic technologies leads to products with more predictable and consistent effects. The future success of the biological control industry will benefit from interdisciplinary research, e.g., on mass production, formulation, interactions, and signaling with the environment, as well as on innovative business management, product marketing, and education. Altogether, the use of microorganisms and the exploitation of beneficial plant-microbe interactions offer promising and environmentally friendly strategies for conventional and organic agriculture worldwide.", "author" : [ { "dropping-particle" : "", "family" : "Berg", "given" : "Gabriele", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Applied Microbiology and Biotechnology", "id" : "ITEM-1", "issue" : "1", "issued" : { "date-parts" : [ [ "2009" ] ] }, "page" : "11-18", "title" : "Plant-microbe interactions promoting plant growth and health: Perspectives for controlled use of microorganisms in agriculture", "type" : "article-journal", "volume" : "84" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Berg, 2009)", "plainTextFormattedCitation" : "(Berg, 2009)", "previouslyFormattedCitation" : "(Berg, 2009)" }, "properties" : { }, "schema" : "" }(Berg, 2009), nematode ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1890/09-2198.1", "ISBN" : "0012-9658", "ISSN" : "0012-9658", "PMID" : "21058562", "abstract" : "Soils are extremely rich in biodiversity, and soil organisms play pivotal roles in supporting terrestrial life, but the role that individual plants and plant communities play in influencing the diversity and functioning of soil food webs remains highly debated. Plants, as primary producers and providers of resources to the soil food web, are of vital importance for the composition, structure, and functioning of soil communities. However, whether natural soil food webs that are completely open to immigration and emigration differ underneath individual plants remains unknown. In a biodiversity restoration experiment we first compared the soil nematode communities of 228 individual plants belonging to eight herbaceous species. We included grass, leguminous, and non-leguminous species. Each individual plant grew intermingled with other species, but all plant species had a different nematode community. Moreover, nematode communities were more similar when plant individuals were growing in the same as compared to different plant communities, and these effects were most apparent for the groups of bacterivorous, carnivorous, and omnivorous nematodes. Subsequently, we analyzed the composition, structure, and functioning of the complete soil food webs of 58 individual plants, belonging to two of the plant species, Lotus corniculatus (Fabaceae) and Plantago lanceolata (Plantaginaceae). We isolated and identified more than 150 taxa?groups of soil organisms. The soil community composition and structure of the entire food webs were influenced both by the species identity of the plant individual and the surrounding plant community. Unexpectedly, plant identity had the strongest effects on decomposing soil organisms, widely believed to be generalist feeders. In contrast, quantitative food web modeling showed that the composition of the plant community influenced nitrogen mineralization under individual plants, but that plant species identity did not affect nitrogen or carbon mineralization or food web stability. Hence, the composition and structure of entire soil food webs vary at the scale of individual plants and are strongly influenced by the species identity of the plant. However, the ecosystem functions these food webs provide are determined by the identity of the entire plant community.", "author" : [ { "dropping-particle" : "", "family" : "Bezemer", "given" : "T. M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Fountain", "given" : "M. T.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Barea", "given" : "J. M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Christensen", "given" : "S.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Dekker", "given" : "S. 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We examined soil mite (Acari) diversity beneath six grass species at the Konza Prairie Biological Station, Kansas, USA. We tested the hypotheses that soil mite species richness, abundance, and taxonomic diversity are greater (1) beneath grasses in dicultures (different species) compared to monocultures (same species), (2) beneath grasses of higher resource quality (lower C:N) compared to lower resource quality, and (3) beneath heterogeneous mixes of grasses (C3 and C4 grasses growing together) compared to homogeneous mixes (C3 or C4 grasses) using natural occurrences of plant species as treatments. This study is the first to examine the interaction between above- and belowground diversity in a natural setting with species-level resolution of a hyper-diverse taxon. Our results indicate that grasses in diculture supported a more species and phylogenetically rich soil mite fauna than was observed for monocultures and that this relationship was significant at depth but not in the upper soil horizon. We noted that mite species richness was not linearly related to grass species richness, which suggests that simple extrapolations of soil faunal diversity based on plant species inventories may underestimate the richness of associated soil mite communities. The distribution of mite size classes in dicultures was considerably different than those for monocultures. There was no difference in soil mite richness between grass combinations of differing resource quality, or resource heterogeneity.", "author" : [ { "dropping-particle" : "", "family" : "John", "given" : "Mark G.", "non-dropping-particle" : "St.", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Wall", "given" : "Diana H.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Behan-Pelletier", "given" : "Valerie M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Ecology", "id" : "ITEM-1", "issue" : "3", "issued" : { "date-parts" : [ [ "2006", "3" ] ] }, "page" : "625-633", "publisher" : "Ecological Society of America", "title" : "Does plant species co-occurrence influence soil mite diversity?", "type" : "article-journal", "volume" : "87" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(St. John et al., 2006)", "plainTextFormattedCitation" : "(St. John et al., 2006)", "previouslyFormattedCitation" : "(St. John et al., 2006)" }, "properties" : { }, "schema" : "" }(St. John et al., 2006) communities. However, it is unclear whether these relationships are driven by shared environmental preferences or by the direct effects of locally dominant plant species on soil communities. While plant invasions can elicit shifts in soil community structure ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/j.1461-0248.2005.00802.x", "ISBN" : "1461-023X", "ISSN" : "1461023X", "PMID" : "22526935", "abstract" : "Plant invasions have dramatic aboveground effects on plant community composition, but their belowground effects remain largely uncharacterized. Soil microorganisms directly interact with plants and mediate many nutrient transformations in soil. We hypothesized that belowground changes to the soil microbial community provide a mechanistic link between exotic plant invasion and changes to ecosystem nutrient cycling. To examine this possible link, monocultures and mixtures of exotic and native species were maintained for 4 years in a California grassland. Gross rates of nitrogen (N) mineralization and nitrification were quantified with N-15 pool dilution and soil microbial communities were characterized with DNA-based methods. Exotic grasses doubled gross nitrification rates, in part by increasing the abundance and changing the composition of ammonia-oxidizing bacteria in soil. These changes may translate into altered ecosystem N budgets after invasion. Altered soil microbial communities and their resulting effects on ecosystem processes may be an invisible legacy of exotic plant invasions.", "author" : [ { "dropping-particle" : "V.", "family" : "Hawkes", "given" : "Christine", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Wren", "given" : "Ian F.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Herman", "given" : "Donald J.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Firestone", "given" : "Mary K.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Ecology Letters", "id" : "ITEM-1", "issue" : "9", "issued" : { "date-parts" : [ [ "2005" ] ] }, "page" : "976-985", "title" : "Plant invasion alters nitrogen cycling by modifying the soil nitrifying community", "type" : "article-journal", "volume" : "8" }, "uris" : [ "" ] }, { "id" : "ITEM-2", "itemData" : { "DOI" : "10.1128/mSystems.00178-16", "ISSN" : "2379-5077", "PMID" : "28289729", "abstract" : "Plant invasions often reduce native plant diversity and increase net primary productivity. Invaded soils appear to differ from surrounding soils in ways that impede restoration of diverse native plant communities. We hypothesize that invader-mediated shifts in edaphic properties reproducibly alter soil microbial community structure and function. Here, we take a holistic approach, characterizing plant, prokaryotic, and fungal communities and soil physicochemical properties in field sites, invasion gradients, and experimental plots for three invasive plant species that cooccur in the Rocky Mountain West. Each invader had a unique impact on soil physicochemical properties. We found that invasions drove shifts in the abundances of specific microbial taxa, while overall belowground community structure and functional potential were fairly constant. Forb invaders were generally enriched in copiotrophic bacteria with higher 16S rRNA gene copy numbers and showed greater microbial carbohydrate and nitrogen metabolic potential. Older invasions had stronger effects on abiotic soil properties, indicative of multiyear successions. Overall, we show that plant invasions are idiosyncratic in their impact on soils and are directly responsible for driving reproducible shifts in the soil environment over multiyear time scales.", "author" : [ { "dropping-particle" : "", "family" : "Gibbons", "given" : "Sean M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Lekberg", "given" : "Ylva", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Mummey", "given" : "Daniel L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Sangwan", "given" : "Naseer", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Ramsey", "given" : "Philip W.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Gilbert", "given" : "Jack A.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "mSystems", "id" : "ITEM-2", "issue" : "2", "issued" : { "date-parts" : [ [ "2017" ] ] }, "page" : "e00178-16", "title" : "Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem", "type" : "article-journal", "volume" : "2" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Hawkes et al., 2005; Gibbons et al., 2017)", "plainTextFormattedCitation" : "(Hawkes et al., 2005; Gibbons et al., 2017)", "previouslyFormattedCitation" : "(Hawkes et al., 2005; Gibbons et al., 2017)" }, "properties" : { }, "schema" : "" }(Hawkes et al., 2005; Gibbons et al., 2017), the effects of plant species identity on the overall composition of belowground communities are often weak or difficult to quantify, with several studies having failed to identify strong links between changes in plant assemblages and corresponding changes in soil communities ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "author" : [ { "dropping-particle" : "", "family" : "Porazinska", "given" : "Dorota L", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Blaauw", "given" : "Maria B", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Hunt", "given" : "H William", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Parsons", "given" : "Andrew N", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Seastedt", "given" : "Timothy R", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Wall", "given" : "Diana H", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Ecological Monographs", "id" : "ITEM-1", "issue" : "3", "issued" : { "date-parts" : [ [ "2003" ] ] }, "page" : "377-395", "title" : "Relationships at the Aboveground-Belowground Interface: Plants, Soil Biota, and Soil Processes", "type" : "article-journal", "volume" : "73" }, "uris" : [ "" ] }, { "id" : "ITEM-2", "itemData" : { "DOI" : "10.1111/j.1365-2745.2006.01158.x", "ISBN" : "0022-0477", "ISSN" : "00220477", "abstract" : "1 Plant species differ in their capacity to influence soil organic matter, soil nutrient availability and the composition of soil microbial communities. Their influences on soil properties result in net positive or negative feedback effects, which influence plant performance and plant community composition. 2 For two grassland systems, one on a sandy soil in the Netherlands and one on a chalk soil in the United Kingdom, we investigated how individual plant species grown in monocultures changed abiotic and biotic soil conditions. Then, we determined feedback effects of these soils to plants of the same or different species. Feedback effects were analysed at the level of plant species and plant taxonomic groups (grasses vs. forbs). 3 In the sandy soils, plant species differed in their effects on soil chemical properties, in particular potassium levels, but PLFA (phospholipid fatty acid) signatures of the soil microbial community did not differ between plant species. The effects of soil chemical properties were even greater when grasses and forbs were compared, especially because potassium levels were lower in grass monocultures. 4 In the chalk soil, there were no effects of plant species on soil chemical properties, but PLFA profiles differed significantly between soils from different monocultures. PLFA profiles differed between species, rather than between grasses and forbs. 5 In the feedback experiment, all plant species in sandy soils grew less vigorously in soils conditioned by grasses than in soils conditioned by forbs. These effects correlated significantly with soil chemical properties. None of the seven plant species showed significant differences between performance in soil conditioned by the same vs. other plant species. 6 In the chalk soil, Sanguisorba minor and in particular Briza media performed best in soil collected from conspecifics, while Bromus erectus performed best in soil from heterospecifics. There was no distinctive pattern between soils collected from forb and grass monocultures, and plant performance could not be related to soil chemical properties or PLFA signatures. 7 Our study shows that mechanisms of plant-soil feedback can depend on plant species, plant taxonomic (or functional) groups and site-specific differences in abiotic and biotic soil properties. Understanding how plant species can influence their rhizosphere, and how other plant species respond to these changes, will greatly enhance our understanding of the functionin\u2026", "author" : [ { "dropping-particle" : "", "family" : "Bezemer", "given" : "T. 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However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se.", "author" : [ { "dropping-particle" : "", "family" : "Tedersoo", "given" : "Leho", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bahram", "given" : "Mohammad", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Cajthaml", "given" : "Tom\u00e1\u0161", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "P\u00f5lme", "given" : "Sergei", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Hiiesalu", "given" : "Indrek", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Anslan", "given" : "Sten", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Harend", "given" : "Helery", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Buegger", "given" : "Franz", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Pritsch", "given" : "Karin", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Koricheva", "given" : "Julia", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Abarenkov", "given" : "Kessy", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "The ISME Journal", "id" : "ITEM-3", "issued" : { "date-parts" : [ [ "2015" ] ] }, "page" : "1-17", "title" : "Tree diversity and species identity effects on soil fungi, protists and animals are context dependent", "type" : "article-journal" }, "uris" : [ "" ] }, { "id" : "ITEM-4", "itemData" : { "DOI" : "10.1016/j.funeco.2016.05.012", "ISSN" : "17545048", "abstract" : "Plant species can influence communities of arbuscular mycorrhizal fungi (AMF) by hosting different AMF taxon identities and/or richness. We used presence/absence data from a recent global survey of AMF communities to assess how often AMF communities differ among plant species, and to explore whether differences result from dissimilarities in AMF taxon identity or richness. We found that AMF communities clustered among plant species in 24% of sites, and that plant species were more likely to differ in AMF taxon richness (23% of sites) than the particular taxa with which they associate (5% of sites). Overall though, the variation in both AMF richness and identity was often as great within as between plant species, suggesting that plant species identity may be less important for structuring local AMF communities than other factors, such as environmental conditions, fungal interactions or even stochastic distributions of AMF. This has implications for how we should view plant-AMF interactions and community patterns.", "author" : [ { "dropping-particle" : "", "family" : "Lekberg", "given" : "Ylva", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Waller", "given" : "Lauren P.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Fungal Ecology", "id" : "ITEM-4", "issued" : { "date-parts" : [ [ "2016" ] ] }, "page" : "10-13", "title" : "What drives differences in arbuscular mycorrhizal fungal communities among plant species?", "type" : "article-journal" }, "uris" : [ "" ] }, { "id" : "ITEM-5", "itemData" : { "DOI" : "10.3389/fmicb.2015.00466", "ISBN" : "1664-302X", "ISSN" : "1664302X", "PMID" : "26042104", "abstract" : "Global and regional environmental changes often co-occur, creating complex gradients of disturbance on the landscape. Soil microbial communities are an important component of ecosystem response to environmental change, yet little is known about how microbial structure and function respond to multiple disturbances, or whether multiple environmental changes lead to unanticipated interactive effects. Our study used experimental semi-arid grassland plots in a Mediterranean-climate to determine how soil microbial communities in a seasonally variable ecosystem respond to one, two, or three simultaneous environmental changes: exotic plant invasion, plant invasion + vegetation clipping (to simulate common management practices like mowing or livestock grazing), plant invasion + nitrogen (N) fertilization, and plant invasion + clipping + N fertilization. We examined microbial community structure 5-6 years after plot establishment via sequencing of >1 million 16S rRNA genes. Abiotic soil properties (soil moisture, temperature, pH, and inorganic N) and microbial functioning (nitrification and denitrification potentials) were also measured and showed treatment-induced shifts, including altered NO3- availability, temperature, and nitrification potential. Despite these changes, bacterial and archaeal communities showed little variation in composition and diversity across treatments. Even communities in plots exposed to three interacting environmental changes were similar to those in restored native grassland plots. Historical exposure to large seasonal and inter-annual variations in key soil properties, in addition to prior site cultivation, may select for a functionally plastic or largely dormant microbial community, resulting in a microbial community that is structurally robust to single and multiple environmental changes.", "author" : [ { "dropping-particle" : "", "family" : "Carey", "given" : "Chelsea J.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Michael Beman", "given" : "J.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Eviner", "given" : "Valerie T.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Malmstrom", "given" : "Carolyn M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Hart", "given" : "Stephen C.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Frontiers in Microbiology", "id" : "ITEM-5", "issue" : "MAY", "issued" : { "date-parts" : [ [ "2015" ] ] }, "title" : "Soil microbial community structure is unaltered by plant invasion, vegetation clipping, and nitrogen fertilization in experimental semi-arid grasslands", "type" : "article-journal", "volume" : "6" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Porazinska et al., 2003; Bezemer et al., 2006; Tedersoo et al., 2015; Lekberg and Waller, 2016; Carey et al., 2015)", "plainTextFormattedCitation" : "(Porazinska et al., 2003; Bezemer et al., 2006; Tedersoo et al., 2015; Lekberg and Waller, 2016; Carey et al., 2015)", "previouslyFormattedCitation" : "(Porazinska et al., 2003; Bezemer et al., 2006; Tedersoo et al., 2015; Lekberg and Waller, 2016; Carey et al., 2015)" }, "properties" : { }, "schema" : "" }(Porazinska et al., 2003; Bezemer et al., 2006; Tedersoo et al., 2015; Lekberg and Waller, 2016; Carey et al., 2015). As such, the existence of a general relationship between plants and soil communities remains uncertain and difficult to predict a priori.There are multiple plant community attributes that could potentially be used to predict variation in soil communities. Plant species identity could be a strong predictor of variation in soil communities ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/j.1574-6941.2009.00654.x", "ISBN" : "0168-6496", "ISSN" : "01686496", "PMID" : "19243436", "abstract" : "The rhizosphere is of central importance not only for plant nutrition, health and quality but also for microorganism-driven carbon sequestration, ecosystem functioning and nutrient cycling in terrestrial ecosystems. A multitude of biotic and abiotic factors are assumed to influence the structural and functional diversity of microbial communities in the rhizosphere. In this review, recent studies on the influence of the two factors, plant species and soil type, on rhizosphere-associated microbial communities are discussed. Root exudates and the response of microorganisms to the latter as well as to root morphology were shown to shape rhizosphere microbial communities. All studies revealed that soil is the main reservoir for rhizosphere microorganisms. Many secrets of microbial life in the rhizosphere were recently uncovered due to the enormous progress in molecular and microscopic tools. Physiological and molecular data on the factors that drive selection processes in the rhizosphere are presented here. Furthermore, implications for agriculture, nature conservation and biotechnology will also be discussed.", "author" : [ { "dropping-particle" : "", "family" : "Berg", "given" : "Gabriele", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Smalla", "given" : "Kornelia", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "FEMS Microbiology Ecology", "id" : "ITEM-1", "issue" : "1", "issued" : { "date-parts" : [ [ "2009" ] ] }, "page" : "1-13", "title" : "Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere", "type" : "article-journal", "volume" : "68" }, "uris" : [ "" ] }, { "id" : "ITEM-2", "itemData" : { "DOI" : "10.1890/09-2198.1", "ISBN" : "0012-9658", "ISSN" : "0012-9658", "PMID" : "21058562", "abstract" : "Soils are extremely rich in biodiversity, and soil organisms play pivotal roles in supporting terrestrial life, but the role that individual plants and plant communities play in influencing the diversity and functioning of soil food webs remains highly debated. Plants, as primary producers and providers of resources to the soil food web, are of vital importance for the composition, structure, and functioning of soil communities. However, whether natural soil food webs that are completely open to immigration and emigration differ underneath individual plants remains unknown. In a biodiversity restoration experiment we first compared the soil nematode communities of 228 individual plants belonging to eight herbaceous species. We included grass, leguminous, and non-leguminous species. Each individual plant grew intermingled with other species, but all plant species had a different nematode community. Moreover, nematode communities were more similar when plant individuals were growing in the same as compared to different plant communities, and these effects were most apparent for the groups of bacterivorous, carnivorous, and omnivorous nematodes. Subsequently, we analyzed the composition, structure, and functioning of the complete soil food webs of 58 individual plants, belonging to two of the plant species, Lotus corniculatus (Fabaceae) and Plantago lanceolata (Plantaginaceae). We isolated and identified more than 150 taxa?groups of soil organisms. The soil community composition and structure of the entire food webs were influenced both by the species identity of the plant individual and the surrounding plant community. Unexpectedly, plant identity had the strongest effects on decomposing soil organisms, widely believed to be generalist feeders. In contrast, quantitative food web modeling showed that the composition of the plant community influenced nitrogen mineralization under individual plants, but that plant species identity did not affect nitrogen or carbon mineralization or food web stability. Hence, the composition and structure of entire soil food webs vary at the scale of individual plants and are strongly influenced by the species identity of the plant. However, the ecosystem functions these food webs provide are determined by the identity of the entire plant community.", "author" : [ { "dropping-particle" : "", "family" : "Bezemer", "given" : "T. M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Fountain", "given" : "M. T.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Barea", "given" : "J. M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Christensen", "given" : "S.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Dekker", "given" : "S. 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G.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Robin", "given" : "C.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Ruiter", "given" : "P. C.", "non-dropping-particle" : "de", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Scheu", "given" : "S.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Set\u00e4l\u00e4", "given" : "H.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Smilauer", "given" : "P", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Putten", "given" : "W. H.", "non-dropping-particle" : "van der", "parse-names" : false, "suffix" : "" } ], "container-title" : "Ecology", "id" : "ITEM-2", "issue" : "10", "issued" : { "date-parts" : [ [ "2010", "10" ] ] }, "page" : "3027-3036", "publisher" : "Ecological Society of America", "title" : "Divergent composition but similar function of soil food webs beneath individual plants: plant species and community effects", "type" : "article-journal", "volume" : "91" }, "uris" : [ "" ] }, { "id" : "ITEM-3", "itemData" : { "DOI" : "10.1016/j.funeco.2016.05.012", "ISSN" : "17545048", "abstract" : "Plant species can influence communities of arbuscular mycorrhizal fungi (AMF) by hosting different AMF taxon identities and/or richness. We used presence/absence data from a recent global survey of AMF communities to assess how often AMF communities differ among plant species, and to explore whether differences result from dissimilarities in AMF taxon identity or richness. We found that AMF communities clustered among plant species in 24% of sites, and that plant species were more likely to differ in AMF taxon richness (23% of sites) than the particular taxa with which they associate (5% of sites). Overall though, the variation in both AMF richness and identity was often as great within as between plant species, suggesting that plant species identity may be less important for structuring local AMF communities than other factors, such as environmental conditions, fungal interactions or even stochastic distributions of AMF. This has implications for how we should view plant-AMF interactions and community patterns.", "author" : [ { "dropping-particle" : "", "family" : "Lekberg", "given" : "Ylva", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Waller", "given" : "Lauren P.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Fungal Ecology", "id" : "ITEM-3", "issued" : { "date-parts" : [ [ "2016" ] ] }, "page" : "10-13", "title" : "What drives differences in arbuscular mycorrhizal fungal communities among plant species?", "type" : "article-journal" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Berg and Smalla, 2009; Bezemer et al., 2010; Lekberg and Waller, 2016)", "plainTextFormattedCitation" : "(Berg and Smalla, 2009; Bezemer et al., 2010; Lekberg and Waller, 2016)", "previouslyFormattedCitation" : "(Berg and Smalla, 2009; Bezemer et al., 2010; Lekberg and Waller, 2016)" }, "properties" : { }, "schema" : "" }(Berg and Smalla, 2009; Bezemer et al., 2010; Lekberg and Waller, 2016), as could evolutionary history (i.e. the phylogeny) of plants, given the potential for more closely related plants to be associated with more similar belowground communities ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/ele.12536", "ISBN" : "1461-023x", "ISSN" : "14610248", "PMID" : "26472095", "abstract" : "The complexities of the relationships between plant and soil microbial communities remain unresolved. We determined the associations between plant aboveground and belowground (root) distributions and the communities of soil fungi and bacteria found across a diverse tropical forest plot. Soil microbial community composition was correlated with the taxonomic and phylogenetic structure of the aboveground plant assemblages even after controlling for differences in soil characteristics, but these relationships were stronger for fungi than for bacteria. In contrast to expectations, the species composition of roots in our soil core samples was a poor predictor of microbial community composition perhaps due to the patchy, ephemeral, and highly overlapping nature of fine root distributions. Our ability to predict soil microbial composition was not improved by incorporating information on plant functional traits suggesting that the most commonly measured plant traits are not particularly useful for predicting the plot-level variability in belowground microbial communities.", "author" : [ { "dropping-particle" : "", "family" : "Barber\u00e1n", "given" : "Albert", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Mcguire", "given" : "Krista L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Wolf", "given" : "Jeffrey A.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Jones", "given" : "F. 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Such patterns could arise as a product of coevolution between plants and soil microbes or if phylogenetic relatedness corresponds to other plant attributes that affect soil organisms ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1016/j.tree.2005.08.009", "ISBN" : "0169-5347", "ISSN" : "01695347", "PMID" : "16701446", "abstract" : "Aboveground and belowground species interactions drive ecosystem properties at the local scale, but it is unclear how these relationships scale-up to regional and global scales. Here, we discuss our current knowledge of aboveground and belowground diversity links from a global to a local scale. Global diversity peaks towards the Equator for large, aboveground organisms, but not for small (mainly belowground) organisms, suggesting that there are size-related biodiversity gradients in global aboveground-belowground linkages. The generalization of aboveground-belowground diversity relationships, and their role in ecosystem functioning, requires surveys at scales that are relevant to the organisms and ecosystem properties. Habitat sizes and diversity gradients can differ significantly between aboveground and belowground organisms and between ecosystems. These gradients in biodiversity and plant community trait perception need to be acknowledged when studying aboveground-belowground biodiversity linkages. ?? 2005 Elsevier Ltd. All rights reserved.", "author" : [ { "dropping-particle" : "", "family" : "Deyn", "given" : "Gerlinde B.", "non-dropping-particle" : "De", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Putten", "given" : "Wim H.", "non-dropping-particle" : "Van Der", "parse-names" : false, "suffix" : "" } ], "container-title" : "Trends in Ecology and Evolution", "id" : "ITEM-1", "issue" : "11", "issued" : { "date-parts" : [ [ "2005" ] ] }, "page" : "625-633", "title" : "Linking aboveground and belowground diversity", "type" : "article-journal", "volume" : "20" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(De Deyn and Van Der Putten, 2005)", "plainTextFormattedCitation" : "(De Deyn and Van Der Putten, 2005)", "previouslyFormattedCitation" : "(De Deyn and Van Der Putten, 2005)" }, "properties" : { }, "schema" : "" }(De Deyn and Van Der Putten, 2005). It has also been proposed that plant functional traits could be used to predict plant-microbe associations a priori given that plant species’ distributions and community diversity are generally predictable based on their traits ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/j.1461-0248.2012.01850.x", "ISSN" : "1461023X", "author" : [ { "dropping-particle" : "", "family" : "Ben-Hur", "given" : "Eyal", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Fragman-Sapir", "given" : "Ori", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Hadas", "given" : "Rivka", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Singer", "given" : "Alon", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Kadmon", "given" : "Ronen", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Ecology Letters", "id" : "ITEM-1", "issue" : "11", "issued" : { "date-parts" : [ [ "2012" ] ] }, "page" : "1276-1282", "title" : "Functional trade-offs increase species diversity in experimental plant communities", "type" : "article-journal", "volume" : "15" }, "uris" : [ "" ] }, { "id" : "ITEM-2", "itemData" : { "DOI" : "10.1111/ele.12157", "ISBN" : "1461-0248", "ISSN" : "1461023X", "PMID" : "23910482", "abstract" : "Recent functional trait studies have shown that trait differences may favour certain species (environmental filtering) while simultaneously preventing competitive exclusion (niche partitioning). However, phenomenological trait-dispersion analyses do not identify the mechanisms that generate niche partitioning, preventing trait-based prediction of future changes in biodiversity. We argue that such predictions require linking functional traits with recognised coexistence mechanisms involving spatial or temporal environmental heterogeneity, resource partitioning and natural enemies. We first demonstrate the limitations of phenomenological approaches using simulations, and then (1) propose trait-based tests of coexistence, (2) generate hypotheses about which plant functional traits are likely to interact with particular mechanisms and (3) review the literature for evidence for these hypotheses. Theory and data suggest that all four classes of coexistence mechanisms could act on functional trait variation, but some mechanisms will be stronger and more widespread than others. The highest priority for future research is studies of interactions between environmental heterogeneity and trait variation that measure environmental variables at within-community scales and quantify species' responses to the environment in the absence of competition. Evidence that similar trait-based coexistence mechanisms operate in many ecosystems would simplify biodiversity forecasting and represent a rare victory for generality over contingency in community ecology.", "author" : [ { "dropping-particle" : "", "family" : "Adler", "given" : "Peter B.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Fajardo", "given" : "Alex", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Kleinhesselink", "given" : "Andrew R.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Kraft", "given" : "Nathan J B", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Ecology Letters", "id" : "ITEM-2", "issue" : "10", "issued" : { "date-parts" : [ [ "2013" ] ] }, "page" : "1294-1306", "title" : "Trait-based tests of coexistence mechanisms", "type" : "article-journal", "volume" : "16" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Ben-Hur et al., 2012; Adler et al., 2013)", "plainTextFormattedCitation" : "(Ben-Hur et al., 2012; Adler et al., 2013)", "previouslyFormattedCitation" : "(Ben-Hur et al., 2012; Adler et al., 2013)" }, "properties" : { }, "schema" : "" }(Ben-Hur et al., 2012; Adler et al., 2013), and soil communities can form associations with plants based on these traits ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1126/science.1094875", "ISSN" : "1095-9203", "PMID" : "15192218", "abstract" : "All terrestrial ecosystems consist of aboveground and belowground components that interact to influence community- and ecosystem-level processes and properties. Here we show how these components are closely interlinked at the community level, reinforced by a greater degree of specificity between plants and soil organisms than has been previously supposed. As such, aboveground and belowground communities can be powerful mutual drivers, with both positive and negative feedbacks. A combined aboveground-belowground approach to community and ecosystem ecology is enhancing our understanding of the regulation and functional significance of biodiversity and of the environmental impacts of human-induced global change phenomena.", "author" : [ { "dropping-particle" : "", "family" : "Wardle", "given" : "David A", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Klironomos", "given" : "John N", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Set\u00e4l\u00e4", "given" : "Heikki", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Putten", "given" : "Wim H", "non-dropping-particle" : "van der", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Wall", "given" : "Diana H", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Science", "id" : "ITEM-1", "issue" : "5677", "issued" : { "date-parts" : [ [ "2004", "6", "11" ] ] }, "page" : "1629-33", "title" : "Ecological linkages between aboveground and belowground biota", "type" : "article-journal", "volume" : "304" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Wardle et al., 2004)", "plainTextFormattedCitation" : "(Wardle et al., 2004)", "previouslyFormattedCitation" : "(Wardle et al., 2004)" }, "properties" : { }, "schema" : "" }(Wardle et al., 2004). Although previous studies have shown that plant traits can explain variation in soil microbial processes involved in C and N cycling ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/j.1365-2745.2010.01679.x", "ISBN" : "0022-0477", "ISSN" : "00220477", "abstract" : "1. Global change is likely to alter plant community structure, with consequences for the structure and functioning of the below-ground community and potential feedbacks to climate change. Understanding the mechanisms behind these plant\u2013soil interactions and feedbacks to the Earth-system is therefore crucial. One approach to understanding such mechanisms is to use plant traits as predictors of functioning.\\r\\n2. We used a field-based monoculture experiment involving nine grassland species that had been growing on the same base soil for 7 years to test whether leaf, litter and root traits associated with different plant growth strategies can be linked to an extensive range of soil properties relevant to carbon, nitrogen and phosphorus cycling. Soil properties included the biomass and structure of the soil microbial community, soil nutrients, soil microclimate and soil process rates.\\r\\n3. Plant species with a high relative growth rate (RGR) were associated with high leaf and litter quality (e.g. low toughness, high nitrogen concentrations), an elevated biomass of bacteria relative to fungi in soil, high rates of soil nitrogen mineralization and concentrations of extractable inorganic nitrogen, and to some extent higher available phosphorus pools.\\r\\n4. In contrast to current theory, species with a high RGR and litter quality were associated with soils with a lower rate of soil respiration and slow decomposition rates. This indicates that predicting processes that influence carbon cycling from plant traits may be more complex than predicting processes that influence nitrogen and phosphorus cycling.\\r\\n5. Root traits did not show strong relationships to RGR, leaf or litter traits, but were strongly correlated with several soil properties, particularly the biomass of bacteria relative to fungi in soil and measures relating to soil carbon cycling.\\r\\n6. Synthesis. Our results indicate that plant species from a single habitat can result in significant divergence in soil properties and functioning when grown in monoculture, and that many of these changes are strongly and predictably linked to variation in plant traits associated with different growth strategies. Traits therefore have the potential to be a powerful tool for understanding the mechanisms behind plant\u2013soil interactions and ecosystem functioning, and for predicting how changes in plant species composition associated with global change will feedback to the Earth-system.", "author" : [ { "dropping-particle" : "", "family" : "Orwin", "given" : "Kate H.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Buckland", "given" : "Sarah M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Johnson", "given" : "David", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Turner", "given" : "Benjamin L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Smart", "given" : "Simon", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Oakley", "given" : "Simon", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Journal of Ecology", "id" : "ITEM-1", "issue" : "5", "issued" : { "date-parts" : [ [ "2010" ] ] }, "page" : "1074-1083", "title" : "Linkages of plant traits to soil properties and the functioning of temperate grassland", "type" : "article-journal", "volume" : "98" }, "uris" : [ "" ] }, { "id" : "ITEM-2", "itemData" : { "DOI" : "10.1111/1365-2745.12014", "ISSN" : "00220477", "author" : [ { "dropping-particle" : "", "family" : "Grigulis", "given" : "Karl", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Lavorel", "given" : "Sandra", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Krainer", "given" : "Ute", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Legay", "given" : "Nicolas", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Baxendale", "given" : "Catherine", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Dumont", "given" : "Maxime", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Kastl", "given" : "Eva", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Arnoldi", "given" : "Cindy", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Poly", "given" : "Franck", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Pommier", "given" : "Thomas", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Schloter", "given" : "Michael", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Tappeiner", "given" : "Ulrike", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bahn", "given" : "Michael", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Cl\u00e9ment", "given" : "Jean-Christophe", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Journal of Ecology", "id" : "ITEM-2", "issue" : "1", "issued" : { "date-parts" : [ [ "2013" ] ] }, "page" : "47-57", "title" : "Relative contributions of plant traits and soil microbial properties to mountain grassland ecosystem services", "type" : "article-journal", "volume" : "101" }, "uris" : [ "" ] }, { "id" : "ITEM-3", "itemData" : { "DOI" : "10.1890/13-2107.1", "ISSN" : "0012-9658", "author" : [ { "dropping-particle" : "", "family" : "Cantarel", "given" : "Am\u00e9lie A. 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However, how plant functional traits are shaping these communities has received less attention though linking plant and microbial traits is crucial for better understanding plant-microbe interactions. Our objective was to determine how plant\u2013microbe interactions were affected by plant traits. Specifically we analyzed how interactions between plant species and microbes involved in nitrogen cycling were affected by plant traits related to nitrogen nutrition in interaction with soil nitrogen availability. Eleven plant species, selected along an oligotrophic\u2013nitrophilic gradient, were grown individually in a nitrogen-poor soil with two levels of nitrate availability. Plant traits for both carbon and nitrogen nutrition were measured and the genetic structure and abundance of rhizosphere microbial communities, in particular the ammonia oxidizer and nitrate reducer guilds, were analyzed. The structure of the bacterial community in the rhizosphere...", "author" : [ { "dropping-particle" : "", "family" : "Moreau", "given" : "Delphine", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Pivato", "given" : "Barbara", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bru", "given" : "David", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Busset", "given" : "Hugues", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Deau", "given" : "Florence", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Faivre", "given" : "C??line", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Matejicek", "given" : "Annick", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Strbik", "given" : "Florence", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Philippot", "given" : "Laurent", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Mougel", "given" : "Christophe", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Ecology", "id" : "ITEM-4", "issue" : "8", "issued" : { "date-parts" : [ [ "2015", "8" ] ] }, "page" : "2300-2310", "publisher" : "Ecological Society of America", "title" : "Plant traits related to nitrogen uptake influence plant-microbe competition", "type" : "article-journal", "volume" : "96" }, "uris" : [ "" ] }, { "id" : "ITEM-5", "itemData" : { "DOI" : "10.1002/ecs2.1448", "ISSN" : "21508925", "author" : [ { "dropping-particle" : "", "family" : "Legay", "given" : "Nicolas", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Lavorel", "given" : "Sandra", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Baxendale", "given" : "Catherine", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Krainer", "given" : "Ute", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bahn", "given" : "Michael", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Binet", "given" : "Marie-No\u00eblle", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Cantarel", "given" : "Am\u00e9lie A. 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Further, past studies show that links between plant traits and the composition of soil communities are not always observed ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/ele.12536", "ISBN" : "1461-023x", "ISSN" : "14610248", "PMID" : "26472095", "abstract" : "The complexities of the relationships between plant and soil microbial communities remain unresolved. We determined the associations between plant aboveground and belowground (root) distributions and the communities of soil fungi and bacteria found across a diverse tropical forest plot. Soil microbial community composition was correlated with the taxonomic and phylogenetic structure of the aboveground plant assemblages even after controlling for differences in soil characteristics, but these relationships were stronger for fungi than for bacteria. In contrast to expectations, the species composition of roots in our soil core samples was a poor predictor of microbial community composition perhaps due to the patchy, ephemeral, and highly overlapping nature of fine root distributions. Our ability to predict soil microbial composition was not improved by incorporating information on plant functional traits suggesting that the most commonly measured plant traits are not particularly useful for predicting the plot-level variability in belowground microbial communities.", "author" : [ { "dropping-particle" : "", "family" : "Barber\u00e1n", "given" : "Albert", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Mcguire", "given" : "Krista L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Wolf", "given" : "Jeffrey A.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Jones", "given" : "F. 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Global change is likely to alter plant community structure, with consequences for the structure and functioning of the below-ground community and potential feedbacks to climate change. Understanding the mechanisms behind these plant\u2013soil interactions and feedbacks to the Earth-system is therefore crucial. One approach to understanding such mechanisms is to use plant traits as predictors of functioning.\\r\\n2. We used a field-based monoculture experiment involving nine grassland species that had been growing on the same base soil for 7 years to test whether leaf, litter and root traits associated with different plant growth strategies can be linked to an extensive range of soil properties relevant to carbon, nitrogen and phosphorus cycling. Soil properties included the biomass and structure of the soil microbial community, soil nutrients, soil microclimate and soil process rates.\\r\\n3. Plant species with a high relative growth rate (RGR) were associated with high leaf and litter quality (e.g. low toughness, high nitrogen concentrations), an elevated biomass of bacteria relative to fungi in soil, high rates of soil nitrogen mineralization and concentrations of extractable inorganic nitrogen, and to some extent higher available phosphorus pools.\\r\\n4. In contrast to current theory, species with a high RGR and litter quality were associated with soils with a lower rate of soil respiration and slow decomposition rates. This indicates that predicting processes that influence carbon cycling from plant traits may be more complex than predicting processes that influence nitrogen and phosphorus cycling.\\r\\n5. Root traits did not show strong relationships to RGR, leaf or litter traits, but were strongly correlated with several soil properties, particularly the biomass of bacteria relative to fungi in soil and measures relating to soil carbon cycling.\\r\\n6. Synthesis. Our results indicate that plant species from a single habitat can result in significant divergence in soil properties and functioning when grown in monoculture, and that many of these changes are strongly and predictably linked to variation in plant traits associated with different growth strategies. Traits therefore have the potential to be a powerful tool for understanding the mechanisms behind plant\u2013soil interactions and ecosystem functioning, and for predicting how changes in plant species composition associated with global change will feedback to the Earth-system.", "author" : [ { "dropping-particle" : "", "family" : "Orwin", "given" : "Kate H.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Buckland", "given" : "Sarah M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Johnson", "given" : "David", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Turner", "given" : "Benjamin L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Smart", "given" : "Simon", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Oakley", "given" : "Simon", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Journal of Ecology", "id" : "ITEM-1", "issue" : "5", "issued" : { "date-parts" : [ [ "2010" ] ] }, "page" : "1074-1083", "title" : "Linkages of plant traits to soil properties and the functioning of temperate grassland", "type" : "article-journal", "volume" : "98" }, "uris" : [ "" ] }, { "id" : "ITEM-2", "itemData" : { "DOI" : "10.1111/j.1461-0248.2012.01844.x", "ISSN" : "1461023X", "author" : [ { "dropping-particle" : "", "family" : "Vries", "given" : "Franciska T.", "non-dropping-particle" : "de", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Manning", "given" : "Pete", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Tallowin", "given" : "Jerry R. B.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Mortimer", "given" : "Simon R.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Pilgrim", "given" : "Emma S.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Harrison", "given" : "Kathryn A.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Hobbs", "given" : "Phil J.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Quirk", "given" : "Helen", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Shipley", "given" : "Bill", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Cornelissen", "given" : "Johannes H. C.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Kattge", "given" : "Jens", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Ecology Letters", "id" : "ITEM-2", "issue" : "11", "issued" : { "date-parts" : [ [ "2012" ] ] }, "page" : "1230-1239", "title" : "Abiotic drivers and plant traits explain landscape-scale patterns in soil microbial communities", "type" : "article-journal", "volume" : "15" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Orwin et al., 2010; de Vries et al., 2012)", "plainTextFormattedCitation" : "(Orwin et al., 2010; de Vries et al., 2012)", "previouslyFormattedCitation" : "(Orwin et al., 2010; de Vries et al., 2012)" }, "properties" : { }, "schema" : "" }(Orwin et al., 2010; de Vries et al., 2012). Likewise, most previous work has focused on the relationships between soil biota and aboveground plant traits, despite increasing evidence that root traits are likely to play a more important role in structuring belowground communities ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1016/j.tree.2014.10.006", "ISBN" : "1872-8383 (Electronic)\\r0169-5347 (Linking)", "ISSN" : "01695347", "PMID" : "25459399", "abstract" : "Ecologists are increasingly adopting trait-based approaches to understand how community change influences ecosystem processes. However, most of this research has focussed on aboveground plant traits, whereas it is becoming clear that root traits are important drivers of many ecosystem processes, such as carbon (C) and nutrient cycling, and the formation and structural stability of soil. Here, we synthesise emerging evidence that illustrates how root traits impact ecosystem processes, and propose a pathway to unravel the complex roles of root traits in driving ecosystem processes and their response to global change. Finally, we identify research challenges and novel technologies to address them.", "author" : [ { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Mommer", "given" : "Liesje", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Vries", "given" : "Franciska T.", "non-dropping-particle" : "De", "parse-names" : false, "suffix" : "" } ], "container-title" : "Trends in Ecology and Evolution", "id" : "ITEM-1", "issue" : "12", "issued" : { "date-parts" : [ [ "2014" ] ] }, "page" : "692-699", "title" : "Going underground: Root traits as drivers of ecosystem processes", "type" : "article", "volume" : "29" }, "uris" : [ "" ] }, { "id" : "ITEM-2", "itemData" : { "DOI" : "10.1093/aob/mcu169", "ISSN" : "0305-7364", "author" : [ { "dropping-particle" : "", "family" : "Legay", "given" : "N.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Baxendale", "given" : "C.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Grigulis", "given" : "K.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Krainer", "given" : "U.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Kastl", "given" : "E.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Schloter", "given" : "M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "R. D.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Arnoldi", "given" : "C.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bahn", "given" : "M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Dumont", "given" : "M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Poly", "given" : "F.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Pommier", "given" : "T.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Clement", "given" : "J. C.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Lavorel", "given" : "S.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Annals of Botany", "id" : "ITEM-2", "issue" : "5", "issued" : { "date-parts" : [ [ "2014" ] ] }, "page" : "1011-1021", "title" : "Contribution of above- and below-ground plant traits to the structure and function of grassland soil microbial communities", "type" : "article-journal", "volume" : "114" }, "uris" : [ "" ] }, { "id" : "ITEM-3", "itemData" : { "DOI" : "10.1093/femsec/fiw091", "ISSN" : "15746941", "PMID" : "27130939", "abstract" : "The influence of plants on archaeal (AOA) and bacterial (AOB) ammonia oxidisers is poorly understood. Higher microbial activity in the rhizosphere, including organic nitrogen (N) mineralisation, may stimulate both groups, while ammonia uptake by plants may favour AOA, considered to prefer lower ammonia concentration. We therefore hypothesised (i) higher AOA and AOB abundances in the rhizosphere than bulk soil and (ii) that AOA are favoured over AOB in the rhizosphere of plants with an exploitative strategy and high N demand, especially (iii) during early growth, when plant N uptake is higher. These hypotheses were tested by growing 20 grassland plants, covering a spectrum of resource-use strategies, and determining AOA and AOB amoA gene abundances, rhizosphere and bulk soil characteristics and plant functional traits. Joint Bayesian mixed models indicated no increase in AO in the rhizosphere, but revealed that AOA were more abundant in the rhizosphere of exploitative plants, mostly grasses, and less abundant under conservative plants. In contrast, AOB abundance in the rhizosphere and bulk soil depended on pH, rather than plant traits. These findings provide a mechanistic basis for plant-ammonia oxidiser interactions and for links between plant functional traits and ammonia oxidiser ecology. Keywords:", "author" : [ { "dropping-particle" : "", "family" : "Thion", "given" : "C\u00e9cile E.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Poirel", "given" : "Jessica D", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Cornulier", "given" : "Thomas", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Vries", "given" : "Franciska T", "non-dropping-particle" : "De", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Prosser", "given" : "James I", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "FEMS Microbiology Ecology", "id" : "ITEM-3", "issue" : "7", "issued" : { "date-parts" : [ [ "2016" ] ] }, "title" : "Plant nitrogen-use strategy as a driver of rhizosphere archaeal and bacterial ammonia oxidiser abundance", "type" : "article-journal", "volume" : "92" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Bardgett et al., 2014; Legay et al., 2014; Thion et al., 2016)", "plainTextFormattedCitation" : "(Bardgett et al., 2014; Legay et al., 2014; Thion et al., 2016)", "previouslyFormattedCitation" : "(Bardgett et al., 2014; Legay et al., 2014; Thion et al., 2016)" }, "properties" : { }, "schema" : "" }(Bardgett et al., 2014; Legay et al., 2014; Thion et al., 2016).Here we provide the first in-depth evaluation of the predictive power of plant community attributes, alongside abiotic factors, for explaining spatial (i.e. horizontal) variation in soil communities at the individual plant and community-scale. While previous work has investigated effects of plant species and community attributes on soil communities, we are not aware of any previous study that has comprehensively assessed these effects across such a wide range of functionally important belowground taxonomic groups. Specifically, we address the overarching question: Can plant community attributes (i.e. taxonomic composition, phylogenetic composition, and plant functional traits) be used to predict spatial variability in soil community composition? To address this question, we sampled soils from both monocultures of 21 common temperate grassland plant species spanning eight families and a range of life history strategies, and we sampled an adjacent field experiment where grassland community composition had been manipulated through plant species additions to create a gradient of plant species and plant functional diversity. We used DNA sequencing-based approaches to target soil fungal, bacterial, protistan, and metazoan (faunal) communities. We first assessed whether the identity, phylogenetic history, and/or functional traits of individual plant species (both leaf and root traits) could be used to explain variation in soil communities. Next, we determined whether observations made at the individual plant scale correspond to similar trends in mixed plant communities in the field.Materials and MethodsMesocosms experimentTo evaluate effects of individual plant species, their phylogeny, and their functional traits on soil communities, mesocosms containing plants grown in monoculture were established in a fenced enclosure at Colt Park within the Ingleborough National Nature Reserve in England (54°11'38.7"N 2°20'54.4”W). Mesocosms were constructed from polypropylene pots (38 x 38 x 30 cm) filled with 10 cm of rinsed gravel and 20 cm sieved and homogenized top soil (pH ~5.8; 8.9 C%; 0.92 N%). Top soil was a brown earth sourced from the adjacent grassland, a mesotrophic temperate grassland under extensive agricultural management, which involved light grazing by sheep and cattle from autumn to spring, but no grazing during the growing season when an annual hay crop was taken, and an occasional light dressing of farmyard manure or mineral fertilizer (~25 kg ha-1 N) in early spring ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/j.1365-2664.2010.01925.x", "ISBN" : "1365-2664", "ISSN" : "00218901", "abstract" : "Summary\\n1. In Europe, grassland agriculture is one of the dominant land uses. A major aim of European agri-environment policy is the management of grassland for botanical diversity conservation and restoration, together with the delivery of ecosystem services including soil carbon (C) sequestration.\\n\\n2. To test whether management for biodiversity restoration has additional benefits for soil C sequestration, we investigated C and nitrogen (N) accumulation rates in soil and C and N pools in vegetation in a long-term field experiment (16 years) in which fertilizer application and plant seeding were manipulated. In addition, the abundance of the legume Trifolium pratense was manipulated for the last 2 years. To unravel the mechanisms underlying changes in soil C and N pools, we also tested for effects of diversity restoration management on soil structure, ecosystem respiration and soil enzyme activities.\\n\\n3. We show that the long-term biodiversity restoration practices increased soil C and N storage especially when these treatments were combined with the recent promotion of the legume Trifolium pratense, sequestering 317 g C and 35 g N m\u22122 year\u22121 in the most successful management treatment. These high rates of C and N accumulation were associated with reduced ecosystem respiration, increased soil organic matter content and improved soil structure. Cessation of fertilizer use, however, reduced the amount of C and N contained in vegetation.\\n\\n4. Synthesis and applications. Our findings show that long-term diversity restoration practices can yield significant benefits for soil C storage when they are combined with increased abundance of a single, sub-ordinate legume species. Moreover, we show that these management practices deliver additional ecosystem benefits such as N storage in soil and improved soil structure.", "author" : [ { "dropping-particle" : "", "family" : "Deyn", "given" : "Gerlinde B.", "non-dropping-particle" : "De", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Shiel", "given" : "Robert S.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Ostle", "given" : "Nick J.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Mcnamara", "given" : "Niall P.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Oakley", "given" : "Simon", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Young", "given" : "Iain", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Freeman", "given" : "Christopher", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Fenner", "given" : "Nathalie", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Quirk", "given" : "Helen", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Journal of Applied Ecology", "id" : "ITEM-1", "issue" : "3", "issued" : { "date-parts" : [ [ "2011" ] ] }, "page" : "600-608", "title" : "Additional carbon sequestration benefits of grassland diversity restoration", "type" : "article-journal", "volume" : "48" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(De Deyn et al., 2011)", "plainTextFormattedCitation" : "(De Deyn et al., 2011)", "previouslyFormattedCitation" : "(De Deyn et al., 2011)" }, "properties" : { }, "schema" : "" }(De Deyn et al., 2011). Twenty-one grassland plant species (Fig. 1) were germinated and grown in a greenhouse from commercial seed (Emorsgate Seeds, Norfolk, PE34 4RT, UK) or from seed collected at the site. Mesocosms were planted and arranged in a randomized block design with four blocks. Plants were actively weeded and harvested annually. Plant biomass and soil was collected in July, approximately two years following planting, during the height of the growing season and before seed filling. Eight to 20 leaves from at least three individuals per mesocosm were clipped and stored in sealed plastic bags at 4 °C prior to processing. A representative 6.8 cm diameter soil core was taken from the complete soil column of each mesocosm, and soil subsamples were frozen and shipped on dry ice to the University of Colorado for molecular soil community analysis. The remainder of the soil was immediately passed through a 4-mm sieve. All root material not passing through the sieve was retained and stored at 4 °C before being washed free of soil prior to processing for root trait measurements.Field plots design and samplingExperimental field plots were established 2 km from the mesocosm enclosure at Selside Shaw, within the Ingleborough National Nature Reserve. The plots were established in 2012, in a mesotrophic grassland with similar management, vegetation and soil to the meadow at Colt Park. The soil was characterized as a clayey brown earth soil with 60% clay, <1% silt, 39% sand, 5.7±0.4 pH (mean ± standard deviation), 4.9±1.4 %C, and 0.46±0.13 %N. Native grassland species were added to the existing plant communities in 6 m × 6 m field plots with the aim of creating a gradient of plant communities of increasing functional diversity and complexity. Over two years the plots were seeded (2014-2015) and planted with seedlings (2013-2015) of species belonging to one of three plant functional groups, namely the grasses (Cynosurus cristatus, Dactylis glomerata, Festuca rubra, Poa trivialis and Briza media), forbs (Achillea millefolium, Geranium sylvaticum, Geum rivale, Leucanthemum vulgare, Plantago lanceolata, Prunella vulgaris, Hypochaeris radicata, Leontodon hispidus, Filipendula ulmaria, and Centaurea nigra), and legumes (Lathyrus pratensis, Lotus corniculatus, Trifolium pretense and Trifolium repens) or their respective two- and three-way combinations. These species are typical of species-rich mesotrohic meadow communities (UK National Vegetation Classification MG3bADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "author" : [ { "dropping-particle" : "", "family" : "Rodwell", "given" : "J.S.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "edition" : "3rd", "editor" : [ { "dropping-particle" : "", "family" : "Rodwell", "given" : "J S", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "id" : "ITEM-1", "issued" : { "date-parts" : [ [ "1992" ] ] }, "publisher" : "Cambridge University Press", "title" : "British plant communities. Volume 3. Grassland and montane communities", "type" : "book" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Rodwell, 1992)", "manualFormatting" : "; Rodwell, 1992)", "plainTextFormattedCitation" : "(Rodwell, 1992)", "previouslyFormattedCitation" : "(Rodwell, 1992)" }, "properties" : { }, "schema" : "" }; Rodwell, 1992), the target plant community for biodiversity ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1046/j.1365-2664.2003.00780.x", "ISBN" : "0021-8901", "ISSN" : "00218901", "abstract" : "1. The enhancement of biodiversity in meadow grassland, an environmental aim of European agricultural policy, requires definition of appropriate management regimes and the rate at which they enhance biodiversity and change ecosystem properties. We describe vegetation changes in a 10-year trial on mesotrophic grassland that was previously agriculturally improved, plus change in the soil microbial community and fertility, important factors that influence biodiversity. 2. Management treatments were three hay-cut dates, plus two mineral fertilizer, two seed addition and two farmyard manure (FYM) applications. Treatment combinations included the traditional management regime (21 July hay-cut date, no mineral fertilizer, autumn grazing with cattle, spring grazing with sheep), modern variants of this (14 June hay-cut date, mineral fertilizer) and exceptional historic variants (1 September hay-cut date). 3. Sowing seed increased species richness and, in the absence of fertilizer and FYM, produced a plant community similar to Geranium sylvaticum\u2013Anthoxanthum odouratum grassland. The greatest cover of sown species was found in seeded treatments, cut for hay on 21 July, in the absence of mineral fertilizer. The target plant community (MG3b grassland) was most rapidly achieved with a 21 July hay cut. Initial decrease in Ellenberg fertility scores only persisted in the 21 July and 1 September cut dates when mineral fertilizer was absent. Soil phosphate was lowest in the joint absence of mineral fertilizer and FYM. 4. There were few treatment effects on the soil microflora. Bacterial biomass was reduced when FYM was applied with the 14 June cut date, but increased when FYM was applied with the 1 September cut date. Fungal biomass decreased when mineral fertilizer was applied. 5. Increased species richness, primarily through an increase in legumes, stress-tolerant and stress-tolerant ruderal plant strategists, was associated with an increase in soil fungi and the abundance of fungi relative to bacteria. All these were associated with seed addition to unfertilized plots cut on 21 July, in the absence of FYM, indicating a functional role for individual species. 6. Synthesis and applications. The enhancement of biodiversity in meadow grassland is a long-term (> 10-year) secondary succession, most rapidly achieved in the absence of mineral fertilizer by cutting for hay in mid-July and autumn grazing with cattle. The sowing of key functional species, i.e. legumes and Rhina\u2026", "author" : [ { "dropping-particle" : "", "family" : "Smith", "given" : "R. S.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Shiel", "given" : "R. S.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "R. D.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Millward", "given" : "D.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Corkhill", "given" : "P.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Rolph", "given" : "G.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Hobbs", "given" : "P. J.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Peacock", "given" : "S.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Journal of Applied Ecology", "id" : "ITEM-1", "issue" : "1", "issued" : { "date-parts" : [ [ "2003" ] ] }, "page" : "51-64", "title" : "Soil microbial community, fertility, vegetation and diversity as targets in the restoration management of a meadow grassland", "type" : "article-journal", "volume" : "40" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Smith et al., 2003)", "plainTextFormattedCitation" : "(Smith et al., 2003)", "previouslyFormattedCitation" : "(Smith et al., 2003)" }, "properties" : { }, "schema" : "" }(Smith et al., 2003). Together with unmodified control communities, this created a total of eight plant community treatments with five replicates of each arranged in a randomized design (n = 40 plots). Details on species added, seedling densities, and sowing rates across all treatments are given in Table S1. We note that most, but not all, of the species contained in the mesocosms were represented in the field plots.We sampled vegetation and soil from four of the eight treatments (control, forb addition, legume addition, and grass-forb-legume addition) in July 2015. To sample vegetation and soil, 30 cm diameter sampling rings were placed at representative locations within plots (n = 4 per plot with 5 plots per treatment; i.e. n = 20 per treatment), and aboveground plant biomass was harvested from within each sampling ring. One 6.8 cm x 10 cm soil core was collected from within the center of each sampling ring and processed identically to the mesocosm soil samples. Root material was processed as above for use in the root-based assessment of plant community composition.Soil community compositionFungal, bacterial, protistan, and metazoan communities were assessed in soil samples following molecular marker gene sequencing protocols as described in Prober et al. 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Briefly, DNA was extracted from each sample, and ribosomal marker genes were amplified using PCR with barcoded primers unique to each sample. We used the ITS1F/ITS2 and the 515f/926r primer pairs for fungi and bacteria, respectively, and the 1391f/EukBr primer set for protists and metazoa. Amplicon pools were sequenced on an Illumina MiSeq instrument using 2x251 bp sequencing kits at the BioFrontiers sequencing facility at the University of Colorado. Appropriate controls were used throughout the laboratory process to ensure there were no contaminants. 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Raw sequences were first demultiplexed by comparing index reads to a key, and paired sequences were trimmed to uniform lengths. Sequences were then dereplicated, and the unique sequence pairs were denoised using the ‘dada’ function with ‘err=NULL’ and ‘selfConsist = TRUE’. Potential primers and adapters were then screened and removed using a custom script (). Next, paired-end sequences were merged and chimeras were removed. 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Zygomycota classifications were changed to Mucoromycota as per ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.3852/16-042", "ISBN" : "0027-5514", "ISSN" : "0027-5514", "PMID" : "27738200", "abstract" : "Zygomycete fungi were classified as a single phylum, Zygomycota, based on sexual reproduction by zygospores, frequent asexual reproduction by sporangia, absence of multicellular sporocarps, and production of coenocytic hyphae, all with some exceptions. Molecular phylogenies based on one or a few genes did not support the monophyly of the phylum, however, and the phylum was subsequently abandoned. Here we present phylogenetic analyses of a genome-scale data set for 46 taxa, including 25 zygomycetes and 192 proteins, and we demonstrate that zygomycetes comprise two major clades that form a paraphyletic grade. A formal phylogenetic classification is proposed herein and includes two phyla, six subphyla, four classes and 16 orders. On the basis of these results, the phyla Mucoromycota and Zoopagomycota are circumscribed. Zoopagomycota comprises Entomophtoromycotina, Kickxellomycotina and Zoopagomycotina; it constitutes the earliest diverging lineage of zygomycetes and contains species that are primarily parasites and pathogens of small animals (e.g. amoeba, insects, etc.) and other fungi, i.e. mycoparasites. Mucoromycota comprises Glomeromycotina, Mortierellomycotina, and Mucoromycotina and is sister to Dikarya. It is the more derived clade of zygomycetes and mainly consists of mycorrhizal fungi, root endophytes, and decomposers of plant material. Evolution of trophic modes, morphology, and analysis of genome-scale data are discussed.", "author" : [ { "dropping-particle" : "", "family" : "Spatafora", "given" : "Joseph W.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Chang", "given" : "Ying", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Benny", "given" : "Gerald L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Lazarus", "given" : "Katy", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Smith", "given" : "Matthew E.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Berbee", "given" : "Mary L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bonito", "given" : "Gregory", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Corradi", "given" : "Nicolas", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Grigoriev", "given" : "Igor", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Gryganskyi", "given" : "Andrii", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "James", "given" : "Timothy Y.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "O\u2019Donnell", "given" : "Kerry", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Roberson", "given" : "Robert W.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Taylor", "given" : "Thomas N.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Uehling", "given" : "Jessie", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Vilgalys", "given" : "Rytas", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "White", "given" : "Merlin M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Stajich", "given" : "Jason E.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Mycologia", "id" : "ITEM-1", "issue" : "5", "issued" : { "date-parts" : [ [ "2016" ] ] }, "page" : "1028-1046", "title" : "A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data", "type" : "article-journal", "volume" : "108" }, "suppress-author" : 1, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(2016)", "manualFormatting" : " Spatafora et al. (2016)", "plainTextFormattedCitation" : "(2016)", "previouslyFormattedCitation" : "(2016)" }, "properties" : { }, "schema" : "" } Spatafora et al. (2016). 16S rRNA gene sequences identified as chloroplasts, mitochondria, or Archaea were removed. To account for differences in sequencing depths, samples were rarefied to 5,300, 1,300, 2,400, and 1,250 sequences per sample for fungi, bacteria, protists, and metazoa, respectively. Putative fungal functional groups were identified using FUNGuild ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1016/j.funeco.2015.06.006", "ISSN" : "17545048", "author" : [ { "dropping-particle" : "", "family" : "Nguyen", "given" : "Nhu H.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Song", "given" : "Zewei", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bates", "given" : "Scott T.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Branco", "given" : "Sara", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Tedersoo", "given" : "Leho", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Menke", "given" : "Jon", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Schilling", "given" : "Jonathan S.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Kennedy", "given" : "Peter G.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Fungal Ecology", "id" : "ITEM-1", "issued" : { "date-parts" : [ [ "2015" ] ] }, "page" : "241-248", "publisher" : "Elsevier Ltd", "title" : "FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild", "type" : "article-journal", "volume" : "20" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Nguyen et al., 2015)", "plainTextFormattedCitation" : "(Nguyen et al., 2015)", "previouslyFormattedCitation" : "(Nguyen et al., 2015)" }, "properties" : { }, "schema" : "" }(Nguyen et al., 2015).Plant community compositionPlant community composition in the field plot samples was assessed in four ways: (1) by sorting the aboveground biomass to species and measuring the biomass (dry weight) of each species, (2) by molecular analysis of the aboveground biomass, (3) by molecular analysis of the roots contained in the soil cores, and (4) by molecular analysis of DNA extracted from the soil samples. For visual inspection, harvested aboveground biomass was identified the same day as collection, and tissue from each species was dried and weighed. For molecular assessments, aboveground and root biomass samples were freeze-dried, ground, and homogenized prior to DNA extraction. We prepared DNA for sequencing following a protocol similar to ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1073/pnas.1503283112", "ISBN" : "0027-8424", "ISSN" : "0027-8424", "PMID" : "26034267", "abstract" : "Niche partitioning facilitates species coexistence in a world of limited resources, thereby enriching biodiversity. For decades, biologists have sought to understand how diverse assemblages of large mammalian herbivores (LMH) partition food resources. Several complementary mechanisms have been identified, including differential consumption of grasses versus nongrasses and spatiotemporal stratification in use of different parts of the same plant. However, the extent to which LMH partition food-plant species is largely unknown because comprehensive species-level identification is prohibitively difficult with traditional methods. We used DNA metabarcoding to quantify diet breadth, composition, and overlap for seven abundant LMH species (six wild, one domestic) in semiarid African savanna. These species ranged from almost-exclusive grazers to almost-exclusive browsers: Grass consumption inferred from mean sequence relative read abundance (RRA) ranged from >99% (plains zebra) to <1% (dik-dik). Grass RRA was highly correlated with isotopic estimates of % grass consumption, indicating that RRA conveys reliable quantitative information about consumption. Dietary overlap was greatest between species that were similar in body size and proportional grass consumption. Nonetheless, diet composition differed between all species-even pairs of grazers matched in size, digestive physiology, and location-and dietary similarity was sometimes greater across grazing and browsing guilds than within them. Such taxonomically fine-grained diet partitioning suggests that coarse trophic categorizations may generate misleading conclusions about competition and coexistence in LMH assemblages, and that LMH diversity may be more tightly linked to plant diversity than is currently recognized.", "author" : [ { "dropping-particle" : "", "family" : "Kartzinel", "given" : "Tyler R.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Chen", "given" : "Patricia a.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Coverdale", "given" : "Tyler C.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Erickson", "given" : "David L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Kress", "given" : "W. 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(2015)", "plainTextFormattedCitation" : "(2015)", "previouslyFormattedCitation" : "(2015)" }, "properties" : { }, "schema" : "" }Kartzinel et al. (2015). We identified the genus-level plant community composition by targeting both the P6 loop of the trnL gene and the rRNA ITS region. We extracted DNA using the PowerSoil DNA Isolation Kit (Mo Bio Laboratories, Inc., Carlsbad, CA, USA), and soil samples were diluted 1:10 prior to amplification. The primer set trnL(UAA)c/trnL(UAA) with included Illumina sequencing adapters was used to amplify the trnL-P6 marker following a PCR protocol of: denaturing at 94 °C for 2 min followed by 36 cycles of 94 °C for 1 min, 55 °C for 30 s, and 72 °C for 30 s, with a 5-min final extension at 72 °C. To amplify the ITS region, we used the forward primer, ITS1-F, and included two reverse primers, ITS1Ast-R and ITS1Poa-R ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1073/pnas.1503283112", "ISBN" : "0027-8424", "ISSN" : "0027-8424", "PMID" : "26034267", "abstract" : "Niche partitioning facilitates species coexistence in a world of limited resources, thereby enriching biodiversity. For decades, biologists have sought to understand how diverse assemblages of large mammalian herbivores (LMH) partition food resources. Several complementary mechanisms have been identified, including differential consumption of grasses versus nongrasses and spatiotemporal stratification in use of different parts of the same plant. However, the extent to which LMH partition food-plant species is largely unknown because comprehensive species-level identification is prohibitively difficult with traditional methods. We used DNA metabarcoding to quantify diet breadth, composition, and overlap for seven abundant LMH species (six wild, one domestic) in semiarid African savanna. These species ranged from almost-exclusive grazers to almost-exclusive browsers: Grass consumption inferred from mean sequence relative read abundance (RRA) ranged from >99% (plains zebra) to <1% (dik-dik). Grass RRA was highly correlated with isotopic estimates of % grass consumption, indicating that RRA conveys reliable quantitative information about consumption. Dietary overlap was greatest between species that were similar in body size and proportional grass consumption. Nonetheless, diet composition differed between all species-even pairs of grazers matched in size, digestive physiology, and location-and dietary similarity was sometimes greater across grazing and browsing guilds than within them. Such taxonomically fine-grained diet partitioning suggests that coarse trophic categorizations may generate misleading conclusions about competition and coexistence in LMH assemblages, and that LMH diversity may be more tightly linked to plant diversity than is currently recognized.", "author" : [ { "dropping-particle" : "", "family" : "Kartzinel", "given" : "Tyler R.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Chen", "given" : "Patricia a.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Coverdale", "given" : "Tyler C.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Erickson", "given" : "David L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Kress", "given" : "W. 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All primers included appropriate Illumina adapters, and PCR reactions were carried out as for trnL amplification. Each PCR was done in duplicate and the amplification product was combined. All products for each sample were combined in equal volumes and cleaned using the UltraClean PCR Clean-Up Kit (Mo Bio Laboratories, Inc.). Illumina Nextera barcodes were added to the amplicons using an 8-cycle PCR, amplicons were cleaned and pooled using the SequalPrep kit (Invitrogen, Carlsbad, CA, USA), and sequenced on an Illumina MiSeq instrument with a 2x151 bp kit at the University of Colorado BioFrontiers sequencing facility.We processed raw plant sequences in a similar manner as for soil community sequences described above. We used the DADA2 pipeline ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1101/024034", "ISSN" : "1548-7091", "PMID" : "27214047", "abstract" : "Microbial communities are commonly characterized by amplifying and sequenc-ing target genes, but errors limit the precision of amplicon sequencing. We present DADA2, a software package that models and corrects amplicon errors. DADA2 identified more real variants than other methods in Illumina-sequenced mock communities, some differing by a single nucleotide, while outputting fewer spurious sequences. DADA2 analysis of vaginal samples revealed a di-versity of Lactobacillus crispatus strains undetected by OTU methods. The importance of microbial communities to human and environmental health has moti-vated methods for their efficient characterization. The most common, and cost-effective, method is the amplification and sequencing of targeted genetic elements. Amplicon se-quencing of taxonomic marker genes such as 16S rRNA [1], the ITS region [2] or 18S rRNA [3] provides a census of a community. Functional diversity can be probed by targeting functional genes [4]. Disentangling errors from biological variation in amplicon sequencing data presents unique challenges, which has prompted the development of amplicon-specific error-correction meth-ods [5, 6, 7, 8]. Most of these methods were designed for pyrosequenced amplicons, and cannot be applied to Illumina sequencing.", "author" : [ { "dropping-particle" : "", "family" : "Callahan", "given" : "Benjamin J", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "McMurdie", "given" : "Paul J", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Rosen", "given" : "Michael J", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Han", "given" : "Andrew W", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Johnson", "given" : "Amy Jo", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Holmes", "given" : "Susan P", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Nature Methods", "id" : "ITEM-1", "issue" : "7", "issued" : { "date-parts" : [ [ "2016" ] ] }, "page" : "581-583", "title" : "DADA2 : High resolution sample inference from amplicon data", "type" : "article-journal", "volume" : "13" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Callahan et al., 2016)", "plainTextFormattedCitation" : "(Callahan et al., 2016)", "previouslyFormattedCitation" : "(Callahan et al., 2016)" }, "properties" : { }, "schema" : "" }(Callahan et al., 2016) to trim forward and reverse paired reads to 145 and 130 bp, respectively. Following the denoising step, Illumina adapters were removed, paired, end reads were merged, and chimeras were filtered. We assigned taxonomy to each sequence using BLAST searches against the GenBank NR database. Sequences were assigned taxonomy only if ≥ 80% of the sequence aligned to a reference sequence and they matched the reference sequence with ≥ 95% identity. If a sequence had multiple best matches to reference sequences, a common genus and/or family name was assigned if one existed. Otherwise, sequences were assigned as ‘unknown’. Taxonomy assignments were manually checked and verified in reference to species known to exist at the site. Separate taxa tables were created based on trnL amplicons and each of the Asteraceae and Poaceae ITS amplicons. Samples with fewer than 550, 1000, and 100 sequences were removed from taxa tables based on trnL, Asteraceae ITS, and Poaceae ITS amplicons, respectively. We calculated the relative abundance of individual plant genera in each sample using the trnL sequence counts. Because the trnL gene yields limited taxonomic resolution for the Asteraceae and Poaceae, we replaced the total relative abundances of taxa (mostly unknown genera) within these two families with normalized relative abundances of genera determined using the ITS sequence data.Plant traitsAll leaf and root traits were measured using standard protocols ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1071/BT02124", "ISBN" : "0067-1924", "ISSN" : "00671924", "PMID" : "3377", "abstract" : "There is growing recognition that classifying terrestrial plant species on the basis of their function (into 'functional types') rather than their higher taxonomic identity, is a promising way forward for tackling important ecological questions at the scale of ecosystems, landscapes or biomes. These questions include those on vegetation responses to and vegetation effects on, environmental changes (e.g. changes in climate, atmospheric chemistry, land use or other disturbances). There is also growing consensus about a shortlist of plant traits that should underlie such functional plant classifications, because they have strong predictive power of important ecosystem responses to environmental change and/or they themselves have strong impacts on ecosystem processes. The most favoured traits are those that are also relatively easy and inexpensive to measure for large numbers of plant species. Large international research efforts, promoted by the IGBP\u2013GCTE Programme, are underway to screen predominant plant species in various ecosystems and biomes worldwide for such traits. This paper provides an international methodological protocol aimed at standardising this research effort, based on consensus among a broad group of scientists in this field. It features a practical handbook with step-by-step recipes, with relatively brief information about the ecological context, for 28 functional traits recognised as critical for tackling large-scale ecological questions.", "author" : [ { "dropping-particle" : "", "family" : "Cornelissen", "given" : "J H C", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Lavorel", "given" : "S", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Garnier", "given" : "E", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "D\u00edaz", "given" : "S.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Buchmann", "given" : "N", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Gurvich", "given" : "D E", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Reich", "given" : "P B", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Steege", "given" : "H", "non-dropping-particle" : "Ter", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Morgan", "given" : "H D", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Heijden", "given" : "M G A", "non-dropping-particle" : "Van Der", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Pausas", "given" : "J G", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Poorter", "given" : "H", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Australian Journal of Botany", "id" : "ITEM-1", "issue" : "4", "issued" : { "date-parts" : [ [ "2003" ] ] }, "page" : "335-380", "title" : "A handbook of protocols for standardised and easy measurement of plant functional traits worldwide", "type" : "article", "volume" : "51" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Cornelissen et al., 2003)", "plainTextFormattedCitation" : "(Cornelissen et al., 2003)", "previouslyFormattedCitation" : "(Cornelissen et al., 2003)" }, "properties" : { }, "schema" : "" }(Cornelissen et al., 2003). Briefly, we measured specific leaf area, specific root length, leaf dry matter content and root dry matter content by weighing and scanning the fresh leaf and root samples. The samples were then oven dried at 60 °C for 48 h and their dry weights measured. The scanned digital images were analyzed in WinRhizo (Reagent Instruments Inc., Ville de Québec, QC, Canada) to determine leaf areas, root lengths and root diameters. Shoot and root N and C contents from the mesocosm-grown plants and the field sample plant communities were measured on an Elementar Vario elemental analyzer (Langenselbold, Germany). In both cases, plant material was freeze-dried and thoroughly homogenized prior to measurement.Soil characteristicsSoil characteristics were measured as in Orwin et al. ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/j.1365-2745.2010.01679.x", "ISBN" : "0022-0477", "ISSN" : "00220477", "abstract" : "1. Global change is likely to alter plant community structure, with consequences for the structure and functioning of the below-ground community and potential feedbacks to climate change. Understanding the mechanisms behind these plant\u2013soil interactions and feedbacks to the Earth-system is therefore crucial. One approach to understanding such mechanisms is to use plant traits as predictors of functioning.\\r\\n2. We used a field-based monoculture experiment involving nine grassland species that had been growing on the same base soil for 7 years to test whether leaf, litter and root traits associated with different plant growth strategies can be linked to an extensive range of soil properties relevant to carbon, nitrogen and phosphorus cycling. Soil properties included the biomass and structure of the soil microbial community, soil nutrients, soil microclimate and soil process rates.\\r\\n3. Plant species with a high relative growth rate (RGR) were associated with high leaf and litter quality (e.g. low toughness, high nitrogen concentrations), an elevated biomass of bacteria relative to fungi in soil, high rates of soil nitrogen mineralization and concentrations of extractable inorganic nitrogen, and to some extent higher available phosphorus pools.\\r\\n4. In contrast to current theory, species with a high RGR and litter quality were associated with soils with a lower rate of soil respiration and slow decomposition rates. This indicates that predicting processes that influence carbon cycling from plant traits may be more complex than predicting processes that influence nitrogen and phosphorus cycling.\\r\\n5. Root traits did not show strong relationships to RGR, leaf or litter traits, but were strongly correlated with several soil properties, particularly the biomass of bacteria relative to fungi in soil and measures relating to soil carbon cycling.\\r\\n6. Synthesis. Our results indicate that plant species from a single habitat can result in significant divergence in soil properties and functioning when grown in monoculture, and that many of these changes are strongly and predictably linked to variation in plant traits associated with different growth strategies. Traits therefore have the potential to be a powerful tool for understanding the mechanisms behind plant\u2013soil interactions and ecosystem functioning, and for predicting how changes in plant species composition associated with global change will feedback to the Earth-system.", "author" : [ { "dropping-particle" : "", "family" : "Orwin", "given" : "Kate H.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Buckland", "given" : "Sarah M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Johnson", "given" : "David", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Turner", "given" : "Benjamin L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Smart", "given" : "Simon", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Oakley", "given" : "Simon", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Journal of Ecology", "id" : "ITEM-1", "issue" : "5", "issued" : { "date-parts" : [ [ "2010" ] ] }, "page" : "1074-1083", "title" : "Linkages of plant traits to soil properties and the functioning of temperate grassland", "type" : "article-journal", "volume" : "98" }, "suppress-author" : 1, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(2010)", "plainTextFormattedCitation" : "(2010)", "previouslyFormattedCitation" : "(2010)" }, "properties" : { }, "schema" : "" }(2010). pH was measured using a ratio of 1 g fresh soil: 2.5 ml dH2O. Dissolved inorganic N, individual ions (NO3-N , NH4-N), and net N mineralization were assessed using 1 M KCl extracts, and dissolved organic N was assessed using water extracts as in Bardgett et al. 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Total soluble N was determined following oxidation of these extracts using potassium persulphate ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "author" : [ { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Streeter", "given" : "Tania C", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bol", "given" : "Roland", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Ecology", "id" : "ITEM-1", "issue" : "5", "issued" : { "date-parts" : [ [ "2003" ] ] }, "page" : "1277-1287", "title" : "Soil microbes compete effectively with plants for organic-nitrogen inputs to temperate grasslands", "type" : "article-journal", "volume" : "84" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Bardgett et al., 2003)", "plainTextFormattedCitation" : "(Bardgett et al., 2003)", "previouslyFormattedCitation" : "(Bardgett et al., 2003)" }, "properties" : { }, "schema" : "" }(Bardgett et al., 2003). Extracted mineral fractions were quantified using standard spectrophotometric protocols on a AA3 segmented flow analyser (SEAL Analytical Inc., Mequon, WI, USA). Total C and N of dried and ground subsamples were measured using an Elementar Vario EL elemental analyzer.Statistical analysesAll statistical analyses were performed in R ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "author" : [ { "dropping-particle" : "", "family" : "R Core Team", "given" : "", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "id" : "ITEM-1", "issued" : { "date-parts" : [ [ "2016" ] ] }, "number" : "3.3.0", "publisher" : "R Foundation for Statistical Computing", "publisher-place" : "Vienna, Austria", "title" : "R: A language and environment for statistical computing", "type" : "article" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(R Core Team, 2016)", "plainTextFormattedCitation" : "(R Core Team, 2016)", "previouslyFormattedCitation" : "(R Core Team, 2016)" }, "properties" : { }, "schema" : "" }(R Core Team, 2016) using specific packages where noted, and the package ‘mctoolsr’ () was used to facilitate data manipulation and analyses. To represent differences in community composition, we calculated Bray-Curtis dissimilarities using square-root transformed relative abundances. Permutational analysis of variance (PERMANOVA), as implemented in the ‘adonis’ function from the ‘vegan’ package, was used to test for differences in soil community composition across factors. We compared the relative abundances of taxa from control (i.e. unplanted) mesocosm communities to the relative abundances of taxa from planted mesocosms using linear mixed effects models based on rank-transformed data with block included as a random effect. P values were corrected for multiple comparisons using false discovery rate corrections, and zeros were replaced with an estimate of the lower detection limit (1×10-5) when creating Fig. S3 to avoid infinite fold changes. To test for differences in soil community composition across mesocosm plant species, we used PERMANOVA and included block identity as a random factor in the model. Network analysis plots were created using the ‘igraph’ package with multidimensional scaling to distribute points. Soil taxa were considered present if their mean relative abundance was ≥ 0.1%, and only taxa with a relative abundance > 0.5% that associated with ≥ 1 plant species are shown. We identified particular soil taxa that associated with specific plant species using indicator analyses ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.2307/2963459", "ISBN" : "0012-9615", "ISSN" : "00129615", "PMID" : "1344", "abstract" : "This paper presents a new and simple method to find indicator species and species assemblages characterizing groups of sites. The novelty of our approach lies in the way we combine a species relative abundance with its relative frequency of occurrence in the various groups of sites. This index is maximum when all individuals of a species are found in a single group of sites and when the species occurs in all sites of that group; it is a symmetric indicator. The statistical significance of the species indicator values is evaluated using a randomization procedure. Contrary to TWINSPAN, our indicator index for a given species is independent of the other species relative abundances, and there is no need to use pseudospecies. The new method identifies indicator species for typologies of species releve \u00b4s obtained by any hierarchical or nonhierarchical classification procedure; its use is independent of the classification method. Because indicator species give ecological meaning to groups of sites, this method provides criteria to compare typologies, to identify where to stop dividing clusters into subsets, and to point out the main levels in a hierarchical classification of sites. Species can be grouped on the basis of their indicator values for each clustering level, the heterogeneous nature of species assemblages observed in any one site being well pre- served. Such assemblages are usually a mixture of eurytopic (higher level) and stenotopic species (characteristic of lower level clusters). The species assemblage approach demon- strates the importance of the \u2018\u2018sampled patch size,\u2019\u2019 i.e., the diversity of sampled ecological combinations, when we compare the frequencies of core and satellite species. A new way to present species\u2013site tables, accounting for the hierarchical relationships among species, is proposed. A large data set of carabid beetle distributions in open habitats of Belgium is used", "author" : [ { "dropping-particle" : "", "family" : "Dufr\u00eane", "given" : "Marc", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Legendre", "given" : "Pierre", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Ecological Monographs", "id" : "ITEM-1", "issue" : "3", "issued" : { "date-parts" : [ [ "1997" ] ] }, "page" : "345-366", "title" : "Species assemblages and indicator species: The need for a flexible asymmetrical approach", "type" : "article-journal", "volume" : "67" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Dufr\u00eane and Legendre, 1997)", "plainTextFormattedCitation" : "(Dufr\u00eane and Legendre, 1997)", "previouslyFormattedCitation" : "(Dufr\u00eane and Legendre, 1997)" }, "properties" : { }, "schema" : "" }(Dufrêne and Legendre, 1997). ‘Cosmopolitan’ soil taxa were defined as those taxa associated with all plant species (i.e. had a mean relative abundance ≥ 0.1% across replicates for each species), ‘intermediate’ as taxa associated with only 2 to 20 plant species, and ‘specialized’ as taxa that associated with only a single plant species.To test the relationship between the composition of soil communities and plant species relatedness in the mesocosms, we used the phylogeny from ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1890/12-0743.1", "ISBN" : "1939-9170", "ISSN" : "0012-9658", "abstract" : "This data set represents a comprehensive, dated phylogeny of a large European flora comprising the vascular plants of the British Isles, Germany, The Netherlands, and Switzerland, totaling 4685 species. The phylogeny thus encompasses all species in the trait databases BIOLFLOR, PLANTATT, and BioBase 2003. The topology of the phylogentic tree is based on a backbone family phylogeny of the Angiosperm Phylogeny Group III. Subsequently, partial phylogenetic subtrees derived from a total of 518 recent molecular studies were manually pruned onto the backbone tree, using multi-gene consensus topologies if possible. Similarly, 1103 internal nodes and the root node were dated based on 261 recent studies. Finally, an ultrametric tree was calculated by placing undated nodes evenly between dated nodes. The phylogeny provides a reference data set for comparative analyses of trait correlations, trait evolution, trait based ecological processes, community assembly, or other phylogenetically informed analyses across a large taxon of European plant species. It can readily be used in phylogenetic analysis tools like ape, phytools, picante, or MESQUITE.", "author" : [ { "dropping-particle" : "", "family" : "Durka", "given" : "Walter", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Michalski", "given" : "Stefan G", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Ecology", "id" : "ITEM-1", "issue" : "10", "issued" : { "date-parts" : [ [ "2012" ] ] }, "page" : "2297", "title" : "Daphne: a dated phylogeny of a large European flora for phylogenetically informed ecological analyses", "type" : "article-journal", "volume" : "93" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Durka and Michalski, 2012)", "manualFormatting" : "Durka and Michalski (2012)", "plainTextFormattedCitation" : "(Durka and Michalski, 2012)", "previouslyFormattedCitation" : "(Durka and Michalski, 2012)" }, "properties" : { }, "schema" : "" }Durka and Michalski (2012). Relationships between difference in soil community composition and plant phylogenetic distances were evaluated using Mantel tests with Spearman correlations. We tested for a phylogenetic signal in the relative abundance of individual protist taxa using the phylosig function in the ‘phytools’ package, where the statistic, K, represents the strength of the signal ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/j.0014-3820.2003.tb00285.x", "ISBN" : "1558-5646", "ISSN" : "1558-5646", "PMID" : "12778543", "abstract" : "Abstract The primary rationale for the use of phylogenetically based statistical methods is that phylogenetic signal, the tendency for related species to resemble each other, is ubiquitous. Whether this assertion is true for a given trait in a given lineage is an empirical question, but general tools for detecting and quantifying phylogenetic signal are inadequately developed. We present new methods for continuous-valued characters that can be implemented with either phylogenetically independent contrasts or generalized least-squares models. First, a simple randomization procedure allows one to test the null hypothesis of no pattern of similarity among relatives. The test demonstrates correct Type I error rate at a nominal \u03b1= 0.05 and good power (0.8) for simulated datasets with 20 or more species. Second, we derive a descriptive statistic, K, which allows valid comparisons of the amount of phylogenetic signal across traits and trees. Third, we provide two biologically motivated branch-length transformations, one based on the Ornstein-Uhlenbeck (OU) model of stabilizing selection, the other based on a new model in which character evolution can accelerate or decelerate (ACDC) in rate (e.g., as may occur during or after an adaptive radiation). Maximum likelihood estimation of the OU (d) and ACDC (g) parameters can serve as tests for phylogenetic signal because an estimate of d or g near zero implies that a phylogeny with little hierarchical structure (a star) offers a good fit to the data. Transformations that improve the fit of a tree to comparative data will increase power to detect phylogenetic signal and may also be preferable for further comparative analyses, such as of correlated character evolution. Application of the methods to data from the literature revealed that, for trees with 20 or more species, 92% of traits exhibited significant phylogenetic signal (randomization test), including behavioral and ecological ones that are thought to be relatively evolutionarily malleable (e.g., highly adaptive) and/or subject to relatively strong environmental (nongenetic) effects or high levels of measurement error. Irrespective of sample size, most traits (but not body size, on average) showed less signal than expected given the topology, branch lengths, and a Brownian motion model of evolution (i.e., K was less than one), which may be attributed to adaptation and/or measurement error in the broad sense (including errors in estimates of phenotypes, branch l\u2026", "author" : [ { "dropping-particle" : "", "family" : "Blomberg", "given" : "Simon P.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Garland", "given" : "Theodore", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Ives", "given" : "Anthony R.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Evolution", "id" : "ITEM-1", "issue" : "4", "issued" : { "date-parts" : [ [ "2003", "4" ] ] }, "page" : "717-745", "title" : "Testing for phylogenetic signal in comparative data: behavioral traits are more labile", "type" : "article-journal", "volume" : "57" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Blomberg et al., 2003)", "plainTextFormattedCitation" : "(Blomberg et al., 2003)", "previouslyFormattedCitation" : "(Blomberg et al., 2003)" }, "properties" : { }, "schema" : "" }(Blomberg et al., 2003). We calculated multivariate dissimilarities in trait values by normalizing and standardizing individual trait values and calculating Euclidian distances. We tested the relationship between Euclidian trait distances and community composition dissimilarities using Mantel tests.For the field samples, we calculated differences in the phylogenetic structure of plant communities (i.e. phylogenetic dissimilarity) using UniFrac ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1038/ismej.2010.133", "ISSN" : "1751-7370", "PMID" : "20827291", "author" : [ { "dropping-particle" : "", "family" : "Lozupone", "given" : "Catherine", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Lladser", "given" : "Manuel E", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Knights", "given" : "Dan", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Stombaugh", "given" : "Jesse", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Knight", "given" : "Rob", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "The ISME journal", "id" : "ITEM-1", "issue" : "2", "issued" : { "date-parts" : [ [ "2011", "2" ] ] }, "page" : "169-72", "publisher" : "Nature Publishing Group", "title" : "UniFrac: an effective distance metric for microbial community comparison.", "type" : "article-journal", "volume" : "5" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Lozupone et al., 2011)", "plainTextFormattedCitation" : "(Lozupone et al., 2011)", "previouslyFormattedCitation" : "(Lozupone et al., 2011)" }, "properties" : { }, "schema" : "" }(Lozupone et al., 2011) as implemented in the package, ‘picante’. We used the plant phylogenetic tree as reported in Durka and Michalski ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1890/12-0743.1", "ISBN" : "1939-9170", "ISSN" : "0012-9658", "abstract" : "This data set represents a comprehensive, dated phylogeny of a large European flora comprising the vascular plants of the British Isles, Germany, The Netherlands, and Switzerland, totaling 4685 species. The phylogeny thus encompasses all species in the trait databases BIOLFLOR, PLANTATT, and BioBase 2003. The topology of the phylogentic tree is based on a backbone family phylogeny of the Angiosperm Phylogeny Group III. Subsequently, partial phylogenetic subtrees derived from a total of 518 recent molecular studies were manually pruned onto the backbone tree, using multi-gene consensus topologies if possible. Similarly, 1103 internal nodes and the root node were dated based on 261 recent studies. Finally, an ultrametric tree was calculated by placing undated nodes evenly between dated nodes. The phylogeny provides a reference data set for comparative analyses of trait correlations, trait evolution, trait based ecological processes, community assembly, or other phylogenetically informed analyses across a large taxon of European plant species. It can readily be used in phylogenetic analysis tools like ape, phytools, picante, or MESQUITE.", "author" : [ { "dropping-particle" : "", "family" : "Durka", "given" : "Walter", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Michalski", "given" : "Stefan G", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Ecology", "id" : "ITEM-1", "issue" : "10", "issued" : { "date-parts" : [ [ "2012" ] ] }, "page" : "2297", "title" : "Daphne: a dated phylogeny of a large European flora for phylogenetically informed ecological analyses", "type" : "article-journal", "volume" : "93" }, "suppress-author" : 1, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(2012)", "plainTextFormattedCitation" : "(2012)", "previouslyFormattedCitation" : "(2012)" }, "properties" : { }, "schema" : "" }(2012), and plants not identified to the genus level were removed. We assessed the relationship between phylogenetic dissimilarity and the Bray-Curtis dissimilarities in soil community composition using Mantel tests with Spearman correlations.To assess whether differences in plant community composition predicted variation in soil community composition beyond the explanatory power of soil characteristics, we built models of soil community composition dissimilarity using multiple regression on distance matrices (MRM) as implemented in the ‘ecodist’ package and compared the explanatory power of the model with and without the addition of plant community dissimilarity as a predictor variable. In these models, each soil variable was transformed using log or inverse transformations where necessary to approximate a normal distribution, and they were standardized prior to calculating Euclidian distances. MRM was implemented with rank (i.e. Spearman) correlations, and the “best” models containing only soil variables were derived by first including all soil variables and using backwards elimination until all predictors explained significant levels of variation in the response dissimilarities.Results and DiscussionThe effect of plant species identity on soil communitiesOverall, the mesocosm soils contained expectedly diverse communities (Fig. S1A). Soil fungal communities were primarily composed of Ascomycota [43% of internal transcribed spacer (ITS) sequence reads, on average], Basidiomycota (31%), and Mucoromycota (21%); bacterial communities were primarily composed of Acidobacteria (31% of 16S rRNA gene reads, on average), Proteobacteria (20%), and Verrucomicrobia (16%); protistan communities were primarily composed of Rhizaria (26%), Amoebozoa (25%), Alveolata (22%), and Stramenopiles (16%); and metazoan communities were primarily composed of Nematoda (33%), Arthropoda (28%), and Annelida (15%; Fig. S1B). The structure of these communities was similar to those found in other temperate grasslands ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1073/pnas.1508382112", "ISSN" : "0027-8424", "author" : [ { "dropping-particle" : "", "family" : "Leff", "given" : "Jonathan W", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Jones", "given" : "Stuart E", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Prober", "given" : "Suzanne M", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Barberan", "given" : "Albert", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Borer", "given" : "Elizabeth T", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Firn", "given" : "Jennifer L", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Harpole", "given" : "W Stanley", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Hobbie", "given" : "Sarah E", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Hofmockel", "given" : "Kirsten S", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Knops", "given" : "Johannes M H", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "McCulley", "given" : "Rebecca L", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Pierre", "given" : "Kimberly", "non-dropping-particle" : "La", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Risch", "given" : "Anita C", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Seabloom", "given" : "Eric W", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Schuetz", "given" : "Martin", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Steenbock", "given" : "Christopher", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Stevens", "given" : "Carly J", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Fierer", "given" : "Noah", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Proceedings of the National Academy of Sciences of the United States of America", "id" : "ITEM-1", "issue" : "35", "issued" : { "date-parts" : [ [ "2015" ] ] }, "page" : "10967-10972", "title" : "Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe", "type" : "article-journal", "volume" : "112" }, "uris" : [ "" ] }, { "id" : "ITEM-2", "itemData" : { "DOI" : "10.1038/ismej.2012.147", "ISBN" : "1751-7362", "ISSN" : "1751-7362", "PMID" : "23235291", "abstract" : "Aim The biogeography and global distribution of protists has long been disputed, with two primary, opposing views. To test these two sets of views in greater detail, we have compiled the available data for marine benthic ciliates and assessed the general patterns of their diversity and distribution compared with Metazoa. Location World-wide. Methods A comprehensive database (1342 species, over 350 sources) was used to analyse the diversity, distribution, species occurrences and range size distribution of free-living ciliates that inhabit marine sediments in 17 geographical regions. Results Twenty-five per cent of the species have been found in a single region only, whereas 18% are widespread (they occur in more than half the regions covering both hemispheres). Only 5\u20137% of regional faunas are endemic, which is much lower than for macroorganisms. Regional diversity depends neither on total area nor on coastline length and does not show any obvious latitudinal trends, but correlates highly with the investigation effort expended in a region and (negatively) with the average salinity. A comparison of species composition reveals distinctions between the Arctic Area (the White, Barents and Kara seas), Laurasian Area (north Atlantic, north Pacific and European seas), Gondwanian Area (Southern Ocean) and the Antarctic. No clear geographical correlations are found for faunistic com-position at the genus or family levels. There is the tendency to narrow the latitudinal ranges for species found at high latitudes (reversal of Rapoport's rule). Main conclusions Undersampling and data insufficiency are the key factors affecting the observed diversity and distribution of microorganisms. Nevertheless, marine benthic ciliates demonstrate certain patterns that generally agree with the 'moderate endemicity' model (Foissner, 2004, 2008), but consistently contradict the regularities commonly observed for multicellular taxa. Thus, ciliates do have a biogeography, but their macroecological patterns may be different in some respects from that of macroorganisms.", "author" : [ { "dropping-particle" : "", "family" : "Bates", "given" : "Scott T", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Clemente", "given" : "Jose C", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Flores", "given" : "Gilberto E", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Walters", "given" : "William Anthony", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Parfrey", "given" : "Laura Wegener", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Knight", "given" : "Rob", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Fierer", "given" : "Noah", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "The ISME Journal", "id" : "ITEM-2", "issue" : "3", "issued" : { "date-parts" : [ [ "2013" ] ] }, "page" : "652-659", "title" : "Global biogeography of highly diverse protistan communities in soil", "type" : "article-journal", "volume" : "7" }, "uris" : [ "" ] }, { "id" : "ITEM-3", "itemData" : { "DOI" : "10.1073/pnas.1103824108", "ISBN" : "0027-8424", "ISSN" : "0027-8424", "PMID" : "22006309", "abstract" : "The global distribution of soil animals and the relationship of below-ground biodiversity to above-ground biodiversity are not well understood. We examined 17,516 environmental 18S rRNA gene sequences representing 20 phyla of soil animals sampled from 11 locations covering a range of biomes and latitudes around the world. No globally cosmopolitan taxa were found and only 14 of 2,259 operational taxonomic units (OTUs) found were common to four or more locations. Half of those were circumpolar and may reflect higher connectivity among circumpolar locations compared with other locations in the study. Even when OTU assembly criteria were relaxed to approximate the family taxonomic level, only 34 OTUs were common to four or more locations. A comparison of our diversity and community structure data to environmental factors suggests that below-ground animal diversity may be inversely related to above-ground biodiversity. Our data suggest that greater soil inorganic N and lower pH could explain the low below-ground biodiversity found at locations of high above-ground biodiversity. Our locations could also be characterized as being dominated by microarthropods or dominated by nematodes. Locations dominated by arthropods were primarily forests with lower soil pH, root biomass, mean annual temperature, low soil inorganic N and higher C:N, litter and moisture compared with nematode-dominated locations, which were mostly grasslands. Overall, our data indicate that small soil animals have distinct biogeographical distributions and provide unique evidence of the link between above-ground and below-ground biodiversity at a global scale.", "author" : [ { "dropping-particle" : "", "family" : "Wu", "given" : "Tiehang", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Ayres", "given" : "Edward", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Wall", "given" : "Diana H", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Garey", "given" : "James R", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Proceedings of the National Academy of Sciences", "id" : "ITEM-3", "issue" : "43", "issued" : { "date-parts" : [ [ "2011" ] ] }, "page" : "17720-17725", "title" : "Molecular study of worldwide distribution and diversity of soil animals", "type" : "article-journal", "volume" : "108" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Leff et al., 2015; Bates et al., 2013; Wu et al., 2011)", "plainTextFormattedCitation" : "(Leff et al., 2015; Bates et al., 2013; Wu et al., 2011)", "previouslyFormattedCitation" : "(Leff et al., 2015; Bates et al., 2013; Wu et al., 2011)" }, "properties" : { }, "schema" : "" }(Leff et al., 2015; Bates et al., 2013; Wu et al., 2011).Plant species identity explained differences in the overall composition of soil fungal (R2 = 0.33; P < 0.001), bacterial (R2 = 0.27; P = 0.02), protistan (R2 = 0.32; P < 0.001), and metazoan (R2 = 0.31; P < 0.001) communities (Fig. 1A). Further, these plant species effects were driven by differences among multiple plant species rather than one or a small number of plant species associating with distinct belowground communities (Fig. 1B, Fig. S2). Certain fungal, protistan, and metazoan taxa tended to be strongly associated with individual plant species, while others tended to have more general associations (Fig. 1C, Fig. S3). For example, the fungal taxa identified as Olpidium brassicae and Phoma sp. associated with Achillea millefolium, while several Ascomycota, Basidiomycota, and Mucoromycota taxa were associated with all plant species (Fig. S4). We used an indicator analysis approach to identify those taxonomic groups that were most strongly associated with each of the individual plant species and found that many of the plant species formed specific associations (Fig. S4). Since there are likely to be different traits associated with more specialized versus more cosmopolitan soil taxa ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1890/11-1745.1", "ISBN" : "0012-9658", "ISSN" : "00129658", "PMID" : "22928415", "abstract" : "The biodiversity of microbial communities has important implications for the stability and functioning of ecosystem processes. Yet, very little is known about the environmental factors that define the microbial niche and how this influences the composition and activity of microbial communities. In this study, we derived niche parameters from physiological response curves that quantified microbial respiration for a diverse collection of soil bacteria and fungi along a soil moisture gradient. On average, soil microorganisms had relatively dry optima (0.3 MPa) and were capable of respiring under low water potentials (-2.0 MPa). Within their limits of activity, microorganisms exhibited a wide range of responses, suggesting that some taxa may be able to coexist by partitioning the moisture niche axis. For example, we identified dry-adapted generalists that tolerated a broad range of water potentials, along with wet-adapted specialists with metabolism restricted to less-negative water potentials. These contrasting ecological strategies had a phylogenetic signal at a coarse taxonomic level (phylum), suggesting that the moisture niche of soil microorganisms is highly conserved. In addition, variation in microbial responses along the moisture gradient was linked to the distribution of several functional traits. In particular, strains that were capable of producing biofilms had drier moisture optima and wider niche breadths. However, biofilm production appeared to come at a cost that was reflected in a prolonged lag time prior to exponential growth, suggesting that there is a trade-off associated with traits that allow microorganisms to contend with moisture stress. Together, we have identified functional groups of microorganisms that will help predict the structure and functioning of microbial communities under contrasting soil moisture regimes.", "author" : [ { "dropping-particle" : "", "family" : "Lennon", "given" : "Jay T.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Aanderud", "given" : "Zachary T.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Lehmkuhl", "given" : "B. K.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Schoolmaster", "given" : "Donald R.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Ecology", "id" : "ITEM-1", "issue" : "8", "issued" : { "date-parts" : [ [ "2012" ] ] }, "page" : "1867-1879", "title" : "Mapping the niche space of soil microorganisms using taxonomy and traits", "type" : "article-journal", "volume" : "93" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Lennon et al., 2012)", "plainTextFormattedCitation" : "(Lennon et al., 2012)", "previouslyFormattedCitation" : "(Lennon et al., 2012)" }, "properties" : { }, "schema" : "" }(Lennon et al., 2012), we investigated whether soil taxa unique to individual plant species tended to represent different taxonomic groups when compared to taxa that were more ubiquitous across plant species. Cosmopolitan taxa were represented by a higher proportion of Mucoromycota, Acidobacteria, Rhizaria, and Nematoda, while more specialized taxa were represented by a greater proportion of Glomeromycota, Planctomycetes, Alveolata, and Rotifera (Fig. 1D). Additionally, cosmopolitan fungal taxa represented a greater proportion of putative saprotrophs compared to more specialized taxa, which had a greater proportion of pathogens and mutualists (Fig. 1E). This suggests that, in temperate grasslands, pathogens and mutualists tend to be more strongly limited to individual plant species, while saprotrophs are more cosmopolitan and less influenced by plant species identity. This finding is in concordance with a previous study conducted in an Amazon rainforest showing stronger plant-soil linkages for pathogenic and mycorrhizal fungi compared to saprotrophs ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1038/ismej.2013.66", "ISBN" : "1751-7362", "ISSN" : "1751-7370", "PMID" : "23598789", "abstract" : "The Amazon basin harbors a diverse ecological community that has a critical role in the maintenance of the biosphere. Although plant and animal communities have received much attention, basic information is lacking for fungal or prokaryotic communities. This is despite the fact that recent ecological studies have suggested a prominent role for interactions with soil fungi in structuring the diversity and abundance of tropical rainforest trees. In this study, we characterize soil fungal communities across three major tropical forest types in the western Amazon basin (terra firme, seasonally flooded and white sand) using 454 pyrosequencing. Using these data, we examine the relationship between fungal diversity and tree species richness, and between fungal community composition and tree species composition, soil environment and spatial proximity. We find that the fungal community in these ecosystems is diverse, with high degrees of spatial variability related to forest type. We also find strong correlations between \u03b1- and \u03b2-diversity of soil fungi and trees. Both fungal and plant community \u03b2-diversity were also correlated with differences in environmental conditions. The correlation between plant and fungal richness was stronger in fungal lineages known for biotrophic strategies (for example, pathogens, mycorrhizas) compared with a lineage known primarily for saprotrophy (yeasts), suggesting that this coupling is, at least in part, due to direct plant-fungal interactions. These data provide a much-needed look at an understudied dimension of the biota in an important ecosystem and supports the hypothesis that fungal communities are involved in the regulation of tropical tree diversity.", "author" : [ { "dropping-particle" : "", "family" : "Peay", "given" : "Kabir G", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Baraloto", "given" : "Christopher", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Fine", "given" : "Paul V A", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "The ISME journal", "id" : "ITEM-1", "issue" : "9", "issued" : { "date-parts" : [ [ "2013" ] ] }, "page" : "1852-61", "title" : "Strong coupling of plant and fungal community structure across western Amazonian rainforests.", "type" : "article-journal", "volume" : "7" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Peay et al., 2013)", "plainTextFormattedCitation" : "(Peay et al., 2013)", "previouslyFormattedCitation" : "(Peay et al., 2013)" }, "properties" : { }, "schema" : "" }(Peay et al., 2013).Can the effect of plant species identity be explained by plant phylogeny or functional traits?We next sought to assess whether plant species identity effects could be explained by plant phylogeny or leaf and root functional traits, two attributes that could potentially be used to predict plant associations with belowground communities a priori. The mesocosm plant species represented eight families including Poaceae, Asteraceae, and Fabaceae, providing an opportunity to evaluate the influence of a wide-ranging phylogeny on the composition of soil communities. Plant phylogenetic distances were not significantly related to differences in fungal, bacterial, or metazoan community composition (P > 0.1 in all cases; Fig. 2A). Differences in protistan community composition were related to plant phylogenetic distance, but this relationship was relatively weak (rho = 0.29, P = 0.002; Fig. 2A). Nonetheless, the relative abundance of Stramenopiles was significantly related to plant species phylogeny (K = 0.51, P = 0.004; Fig. S5). We might expect plant phylogenetic differences to be associated with the structure of belowground communities due to coevolution with mutualists or pathogens ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1016/j.tree.2005.08.009", "ISBN" : "0169-5347", "ISSN" : "01695347", "PMID" : "16701446", "abstract" : "Aboveground and belowground species interactions drive ecosystem properties at the local scale, but it is unclear how these relationships scale-up to regional and global scales. Here, we discuss our current knowledge of aboveground and belowground diversity links from a global to a local scale. Global diversity peaks towards the Equator for large, aboveground organisms, but not for small (mainly belowground) organisms, suggesting that there are size-related biodiversity gradients in global aboveground-belowground linkages. The generalization of aboveground-belowground diversity relationships, and their role in ecosystem functioning, requires surveys at scales that are relevant to the organisms and ecosystem properties. Habitat sizes and diversity gradients can differ significantly between aboveground and belowground organisms and between ecosystems. These gradients in biodiversity and plant community trait perception need to be acknowledged when studying aboveground-belowground biodiversity linkages. ?? 2005 Elsevier Ltd. All rights reserved.", "author" : [ { "dropping-particle" : "", "family" : "Deyn", "given" : "Gerlinde B.", "non-dropping-particle" : "De", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Putten", "given" : "Wim H.", "non-dropping-particle" : "Van Der", "parse-names" : false, "suffix" : "" } ], "container-title" : "Trends in Ecology and Evolution", "id" : "ITEM-1", "issue" : "11", "issued" : { "date-parts" : [ [ "2005" ] ] }, "page" : "625-633", "title" : "Linking aboveground and belowground diversity", "type" : "article-journal", "volume" : "20" }, "uris" : [ "" ] }, { "id" : "ITEM-2", "itemData" : { "DOI" : "10.1111/ele.12378", "ISBN" : "1461-0248", "ISSN" : "14610248", "PMID" : "25328022", "abstract" : "We examined whether plant-soil feedback and plant-field abundance were phylogenetically conserved. For 57 co-occurring native and exotic plant species from an old field in Canada, we collected a data set on the effects of three\u00a0soil biota treatments on plant growth: net whole-soil feedback (combined effects of mutualists and antagonists), feedback with arbuscular mycorrhizal fungi (AMF) collected from soils of conspecific plants, and feedback with Glomus etunicatum, a dominant mycorrhizal fungus. We found phylogenetic signal in both net whole-soil feedback and feedback with AMF of conspecifics; conservatism was especially strong among native plants but absent among exotics. The abundance of plants in the field was also conserved, a pattern underlain by shared plant responses to soil biota. We conclude that soil biota influence the abundance of close plant relatives in nature.", "author" : [ { "dropping-particle" : "", "family" : "Anacker", "given" : "Brian L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Klironomos", "given" : "John N.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Maherali", "given" : "Hafiz", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Reinhart", "given" : "Kurt O.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Strauss", "given" : "Sharon Y.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Ecology Letters", "id" : "ITEM-2", "issue" : "12", "issued" : { "date-parts" : [ [ "2014" ] ] }, "page" : "1613-1621", "title" : "Phylogenetic conservatism in plant-soil feedback and its implications for plant abundance", "type" : "article-journal", "volume" : "17" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(De Deyn and Van Der Putten, 2005; Anacker et al., 2014)", "plainTextFormattedCitation" : "(De Deyn and Van Der Putten, 2005; Anacker et al., 2014)", "previouslyFormattedCitation" : "(De Deyn and Van Der Putten, 2005; Anacker et al., 2014)" }, "properties" : { }, "schema" : "" }(De Deyn and Van Der Putten, 2005; Anacker et al., 2014); however, this did not appear to be the case for most soil taxonomic groups. Further, the general lack of a relationship between plant phylogeny and belowground communities found in our study is consistent with studies of plant-soil feedbacks, which likewise have shown no relation to plant phylogeny ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/nph.13238", "ISBN" : "1469-8137", "ISSN" : "14698137", "PMID" : "25557183", "abstract" : "* Understanding the mechanisms underlying negative plant\u2013soil feedbacks remains a critical challenge in plant ecology. If closely related species are more similar, then phylogeny could be used as a predictor for plant species interactions, simplifying our understanding of how plant\u2013soil feedbacks structure plant communities, underlie invasive species dynamics, or reduce agricultural productivity. * Here, we test the utility of phylogeny for predicting plant\u2013soil feedbacks by undertaking a hierarchical Bayesian meta-analysis on all available pairwise plant\u2013soil feedback experiments conducted over the last two decades, including 133 plant species in 329 pairwise interactions. * We found that the sign and magnitude of plant\u2013soil feedback effects were not explained by the phylogenetic distance separating interacting species. This result was consistent across different life forms, life cycles, provenances, and phylogenetic scales. * Our analysis shows that, contrary to widespread assumption, relatedness is a poor predictor of plant\u2013soil feedback effects.", "author" : [ { "dropping-particle" : "", "family" : "Mehrabi", "given" : "Zia", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Tuck", "given" : "Sean L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "New Phytologist", "id" : "ITEM-1", "issue" : "3", "issued" : { "date-parts" : [ [ "2015" ] ] }, "page" : "1071-1075", "title" : "Relatedness is a poor predictor of negative plant-soil feedbacks", "type" : "article-journal", "volume" : "205" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Mehrabi and Tuck, 2015)", "plainTextFormattedCitation" : "(Mehrabi and Tuck, 2015)", "previouslyFormattedCitation" : "(Mehrabi and Tuck, 2015)" }, "properties" : { }, "schema" : "" }(Mehrabi and Tuck, 2015).The measured leaf and root traits were highly variable across the mesocosm species. Grassland plants vary in their ecological strategies. Exploitative species grow fast under high nutrient conditions and have characteristically high specific leaf areas and N contents while conservative species are selected to survive under lower nutrient conditions and have opposite traits ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1046/j.1365-2435.2002.00664.x", "ISSN" : "0269-8463", "author" : [ { "dropping-particle" : "", "family" : "Lavorel", "given" : "S.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Garnier", "given" : "E.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Functional Ecology", "id" : "ITEM-1", "issue" : "5", "issued" : { "date-parts" : [ [ "2002", "10" ] ] }, "page" : "545-556", "title" : "Predicting changes in community composition and ecosystem functioning from plant traits: revisiting the Holy Grail", "type" : "article-journal", "volume" : "16" }, "uris" : [ "" ] }, { "id" : "ITEM-2", "itemData" : { "DOI" : "10.1111/nph.13828", "ISBN" : "8224406113", "ISSN" : "14698137", "PMID" : "25869851", "abstract" : "Although fine roots are important components of the global carbon cycle, there is limited understanding of root structure\u2013function relationships among species. We determined whether root respiration rate and decomposability, two key processes driving carbon cycling but always studied separately, varied with root morphological and chemical traits, in a coordi- nated way that would demonstrate the existence of a root economics spectrum (RES). ? Twelve traits were measured on fine roots (diameter \u2264 2 mm) of 74 species (31 graminoids and 43 herbaceous and dwarf shrub eudicots) collected in three biomes. ? The findings of this study support the existence of a RES representing an axis of trait varia- tion in which root respiration was positively correlated to nitrogen concentration and specific root length and negatively correlated to the root dry matter content, lignin : nitrogen ratio and the remaining mass after decomposition. This pattern of traits was highly consistent within graminoids but less consistent within eudicots, as a result of an uncoupling between decomposability and morphology, and of heterogeneity of individual roots of eudicots within the fine-root pool. ? The positive relationship found between root respiration and decomposability is essential for a better understanding of vegetation\u2013soil feedbacks and for improving terrestrial bio- sphere models predicting the consequences of plant community changes for carbon cycling. Introduction", "author" : [ { "dropping-particle" : "", "family" : "Roumet", "given" : "Catherine", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Birouste", "given" : "Marine", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Picon-Cochard", "given" : "Catherine", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Ghestem", "given" : "Murielle", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Osman", "given" : "Normaniza", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Vrignon-Brenas", "given" : "Sylvain", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Cao", "given" : "Kun fang", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Stokes", "given" : "Alexia", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "New Phytologist", "id" : "ITEM-2", "issued" : { "date-parts" : [ [ "2016" ] ] }, "title" : "Root structure-function relationships in 74 species: Evidence of a root economics spectrum related to carbon economy", "type" : "article-journal" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Lavorel and Garnier, 2002; Roumet et al., 2016)", "plainTextFormattedCitation" : "(Lavorel and Garnier, 2002; Roumet et al., 2016)", "previouslyFormattedCitation" : "(Lavorel and Garnier, 2002; Roumet et al., 2016)" }, "properties" : { }, "schema" : "" }(Lavorel and Garnier, 2002; Roumet et al., 2016). For each plant species in the mesocosms, we measured the plant traits that are known to be indicative of the tradeoffs in these life history strategies (Fig. S6A, Table S2). For example, the Fabaceae species tended to have a greater shoot and root N and C content, while Poaceae species tended to have high leaf dry matter contents (Fig. S6B). Yet, there were no strong or significant relationships (i.e., Bonferroni corrected P < 0.05) between belowground community composition and individual leaf or root traits (Fig. 2C). Furthermore, multivariate dissimilarity in leaf and root traits of plant species was not predictive of differences in communities of any of the soil taxonomic groups (P > 0.1 in all cases; Fig. 2B).These results suggest that the plant traits we measured are not effective indicators of the specific relationships plants form with belowground communities. Previous studies have detected relationships between plant traits and coarse measures of microbial community composition ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/j.1365-2745.2010.01679.x", "ISBN" : "0022-0477", "ISSN" : "00220477", "abstract" : "1. Global change is likely to alter plant community structure, with consequences for the structure and functioning of the below-ground community and potential feedbacks to climate change. Understanding the mechanisms behind these plant\u2013soil interactions and feedbacks to the Earth-system is therefore crucial. One approach to understanding such mechanisms is to use plant traits as predictors of functioning.\\r\\n2. We used a field-based monoculture experiment involving nine grassland species that had been growing on the same base soil for 7 years to test whether leaf, litter and root traits associated with different plant growth strategies can be linked to an extensive range of soil properties relevant to carbon, nitrogen and phosphorus cycling. Soil properties included the biomass and structure of the soil microbial community, soil nutrients, soil microclimate and soil process rates.\\r\\n3. Plant species with a high relative growth rate (RGR) were associated with high leaf and litter quality (e.g. low toughness, high nitrogen concentrations), an elevated biomass of bacteria relative to fungi in soil, high rates of soil nitrogen mineralization and concentrations of extractable inorganic nitrogen, and to some extent higher available phosphorus pools.\\r\\n4. In contrast to current theory, species with a high RGR and litter quality were associated with soils with a lower rate of soil respiration and slow decomposition rates. This indicates that predicting processes that influence carbon cycling from plant traits may be more complex than predicting processes that influence nitrogen and phosphorus cycling.\\r\\n5. Root traits did not show strong relationships to RGR, leaf or litter traits, but were strongly correlated with several soil properties, particularly the biomass of bacteria relative to fungi in soil and measures relating to soil carbon cycling.\\r\\n6. Synthesis. Our results indicate that plant species from a single habitat can result in significant divergence in soil properties and functioning when grown in monoculture, and that many of these changes are strongly and predictably linked to variation in plant traits associated with different growth strategies. Traits therefore have the potential to be a powerful tool for understanding the mechanisms behind plant\u2013soil interactions and ecosystem functioning, and for predicting how changes in plant species composition associated with global change will feedback to the Earth-system.", "author" : [ { "dropping-particle" : "", "family" : "Orwin", "given" : "Kate H.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Buckland", "given" : "Sarah M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Johnson", "given" : "David", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Turner", "given" : "Benjamin L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Smart", "given" : "Simon", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Oakley", "given" : "Simon", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Journal of Ecology", "id" : "ITEM-1", "issue" : "5", "issued" : { "date-parts" : [ [ "2010" ] ] }, "page" : "1074-1083", "title" : "Linkages of plant traits to soil properties and the functioning of temperate grassland", "type" : "article-journal", "volume" : "98" }, "uris" : [ "" ] }, { "id" : "ITEM-2", "itemData" : { "DOI" : "10.1111/j.1461-0248.2012.01844.x", "ISSN" : "1461023X", "author" : [ { "dropping-particle" : "", "family" : "Vries", "given" : "Franciska T.", "non-dropping-particle" : "de", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Manning", "given" : "Pete", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Tallowin", "given" : "Jerry R. B.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Mortimer", "given" : "Simon R.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Pilgrim", "given" : "Emma S.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Harrison", "given" : "Kathryn A.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Hobbs", "given" : "Phil J.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Quirk", "given" : "Helen", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Shipley", "given" : "Bill", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Cornelissen", "given" : "Johannes H. C.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Kattge", "given" : "Jens", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Ecology Letters", "id" : "ITEM-2", "issue" : "11", "issued" : { "date-parts" : [ [ "2012" ] ] }, "page" : "1230-1239", "title" : "Abiotic drivers and plant traits explain landscape-scale patterns in soil microbial communities", "type" : "article-journal", "volume" : "15" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Orwin et al., 2010; de Vries et al., 2012)", "plainTextFormattedCitation" : "(Orwin et al., 2010; de Vries et al., 2012)", "previouslyFormattedCitation" : "(Orwin et al., 2010; de Vries et al., 2012)" }, "properties" : { }, "schema" : "" }(Orwin et al., 2010; de Vries et al., 2012) or specific microbial groups, such as ammonia oxidizers ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1093/femsec/fiw091", "ISSN" : "15746941", "PMID" : "27130939", "abstract" : "The influence of plants on archaeal (AOA) and bacterial (AOB) ammonia oxidisers is poorly understood. Higher microbial activity in the rhizosphere, including organic nitrogen (N) mineralisation, may stimulate both groups, while ammonia uptake by plants may favour AOA, considered to prefer lower ammonia concentration. We therefore hypothesised (i) higher AOA and AOB abundances in the rhizosphere than bulk soil and (ii) that AOA are favoured over AOB in the rhizosphere of plants with an exploitative strategy and high N demand, especially (iii) during early growth, when plant N uptake is higher. These hypotheses were tested by growing 20 grassland plants, covering a spectrum of resource-use strategies, and determining AOA and AOB amoA gene abundances, rhizosphere and bulk soil characteristics and plant functional traits. Joint Bayesian mixed models indicated no increase in AO in the rhizosphere, but revealed that AOA were more abundant in the rhizosphere of exploitative plants, mostly grasses, and less abundant under conservative plants. In contrast, AOB abundance in the rhizosphere and bulk soil depended on pH, rather than plant traits. These findings provide a mechanistic basis for plant-ammonia oxidiser interactions and for links between plant functional traits and ammonia oxidiser ecology. Keywords:", "author" : [ { "dropping-particle" : "", "family" : "Thion", "given" : "C\u00e9cile E.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Poirel", "given" : "Jessica D", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Cornulier", "given" : "Thomas", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Vries", "given" : "Franciska T", "non-dropping-particle" : "De", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Prosser", "given" : "James I", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "FEMS Microbiology Ecology", "id" : "ITEM-1", "issue" : "7", "issued" : { "date-parts" : [ [ "2016" ] ] }, "title" : "Plant nitrogen-use strategy as a driver of rhizosphere archaeal and bacterial ammonia oxidiser abundance", "type" : "article-journal", "volume" : "92" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Thion et al., 2016)", "plainTextFormattedCitation" : "(Thion et al., 2016)", "previouslyFormattedCitation" : "(Thion et al., 2016)" }, "properties" : { }, "schema" : "" }(Thion et al., 2016). However, our findings are in line with other studies. For example, Porazinska et al. ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "author" : [ { "dropping-particle" : "", "family" : "Porazinska", "given" : "Dorota L", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Blaauw", "given" : "Maria B", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Hunt", "given" : "H William", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Parsons", "given" : "Andrew N", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Seastedt", "given" : "Timothy R", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Wall", "given" : "Diana H", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Ecological Monographs", "id" : "ITEM-1", "issue" : "3", "issued" : { "date-parts" : [ [ "2003" ] ] }, "page" : "377-395", "title" : "Relationships at the Aboveground-Belowground Interface: Plants, Soil Biota, and Soil Processes", "type" : "article-journal", "volume" : "73" }, "suppress-author" : 1, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(2003)", "plainTextFormattedCitation" : "(2003)", "previouslyFormattedCitation" : "(2003)" }, "properties" : { }, "schema" : "" }(2003) found that certain soil communities were linked to individual plant species in a prairie grassland, but they were unable to identify traits that could predict soil communities. Likewise, Barberán et al. (ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "abstract" : "We spend the majority of our lives indoors; yet, we currently lack a comprehensive understanding of how the microbial communities found in homes vary across broad geographical regions and what factors are most important in shaping the types of microorganisms found inside homes. Here, we investigated the fungal and bacterial communities found in settled dust collected from inside and outside approximately 1200 homes located across the continental US, homes that represent a broad range of home designs and span many climatic zones. Indoor and outdoor dust samples harboured distinct microbial communities, but these differences were larger for bacteria than for fungi with most indoor fungi originating outside the home. Indoor fungal communities and the distribution of potential allergens varied predictably across climate and geographical regions; where you live determines what fungi live with you inside your home. By contrast, bacterial communities in indoor dust were more strongly influenced by the number and types of occupants living in the homes. In particular, the female : male ratio and whether a house had pets had a significant influence on the types of bacteria found inside our homes highlighting that who you live with determines what bacteria are found inside your home.", "author" : [ { "dropping-particle" : "", "family" : "Barber\u00e1n", "given" : "Albert", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Dunn", "given" : "Robert R.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Reich", "given" : "Brian J.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Pacifici", "given" : "Krishna", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Laber", "given" : "Eric B.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Menninger", "given" : "Holly L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Morton", "given" : "James M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Henley", "given" : "Jessica B.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Leff", "given" : "Jonathan W.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Miller", "given" : "Shelly L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Fierer", "given" : "Noah", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Proc R Soc B", "id" : "ITEM-1", "issue" : "20151139", "issued" : { "date-parts" : [ [ "2015", "8", "26" ] ] }, "note" : "Abstract\n\nWe spend the majority of our lives indoors; yet, we currently lack a comprehensive understanding of how the microbial communities found in homes vary across broad geographical regions and what factors are most important in shaping the types of microorganisms found inside homes. Here, we investigated the fungal and bacterial communities found in settled dust collected from inside and outside approximately 1200 homes located across the continental US, homes that represent a broad range of home designs and span many climatic zones. Indoor and outdoor dust samples harboured distinct microbial communities, but these differences were larger for bacteria than for fungi with most indoor fungi originating outside the home. Indoor fungal communities and the distribution of potential allergens varied predictably across climate and geographical regions; where you live determines what fungi live with you inside your home. By contrast, bacterial communities in indoor dust were more strongly influenced by the number and types of occupants living in the homes. In particular, the female : male ratio and whether a house had pets had a significant influence on the types of bacteria found inside our homes highlighting that who you live with determines what bacteria are found inside your home", "page" : "1-9", "title" : "The ecology of microscopic life in household dust", "type" : "article-journal", "volume" : "282" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Barber\u00e1n et al., 2015a)", "manualFormatting" : "2015a)", "plainTextFormattedCitation" : "(Barber\u00e1n et al., 2015a)", "previouslyFormattedCitation" : "(Barber\u00e1n et al., 2015a)" }, "properties" : { }, "schema" : "" }2015a) demonstrated that plant species identity is more predictive of soil communities than plant traits. Nonetheless, it is possible that the plant-soil organism associations we observed could have been driven by unmeasured plant traits given that certain plant characteristics must explain the species identity effects we observed. For example, variations in the quantity and quality of root exudates can influence soil community composition ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1038/ismej.2008.80", "ISBN" : "1751-7370 (Electronic)", "ISSN" : "1751-7362", "PMID" : "18754043", "abstract" : "The rhizosphere is active and dynamic in which newly generated carbon, derived from root exudates, and ancient carbon, in soil organic matter (SOM), are available for microbial growth. Stable isotope probing (SIP) was used to determine bacterial communities assimilating each carbon source in the rhizosphere of four plant species. Wheat, maize, rape and barrel clover (Medicago truncatula) were grown separately in the same soil under (13)CO(2) (99% of atom (13)C) and DNA extracted from rhizosphere soil was fractionated by isopycnic centrifugation. Bacteria-assimilating root exudates were characterized by denaturing gradient gel electrophoresis (DGGE) analysis of (13)C-DNA and root DNA, whereas those assimilating SOM were identified from (12)C-DNA. Plant species root exudates significantly shaped rhizosphere bacterial community structure. Bacteria related to Sphingobacteriales and Myxococcus assimilated root exudates in colonizing roots of all four plants, whwereas bacteria related to Sphingomonadales utilized both carbon sources, and were identified in light, heavy and root compartment DNA. Sphingomonadales were specific to monocotyledons, whereas bacteria related to Enterobacter and Rhizobiales colonized all compartments of all four plants, used both fresh and ancient carbon and were considered as generalists. There was also evidence for an indirect important impact of root exudates, through stimulation of SOM assimilation by a diverse bacterial community.", "author" : [ { "dropping-particle" : "", "family" : "Haichar", "given" : "Feth El Zahar", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Marol", "given" : "Christine", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Berge", "given" : "Odile", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Rangel-Castro", "given" : "J Ignacio", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Prosser", "given" : "James I", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Balesdent", "given" : "J\u00e9r\u00f4me", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Heulin", "given" : "Thierry", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Achouak", "given" : "Wafa", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "The ISME journal", "id" : "ITEM-1", "issue" : "12", "issued" : { "date-parts" : [ [ "2008" ] ] }, "page" : "1221-1230", "title" : "Plant host habitat and root exudates shape soil bacterial community structure.", "type" : "article-journal", "volume" : "2" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Haichar et al., 2008)", "plainTextFormattedCitation" : "(Haichar et al., 2008)", "previouslyFormattedCitation" : "(Haichar et al., 2008)" }, "properties" : { }, "schema" : "" }(Haichar et al., 2008). Likewise, leaf litter chemistry has been shown to be related to coarse measures of soil microbial community composition in a manner broadly consistent with the leaf economic spectrum ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/j.1365-2745.2010.01679.x", "ISBN" : "0022-0477", "ISSN" : "00220477", "abstract" : "1. Global change is likely to alter plant community structure, with consequences for the structure and functioning of the below-ground community and potential feedbacks to climate change. Understanding the mechanisms behind these plant\u2013soil interactions and feedbacks to the Earth-system is therefore crucial. One approach to understanding such mechanisms is to use plant traits as predictors of functioning.\\r\\n2. We used a field-based monoculture experiment involving nine grassland species that had been growing on the same base soil for 7 years to test whether leaf, litter and root traits associated with different plant growth strategies can be linked to an extensive range of soil properties relevant to carbon, nitrogen and phosphorus cycling. Soil properties included the biomass and structure of the soil microbial community, soil nutrients, soil microclimate and soil process rates.\\r\\n3. Plant species with a high relative growth rate (RGR) were associated with high leaf and litter quality (e.g. low toughness, high nitrogen concentrations), an elevated biomass of bacteria relative to fungi in soil, high rates of soil nitrogen mineralization and concentrations of extractable inorganic nitrogen, and to some extent higher available phosphorus pools.\\r\\n4. In contrast to current theory, species with a high RGR and litter quality were associated with soils with a lower rate of soil respiration and slow decomposition rates. This indicates that predicting processes that influence carbon cycling from plant traits may be more complex than predicting processes that influence nitrogen and phosphorus cycling.\\r\\n5. Root traits did not show strong relationships to RGR, leaf or litter traits, but were strongly correlated with several soil properties, particularly the biomass of bacteria relative to fungi in soil and measures relating to soil carbon cycling.\\r\\n6. Synthesis. Our results indicate that plant species from a single habitat can result in significant divergence in soil properties and functioning when grown in monoculture, and that many of these changes are strongly and predictably linked to variation in plant traits associated with different growth strategies. Traits therefore have the potential to be a powerful tool for understanding the mechanisms behind plant\u2013soil interactions and ecosystem functioning, and for predicting how changes in plant species composition associated with global change will feedback to the Earth-system.", "author" : [ { "dropping-particle" : "", "family" : "Orwin", "given" : "Kate H.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Buckland", "given" : "Sarah M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Johnson", "given" : "David", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Turner", "given" : "Benjamin L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Smart", "given" : "Simon", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Oakley", "given" : "Simon", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Journal of Ecology", "id" : "ITEM-1", "issue" : "5", "issued" : { "date-parts" : [ [ "2010" ] ] }, "page" : "1074-1083", "title" : "Linkages of plant traits to soil properties and the functioning of temperate grassland", "type" : "article-journal", "volume" : "98" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Orwin et al., 2010)", "plainTextFormattedCitation" : "(Orwin et al., 2010)", "previouslyFormattedCitation" : "(Orwin et al., 2010)" }, "properties" : { }, "schema" : "" }(Orwin et al., 2010). Also, while we did not observe relationships between plant traits and the overall composition of soil communities, it is possible that specific soil organisms do respond to plant traits, including those taxa directly involved with N cycling ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1093/aob/mcu169", "ISSN" : "0305-7364", "author" : [ { "dropping-particle" : "", "family" : "Legay", "given" : "N.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Baxendale", "given" : "C.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Grigulis", "given" : "K.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Krainer", "given" : "U.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Kastl", "given" : "E.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Schloter", "given" : "M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "R. 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Our objective was to determine how plant\u2013microbe interactions were affected by plant traits. Specifically we analyzed how interactions between plant species and microbes involved in nitrogen cycling were affected by plant traits related to nitrogen nutrition in interaction with soil nitrogen availability. Eleven plant species, selected along an oligotrophic\u2013nitrophilic gradient, were grown individually in a nitrogen-poor soil with two levels of nitrate availability. Plant traits for both carbon and nitrogen nutrition were measured and the genetic structure and abundance of rhizosphere microbial communities, in particular the ammonia oxidizer and nitrate reducer guilds, were analyzed. The structure of the bacterial community in the rhizosphere...", "author" : [ { "dropping-particle" : "", "family" : "Moreau", "given" : "Delphine", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Pivato", "given" : "Barbara", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bru", "given" : "David", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Busset", "given" : "Hugues", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Deau", "given" : "Florence", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Faivre", "given" : "C??line", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Matejicek", "given" : "Annick", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Strbik", "given" : "Florence", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Philippot", "given" : "Laurent", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Mougel", "given" : "Christophe", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Ecology", "id" : "ITEM-2", "issue" : "8", "issued" : { "date-parts" : [ [ "2015", "8" ] ] }, "page" : "2300-2310", "publisher" : "Ecological Society of America", "title" : "Plant traits related to nitrogen uptake influence plant-microbe competition", "type" : "article-journal", "volume" : "96" }, "uris" : [ "" ] }, { "id" : "ITEM-3", "itemData" : { "DOI" : "10.1093/femsec/fiw091", "ISSN" : "15746941", "PMID" : "27130939", "abstract" : "The influence of plants on archaeal (AOA) and bacterial (AOB) ammonia oxidisers is poorly understood. Higher microbial activity in the rhizosphere, including organic nitrogen (N) mineralisation, may stimulate both groups, while ammonia uptake by plants may favour AOA, considered to prefer lower ammonia concentration. We therefore hypothesised (i) higher AOA and AOB abundances in the rhizosphere than bulk soil and (ii) that AOA are favoured over AOB in the rhizosphere of plants with an exploitative strategy and high N demand, especially (iii) during early growth, when plant N uptake is higher. These hypotheses were tested by growing 20 grassland plants, covering a spectrum of resource-use strategies, and determining AOA and AOB amoA gene abundances, rhizosphere and bulk soil characteristics and plant functional traits. Joint Bayesian mixed models indicated no increase in AO in the rhizosphere, but revealed that AOA were more abundant in the rhizosphere of exploitative plants, mostly grasses, and less abundant under conservative plants. In contrast, AOB abundance in the rhizosphere and bulk soil depended on pH, rather than plant traits. These findings provide a mechanistic basis for plant-ammonia oxidiser interactions and for links between plant functional traits and ammonia oxidiser ecology. 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Other potential reasons exist for our failure to detect strong associations between soil communities and plant traits or phylogeny. First, it is possible that if the experiment had a longer duration, additional effects on soil communities would become evident, and these effects would more strongly correspond to differences in plant traits and/or phylogeny. Second, soil can contain DNA from cells that are no longer viable ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1038/nmicrobiol.2016.242", "ISBN" : "9788578110796", "ISSN" : "20585276", "PMID" : "25246403", "abstract" : "applicability for this approach.", "author" : [ { "dropping-particle" : "", "family" : "Carini", "given" : "Paul", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Marsden", "given" : "Patrick J.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Leff", "given" : "Jonathan W.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Morgan", "given" : "Emily E.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Strickland", "given" : "Michael S.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Fierer", "given" : "Noah", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Nature Microbiology", "id" : "ITEM-1", "issue" : "December", "issued" : { "date-parts" : [ [ "2016" ] ] }, "publisher" : "Nature Publishing Group", "title" : "Relic DNA is abundant in soil and obscures estimates of soil microbial diversity", "type" : "article-journal", "volume" : "2" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Carini et al., 2016)", "plainTextFormattedCitation" : "(Carini et al., 2016)", "previouslyFormattedCitation" : "(Carini et al., 2016)" }, "properties" : { }, "schema" : "" }(Carini et al., 2016), and this ‘relic’ DNA could obscure ecological relationships among organisms.Are soil communities in the field predictable based on plant community attributes?The results from the mesocosm study demonstrated that plant species identity is a more important determinant of soil community composition than plant phylogeny or plant traits. Given this, we would hypothesize that knowledge of the species composition of mixed plant communities in the field should be an effective predictor of soil communities. We tested this hypothesis by analyzing plant and soil samples from a series of experimental plots established at a grassland site close to the mesocosm experiment, where grassland community composition had been manipulated for three years to create a gradient of plant species composition and diversity. Plant community composition was assessed using marker gene sequencing of plant DNA extracted from dried and ground representative samples of plant biomass collected immediately above each soil sample, and this molecular approach was verified for efficacy by comparing it to visual assessments of aboveground biomass (Fig. S7).Differences in the composition of each soil taxonomic group were related to differences in plant community composition (P < 0.05 in all cases). By comparing the compositions of the plant communities across experimental plots (using the first principal coordinate score based on aboveground assessments), we could identify specific plant genera that drove variation in soil community composition across the samples (Fig. 3A, Table S3). For instance, some samples had comparatively high relative abundances of Lolium spp. while other samples had high relative abundances of Agrostis spp. These differences in plant community composition were related to the relative abundance of certain groups of soil taxa, including the Ascomycota, Mucoromycota, Acidobacteria, Amoebozoa, Stramenopiles, and Arthropoda (Fig. 3A). These specific associations between plant and soil taxa can ultimately be used to predict the composition of soil communities from plant species abundances. For example, our results suggest that plant communities dominated by Agrostis spp. are likely to have greater relative abundances of Ascomycota and lower relative abundances of Acidobacteria in the soils in which they grow.We also evaluated whether the phylogenetic structure or community-aggregated plant traits ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/j.1461-0248.2012.01844.x", "ISSN" : "1461023X", "author" : [ { "dropping-particle" : "", "family" : "Vries", "given" : "Franciska T.", "non-dropping-particle" : "de", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Manning", "given" : "Pete", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Tallowin", "given" : "Jerry R. 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We did this by testing whether plant communities containing genera with more similar phylogenetic histories or trait values were associated with more similar soil communities. However, plant community phylogenetic structure was not significantly related to the composition of any of the soil taxonomic groups (P > 0.3 in all cases), suggesting that phylogenetic relatedness is not predictive of soil community composition. This finding is in agreement with the monoculture mesocosm study described above and a field study conducted in a tropical rainforest that failed to find a strong effect of tree species phylogenetic relationships on soil communities ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/ele.12536", "ISBN" : "1461-023x", "ISSN" : "14610248", "PMID" : "26472095", "abstract" : "The complexities of the relationships between plant and soil microbial communities remain unresolved. We determined the associations between plant aboveground and belowground (root) distributions and the communities of soil fungi and bacteria found across a diverse tropical forest plot. Soil microbial community composition was correlated with the taxonomic and phylogenetic structure of the aboveground plant assemblages even after controlling for differences in soil characteristics, but these relationships were stronger for fungi than for bacteria. In contrast to expectations, the species composition of roots in our soil core samples was a poor predictor of microbial community composition perhaps due to the patchy, ephemeral, and highly overlapping nature of fine root distributions. 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Furthermore, differences in community-aggregated trait values, including leaf and root N and C content, also did not significantly relate to the composition of any of the soil taxonomic groups (P > 0.1 in all cases). The trait values we measured were not predictive of soil community composition in mixed grassland communities, results that are consistent with those from the mesocosm experiment of individual plant species.In addition to assessing relationships between the composition of soil taxonomic groups and plant communities based on aboveground biomass, we evaluated plant community composition in two other ways: using root DNA and plant DNA in soil. We used these approaches because roots of different species are intermingled and difficult to identify visually, and assessing plant communities via soil DNA provides an alternate approach to determine which plant species have occupied a given location currently or in the past ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/j.1365-294X.2012.05545.x", "ISBN" : "1365-294X", "ISSN" : "09621083", "PMID" : "22507540", "abstract" : "Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually <100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from environmental samples. 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Roots might also might be more strongly associated with soil community structure than aboveground tissue ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/j.1365-2745.2010.01679.x", "ISBN" : "0022-0477", "ISSN" : "00220477", "abstract" : "1. Global change is likely to alter plant community structure, with consequences for the structure and functioning of the below-ground community and potential feedbacks to climate change. Understanding the mechanisms behind these plant\u2013soil interactions and feedbacks to the Earth-system is therefore crucial. One approach to understanding such mechanisms is to use plant traits as predictors of functioning.\\r\\n2. We used a field-based monoculture experiment involving nine grassland species that had been growing on the same base soil for 7 years to test whether leaf, litter and root traits associated with different plant growth strategies can be linked to an extensive range of soil properties relevant to carbon, nitrogen and phosphorus cycling. Soil properties included the biomass and structure of the soil microbial community, soil nutrients, soil microclimate and soil process rates.\\r\\n3. Plant species with a high relative growth rate (RGR) were associated with high leaf and litter quality (e.g. low toughness, high nitrogen concentrations), an elevated biomass of bacteria relative to fungi in soil, high rates of soil nitrogen mineralization and concentrations of extractable inorganic nitrogen, and to some extent higher available phosphorus pools.\\r\\n4. In contrast to current theory, species with a high RGR and litter quality were associated with soils with a lower rate of soil respiration and slow decomposition rates. This indicates that predicting processes that influence carbon cycling from plant traits may be more complex than predicting processes that influence nitrogen and phosphorus cycling.\\r\\n5. Root traits did not show strong relationships to RGR, leaf or litter traits, but were strongly correlated with several soil properties, particularly the biomass of bacteria relative to fungi in soil and measures relating to soil carbon cycling.\\r\\n6. Synthesis. Our results indicate that plant species from a single habitat can result in significant divergence in soil properties and functioning when grown in monoculture, and that many of these changes are strongly and predictably linked to variation in plant traits associated with different growth strategies. Traits therefore have the potential to be a powerful tool for understanding the mechanisms behind plant\u2013soil interactions and ecosystem functioning, and for predicting how changes in plant species composition associated with global change will feedback to the Earth-system.", "author" : [ { "dropping-particle" : "", "family" : "Orwin", "given" : "Kate H.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Buckland", "given" : "Sarah M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Johnson", "given" : "David", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Turner", "given" : "Benjamin L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Smart", "given" : "Simon", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Oakley", "given" : "Simon", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Journal of Ecology", "id" : "ITEM-1", "issue" : "5", "issued" : { "date-parts" : [ [ "2010" ] ] }, "page" : "1074-1083", "title" : "Linkages of plant traits to soil properties and the functioning of temperate grassland", "type" : "article-journal", "volume" : "98" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Orwin et al., 2010)", "plainTextFormattedCitation" : "(Orwin et al., 2010)", "previouslyFormattedCitation" : "(Orwin et al., 2010)" }, "properties" : { }, "schema" : "" }(Orwin et al., 2010). As with the aboveground plant biomass-based analysis, differences in the compositions of each of the soil taxonomic groups were related to differences in plant community composition assessed using the plant DNA extracted from soil (P < 0.05 in all cases). However, the differences in the composition of soil communities were not significantly related to differences in plant community composition assessed using root DNA (P > 0.1 in all cases; Fig. 3B). It is possible that the composition of plant communities as assessed via roots were unrelated to soil communities because much of the root biomass consisted of dormant plants or dead tissue ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/j.1365-294X.2011.05390.x", "ISBN" : "1365-294X", "ISSN" : "09621083", "PMID" : "22168247", "abstract" : "Variation in plant species richness has been described using only aboveground vegetation. The species richness of roots and rhizomes has never been compared with aboveground richness in natural plant communities. We made direct comparisons of grassland plant richness in identical volumes (0.1 \u00d7 0.1 \u00d7 0.1 m) above and below the soil surface, using conventional species identification to measure aboveground richness and 454 sequencing of the chloroplast trnL(UAA) intron to measure belowground richness. We described above- and belowground richness at multiple spatial scales (from a neighbourhood scale of centimetres to a community scale of hundreds of metres), and related variation in richness to soil fertility. Tests using reference material indicated that 454 sequencing captured patterns of species composition and abundance with acceptable accuracy. At neighbourhood scales, belowground richness was up to two times greater than aboveground richness. The relationship between above- and belowground richness was significantly different from linear: beyond a certain level of belowground richness, aboveground richness did not increase further. Belowground richness also exceeded that of aboveground at the community scale, indicating that some species are temporarily dormant and absent aboveground. Similar to other grassland studies, aboveground richness declined with increasing soil fertility; in contrast, the number of species found only belowground increased significantly with fertility. These results indicate that conventional aboveground studies of plant richness may overlook many coexisting species, and that belowground richness becomes relatively more important in conditions where aboveground richness decreases. Measuring plant belowground richness can considerably alter perceptions of biodiversity and its responses to natural and anthropogenic factors.", "author" : [ { "dropping-particle" : "", "family" : "Hiiesalu", "given" : "Inga", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "\u00d6pik", "given" : "Maarja", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Metsis", "given" : "Madis", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Lilje", "given" : "Liisa", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Davison", "given" : "John", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Vasar", "given" : "Martti", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Moora", "given" : "Mari", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Zobel", "given" : "Martin", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Wilson", "given" : "Scott D.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "P\u00e4rtel", "given" : "Meelis", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Molecular Ecology", "id" : "ITEM-1", "issue" : "8", "issued" : { "date-parts" : [ [ "2012", "4" ] ] }, "page" : "2004-2016", "publisher" : "Blackwell Publishing Ltd", "title" : "Plant species richness belowground: Higher richness and new patterns revealed by next-generation sequencing", "type" : "article-journal", "volume" : "21" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Hiiesalu et al., 2012)", "plainTextFormattedCitation" : "(Hiiesalu et al., 2012)", "previouslyFormattedCitation" : "(Hiiesalu et al., 2012)" }, "properties" : { }, "schema" : "" }(Hiiesalu et al., 2012). Further, it is possible that root distributions are so variable over time that they obscure plant species effects on belowground communities.Differences in aboveground plant community composition were unrelated to differences in root community composition (P = 0.11), but they were related to differences in the plant community composition as assessed using plant DNA in soil (rho = 0.2; P < 0.001; Fig. 3C). This shows that shoot and root biomass in a given location do not represent the same plant community, as also found in a tropical rainforest ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/ele.12536", "ISBN" : "1461-023x", "ISSN" : "14610248", "PMID" : "26472095", "abstract" : "The complexities of the relationships between plant and soil microbial communities remain unresolved. We determined the associations between plant aboveground and belowground (root) distributions and the communities of soil fungi and bacteria found across a diverse tropical forest plot. Soil microbial community composition was correlated with the taxonomic and phylogenetic structure of the aboveground plant assemblages even after controlling for differences in soil characteristics, but these relationships were stronger for fungi than for bacteria. In contrast to expectations, the species composition of roots in our soil core samples was a poor predictor of microbial community composition perhaps due to the patchy, ephemeral, and highly overlapping nature of fine root distributions. Our ability to predict soil microbial composition was not improved by incorporating information on plant functional traits suggesting that the most commonly measured plant traits are not particularly useful for predicting the plot-level variability in belowground microbial communities.", "author" : [ { "dropping-particle" : "", "family" : "Barber\u00e1n", "given" : "Albert", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Mcguire", "given" : "Krista L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Wolf", "given" : "Jeffrey A.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Jones", "given" : "F. 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Additionally, these results suggest that plant DNA in soil can be used as a proxy for the community composition of the aboveground biomass ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/j.1365-294X.2012.05545.x", "ISBN" : "1365-294X", "ISSN" : "09621083", "PMID" : "22507540", "abstract" : "Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually <100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from environmental samples. All analyses included amplification using plant-specific versa-tile primers, sequencing and estimation of taxonomic diversity. We tested in three steps whether degraded DNA from dead material in soil has the potential of efficiently assessing biodiversity in different biomes. First, soil DNA from eight boreal plant communities located in two different vegetation types (meadow and heath) was amplified. Plant diversity detected from boreal soil was highly consistent with plant taxonomic and growth form diversity estimated from conventional above-ground surveys. Second, we assessed DNA persistence using samples from formerly cultivated soils in temperate environments. We found that the number of crop DNA sequences retrieved strongly varied with years since last cultivation, and crop sequences were absent from nearby, uncultivated plots. Third, we assessed the universal applicability of DNA metabarcoding using soil samples from tropical environments: a large proportion of species and families from the study site were efficiently recovered. The results open unprecedented opportunities for large-scale DNA-based biodiversity studies across a range of taxonomic groups using standardized metabarcoding approaches.", "author" : [ { "dropping-particle" : "", "family" : "Yoccoz", "given" : "N. G.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Br\u00e5then", "given" : "K. A.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Gielly", "given" : "L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Haile", "given" : "J.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Edwards", "given" : "M. 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H.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Miquel", "given" : "C.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Valentini", "given" : "A.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bello", "given" : "F.", "non-dropping-particle" : "De", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Chave", "given" : "J.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Thuiller", "given" : "W.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Wincker", "given" : "P.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Cruaud", "given" : "C.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Gavory", "given" : "F.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Rasmussen", "given" : "M.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Gilbert", "given" : "M. T P", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Orlando", "given" : "L.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Brochmann", "given" : "C.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Willerslev", "given" : "E.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Taberlet", "given" : "P.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Molecular Ecology", "id" : "ITEM-1", "issue" : "15", "issued" : { "date-parts" : [ [ "2012" ] ] }, "page" : "3647-3655", "title" : "DNA from soil mirrors plant taxonomic and growth form diversity", "type" : "article-journal", "volume" : "21" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Yoccoz et al., 2012)", "plainTextFormattedCitation" : "(Yoccoz et al., 2012)", "previouslyFormattedCitation" : "(Yoccoz et al., 2012)" }, "properties" : { }, "schema" : "" }(Yoccoz et al., 2012). This has implications for future research since it is often logistically easier to obtain a representative sample of surface soils rather than sampling and homogenizing aboveground plant biomass.Are the associations between plant and soil communities driven by soil characteristics?We aimed to assess whether relationships between soil communities and plant communities in the field plots were attributable to the direct effects of the plants, shared environmental drivers, or intermediary effects of the plants on soil properties. Therefore, we evaluated whether plant community composition contributed additional explanatory power to the observed variation in soil community composition given differences in edaphic characteristics. Shifts in the composition of soil communities across the field plots were significantly correlated with multiple, individual edaphic properties (Table S4), and combinations of these properties explained 13 – 29% of the variation in soil community composition (P = 0.001 in all cases; Fig. S8A). For example, soil N content and pH were typically predictive of the composition of the four taxonomic soil groups. Only differences in fungal community composition could be predicted more accurately when information on aboveground plant community composition was added to the models containing only soil characteristics as predictor variables (P = 0.01; Fig. S8). When soil DNA-based plant community composition information was used instead of aboveground plant community composition, fungal, bacterial, and protistan community composition could all be predicted more accurately with the addition of information on plant community composition (R2 increased 9 – 24%; P < 0.02 in all cases; Fig. S8). These results suggest that shifts in aboveground community composition likely influence soil communities in ways not accounted for in commonly measured soil properties, and indicate that the structure of complex soil communities in grasslands is controlled by a combination of plant and soil characteristics ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1111/j.1574-6941.2009.00654.x", "ISBN" : "0168-6496", "ISSN" : "01686496", "PMID" : "19243436", "abstract" : "The rhizosphere is of central importance not only for plant nutrition, health and quality but also for microorganism-driven carbon sequestration, ecosystem functioning and nutrient cycling in terrestrial ecosystems. A multitude of biotic and abiotic factors are assumed to influence the structural and functional diversity of microbial communities in the rhizosphere. In this review, recent studies on the influence of the two factors, plant species and soil type, on rhizosphere-associated microbial communities are discussed. Root exudates and the response of microorganisms to the latter as well as to root morphology were shown to shape rhizosphere microbial communities. All studies revealed that soil is the main reservoir for rhizosphere microorganisms. Many secrets of microbial life in the rhizosphere were recently uncovered due to the enormous progress in molecular and microscopic tools. Physiological and molecular data on the factors that drive selection processes in the rhizosphere are presented here. Furthermore, implications for agriculture, nature conservation and biotechnology will also be discussed.", "author" : [ { "dropping-particle" : "", "family" : "Berg", "given" : "Gabriele", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Smalla", "given" : "Kornelia", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "FEMS Microbiology Ecology", "id" : "ITEM-1", "issue" : "1", "issued" : { "date-parts" : [ [ "2009" ] ] }, "page" : "1-13", "title" : "Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere", "type" : "article-journal", "volume" : "68" }, "uris" : [ "" ] }, { "id" : "ITEM-2", "itemData" : { "DOI" : "10.1111/j.1365-2745.2009.01614.x", "ISBN" : "1365-2745", "ISSN" : "00220477", "PMID" : "16417727", "abstract" : "1.\u2002Our aim was to explore plant\u2013soil feedback in mixed grassland communities and its significance for plant productivity and community composition relative to abiotic factors of soil type and fertility. 2.\u2002We carried out a 4-year, field-based mesocosm experiment to determine the relative effects of soil type, historic management intensity and soil conditioning by a wide range of plant species of mesotrophic grassland on the productivity and evenness of subsequent mixed communities. 3.\u2002The study consisted of an initial soil conditioning phase, whereby soil from two locations each with two levels of management intensity was conditioned with monocultures of nine grassland species, and a subsequent feedback phase, where mixed communities of the nine species were grown in conditioned soil to determine relative effects of experimental factors on the productivity and evenness of mixed communities and individual plant species performance. 4.\u2002In the conditioning phase of the experiment, individual plant species differentially influenced soil microbial communities and nutrient availability. However, these biotic effects were much less important as drivers of soil microbial properties and nutrient availability than were abiotic factors of soil type and fertility. 5.\u2002Significant feedback effects of conditioning were detected during the second phase of the study in terms of individual plant growth in mixed communities. These feedback effects were generally independent of soil type or fertility, and were consistently negative in nature. In most cases, individual plant species performed less well in mixed communities planted in soil that had previously supported their own species. 6.\u2002Synthesis. These findings suggest that despite soil abiotic factors acting as major drivers of soil microbial communities and nutrient availability, biotic interactions in the form of negative feedback play a significant role in regulating individual plant performance in mixed grassland communities across a range of soil conditions.", "author" : [ { "dropping-particle" : "", "family" : "Harrison", "given" : "Kathryn A.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "Journal of Ecology", "id" : "ITEM-2", "issue" : "2", "issued" : { "date-parts" : [ [ "2010" ] ] }, "page" : "384-395", "title" : "Influence of plant species and soil conditions on plant-soil feedback in mixed grassland communities", "type" : "article-journal", "volume" : "98" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Berg and Smalla, 2009; Harrison and Bardgett, 2010)", "plainTextFormattedCitation" : "(Berg and Smalla, 2009; Harrison and Bardgett, 2010)", "previouslyFormattedCitation" : "(Berg and Smalla, 2009; Harrison and Bardgett, 2010)" }, "properties" : { }, "schema" : "" }(Berg and Smalla, 2009; Harrison and Bardgett, 2010).ConclusionsWe demonstrate that plant community composition is an effective predictor of the structure of complex grassland soil communities, especially when combined with information on soil abiotic properties. Furthermore, we show that plant community composition is particularly effective for predicting distributions of certain groups of soil organisms, such as fungal symbionts and pathogens. Importantly, we found that plant species identity, rather than plant phylogeny or functional traits, was the best predictor of soil community composition at both the individual plant and community scale. This is significant because it raises questions about the effectiveness of phylogenetic and trait-based approaches for explaining spatial variation in soil community composition at a local scale. Such approaches are increasingly being used to predict how changes in plant community composition impact soil properties and functions ADDIN CSL_CITATION { "citationItems" : [ { "id" : "ITEM-1", "itemData" : { "DOI" : "10.1016/j.tree.2014.10.006", "ISBN" : "1872-8383 (Electronic)\\r0169-5347 (Linking)", "ISSN" : "01695347", "PMID" : "25459399", "abstract" : "Ecologists are increasingly adopting trait-based approaches to understand how community change influences ecosystem processes. However, most of this research has focussed on aboveground plant traits, whereas it is becoming clear that root traits are important drivers of many ecosystem processes, such as carbon (C) and nutrient cycling, and the formation and structural stability of soil. Here, we synthesise emerging evidence that illustrates how root traits impact ecosystem processes, and propose a pathway to unravel the complex roles of root traits in driving ecosystem processes and their response to global change. Finally, we identify research challenges and novel technologies to address them.", "author" : [ { "dropping-particle" : "", "family" : "Bardgett", "given" : "Richard D.", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Mommer", "given" : "Liesje", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" }, { "dropping-particle" : "", "family" : "Vries", "given" : "Franciska T.", "non-dropping-particle" : "De", "parse-names" : false, "suffix" : "" } ], "container-title" : "Trends in Ecology and Evolution", "id" : "ITEM-1", "issue" : "12", "issued" : { "date-parts" : [ [ "2014" ] ] }, "page" : "692-699", "title" : "Going underground: Root traits as drivers of ecosystem processes", "type" : "article", "volume" : "29" }, "uris" : [ "" ] }, { "id" : "ITEM-2", "itemData" : { "DOI" : "10.1111/nph.14247", "ISSN" : "0028646X", "author" : [ { "dropping-particle" : "", "family" : "Lalibert\u00e9", "given" : "Etienne", "non-dropping-particle" : "", "parse-names" : false, "suffix" : "" } ], "container-title" : "New Phytologist", "id" : "ITEM-2", "issue" : "4", "issued" : { "date-parts" : [ [ "2017", "3" ] ] }, "page" : "1597-1603", "title" : "Below-ground frontiers in trait-based plant ecology", "type" : "article-journal", "volume" : "213" }, "uris" : [ "" ] } ], "mendeley" : { "formattedCitation" : "(Bardgett et al., 2014; Lalibert\u00e9, 2017)", "plainTextFormattedCitation" : "(Bardgett et al., 2014; Lalibert\u00e9, 2017)", "previouslyFormattedCitation" : "(Bardgett et al., 2014; Lalibert\u00e9, 2017)" }, "properties" : { }, "schema" : "" }(Bardgett et al., 2014; Laliberté, 2017), but our findings indicate that, at a local scale in temperate grassland, they are ineffective for explaining variation in soil communities. Finally, it is important to note that much of the variation in soil community composition could not be explained by the measured soil characteristics or plant community attributes, highlighting the difficulty of predicting complex soil communities in situ and the need to build a mechanistic understanding of which specific plant attributes are responsible for driving plant species effects on the biodiversity of soil. Combined, our findings provide new evidence that associations between specific plant species and complex soil communities, associations that are not explained by plant phylogeny or commonly measured plant traits, act as key determinants of spatial patterns of biodiversity in grassland soils.AcknowledgementsThis research was supported by a grant from the UK Biotechnology and Biological Sciences Research Council (BBSRC) (Grant BB/I009000/2), initiated and led by RDB, a BBSRC International Exchange Grant (BB/L026406/1) between RDB and NF, and a grant from the U.S. National Science Foundation (NSF) (DEB 1542653) awarded to NF. We thank Emily Morgan for her assistance with the microbial community analyses, Colin Newlands of Natural England for permission to use the field sites, and Marina Semchenko for comments on a previous version of this manuscript. We also thank all who helped establish the field experimental site and collect and process the plant and soil samples: Aurore Kaisermann, Debora Ashworth, Angela Straathof, Imelda Uwase, Marina Semchenko, Maatren Schrama, Melanie Edgar, Mark Bradford, Mike Whitfield, Rachel Marshall, and Andrew Cole.Supplementary information is available at The ISME Journal’s website.ReferencesADDIN Mendeley Bibliography CSL_BIBLIOGRAPHY Abarenkov K, Henrik Nilsson R, Larsson K-H, Alexander IJ, Eberhardt U, Erland S, et al. (2010). The UNITE database for molecular identification of fungi – recent updates and future perspectives. New Phytol 186: 281–285.Adler PB, Fajardo A, Kleinhesselink AR, Kraft NJB. (2013). Trait-based tests of coexistence mechanisms. Ecol Lett 16: 1294–1306.Anacker BL, Klironomos JN, Maherali H, Reinhart KO, Strauss SY. (2014). Phylogenetic conservatism in plant-soil feedback and its implications for plant abundance. Ecol Lett 17: 1613–1621.Barberán A, Dunn RR, Reich BJ, Pacifici K, Laber EB, Menninger HL, et al. (2015a). The ecology of microscopic life in household dust. Proc R Soc B 282: 1–9.Barberán A, Mcguire KL, Wolf JA, Jones FA, Wright SJ, Turner BL, et al. (2015b). Relating belowground microbial composition to the taxonomic, phylogenetic, and functional trait distributions of trees in a tropical forest. Ecol Lett 18: 1397–1405.Bardgett RD, Mawdsley JL, Edwards S, Hobbs PJ, Rodwell JS, Davies WJ. (1999). Plant species and nitrogen effects on soil biological properties of temperate upland grasslands. Funct Ecol 13: 650–660.Bardgett RD, Mommer L, De Vries FT. (2014). Going underground: Root traits as drivers of ecosystem processes. Trends Ecol Evol 29: 692–699.Bardgett RD, Streeter TC, Bol R. (2003). Soil microbes compete effectively with plants for organic-nitrogen inputs to temperate grasslands. Ecology 84: 1277–1287.Bardgett RD, Wardle DA. (2010). Aboveground-belowground linkages: biotic interactions, ecosystem processes, and global change. Oxford University Press Oxford: New York, NY, USA.Bates ST, Clemente JC, Flores GE, Walters WA, Parfrey LW, Knight R, et al. (2013). Global biogeography of highly diverse protistan communities in soil. ISME J 7: 652–659.Ben-Hur E, Fragman-Sapir O, Hadas R, Singer A, Kadmon R. (2012). Functional trade-offs increase species diversity in experimental plant communities. Ecol Lett 15: 1276–1282.Berg G. (2009). Plant-microbe interactions promoting plant growth and health: Perspectives for controlled use of microorganisms in agriculture. Appl Microbiol Biotechnol 84: 11–18.Berg G, Smalla K. (2009). Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 68: 1–13.Bezemer TM, Fountain MT, Barea JM, Christensen S, Dekker SC, Duyts H, et al. (2010). Divergent composition but similar function of soil food webs beneath individual plants: plant species and community effects. Ecology 91: 3027–3036.Bezemer TM, Lawson CS, Hedlund K, Edwards AR, Brook AJ, Igual JM, et al. (2006). Plant species and functional group effects on abiotic and microbial soil properties and plant-soil feedback responses in two grasslands. J Ecol 94: 893–904.Blomberg SP, Garland T, Ives AR. (2003). Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution (N Y) 57: 717–745.Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. (2016). DADA2?: High resolution sample inference from amplicon data. Nat Methods 13: 581–583.Cantarel AAM, Pommier T, Desclos-Theveniau M, Diquélou S, Dumont M, Grassein F, et al. (2015). Using plant traits to explain plant–microbe relationships involved in nitrogen acquisition. Ecology 96: 788–799.Carey CJ, Michael Beman J, Eviner VT, Malmstrom CM, Hart SC. (2015). Soil microbial community structure is unaltered by plant invasion, vegetation clipping, and nitrogen fertilization in experimental semi-arid grasslands. Front Microbiol 6. e-pub ahead of print, doi: 10.3389/fmicb.2015.00466.Carini P, Marsden PJ, Leff JW, Morgan EE, Strickland MS, Fierer N. (2016). Relic DNA is abundant in soil and obscures estimates of soil microbial diversity. Nat Microbiol 2. e-pub ahead of print, doi: 10.1038/nmicrobiol.2016.242.Cornelissen JHC, Lavorel S, Garnier E, Díaz S, Buchmann N, Gurvich DE, et al. (2003). A handbook of protocols for standardised and easy measurement of plant functional traits worldwide. Aust J Bot 51: 335–380.De Deyn GB, Van Der Putten WH. (2005). Linking aboveground and belowground diversity. Trends Ecol Evol 20: 625–633.De Deyn GB, Shiel RS, Ostle NJ, Mcnamara NP, Oakley S, Young I, et al. (2011). Additional carbon sequestration benefits of grassland diversity restoration. J Appl Ecol 48: 600–608.Dufrêne M, Legendre P. (1997). Species assemblages and indicator species: The need for a flexible asymmetrical approach. Ecol Monogr 67: 345–366.Durka W, Michalski SG. (2012). Daphne: a dated phylogeny of a large European flora for phylogenetically informed ecological analyses. Ecology 93: 2297.Fierer N, Strickland MS, Liptzin D, Bradford M a., Cleveland CC. (2009). Global patterns in belowground communities. Ecol Lett 12: 1238–1249.Gibbons SM, Lekberg Y, Mummey DL, Sangwan N, Ramsey PW, Gilbert JA. (2017). Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem. mSystems 2: e00178-16.Grayston SJ, Griffith GS, Mawdsley JL, Campbell CD, Bardgett RD. (2001). Accounting for variability in soil microbial communities of temperate upland grassland ecosystems. Soil Biol Biochem 33: 533–551.Grayston SJ, Wang S, Campbell CD, Edwards AC. (1998). Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biol Biochem 30: 369–378.Grigulis K, Lavorel S, Krainer U, Legay N, Baxendale C, Dumont M, et al. (2013). Relative contributions of plant traits and soil microbial properties to mountain grassland ecosystem services. J Ecol 101: 47–57.Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, et al. (2013). The Protist Ribosomal Reference database (PR2): A catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Res 41: 597–604.Haichar FEZ, Marol C, Berge O, Rangel-Castro JI, Prosser JI, Balesdent J, et al. (2008). Plant host habitat and root exudates shape soil bacterial community structure. ISME J 2: 1221–1230.Harrison KA, Bardgett RD. (2010). Influence of plant species and soil conditions on plant-soil feedback in mixed grassland communities. J Ecol 98: 384–395.Hawkes C V., Wren IF, Herman DJ, Firestone MK. (2005). Plant invasion alters nitrogen cycling by modifying the soil nitrifying community. Ecol Lett 8: 976–985.van der Heijden MGA, Klironomos JN, Ursic M, Moutoglis P, Streitwolf-Engel R, Boller T, et al. (1998). Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature 396: 69–72.Hiiesalu I, ?pik M, Metsis M, Lilje L, Davison J, Vasar M, et al. (2012). Plant species richness belowground: Higher richness and new patterns revealed by next-generation sequencing. Mol Ecol 21: 2004–2016.Hiiesalu I, P?rtel M, Davison J, Gerhold P, Metsis M, Moora M, et al. (2014). Species richness of arbuscular mycorrhizal fungi: Associations with grassland plant richness and biomass. New Phytol 203: 233–244.St. John MG, Wall DH, Behan-Pelletier VM. (2006). Does plant species co-occurrence influence soil mite diversity? Ecology 87: 625–633.Kaiser K, Wemheuer B, Korolkow V, Wemheuer F, Nacke H, Sch?ning I, et al. (2016). Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests. Sci Rep 6: 33696.Kartzinel TR, Chen P a., Coverdale TC, Erickson DL, Kress WJ, Kuzmina ML, et al. (2015). DNA metabarcoding illuminates dietary niche partitioning by African large herbivores. Proc Natl Acad Sci 112: 8019–8024.Laliberté E. (2017). Below-ground frontiers in trait-based plant ecology. New Phytol 213: 1597–1603.Lavorel S, Garnier E. (2002). Predicting changes in community composition and ecosystem functioning from plant traits: revisiting the Holy Grail. Funct Ecol 16: 545–556.Leff JW, Jones SE, Prober SM, Barberan A, Borer ET, Firn JL, et al. (2015). Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. Proc Natl Acad Sci U S A 112: 10967–10972.Legay N, Baxendale C, Grigulis K, Krainer U, Kastl E, Schloter M, et al. (2014). Contribution of above- and below-ground plant traits to the structure and function of grassland soil microbial communities. Ann Bot 114: 1011–1021.Legay N, Lavorel S, Baxendale C, Krainer U, Bahn M, Binet M-N, et al. (2016). Influence of plant traits, soil microbial properties, and abiotic parameters on nitrogen turnover of grassland ecosystems. Ecosphere 7: 1–17.Lekberg Y, Waller LP. (2016). What drives differences in arbuscular mycorrhizal fungal communities among plant species? Fungal Ecol 10–13.Lennon JT, Aanderud ZT, Lehmkuhl BK, Schoolmaster DR. (2012). Mapping the niche space of soil microorganisms using taxonomy and traits. Ecology 93: 1867–1879.Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. (2011). UniFrac: an effective distance metric for microbial community comparison. ISME J 5: 169–72.McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, et al. (2012). An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6: 610–618.Mehrabi Z, Tuck SL. (2015). Relatedness is a poor predictor of negative plant-soil feedbacks. New Phytol 205: 1071–1075.Moreau D, Pivato B, Bru D, Busset H, Deau F, Faivre C, et al. (2015). Plant traits related to nitrogen uptake influence plant-microbe competition. Ecology 96: 2300–2310.Nguyen NH, Song Z, Bates ST, Branco S, Tedersoo L, Menke J, et al. (2015). FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol 20: 241–248.Orwin KH, Buckland SM, Johnson D, Turner BL, Smart S, Oakley S, et al. (2010). Linkages of plant traits to soil properties and the functioning of temperate grassland. J Ecol 98: 1074–1083.Peay KG, Baraloto C, Fine PVA. (2013). Strong coupling of plant and fungal community structure across western Amazonian rainforests. ISME J 7: 1852–61.Porazinska DL, Bardgett RD, Blaauw MB, Hunt HW, Parsons AN, Seastedt TR, et al. (2003). Relationships at the Aboveground-Belowground Interface: Plants, Soil Biota, and Soil Processes. Ecol Monogr 73: 377–395.Prober SM, Leff JW, Bates ST, Borer ET, Firn J, Harpole WS, et al. (2015). Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide. Ecol Lett 18: 85–95.Van der Putten WH, Bardgett RD, Bever JD, Bezemer TM, Casper BB, Fukami T, et al. (2013). Plant-soil feedbacks: The past, the present and future challenges Hutchings M (ed). J Ecol 101: 265–276.R Core Team. (2016). R: A language and environment for statistical computing.Ramirez KS, Leff JW, Barberán A, Bates ST, Betley J, Crowther TW, et al. (2014). Biogeographic patterns in below-ground diversity in New York City’s Central Park are similar to those observed globally. Proc R Soc B Biol Sci 281: 1–9.Rodwell JS. (1992). British plant communities. Volume 3. Grassland and montane communities. 3rd ed. Cambridge University Press.Roumet C, Birouste M, Picon-Cochard C, Ghestem M, Osman N, Vrignon-Brenas S, et al. (2016). Root structure-function relationships in 74 species: Evidence of a root economics spectrum related to carbon economy. New Phytol. e-pub ahead of print, doi: 10.1111/nph.13828.Singh BK, Millard P, Whiteley AS, Murrell JC. (2004). Unravelling rhizosphere–microbial interactions: opportunities and limitations. Trends Microbiol 12: 386–393.Smith RS, Shiel RS, Bardgett RD, Millward D, Corkhill P, Rolph G, et al. (2003). Soil microbial community, fertility, vegetation and diversity as targets in the restoration management of a meadow grassland. J Appl Ecol 40: 51–64.Spatafora JW, Chang Y, Benny GL, Lazarus K, Smith ME, Berbee ML, et al. (2016). A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia 108: 1028–1046.Tedersoo L, Bahram M, Cajthaml T, P?lme S, Hiiesalu I, Anslan S, et al. (2015). Tree diversity and species identity effects on soil fungi, protists and animals are context dependent. ISME J 1–17.Tedersoo L, Bahram M, Polme S, Koljalg U, Yorou NS, Wijesundera R, et al. (2014). Global diversity and geography of soil fungi. Science (80- ) 346: 1256688–1256688.Thion CE, Poirel JD, Cornulier T, De Vries FT, Bardgett RD, Prosser JI. (2016). Plant nitrogen-use strategy as a driver of rhizosphere archaeal and bacterial ammonia oxidiser abundance. FEMS Microbiol Ecol 92. e-pub ahead of print, doi: 10.1093/femsec/fiw091.de Vries FT, Manning P, Tallowin JRB, Mortimer SR, Pilgrim ES, Harrison KA, et al. (2012). Abiotic drivers and plant traits explain landscape-scale patterns in soil microbial communities. Ecol Lett 15: 1230–1239.Wardle DA, Bardgett RD, Klironomos JN, Set?l? H, van der Putten WH, Wall DH. (2004). Ecological linkages between aboveground and belowground biota. Science (80- ) 304: 1629–33.Wu T, Ayres E, Bardgett RD, Wall DH, Garey JR. (2011). Molecular study of worldwide distribution and diversity of soil animals. Proc Natl Acad Sci 108: 17720–17725.Yoccoz NG, Br?then KA, Gielly L, Haile J, Edwards ME, Goslar T, et al. (2012). DNA from soil mirrors plant taxonomic and growth form diversity. Mol Ecol 21: 3647–3655.Figure legendsFigure 1. The effects of plant species identity on the composition of soil communities from mesocosms containing monocultures. Boxplots represent pairwise Bray-Curtis dissimilarities in community composition between vs. within soils from the same plant species (A). Hierarchical clustering diagrams based on mean dissimilarities across the plant species (B). Bipartite network diagram, where edges (lines) connect plant species (green circles) to fungal taxa (red points) that occurred in the same mesocosm (C). The composition of cosmopolitan soil taxa (those taxa associated with all plant species), intermediate (taxa associated with only 2 to 20 plant species), and specialized (taxa that associate with only a single plant species) (D). The composition of functional groups of fungal taxa identified as being cosmopolitan, intermediate, and specialized across plant species (E).Figure 2. Relationships between plant species’ relatedness and differences in the composition of soil communities. Panel A shows a plant phylogenetic tree with species names colored by family (key shown in Fig. 1) with the corresponding heatmap showing the dissimilarities in the composition of each soil community. Colors represent the first principal coordinate analysis axis calculated from Bray-Curtis dissimilarities (A). The relationship between differences in the composition of soil communities and plant trait distances (B). Euclidean trait distances were calculated using all the traits shown in panel C. The relationship between differences in the composition of soil communities and individual plant traits (C). Points represent Spearman correlation coefficients (rho) and Mantel test results (P value).Figure 3. Soil community composition is related to plant community composition in the field. Variation in plant community composition across the field samples ordered by the first principal coordinate score (i.e. the x-axis represents a gradient of plant community compositions where communities further apart are more dissimilar), and relationships between soil taxonomic group relative abundance and the plant first principal coordinate score (A). Linear trend lines were only plotted for groups that had a Pearson correlation P ≤ 0.05. Relationship strength between dissimilarities in soil communities and dissimilarities in plant communities (* = P < 0.05, ** = P < 0.01, *** = P = 0.001; Mantel tests; B). Pairwise Bray-Curtis dissimilarities in plant community composition, as assessed using aboveground tissue, are not related to dissimilarities in plant community composition as assessed using root tissue, but they are related to dissimilarities in plant community composition as assessed using plant DNA in soil (C). ................
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