Vitae - USC Dana and David Dornsife College of Letters ...



CURRICULUM VITAE updated 10/1/20 Jed Alan Fuhrman Address: Department of Biological Sciences University of Southern California Los Angeles, CA 90089-0371Birth: October 1956. U.S. Citizen.Contact: (213) 740-5757 or -5759 FAX: 740-8123 email: fuhrman@usc.eduWebsites:, scholar.citations?user=VjvupJUAAAAJ&hl=enEDUCATIONPh.D., Oceanography, 1981. Scripps Institution of Oceanography, University of California, San DiegoS.B., Biology, 1977. Massachusetts Institute of TechnologyPROFESSIONAL EXPERIENCEFaculty positions:Assistant Professor of Oceanography, SUNY Stony Brook, 1981-1986 Associate Professor of Oceanography, State University of New York at Stony Brook, 1986-88 Associate Professor of Biological Sciences, University of Southern California, 1988 -1992Professor of Biological Sciences, University of Southern California, 1992-present Department Chair (Biological Sciences), 1994-1996 McCulloch-Crosby Chair of Marine Biology 1995 – presentSection Head, Marine Biology and Biological Oceanography 2009-12 Other: Research Collaborator, Brookhaven National Laboratory, 1985-1988Editorial Advisor of Marine Ecology - Progress Series, 1988-93, Senior Editorial Advisor (sub-editor) 1993-97; Contributing Editor, 1997-2003; Editorial Board 2003-2006Editorial Advisor of Marine Microbial Food Webs, 1992-1995 Editorial Board, Microbial Ecology 2006-2007Editorial Board, Applied and Environmental Microbiology, 1997 -2000Subject Editor (empowered to accept/reject manuscripts) of Aquatic Microbial Ecology, 1995 - presentEditorial Board, Environmental Microbiology 2003-presentEditorial Board, ISME Journal, 2006- 2018Editorial Board, Microbiome (BioMed Central), 2012-PROFESSIONAL SOCIETIESAmerican Society of Limnology and OceanographyAmerican Association for the Advancement of Science (ASLO representative to the Biological Sciences Section of AAAS 1984-93)American Society for MicrobiologySigma XiThe Oceanography Society (charter member)American Geophysical UnionInternational Society for Microbial Ecology (charter member)HONORS, FELLOWSHIPS, SCHOLARSHIPS, VISITING POSITIONSMajor Career Awards and Recognition: McCulloch-Crosby Chair of Marine Biology (at USC), 1995 - presentFellow of the American Association for the Advancement of Science, 1997 Highly Cited Researcher, Institute for Scientific Information, , 2001,2002Fellow of the American Academy of Microbiology, 2003G. Evelyn Hutchinson Medal (American Society of Limnology & Oceanography) 2006Albert S. Raubenheimer Outstanding Faculty Award (USC) 2006Faculty of 1000 member 2012-Gordon and Betty Moore Foundation Marine Microbiology Initiative Investigator, 2013-2020Fellow, American Academy of Arts and Sciences, 2013Sustaining Fellow (Inaugural class), Assoc for the Sciences of Limnology and Oceanography 2015USC Associates Award for Creativity in Research and Scholarship 2016Highly Cited Researcher, Clarivate Analytics 2018 top 1% by citations for field & year, Web of Science, Publon. Also 2019Other:Phi Beta Kappa (MIT chapter), 1977National Science Foundation Graduate Fellowship, 1977-80Riker Fellowship at Bermuda Biological Station, summer 1987 Visiting Professor, University of Copenhagen, spring 1988Visiting Distinguished Scientist, Texas A&M University, April 1997Steinbach Scholar, Woods Hole Oceanographic Institution, July 2000Eminent Scholar Series Lecturer, University of South Florida, 2009Van Neil Lecturer, Hopkins Marine Station, Stanford University, 2012Visiting Professor, University of Pierre and Marie Curie, Banyuls sur mer, France, 2012Visiting Professor, Institute for Marine Sciences, Barcelona, Spain, 2012RESEARCH INTERESTSAquatic microbial ecology and biological oceanography; functioning of microbial systems - particularly, roles of bacteria, archaea, protists, and viruses in natural systems; microbial biodiversity and identification of nonculturable bacteria, archaea, and protists and their functions; microbial biogeography and its causal factors; interactions with dissolved and particulate organic matter; two-way interactions with other chemical and physical processes; rates of bactivory and viral infection; rates of nutrient regeneration; application of biochemical and molecular biological approaches to these problems; connections to global cycles; microbial association networks; human impacts on aquatic systems, pathogens and related health hazards. Rapid measurements of human pathogenic viruses and bacteria in environmental samples of water and air.PUBLICATIONS (h-index = 100 by Google Scholar as of September 2020)1. Fuhrman, J.A., S.W. Chisholm, and R.R.L. Guillard. 1978. Marine alga Platymonas sp. accumulates silicon without apparent requirement. Nature (London) 272: 244-2462. Hollibaugh, J.T., J.A. Fuhrman, and F. Azam. 1980. Radioactively labeling of natural assemblages of bacterioplankton for use in trophic studies. Limnol. Oceanogr. 25: 172-1813. Fuhrman, J.A., and F. Azam. 1980. Bacterioplankton secondary production estimates for coastal waters of British Columbia, Antarctica, and California. Appl. Envir. Microbiol. 39:1085-1095 (an ISI "Citation Classic")4. Hollibaugh, J,T., A.B. Carruthers, J.A. Fuhrman, and F. Azam. 1980. Cycling of organic nitrogen in marine plankton communities studied in enclosed water columns. Mar. Biol. 59: 15-215. Fuhrman, J.A., J.W. Ammerman, and F. Azam. 1980. Bacterioplankton in the coastal euphotic zone: distribution, activity, and possible relationships with phytoplankton. Mar. Biol. 60: 201-2076. Hodson, R.E., F. Azam, A.F. Carlucci, J.A. Fuhrman, D.M. Karl, and O. Holm- Hansen. 1981. Microbial uptake of dissolved organic matter in McMurdo Sound, Antarctica. Mar. Biol. 61: 89-947. Fuhrman, J.A. 1981. Influence of method on the apparent size distribution of bacterioplankton cells: epifluorescence microscopy compared to scanning electron microscopy. Mar. Ecol. Prog. Ser. 5: 103-1068. Eppley, R.W., S.G. Horrigan, J.A. Fuhrman, E.R. Brooks, C.C. Price, and K. Sellner. 1981. Origins of dissolved organic matter in Southern California coastal waters: experiments on the role of zooplankton. Mar. Ecol. Prog. Ser. 6: 149-1599. Fuhrman, J.A., and F. Azam. 1982. Thymidine incorporation as a measure of heterotrophic bacterioplankton production in marine surface waters: evaluation and field results. Mar. Biol. 66:109-120 (An "ISI Citation Classic")10. Riemann, B., J.A. Fuhrman, and F. Azam. 1982. Bacterial secondary production in freshwater measured by the tritiated thymidine incorporation method. Microb. Ecol. 8:101-11411. Fuhrman, J.A.,and F. Azam. 1983. Adaptations of bacteria to marine subsurface waters studied by temperature response. Mar. Ecol. Prog. Ser. 13:95-9812. Azam, F., J.W. Ammerman, J.A. Fuhrman, and A. Hagstrom. 1984. Role of bacteria in polluted marine ecosystems. In H. H. White (ed.) Concepts in Marine Pollution Measurements. University of Maryland Sea Grant, College Park. pp 431-442 13. Ammerman, J.W., J.A. Fuhrman, A. Hagstrom, and F. Azam. 1984. Growth characteristics of marine bacteria grown in "seawater cultures" (unsupplemented particle-free seawater). Mar. Ecol. Prog. Ser. 18:31-3914. Azam, F. and J.A. Fuhrman. 1984. Measurement of bacterioplankton growth in the sea and its regulation by environmental conditions. In: Heterotrophic activity in the sea. J. Hobbie and P.J.leB. Williams (eds). Plenum Press. pp. 179-196 15. Fuhrman, J.A. and G.B. McManus. 1984. Do bacteria-sized marine eukaryotes consume significant bacterial production? Science 224: 1257-1260 16. Riemann, B., P. Nielsen, M. Jeppesen, B. Marcussen and J.A. Fuhrman. 1984. Diel changes in bacterial biomass and growth rates in coastal environments, determined by means of thymidine incorporation into DNA, frequency of dividing cells (FDC), and microautoradiography. Mar. Ecol. Prog. Ser. 17: 227-23517. Fuhrman, J.A and T. Bell. 1985. Biological considerations in the measurement of dissolved free amino acids in seawater and implications for chemical and microbiological studies. Mar. Ecol. Prog. Ser. 25: 13-2118. Mitchell, J.G., A. Okubo, and J.A. Fuhrman. 1985. Microzones form the basis for a stratified microbial ecosystem. Nature (London) 316: 58-5919. Fuhrman, J.A., R.W. Eppley, A. Hagstrom, and F. Azam. 1985. Diel variations in bacterioplankton, phytoplankton, and related parameters in the Southern California Bight. Mar. Ecol. Prog. Ser. 27: 9-2020. Legier-Visser, M., J. Mitchell, A. Okubo, and J.A. Fuhrman. 1986. Mechanoreception in calanoid copepods: a mechanism for prey detection. Mar. Biol. 90: 526-53521. McManus, G.B. and J.A. Fuhrman. 1986. Photosynthetic pigments in the ciliate Laboea strobila from Long Island Sound, USA. J. Plankton Res. 8:317-32722. McManus, G.B. and J.A. Fuhrman. 1986. Bactivory in seawater studied with the use of inert fluorescent particles. Limnol. Oceanogr. 31: 420-42623. Riemann, B., N.O.G. Jorgensen, W. Lampert, and J.A. Fuhrman. 1986. Zooplankton-induced changes in dissolved free amino acids and in production rates of freshwater bacteria. Microb. Ecol. 12: 247-25824. Fuhrman, J.A., H.W. Ducklow, D. Kirchman, J.P. Hudak, G.B. McManus, J. Kramer. 1986. Does adenine incorporation into nucleic acids measure total microbial production? Limnol. Oceanogr. 31: 627-63625. Fuhrman, J.A., H.W. Ducklow, D.L. Kirchman, and G.B. McManus. 1986. Adenine and total microbial production: a reply. Limnol Oceanogr. 31: 1395-1400 26. Fuhrman, J.A. and R. L. Ferguson. 1986. Low concentrations and rapid turnover of dissolved free amino acids in seawater: chemical and microbiological measurements. Mar. Ecol. Prog. Ser. 33: 237-24227. Fuhrman, J.A. 1987. Close coupling between release and uptake of dissolved free amino acids in seawater studied by an isotope dilution approach. Mar. Ecol. Prog. Ser. 37: 45-5228. Lee, S. and J.A. Fuhrman. 1987. Relationships between biovolume and biomass of naturally-derived marine bacterioplankton. Appl. Environ. Microbiol. 53: 1298-130329. Boicourt, W.C., S.-Y.Chao, H.W. Ducklow, P.M. Glibert, T.C. Malone, M.R. Roman, J.A. Fuhrman, C. Garside, and R.W. Garvine. 1987. Physics and microbial ecology of a buoyant estuarine plume on the continental shelf. EOS, Trans. Am. Geophys. Union 68: 666-66830. McManus, G.B. and J.A. Fuhrman. 1988. Control of marine bacterioplankton populations: a review of grazing rate methodologies and estimates. Hydrobiologia 159: 51-62.31. Roman, M.R., H.W. Ducklow, J.A. Fuhrman, C. Garside, P.M. Glibert, T.C. Malone, and G.B. McManus. 1988. Production, consumption and nutrient cycling in a laboratory mesocosm. Mar. Ecol. Prog. Ser. 42: 39-5232. McManus, G.B. and J.A. Fuhrman. 1988. Clearance of bacteria-sized particles by natural populations of nanoplankton in the Chesapeake Bay outflow plume. Mar. Ecol. Prog. Ser. 42: 199-20633. Fuhrman, J.A., D.E. Comeau, ?. Hagstr?m, and A.M. Chan. 1988. Extraction of DNA suitable for molecular biological studies from natural planktonic microorganisms. Appl. Environ. Microbiol. 54: 1426-142934. Hudak, J.P. and J.A. Fuhrman. 1988. Effects of four organic pollutants on the growth of natural marine bacterioplankton populations. Mar. Ecol. Prog. Ser. 47: 185-194 35. Fuhrman, J.A., S.G. Horrigan, and D.G. Capone. 1988. The use of 13N as tracer for bacterial and algal uptake of ammonium from seawater. Mar. Ecol. Prog. Ser. 45: 271-27836. Hudak, J.P., J. McDaniel, S. Lee, and J.A. Fuhrman. 1988. Mineralization potentials of aromatic hydrocarbons by estuarine microorganisms: variations with season, location, and bacterioplankton production. Mar. Ecol. Prog. Ser. 47: 97-10237. Mitchell, J.G. and J.A. Fuhrman. 1989. Centimeter scale vertical heterogeneity in bacteria and chlorophyll a. Mar. Ecol. Prog. Ser. 54: 141- 14838. Fuhrman, J.A., T.D. Sleeter, C. Carlson, and L.M. Proctor. 1989. Dominance of bacterial biomass in the Sargasso Sea and its ecological implications. Mar. Ecol. Prog. Ser. 57: 207-21739. Fuhrman, J.A. and S. Lee. 1989. Natural microbial species variations studied at the DNA level. In: Recent advances in microbial ecology. T. Hattori, Y. Ishida, Y. Maruyama, R.Y. Morita, and A. Uchida, eds. Japan Scientific Societies Press, Tokyo. pp. 687-69140. Mitchell, J.G., A. Okubo, J.A. Fuhrman, and W. Cochlan. 1989. The contribution of phytoplankton to ocean density gradients. Deep Sea Res. 36: 1277-128241. Proctor, L.M. and J.A. Fuhrman. 1990. Viral mortality of marine cyanobacteria and bacteria. Nature 343: 60-6242. McManus, G.B., and J.A. Fuhrman. 1990. Mesoscale and seasonal variability of heterotrophic nanoflagellate abundance in an estuarine outflow plume. Mar. Ecol. Prog. Ser. 61: 207-21343. Lee, S. and J.A. Fuhrman. 1990. DNA hybridization to compare species compositions of natural bacterioplankton assemblages. Appl. Environ. Microbiol. 56: 739-74644. Suttle, C.A., J.A. Fuhrman, and D.G. Capone. 1990. Rapid ammonium cycling and concentration-dependent partitioning of ammonium and phosphate: implications for carbon transfer in planktonic communities. Limnol. Oceanogr. 35: 424-433 45. Mitchell, J.G., A. Okubo, and J.A. Fuhrman. 1990. Gyrotaxis as a new mechanism for generating plankton heterogeneity and migration. Limnol. Oceanogr. 35: 123-13046. Fuhrman, J.A. 1990. Dissolved free amino acid cycling in an estuarine outflow plume. Mar. Ecol. Prog. Ser. 66: 197-20347. Proctor. L.M. and J.A. Fuhrman. 1991. The roles of viral infection in organic particle flux. Mar. Ecol. Prog. Ser. 69: 133-142 48. Suttle, C.A., A.M. Chan, and J.A. Fuhrman. 1991. Dissolved free amino acids in the Sargasso Sea: uptake and respiration rates, turnover times, and concentrations. Mar. Ecol. Prog. Ser. 70: 189-19949. Glibert, P.M, C. Garside, J.A. Fuhrman, and M.R. Roman. 1991.Time-dependent coupling of inorganic and organic nitrogen uptake and ammonium regeneration in the plume of Chesapeake Bay Estuary, USA and its regulation by large heterotrophs. Limnol. Oceanogr. 36: 895-90950. Lee, S.H. and J.A. Fuhrman. 1991. Spatial and temporal variation of natural bacterioplankton assemblages studied by total genomic DNA cross-hybridization. Limnol. Oceanogr. 36: 1277-128751. Fuhrman, J.A. and D.G. Capone. 1991. Possible biogeochemical consequences of ocean fertilization. Limnol. Oceanogr. 36: 1951-195952. Lee, S.H. and J.A. Fuhrman. 1991. Confinement effect on species composition of bacterioplankton studied at the level of community DNA. Mar. Ecol. Prog. Ser. 79: 195-201 53. Fuhrman, J.A., K. McCallum, and A.A. Davis. 1992. Novel major archaebacterial group from marine plankton. Nature (London) 356: 148-14954. Fuhrman, J.A. 1992. Bacterioplankton roles in cycling of organic matter: the microbial food web. In P.G. Falkowski and A.D. Woodhead (editors), Primary Productivity and Biogeochemical Cycles in the Sea. Plenum Press, New York. pp. 361-38355. Kristiansen, K., H. Nielsen, B. Riemann, and J.A. Fuhrman. 1992. Growth efficiencies of freshwater bacterioplankton. Microb. Ecol. 24: 145-16056. Fuhrman, J.A. 1992. Bacterial growth in the sea (Current Contents Citation Classic). Current Contents: Agriculture, Biology, and Environmental Sciences, 23: 8 (not reviewed)57. Proctor, L.M. and J.A. Fuhrman. 1992. Mortality of marine bacteria in response to enrichments of the virus size fraction from seawater. Mar. Ecol. Prog. Ser.87: 283-29358. Fuhrman, J.A., K. McCallum, and A.A. Davis. 1993. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl. Environ. Microbiol. 59: 1294-130259. Proctor, L.M., A. Okubo, and J.A. Fuhrman. 1993. Calibrating estimates of phage-induced mortality in marine bacteria: Ultrastructural studies of marine bacteriophage development from one-step growth experiments. Microb. Ecol. 25: 161-182 60. Fuhrman, J.A. and C. A. Suttle. 1993. Viruses in marine plankton. Oceanography 6: 51-63 61. Fuhrman, J.A. 1993. Measuring marine bacterial growth (Current Contents Citation Classic). Current Contents: Agriculture, Biology, and Environmental Sciences 24: 8 (not reviewed)62. Fuhrman, J.A., R.M. Wilcox, R.T. Noble, and N.C. Law. 1993. Viruses in marine food webs.In Guerrero, R. and C. Pedros-Alio (eds). Trends in microbial ecology. Spanish Society for Microbiology, Barcelona. pp. 295-298.63. Fuhrman, J.A., S.H. Lee, Y. Masuchi, A.A. Davis, and R.M. Wilcox. 1994. Characterization of marine prokaryotic communities via DNA and RNA. Microb. Ecol. 28:133-14564. Wilcox, R.M. and J.A. Fuhrman. 1994. Bacterial viruses in coastal seawater: lytic rather than lysogenic production. Mar. Ecol. Prog. Ser. 114: 35-4565. Lee, S.H., Y-C. Kang, and J.A. Fuhrman. 1995. Imperfect retention of natural bacterioplankton cells by glass fiber filters. Mar. Ecol. Prog. Ser. 119: 285-29066. Fuhrman, J.A. and R.T. Noble. 1995. Viruses and protists cause similar bacterial mortality in coastal seawater. Limnol. Oceanogr. 40: 1236-124267. Thingstad, T.F., J.R. Dolan, and J.A. Fuhrman. 1996. Loss rate estimates of an oligotrophic bacterial assemblage as measured by 3H-thymidine and 32PO4: good agreement and near-balance with production. Aquat. Microb. Ecol. 10: 29-3668. Fuhrman, J.A. 1997. Community structure: Bacteria and Archaea. In: C.J. Hurst, G.R. Knudsen, M.J. McInerney, L.D. Stetzenbach, M.V. Walter, eds., Manual of Environmental Microbiology. ASM Press, Washington DC, pp. 278-28369. Noble, R.T., and J.A. Fuhrman. 1997. Virus decay and its causes in coastal waters. Appl. Environ. Microbiol. 63:77-8370. Karner, M. and J.A. Fuhrman. 1997. Determination of “active” marine bacterioplankton: a comparison of universal 16S rRNA probes, autoradiography, and nucleoid staining. Appl. Environ. Microbiol. 63: 1208-121371. Fuhrman, J.A., and A.A. Davis.1997. Widespread Archaea and novel Bacteria from the deep sea as shown by 16S rRNA gene sequences. Mar. Ecol. Prog. Ser. 150: 275-285 72. Ouverney, C.C. and J.A. Fuhrman. 1997. Increasing fluorescence of 16S rRNA in situ hybridization with chloramphenicol. Appl. Environ. Microbiol. 63: 2735-2740 73. Noble, R.T., and J.A. Fuhrman. 1998. Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat. Microb. Ecol. 14: 113-11874. Fuhrman, J.A. and L. Campbell. 1998. Microbial microdiversity. Nature (London) 393: 410-41175. Fuhrman, J.A. and C. C. Ouverney. 1998. Marine microbial diversity studied via 16S rRNA sequences: cloning results from coastal waters and counting of native archaea with fluorescent single cell probes. Aquat. Ecol. 32: 3-1576. Ouverney, C.C. and J.A. Fuhrman. 1999. Combined microautoradiography -16S rRNA probe technique for the determination of radioisotope uptake by specific microbial cell types in situ. Appl. Environ. Microbiol. 65:1746-175277. Noble, R.T., M. Middelboe, and J.A. Fuhrman. 1999. The effects of viral enrichment on the mortality and growth of heterotrophic bacterioplankton. Aquat. Microb. Ecol. 18:1-1378. Fuhrman, J.A. 1999. Marine viruses and their biogeochemical and ecological effects. Nature (London) 399: 541-54879. Noble, R.T. and J.A. Fuhrman. 1999. Breakdown and microbial uptake of marine viruses and other lysis products. Aquat. Microb. Ecol. 20:1-11 80. Gasol, J.M.,U. L. Zweifel, F. Peters, J.A. Fuhrman, and ?. Hagstr?m. 1999. Significance of size and nucleic acid content heterogeneity as measured by flow cytometry in natural planktonic bacteria. Appl. Environ. Microbiol. 65:4475-4483 81. Fuhrman, J.A. and R.T. Noble. 2000. Causative agents of bacterial mortality and the consequences to marine food webs. In Microbial biosystems: new frontiers. Proc 8th Int Symp Microb. Ecol. (ed. Bell, C.R., Brylinsky, M, & Johnson-Green, P.). Atlantic Canada Society for Microbial Ecology, Halifax, Canada pp. 145-15182. Fuhrman, J.A. 2000. Impact of viruses on planktonic bacteria. In: Microbial Ecology of the Oceans, D.L. Kirchman (ed.), Wiley & Sons. pp 327 - 350 83. Noble, R.T and, J. A. Fuhrman. 2000. Rapid viral production and removal as measured with fluorescently labeled viruses as tracers. Appl. Environ. Microbiol.. 66:3790-379784. Ouverney, C.C. and J.A. Fuhrman. 2000. Marine planktonic Archaea take up amino acids. Appl. Environ. Microbiol. 66:4829-483385. Fuhrman, J.A. 2000. Microbial Contamination. In: Opportunities for Environmental Applications of Marine Biotechnology. National Academy Press, Washington DC, pp. 102-11186. Fuhrman, J.A., and D.G. Capone. 2001. Nifty nanoplankton. Nature (London) 412: 593-59487. Hewson, I., J. M. O’Neil, J. A. Fuhrman, W.C. Dennison. 2001. Virus-like particle distribution and abundance in sediments and overlying waters along eutrophication gradients in two subtropical estuaries. Limnol Oceanogr. 46:1734-1746 88. Noble, R.T. and J.A. Fuhrman. 2001. Enteroviruses detected by reverse transcriptase polymerase chain reaction from the coastal waters of Santa Monica Bay, California: Low correlation to bacterial indicator levels. Hydrobiologia 460:175-184.89. Fuhrman, J.A. 2001. Plankton Viruses. In: Encyclopedia of Ocean Sciences, vol. 1, J. Steele, S. Thorpe and K. Turekian, eds. Academic Press, London. pages 2200-2207 90. Fuhrman, J.A. 2001. Community structure: Bacteria and Archaea. In: C.J. Hurst, R.L. Crawford, G.R. Knudsen, M.J. McInerney, L.D. Stetzenbach, eds., Manual of Environmental Microbiology, 2nd edition. ASM Press, Washington DC , pages 371-377change, H.A. Mooney and J.G. Canadell, editors. Wiley & Sons, Chichester UK. pp 421-42591. Fuhrman, J. A., J. F. Griffith, and M. S. Schwalbach. 2002. Prokaryotic and viral diversity patterns in marine plankton. Ecological Research 17 (2): 183-19492. Fuhrman, J.A. 2002. Viruses in the Marine Environment. In: Encyclopedia of Environmental Microbiology, G. Bitton, ed., Wiley & Sons, New York pages 3300-331093. Staley, J.T. and J.A. Fuhrman. 2002. Microbial Diversity. In: Encyclopedia of global environmental change, vol. 2, The Earth system: biological and ecological dimensions of global environmental94. Fuhrman, J.A. 2002. Community structure and function in prokaryotic marine plankton. Antonie van Leeuwenhoek 81:521-52795. Jiang, S., W. Fu, W, Chu, and J.A. Fuhrman. 2003. The vertical distribution and diversity of marine bacteriophage at a station off Southern California. Microb. Ecol. 45:399-410. Online DOI: 10.1007/s00248-002-1059-396. Hewson I, and J. A. Fuhrman. 2003. Viriobenthos production and virioplankton sorptive scavenging by suspended sediment particles in coastal and pelagic waters. Microbial Ecology 46: 337-34797. Gonzalez, J. M., J. S. Covert, W. B. Whitman, J. R. Henriksen, F. Mayer, B. Scharf, R. Schmitt, A. Buchan, J. A. Fuhrman, R. P. Kiene and M. A. Moran. 2003. Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments. Int. J. Syst. Evol. Microbiol. 53:1261-1269.98. Boehm, A.B, J.A.Fuhrman, R.D.Mr?e, and S. B.Grant. 2003 A tiered approach for identfication of a human fecal pollution source at a recreational beach:case study at Avalon Bay, Catalina Island, California, USA. Env. Sci. & Tech. 37(4):673-680 99. Fuhrman, J.A. and M.S. Schwalbach. 2003. Viral influence on aquatic bacterial communities. Biol. Bulletin. 204: 192-195100. Fuhrman, J. 2003. Genome sequences from the sea. Nature 424: 1001-1002 101. Hewson, I., G. A. Vargo, and J.A. Fuhrman. 2003. Bacterial diversity in shallow oligotrophic marine benthos and overlying waters: effects of virus infection, containment, and nutrient enrichment. Microbial Ecology 46: 322-336102. Field, K.G., E. C. Chern, L. K. Dick, J. A. Fuhrman, J. Griffith, P. A. Holden, M.G. LaMontagne, J. Le, B. Olson, and M. T. Simonich. 2003. A comparative study of culture-independent, library-independent genotypic methods of fecal source tracking. J. Wat. Health 1(4): 181-194 103. Schwalbach, M.S., I. Hewson, and J.A. Fuhrman. 2004. Viral effects on bacterial community composition in marine plankton mesocosms. Aquat. Microb. Ecol. 34:117-127104. Ouverney C.C., Fuhrman J.A. 2004. Correlating single-cell count with function in mixed natural microbial communities through STARFISH. In G. A. Kowalchuk, F. J. de Bruijn, I. M. Head, Akkermans, A.D.L., and J. D. van Elsas, editors. Molecular Microbial Ecology Manual, 2nd edition. Chapter 8.08: 1689-1710. Kluwer Academic Publishers, Dordrecht.105. Hewson, I., Govil, S.R., Capone, D.G., Carpenter, E.J. and Fuhrman J.A. 2004 Evidence of Trichodesmium viral lysis and potential significance for biogeochemical cycling in the oligotrophic ocean. Aquatic Microbial Ecology 36: 1 - 8106. Hewson, I, and J. A. Fuhrman. 2004. Bacterioplankton species richness and diversity along an estuarine gradient in Moreton Bay, Australia. Appl. Environ. Microbiol. 70(6): 3425-3433107. Schwalbach, M.S. and J. A. Fuhrman. 2005. Wide-ranging abundances of aerobic anoxygenic phototrophic bacteria in the world ocean revealed by epifluorescence microscopy and quantitative PCR. Limnol. Oceanogr. 50: 620-628.108. Brown, M.V., M.S. Schwalbach, I. Hewson and J. A. Fuhrman. 2005. Coupling 16S-ITS rDNA clone libraries and amplified ribosomal intergenic spacer analysis to show marine microbial diversity; development and application to a time series. Environ. Microbiol. 7: 1466-1479109. Fuhrman, J.A., R.T. Noble, and X. Liang. 2005. Rapid detection of enteroviruses from small volumes of natural waters by real time RT-PCR. Appl. Environ Microbiol. 71:4523-4530110. Schwalbach, M.S., M. Brown and J. A.. Fuhrman. 2005. Impact of light on marine bacterioplankton community structure. Aquat. Microb. Ecol. 39: 235-245111. Oremland, R.S., D. G. Capone, J.F. Stolz, and J.A. Fuhrman. 2005. Whither or Wither Geomicrobiology in the Era of “Community Metagenomics.” Nature Reviews Microbiology 3: 572-578 112. Brown, M.V.and J.A. Fuhrman. 2005. Marine bacterial microdiversity as revealed by internal transcribed spacer analysis. Aquat. Microb. Ecol. 41:15-23113. Steele, J.A., F. Ozis, J.A. Fuhrman, J.S. Devinny. 2005. Structure of microbial communities in ethanol biofilters. Chemical Engineering Journal 113: 135-143114. Hewson, I, and J.A. Fuhrman. 2006. Spatial and vertical biogeography of coral reef sediment bacterial and diazotroph communities . Marine Ecology Progress Series 306:79-86 115. Hewson, I, J. A. Steele, D.G. Capone , J.A. Fuhrman. 2006. Temporal and spatial scales of variation in bacterioplankton assemblages of oligotrophic surface waters. Mar. Ecol. Ecol. Ser. 311: 67-77116. Hewson, I., and J. A. Fuhrman. 2006. Improved strategy for comparing community fingerprints. Microbial Ecology. 51: 147-153 DOI: 10.1007/s00248-005-0144-9117. Noble, R.T., J F. Griffith, A.D. Blackwood, J.A. Fuhrman, J B. Gregory, X Hernandez, X Liang, A.A. Bera, K. Schiff. 2006. Multi-tiered approach using quantitative polymerase chain reaction for tracking sources of fecal pollution to Santa Monica Bay, California. Appl. Environ. Microbiol. 72: 1604-1612118. Hewson, I, J. A. Steele, D.G. Capone , J.A. Fuhrman. 2006. Remarkable heterogeneity in meso- and bathypelagic bacterioplankton community composition. Limnol. Oceanogr. 51: 1274-1283119. Hughes Martiny, J. B. , B.J.M. Bohannan, J.H. Brown, R. Colwell, J.A. Fuhrman, J. Green, M. C. Horner-Devine, M. Kane, J. A. Krumins, C. R. Kuske, P. Morin, S. Naeem, L. ?vre?s, A-L. Reysenbach, V. Smith, J. Staley. 2006. Microbial biogeography: Putting microorganisms on the map. Nature Reviews Microbiology 4:102-112120. Ruan, Q. , J. A. Steele, M..S. Schwalbach, J.A. Fuhrman, F. Sun. 2006. A Dynamic Programming Algorithm for Binning Microbial Community Profiles. Bioinformatics 22: 1508-1514 doi:10.1093/bioinformatics/btl114 121. Fuhrman, J.A., I. Hewson, M.S. Schwalbach, J. Steele, Mark V. Brown, and S. Naeem. 2006. Annually reoccurring bacterial communities are predictable from ocean conditions. Proc. Natl. Acad. Sci. USA, 103:13104-13109122. Ruan, Q., D. Dutta, M.S. Schwalbach, J. A. Steele, J.A. Fuhrman, and F. Sun. 2006. Local Similarity Analysis Reveals Unique Associations Among Marine Bacterioplankton Species and Environmental Factors. Bioinformatics. 20: 2532-2538. PMID: 16882654 123. Honjo, M, K. Matsui, M. Ueki, R. Nakamura, J.A. Fuhrman, and Z. Kawabata. 2006. Diversity of virus like agents killing Microcystis aeruginosa in a hyper-eutrophic pond. Journal of Plankton Research 28:407-412124. Hewson, I., D.G. Capone, J. A. Steele, and J.A. Fuhrman. 2006. Influence of Amazon and Orinoco offshore surface water plumes on oligotrophic bacterioplankton diversity in the West Tropical Atlantic. Aquat. Microb. Ecol. 43:11-22125 Hewson, Ian, and Jed A. Fuhrman. 2006. Viral impacts upon marine bacterioplankton assemblage structure. J. Mar. Biol. Asoc U.K. 86: 577-589126. Hewson I., D.M. Winget, K.E.Williamson, J.A. Fuhrman and K. E. Wommack. 2006. Viral and bacterial assemblage covariance in oligotrophic waters of the West Florida Shelf (Gulf of Mexico). J. Mar. Biol. Asoc U.K. 86: 591-603127. Fuhrman, J.A. Community Structure: Bacteria and Archaea. 2007. In: Christon J. Hurst, Ronald L. Crawford, Jay L. Garland, David A. Lipson, Aaron L. Mills, Linda D. Stetzenbach (eds.). Manual of Environmental Microbiology, 3rd edition. ASM Press, Washington, D.C. Section IV, Chap 35.128. Hewson, I. and J.A. Fuhrman. 2007. Characterization of lysogens in bacterioplankton assemblages of the Southern California Borderland. Microbial Ecology 53: 631-638129. Horner-Devine, M. Claire , Jessica M. Silver, Mathew A. Leibold, Brendan J. M. Bohannan,Robert K. Colwell, Jed A. Fuhrman, Jessica L. Green, Cheryl R. Kuske, Jennifer B. H. Martiny,Gerard Muyzer, Lise ?vreas, Anna-Louise Reysenbach, and Val H. Smith. 2007. A comparison of taxon co-occurrence patterns for macro- and microorganisms. Ecology 88:1345-1353130. Hewson, I., Fuhrman, J.A. 2007. Covariation between viral parameters with bacterial assemblage richness and diversity in the water column and sediments. Deep Sea Research I. 54: 811-830 idoi:10.1016/j.dsr.2007.02.003131. Hewson, I., Myrna E. Jacobson/Meyers and J. A. Fuhrman. 2007. Diversity and biogeography of bacterial assemblages in surface sediments across the San Pedro Basin, Southern California Borderlands. Environmental Microbiology 9: 923–933132. Patel, A, R.T. Noble, J.A. Steele, M.S. Schwalbach, I. Hewson, and J.A. Fuhrman. 2007. Virus and prokaryote enumeration from planktonic marine environments by epifluorescence microscopy with SYBR Green I. Nature Protocols 2: 269-276133. Fuhrman, J.A. and ?ke Hagstr?m. 2008. Bacterial and archaeal community structure and its patterns. In D.L. Kirchman (ed.) Microbial Ecology of the Oceans, 2nd edition. Wiley ISBN 978-0-470-04344-8. 593 pp.134. Fuhrman, J.A. 2008. Measuring diversity. In K. Zengler (ed.) Accessing Uncultivated Microorganisms. ASM Press. ISBN:978-1-55581-406-9. 320 pages135. Fuhrman, J.A., M.S. Schwalbach, U. Stingl. 2008. Proteorhodopsins: an array of physiological roles? Nature Reviews Microbiology. 6: 488-494136. Fuhrman, J.A., J. A. Steele, I. Hewson, M. S. Schwalbach, M.V. Brown, J. L. Green, J. H. Brown. 2008. A latitudinal diversity gradient in planktonic marine bacteria.. Proc. Nat. Acad. Sci. USA. 105: 7774-7778137. Hewson, I. and J.A. Fuhrman. 2008. Viruses, bacteria and the microbial loop. In D.G. Capone, D. A. Bronk, M. R. Mulholland and E. J. Carpenter (ed.), Nitrogen in the marine environment, Second edition. Elsevier.138. Fuhrman, J.A. and J.A. Steele. 2008. Community structure of marine bacterioplankton: patterns, networks, and relationships to function. Aquat. Microb. Ecol. 53: 69-81139. Fuhrman, J.A. 2009. Microbial community structure and its functional implications. Nature. 459: 193-199140. Brown, M.V., G.K. Philip, J.A. Bunge, M.C. Smith, A. Bissett, F.M. Lauro, J.A. Fuhrman, S. P. Donachie. 2009. Microbial community structure in the North Pacific Ocean. ISME Journal.3: 1374-1386. doi: 10.1038/ismej.2009.86141. B?er, Simone, Stefanie Hedtkamp, Justus van Beusekom, Jed A. Fuhrman, Antje Boetius, Alban Ramette. 2009. Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sandy sediments. ISME Journal 3:780-791142. Griffith, J.F. K. D. Schiff, G. Lyon and J.A. Fuhrman. 2010. Microbiological water quality at non-human impacted reference beaches in Southern California during wet weather. Marine Pollution Bulletin. 60(4): 500-508. doi:10.1016/j.marpolbul.2009.11.015143. Beman, J. M., R. Sachdeva, and J.A. Fuhrman. 2010. Population ecology of nitrifying Archaea and Bacteria in the Southern California Bight. Envir. Microbiol. 12: 1282-1292. Online doi:10.1111/j.1462-2920.2010.02172.x 144. Suttle, C. A., and J. A. Fuhrman. 2010. Enumeration of virus particles in aquatic or sediment samples by epifluorescence microscopy, p. 145–153. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7. . Bertics V.J. , J A. Sohm, T. Treude, C-E T. Chow, D. G. Capone, J. A. Fuhrman, and W. Ziebis. 2010. Burrowing deeper into benthic nitrogen fixation: The impact of bioturbation on nitrogen fixation coupled to sulfate reduction in coastal sediments. Mar. Ecol. Prog. Ser. 409: 1–15146. Beman, J.M., C.-E. Chow, B. N. Popp, J.A. Fuhrman, A. Andersson, Y. Feng, A.L. King, D.A. Hutchins. 2011. Global declines in ammonia oxidation as a consequence of ocean acidification. Proc. Nat. Acad. Sci USA. 108: 208-213 (online 20 December 2010) doi:10.1073/pnas.1011053108147. Perrings, C., Naeem, S., Ahrestani, F., Bunker, D. E., Burkill, P., Canziani, G., Elmqvist, T., Ferrati, R., Fuhrman, J., Jaksic, F., Kawabata, Z., Kinzig, A., Mace, G. M., Milano, F., Mooney, H., Prieur-Richard, A.-H., Tschirhart, J. & Weisser, W. 2010. Ecosystem Services for 2020. Science 330: 323-324.148. Hewson, Ian; Chow, Cheryl; and Fuhrman, Jed A. 2010. Ecological Role of Viruses in Aquatic Ecosystems. In: Encyclopedia of Life Sciences 2010, John Wiley & Sons, Ltd: Chichester [DOI: 10.1002/9780470015902.a0022546]149. Danovaro, Roberto, Cinzia Corinaldesi, Antonio Dell’Anno, Jed A. Fuhrman, Jack J. Middelburg, Rachel T. Noble and Curtis Suttle. 2011. Marine viruses and global climate change. FEMS Microbiology Reviews. 35: 993–1034 doi:?10.1111/j.1574-6976.2010.00258.x150. Beman J. Michael, Joshua A. Steele, and Jed A. Fuhrman. 2011. Co-occurrence patterns for abundant marine archaeal and bacterial lineages in the deep chlorophyll maximum of coastal California. ISME Journal 5:1077–1085; doi:10.1038/ismej.2010.204151. Steele , J. A., Peter D. Countway, L. Xia, P. D. Vigil, J. M. Beman, D. Y.Kim, C-E. T. Chow, R. Sachdeva, A. C. Jones, M. S. Schwalbach, J. M. Rose, I. Hewson, A. Patel, F. Sun, D. A. Caron, J. A. Fuhrman. 2011. Marine bacterial, archaeal, and protistan association networks reveal ecological linkages. ISME J. 5(9):1414-25. doi: 10.1038/ismej.2011.24. 152. Perrings, C., Shahid Naeem, Farshid S Ahrestani, Daniel E Bunker, Peter Burkill, Graciela Canziani, Thomas Elmqvist, Jed A Fuhrman, Fabian M Jaksic, Zen'ichiro Kawabata, Ann Kinzig, Georgina M Mace, Harold Mooney, Anne-Hélène Prieur-Richard, John Tschirhart, Wolfgang Weisser. 2011. Ecosystem services, targets, and indicators for the conservation and sustainable use of biodiversity. Frontiers in Ecology and the Environment. 9: 512-520 doi:10.1890/100212153. Romero, Isabel C., Myrna Jacobson, Jed A. Fuhrman, Marilyn Fogel Douglas G. Capone, 2011. Long-term nitrogen and phosphorus fertilization effects on N2 fixation rates and nifH gene community patterns in mangrove sediments. Mar. Ecol (2012) 33: 117–127. Article first published online : 14 JUN 2011, DOI:?10.1111/j.1439-0485.2011.00465. 154. Yilmaz, Pelin; Renzo Kottmann, Dawn Field, Rob Knight, James R. Cole, Linda Amaral-Zettler, Jack A. Gilbert, Ilene Karsch-Mizrachi, Anjanette Johnston, Guy Cochrane, Robert Vaughan, Christopher Hunter, Joonhong Park, Norman Morrison, Phillipe Rocca-Serra, Peter Sterk, Mani Arumugam, Laura Baumgartner, Bruce W. Birren, Martin J. Blaser, Vivien Bonazzi, Peer Bork, Pier Luigi Buttigieg, Patrick Chain, Elizabeth K. Costello, Heather Huot-Creasy, Peter Dawyndt, Todd DeSantis, Noah Fierer, Jed Fuhrman, Rachel E. Gallery, Richard A. Gibbs, Michelle Gwinn Giglio, Inigo San Gil, Elizabeth M. Glass, Antonio Gonzalez, Jeffrey I. Gordon, Robert Guralnick, Wolfgang Hankeln, Sarah Highlander, Philip Hugenholtz, Janet Jansson, Jerry Kennedy, Dan Knights, Omry Koren, Justin Kuczynski, Nikos Kyrpides, Robert Larsen, Christian L. Lauber, Teresa Legg, Ruth E. Ley, Catherine A. Lozupone, Wolfgang Ludwig, Donna Lyons, Eamonn Maguire, Barbara A. Methé, Folker Meyer, Sara Nakielny, Karen E. Nelson, Diana Nemergut, Josh D. Neufeld, Norman R. Pace, Giriprakash Palanisamy, J?rg Peplies, Jane Peterson, Joseph Petrosino, Lita Proctor, Jeroen Raes, Sujeevan Ratnasingham, Jacques Ravel, David A. Relman, Susanna Assunta-Sansone, Lynn Schriml, Erica Sodergren, Aymé Spor, Jesse Stombaugh, James M. Tiedje, Doyle V. Ward, George M. Weinstock, Doug Wendel, Owen White, Andreas Wilke, Jennifer Wortmann & Frank Oliver Gl?ckner. 2011. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology. 29:415–420 doi:10.1038/nbt.1823155. Zinger L., Amaral-Zettler, L.A., Fuhrman, J.A., Horner-Devine, M.C., Huse, S.M., Mark Welch, D.B., Martiny, J.B.H., Neal, P.R., Sogin, M., Boetius A., Ramette A. 2011. Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS ONE 6(9): e24570. doi:10.1371/journal.pone.0024570 156. Gilbert, Jack A., Joshua Steele, J. Gregory Caporaso, Lars Steinbrück, Jens Reeder, Ben Temperton, Susan Huse, Ian Joint, Alice C. McHardy, Rob Knight, Paul Somerfield, Jed A. Fuhrman, Dawn Field. 2011. Defining seasonal marine microbial community dynamics. The ISME Journal (2012) 6: 298–308; doi:10.1038/ismej.2011.107; published online 18 August 2011157. Fuhrman, J.A. 2011. Oceans of Crenarchaeota: a personal history describing this paradigm shift. Microbe. 6: 531-537. HYPERLINK ""online version158. Xia L.C., Cram J.A., Chen T., Fuhrman J.A., Sun F. 2011. Accurate genome relative abundance estimation based on shotgun metagenomic reads. PLoS ONE 6(12): e27992. doi:10.1371/journal.pone.0027992159. Xia, Li C., Joshua A. Steele, Jacob A. Cram, Zoe G. Cardon , Sheri L. Simmons , Joseph J. Vallino, Jed A. Fuhrman , Fengzhu Sun. 2011. Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. BMC Systems Biology. 5(Suppl 2):S15? doi:10.1186/1752-0509-5-S2-S15160. Hanson China, Horner-Devine M. Claire, Martiny Jennifer B.H., and Fuhrman Jed A. 2013. Microbial Biogeography. In: Levin S.A. (ed.) Encyclopedia of Biodiversity, second edition, Volume 5, pp. 271-279. Waltham, MA: Academic Press161. Chang, Qin, Yihui Luan, Ting Chen, Jed A. Fuhrman, Fengzhu Sun. 2012. Computational methods for the analysis of tag sequences in metagenomics studies. Frontiers in Bioscience. S4: 1333-1343 . doi 10.2741/335162. Freitas, Sara, Stephen Hatosy, Jed A. Fuhrman, Susan M. Huse, David B. Mark Welch, Mitchell L. Sogin, and Adam C. Martin. 2012. Global Distribution and Diversity of Marine Verrucomicrobia. ISME Journal 6: 1499–1505; doi:10.1038/ismej.2012.3163. Knight, Rob, Janet Jansson, Dawn Field, Noah Fierer, Narayan Desai, Jed A. Fuhrman, Phil Hugenholtz, Folker Meyer, Rick Stevens, Mark J. Bailey, Jeffrey I. Gordon, George A. Kowalchuk, Daniel van der Lelie, Jack A. Gilbert. 2012. The hype, the promises and developing hypotheses: Towards replicated experimental designs that deliver on the true potential of metagenomics. Nature Biotechnology 30(6):513-20 doi:10.1038/nbt.2235164. Chow, C-E.T., and J.A. Fuhrman. 2012. Seasonality and monthly dynamics of marine myovirus communities. Envir. Microbiol. 14(8): 2171–2183 DOI:?10.1111/j.1462-2920.2012.02744.x165. Hanson, China, Claire Horner-Devine, Jed A. Fuhrman, Jennifer B. H. Martiny. 2012. Beyond biogeographic patterns: evolutionary and ecological processes that shape the microbial landscape. Nature Reviews Microbiology 10: 497-506. doi:10.1038/nrmicro2795166. Brown, Mark V, Federico M. Lauro, Les Muir, David Wilkins, Matthew Z. DeMaere, Torsten Thomas, Martin Riddle, Jed A. Fuhrman, Cynthia Andrews-Pfannkoch, Matthew Lewis, Jeffrey M. Hoffman, Andrew Allen, Stephen R. Rintoul & Ricardo Cavicchioli. 2012. Global biogeography of SAR11 marine bacteria. Molecular Systems Biology 8: 595; doi:10.1038/msb.2012.28167. Fuhrman, J.A. 2012. Metagenomics and its connection to microbial community organization. F1000 Biology Reports 2012, 4:15 (doi:10.3410/B4-15) URL: . Amend, Anthony S., Tom A. Oliver, Linda A. Amaral-Zettler, Antje Boetius, Jed A. Fuhrman, M. Claire Horner-Devine, Susan M. Huse, David B. Mark Welch, Adam C. Martiny, Alban Ramette, Lucie Zinger, Mitchell L. Sogin, and Jennifer H. Martiny. 2013. Macroecological patterns of marine Bacteria on a global scale. J. Biogeography. 40:800-811 doi:10.1111/jbi.12034 ?169. Xia, Li, Dongmei Ai, Jacob Cram, Jed Fuhrman, Fengzhu Sun. 2013. Efficient statistical significance approximation for local association analysis of high-throughput time series data. Bioinformatics 29(2):230-7. doi: 10.1093/bioinformatics/bts668. Epub 2012 Nov 23.170. Needham, David M., Cheryl-Emiliane T. Chow, Jacob A. Cram, Rohan Sachdeva, Alma Parada, Jed A. Fuhrman.2013. Short-term observations of marine bacterial and viral communities: patterns, connections, and resilience. ISME J 7:1274–1285;online February 2013 doi:10.1038/ismej.2013.19.171. Riedel, Thomas, Laura Gómez-Consarnau, Jurgen Tomasch, Madeleine Martin, Michael Jarek,Jose? M. Gonzalez, Stefan Spring, Meike Rohlfs, Thorsten Brinkhoff, Heribert Cypionka,Markus Goeker, Anne Fiebig, Johannes Klein, Alexander Goesmann, Jed A. Fuhrman, Irene Wagner-Doebler. 2013. Genomics and Physiology of a Marine Flavobacterium Encoding a Proteorhodopsin and a Xanthorhodopsin-Like Protein. PLoS ONE 8(3): 57487 DOI: 10.1371/journal.pone.0057487172. Harwood, Valerie J., Alexandria B. Boehm, Lauren Sassoubre, Vijay Kannappan, Jill R. Stewart, Theng-Theng Fong, Marie-Paule Caprais, Reagan R. Converse, David Diston, James Ebdon, Jed A. Fuhrman, Michele Gourmelon, Jennifer Gentry-Shields, John F. Griffith, Donna Kashian, Rachel T. Noble, Huw Taylor, and Melanie Wicki. 2013. Performance of Viruses and Bacteriophages for Fecal Source Determination in a Multi-Laboratory, Comparative Study (SIPP). Water Research 47: 6929-6943. . 173. Hatosy, Stephen M., Jennifer B. H. Martiny, Rohan Sachdeva, Joshua Steele, Jed A. Fuhrman, Adam C. Martiny. 2013. Beta-diversity of marine bacteria depends on temporal scale. Ecology, 94:1898-1904; doi 10.1890/12-2125.1 (online May 2013)174. Chow, Cheryl-Emiliane T., Rohan Sachdeva, Jacob A. Cram, Joshua A Steele, David M. Needham, Anand Patel, Alma E. Parada, and Jed A. Fuhrman. 2013. Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight. The ISME Journal (2013) 7, 2259–2273; doi:10.1038/ismej.2013.122; published online 18 July 2013175. Pagarete, A., Chow, C-E.T., Johannessen, T., Fuhrman, J.A., Thingstad, T.F., Sandaa, R.A. 2013. Strong seasonality and inter-annual recurrence in marine myovirus communities. Appl. Environ Microbiol. 79:20 6253-6259; online August 2013 doi:10.1128/AEM.01075-13176. Chow, Cheryl-Emiliane T., Diane Y. Kim, Rohan Sachdeva, David A. Caron, and Jed A. Fuhrman. 2014. Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists. ISME Journal 8: 816-829 doi:10.1038/ismej.2013.199 177. Cram, Jacob A., Cheryl-Emiliane T. Chow, Rohan Sachdeva, David M. Needham, Alma E. Parada, Joshua A. Steele, Jed A. Fuhrman. 2014. Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years. ISME Journal 9, 563–580 doi:10.1038/ismej.2014.153178. Cram, Jacob, Fengzhu Sun and Jed A. Fuhrman. 2014. “Marine Bacterial, Archaeal, and Protistan Association Networks.” in Encyclopedia of Metagenomics. Springer. DOI 10.1007/978-1-4614-6418-1_721-3179. Weitz, Joshua S., Charles A. Stock, Steven W. Wilhelm, Lydia Bourouiba, Alison Buchan, Maureen L. Coleman, Michael J. Follows, Jed A. Fuhrman, Luis F. Jover, Jay T. Lennon, Mathias Middelboe, Derek L. Sonderegger, Curtis A. Suttle, Bradford P. Taylor, T. Frede Thingstad, Willie H. Wilson and K. Eric Wommack. 2014. A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes. ISME Journal, 9, 1352–1364; doi: 10.1038/ismej.2014.220180. Fuhrman, Jed A, Jacob Cram, David M. Needham. 2015. Marine microbial dynamics and their ecological interpretation. Nature Reviews Microbiology, 13: 133 - 146 doi:10.1038/nrmicro3417181. Cram, Jacob A, Li C. Xia, David M. Needham, Rohan Sachdeva, Fengzhu Sun, Jed A. Fuhrman. 2015. Cross-depth analysis of marine bacterial networks suggests downward propagation of temporalChanges. The ISME Journal 9, 2573–258, online publication 19?May?2015; doi: 10.1038/ismej.2015.76182. Romero, Isabel C., Myrna E. Jacobson-Meyers, Jed A. Fuhrman, Douglas G. Capone. 2015 Phylogenetic diversity of diazotrophs along an experimental nutrient gradient in mangrove sediments. J. Mar. Sci. Eng. 2015, 3(3), 699-719; doi:10.3390/jmse3030699 183. Fuhrman J, Caron D. 2015. Heterotrophic Planktonic Microbes: Virus, Bacteria, Archaea, and Protozoa, p 4.2.2-1-4.2.2-34. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, 4th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch4.2.2184. Xia, Li Charlie, Dongmei Ai, Jacob Cram, Xiaoyi Liang, Jed A Fuhrman, Fengzhu Sun. 2015 Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains. BMC Bioinformatics, 16:301 DOI: 10.1186/s12859-015-0732-8185. Walters, William, Embriette R. Hyde, Donna Berg-Lyons, Gail Ackermann, Greg Humphrey, Alma Parada, Jack Gilbert, Janet K. Jansson, Greg Caporaso, Jed A. Fuhrman, Amy Apprill, Rob Knight. 2015.Improved V4, V4-5, and ITS marker gene primers for microbial community survey. mSystems Dec 2015, 1 (1), DOI: 10.1128/mSystems.00009-15186. Parada, Alma, David M. Needham, and Jed A. Fuhrman. 2016. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time-series and global field samples. Envir. Microbiol. 18, (5)1403–1414, DOI:?10.1111/1462-2920.13023. Advanced online publication 18 August 2015 187. Gómez-Consarnau, L., J. M. González, T. Riedel, S. Jaenicke, S. A. Sa?udo-Wilhelmy, I. Wagner-D?bler, J. A. Fuhrman. 2016. Proteorhodopsin light-enhanced growth linked to vitamin B1 acquisition in marine Flavobacteria. The ISME Journal 10: 1102–1112; doi:10.1038/ismej.2015.196; published online 17 November 2015188. Cram, Jacob A., Alma E. Parada and Jed A. Fuhrman. 2016. Dilution reveals how viral lysis and grazing shape microbial communities. Limnol. Oceanogr. 61, 2016, 889–905. Advanced online 8 February 2016. DOI: 10.1002/lno.10259 PMID:25989373189. Weiss S., Van Treuren W., Lozupone C., Faust K., Friedman J., Deng Y., Xia L.C., Xu Z.Z., Ursell L., Alm E.J., Birmingham A., Cram J.A., Fuhrman J.A., Raes J., Sun F., Zhou J., Knight R. 2016. Correlation detection strategies in microbial datasets vary widely in sensitivity and precision. ISME J. 10, 1669–1681; doi:10.1038/ismej.2015.235, advance online Feb 23 2016190. Needham, David M., and J. A. Fuhrman. 2016. Pronounced daily succession of bloom associated phytoplankton, archaea, & bacteria. Nature Microbiology 1, 16005. 29 February 2016 doi: 10.1038/nmicrobiol.2016.5191. Wigington, Charles H, Derek L Sonderegger, Corina PD Brussaard, Alison Buchan, Jan F Finke, Jed A Fuhrman,Jay Lennon, Mathias Middelboe, Charles A Stock, Curtis A Suttle, William H Wilson, K. Eric Wommack, Steven W. Wilhelm, Joshua S Weitz. 2016. Re-examination of the relationship between marine virus and microbial cell abundances" Nature Microbiology 1: 15024, doi:10.1038/nmicrobiol.2015.24 . 192. Yang Lu, Ting Chen, Jed A. Fuhrman, and Fengzhu Sun. 2016. COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read LinkAge. Bioinformatics. 33 (6): 791-798. doi:10.1093/bioinformatics/btw290193. Bálint, Miklós; Mohammad Bahram, A. Murat Eren, Karoline Faust, Jed A. Fuhrman, Bj?rn Lindahl, Robert B. O'Hara, Maarja ?pik, Mitchell L. Sogin, Martin Unterseher, Leho Tedersoo. 2016. Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes. FEMS Microbiol Rev. 40 (5): 686-700. DOI: 686-700 194. Zhang, Mengge, Lianping Yang, Jie Ren, Nathan Ahlgren, Jed Fuhrman and Fengzhu Sun. 2017. Prediction of virus-host infectious association by supervised learning methods. BMC Bioinformatics 2017 18(Suppl 3):60 195. Ahlgren, Nathan A., Jie Ren, Yang Young Lu, Jed A. Fuhrman, Fengzhu Sun. 2017. Alignment-free ?2? oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences. Nucleic Acids Res. 45 (1): 39-53., doi: 10.1093/nar/gkw1002196. David A. Caron, Paige E. Connell, Rebecca A. Schaffner, Astrid Schnetzer, Jed A. Fuhrman, Peter D. Countway, Diane Y. Kim. 2017. Planktonic food web structure at a coastal time-series site: I. Partitioning of microbial abundances and carbon biomass. Deep-Sea Research Part 1. 121: 14-29. Advance online publication 3 Jaunary 2017, . Needham, David M., Rohan Sachdeva, Jed A. Fuhrman. 2017. Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters.ISME Journal 11: 1614–1629. doi: 10.1038/ismej.2017.29198. Parada, Alma and Jed A. Fuhrman. 2017. Marine archaeal dynamics and interactions with the microbial community over 5 years from surface to seafloor. ISME Journal 11: 2510–2525;advance online publication 21?July?2017; doi: 10.1038/ismej.2017.104199. Yang Young Lu, Kujin Tang, Jie Ren, Jed A. Fuhrman, Michael S. Waterman and Fengzhu Sun. 2017. CAFE: aCcelerated Alignment-FrEe sequence analysis. Nucl. Acids Res.45: W554-W559. DOI: 10.1093/nar/gkx351200. Ahlgren, Nathan A., Yangyang Chen, David Needham, Alma E. Parada, RohanSachdeva, Vickie Trinh, Ting Chen, Jed A. Fuhrman. 2017. Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification, and multiple restriction systems. Envir. Microbiol. 19:2434-2452. doi 10.1111/1462-2920.13768201. Gómez-Consarnau L., R. Sachdeva, S. Gifford, L. S. Cutter, J. A. Fuhrman, S. A. Sa?udo-Wilhelmy, M.A. Moran. 2018. Mosaic patterns of B-vitamin synthesis and utilization?in a natural marine microbial community. Envir. Microbiol. 8: 2809 – 2823 doi 10.1111/1462-2920.14133 ?202. Ren, Jie, Nathan A. Ahlgren, Yang Young Lu, Jed A .Fuhrman, Fengzhu Sun. 2017. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. Microbiome 5:69, DOI: 10.1186/s40168-017-0283-5 203. Lu, Yang Young, Jinchi Lv, Jed A Fuhrman, Fengzhu Sun. 2017. Towards enhanced and interpretable clustering/classification in integrative genomics. Nucleic Acids Research, 45 (20): e169, gkx767, 204. Thompson, Luke R., Jon G. Sanders, Daniel McDonald, Amnon Amir, Joshua Ladau, Kenneth J.Locey, Robert J. Prill, Anupriya Tripathi, Sean M. Gibbons, Gail Ackermann, Jose A. Navas-Molina, Evguenia Kopylova, Yoshiki Vázquez-Baeza, Stefan Janssen, James T. Morton, Siavash Mirarab, Zhenjiang Zech Xu, Mohamed F. Haroon, Jad Kanbar, Qiyun Zhu, Antonio Gonzalez, Se Jin Song, Tomasz Kosciolek, Nicholas A. Bokulich, Joshua Lefler, Colin J. Brislawn, Greg C.Humphrey, Sarah M. Owens, Jarrad Hampton-Marcell, Donna Berg-Lyons, Valerie McKenzie,Noah Fierer, Jed A. Fuhrman, Aaron Clauset, Rick L. Stevens, Ashley Shade, Katherine S. Pollard, Kelly D. Goodwin, Janet K. Jansson, Jack A. Gilbert, Rob Knight & The Earth Microbiome Project Consortium. 2017. A communal catalogue reveals Earth's multiscale microbial diversity. Nature, 551:457-466. doi:10.1038/nature24621205. Wang Y, Wang K, Lu YY, Sun FZ* (2017) Improving contig binning of metagenomic data using d2S oligonucleotide frequency dissimilarity. BMC Bioinformatics 18:425. 206. Brown, Mark, Jodie van de Kamp , Martin Ostrowski , Justin Seymour, Tim Ingleton , Lauren Messer , Thomas Jeffries , Nashon Siboni , Bonnie Laverock , Jaume Bibiloni-Isaksson , Tiffanie Nelson, Frank Coman , Claire Davies , Dion Frampton , Mark Rayner , Kirianne Goossen , Stan Robert , Bronwyn Holmes , Guy Abell , Pascal Craw , Tim Kahlke , Swanlisan Sow ,. Kirsty McAllister , Jonathon Windsor , Michele Skuza , Ryan Crossing , Nicole Patten , Paul Malthouse , Paul van Ruth , Ian Paulsen , Jed Fuhrman , Anthony Richardson , Jason Koval , Andrew Bissett , Anna Fitzgerald , Tim Moltmann , Levente Bodrossy. 2018. Continental scale monitoring of marine microbiota by the Australian Marine Microbial Biodiversity Initiative. Scientific Data 5, 180130. 207. Hernando-Morales, Víctor, Marta M Varela, David M. Needham, Jacob Cram, Jed A. Fuhrman, Eva Teira. 2018. Vertical and seasonal patterns control bacterioplankton communities at two horizontally coherent coastal upwelling sites off Galicia (NW Spain). Microb. Ecol. online April 2018. . Berdjeb, Lyria. Alma Parada, David M. Needham, Jed A Fuhrman. 2018. Short-term dynamics and interactions of marine protist communities during the spring-summer transition. ISME J 12:1907–1917. . . 209. Ignacio-Espinoza, J.Cesar and Jed A. Fuhrman. 2018. A non-tailed twist in the viral tale. Nature, 554: 39-39. online 24 January 2018. doi:10.1038/d41586-018-00923-8 . Yeh, Yi-Chun, David M. Needham, Ella T.?Sieradzki,and Jed A. Fuhrman. 2018.Taxon disappearance from microbiome analysis reinforces the value of?mock?communities as a standard?in every sequencing run. mSystems, 3 e00023-18. . Also bioRxiv 211. Needham, David M., Erin B. Fichot, Ellice Wang, Lyria Berdjeb, Jacob A. Cram, Cedric G. Fichot, Jed A. Fuhrman. 2018. Dynamics and interactions of highly resolved marine plankton via automated high frequency sampling . ISME Journal, 12:2417-32. . . Also bioRxiv212. Sieradzki E.T., J.A. Fuhrman, S Rivero-Calle, and L.Gómez-Consarnau (2018) Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities. 2018. PeerJ 6:e5798; DOI 10.7717/peerj.5798 213. Ahlgren, Nathan A., Clara Fuchsman, Gabrielle Rocap, Jed A. Fuhrman. 2019. Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode nitrifying genes. ISME J 13:618–631. Online 12 Oct 2018. , Editor’s Choice 2018214. Gómez-Consarnau, Laura, John A. Raven, Naomi M. Levine, Lynda S. Cutter, Deli Wang, Brian Seegers, Javier Arístegui, Jed A. Fuhrman, Josep M. Gasol & Sergio A. Sa?udo-Wilhelmy. 2019. Microbial rhodopsins are major contributors to the solar energy captured in the sea. Science Advances Vol. 5, No. 8. DOI: 10.1126/sciadv.aaw8855 bioRxiv 231167; doi: 215. Monteverde, Danielle, Jason Sylvan, Christopher Suffridge, Jotautas Baronas, Erin Fichot, Jed Fuhrman, William Berelson, and Sergio Sa?udo-Wilhelmy. 2018. Distribution of extracellular flavins in a coastal marine basin and their relationship to redox gradients and microbial community members Environ. Sci. Technol 52 (21):12265–12274 216. Dekas, Anne E, Alma E Parada, Xavier Mayali, Jed Fuhrman, Jessica Wollard, Peter K Weber, Jennifer Pett-Ridge. 2019. Characterizing chemoautotrophy and heterotrophy in marine archaea and bacteria with single-cell multi-isotope nanoSIP. Front. Microbiol., 17 December 2019 | . Sieradzki, Ella T., J. Cesar Ignacio-Espinoza, David M. Needham, Erin B Fichot, and Jed A. Fuhrman. 2019. Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes. Nature Communications, 10:1169 | and bioRxiv218. Wang, Ziye, Ying Wang, Jed A. Fuhrman, Fengzhu Sun and Shanfeng Zhu. 2019. Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences. Briefings in Bioinformatics bbz025, . Ahlgren, N. A., J. Perelman,Yi-chun Yeh, and J.A. Fuhrman. 2019. Multi-year dynamics of fine-scale marine cyanobacterial populations are more strongly explained by phage interactions than abiotic, bottom-up factors. Envir Microbiol.21(8), 2948–2963. 220. Roux, Simon, Evelien M. Adriaenssens, Bas E. Dutilh, Eugene V. Koonin, Andrew M. Kropinski,Mart Krupovic, Jens H. Kuhn, Rob Lavigne, J. Rodney Brister, Arvind Varsani,Clara Amid, Ramy K. Aziz, Seth R. Bordenstein, Peer Bork, Mya Breitbart, Guy R. Cochrane, Rebecca A.Daly, Christelle Desnues, Melissa B. Duhaime, Joanne B. Emerson, Fran?ois Enault, Jed A.Fuhrman, Pascal Hingamp, Philip Hugenholtz, Bonnie L. Hurwitz, Natalia N. Ivanova, JessicaM. Labonte, Rex R. Malmstrom, Manuel Martinez-Garcia, Ilene Mizrachi, Hiroyuki Ogata,David Páez-Espino, Marie-Agnès Petit, Catherine Putonti, Thomas Rattei, Alejandro Reyes, Francisco Rodriguez-Valera, Karyna Rosario, Lynn Schriml, Frederik Schulz, Grieg F. Steward, Matthew B. Sullivan, Shinichi Sunagawa, Curtis A. Suttle, Ben Temperton, Susannah G. Tringe, Rebecca Vega Thurber, Nicole S. Webster,, Katrine L. Whiteson, Steven W. Wilhelm, K. Eric Wommack, Tanja Woyke,, Kelly Wrighton, Pelin Yilmaz, Takashi Yoshida, Mark J. Young, Natalya Yutin, Lisa Zeigler Allen, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh. 2019. Minimum Information about Uncultivated Virus Genomes (MIUViG): a community consensus on standards and best practices for describing genome sequences from uncultivated viruses. Nature Biotechnology 37: 29–37 221. Roux, Simon, Gareth Trubl, Danielle Goudeau, Nandita Nath, Estelle Couradeau, Nathan A. Ahlgren, Yuanchao Zhan, David Marsan, Feng Chen, Jed A. Fuhrman, Trent R. Northen, Matthew B. Sullivan, Virginia I. Rich, Rex R. Malmstrom, and Emiley A. Eloe-Fadrosh. 2019. Optimizing de novo genome assembly from PCR-amplified metagenomes. PeerJ 7:e6902 . Paterson James S., Renee J. Smith, Jody C McKerral, Lisa M. Dann, Elise Launer, Peter Goonan, Tavis Kleinig, Jed A. Fuhrman and James G. Mitchell. 2019. A hydrocarbon contaminated aquifer reveals a Piggyback-the-Persistent viral strategy. FEMS Microbiology Ecology, fiz116,. Gomez-Consarnau, Laura, David M Needham, Peter K Weber, Jed A Fuhrman and Xavier Mayali. 2019. Influence of light on particulate organic matter utilization by attached and free-living marine bacteria. Frontiers in Microbiology 10:1204.doi: 10.3389/fmicb.2019.01204224. Ignacio-Espinoza, J. Cesar, Nathan A. Ahlgren, and Jed A. Fuhrman. 2020. Long-term stability and Red Queen-like strain dynamics in marine viruses. Nature Microbiology 5: 265–271 (online 2019)DOI 10.1038/s41564-019-0628-x 225. Ren J, K, Song, C Deng, NA Ahlgren, JA Fuhrman, Y Li, XH Xie, R Poplin, FZ Sun. (2020) Identifying viruses from metagenomic data by deep learning. Quantitative Biology 8 (1): 64-67 . 226. Wang, Weili, Jie Ren, Kujin Tang; Emily Dart, J. Cesar Ignacio-Espinoza , Jed A. Fuhrman, Jonathan Braun, Fengzhu Sun, Nathan A. Ahlgren. 2020. A network-based integrated framework for predicting Virus-host interactions. NAR Genomics and Bioinformatics, Volume 2, Issue 2, June 2020, lqaa044, . Messer L.F., Ostrowski M., Doblin M.A., Petrou K., Baird M.E., Ingleton T., Bissett A., Van de Kamp J., Nelson T., Paulsen I., Bodrossy L. Fuhrman J.A., Seymour J.R., Brown M.V. 2020. Tropicalisation driven by a strengthening western boundary current. Glob Change Biol. 26:5613–5629, HYPERLINK "" . Sieradzki, Ella T., Michael Morando and Jed A. Fuhrman. Metagenomics and stable isotope probing offer insights into metabolism of polycyclic aromatic hydrocarbons biodegraders in chronically polluted seawater. Submitted. Also bioRxiv . Long, A.M., Hou, S., Ignacio-Espinoza, J.C. et al. Benchmarking microbial growth rate predictions from metagenomes. ISME J (2020). bioRxiv . Yi-Chun Yeh, Jesse C McNichol, David M Needham, Erin B Fichot, Jed A Fuhrman. Comprehensive single-PCR 16S and 18S rRNA community analysis validated with mock communities and denoising algorithms. Submitted to Envir. Microbiol.Also bioRxiv : . Weissman, Jake L, Shengwei Hou, Jed A Fuhrman. 2020. Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns. Submitted to PNAS. Also bioRxiv \232. Weissman, Jake L, Ellinor O Alseth, Sean Meaden, Edze R Westra, Jed A Fuhrman.Immune Lag Is a Major Cost of Prokaryotic Adaptive Immunity During Viral Outbreaks. Submitted to Ecol Letters. bioRxiv . Steele, Joshua A., Michael S. Schwalbach, Rohan Sachdeva, Jed A. Fuhrman. Spatial scales of marine bacterioplankton assemblages in the Southern California Bight. SubmittedBOOK REVIEWSAquatic Microbiology, by G. Rheinheimer. American Scientist 76: 90 (1988)PUBLISHED CORRESPONDENCEPerrings, C., Naeem, S., Ahrestani, F., Bunker, D. E., Burkill, P., Canziani, G., Elmqvist, T., Ferrati, R., Fuhrman, J., Jasic, F., Kawabata, Z., Kinzig, A., Mace, G. M., Milano, F., Mooney, H., Richard, A.-H. P., Tschirhart, J. & Weisser, W. (2010) Biodiversity Transcends Services? Response. Science, 330: 1745.Reports/Commentary:Dagit, Rosi, Steve Williams, and Jed Fuhrman. 2005. Topanga Creek Watershed Water Quality Study Final Report. Resource Conservation District of the Santa Monica Mountians, Topanga, CANoble T., Rachel, J.F. Griffith, A.D. Blackwood, J.A. Fuhrman, J.B. Gregory, X. Hernandez, X. Liang, A. A. Bera, K. Schiff. 2005. Multi-tiered approach using quantitative polymerase chain reaction for tracking sources of fecal pollution to Santa Monica Bay, California. Southern California Coastal Water Research Project, Westminster, CA.Perrings, Charles, Shahid Naeem, Farshid Ahrestani, Dan Bunker, Peter Burkill , Graciela Canziani, Thomas Elmqvist, Rosana Ferrati, Jed Fuhrman, Fabian Jaksic, Zen Kawabata, Ann Kinzig, Georgina Mace, Fernando Milano, Harold Mooney, John Tschirhart, Wolfgang Weisser. 2010.Ecosystem services and target-setting for the protection of the global common wealth. DIVERSITAS Ecoservices Committee report to United Nations Environment Programme (UNEP). New York.Jed A Fuhrman, Michael Follows, and Samantha Forde. 2013. Merging complex "-omic" data and computational ecosystem models. EOS 94:241 DOI:?10.1002/2013EO270006Davies ?Neil, Field, ?Dawn, Amaral-Zettler ?Linda, Clark S Melody, Deck ?John, Drummond ?Alexei, Faith P Daniel, Geller ?Jonathan, Gilbert ?Jack, Gl?ckner Oliver Frank, Hirsch ?Penny, Leong ?Jo-Ann, Meyer ?Chris, Obst ?Matthias, Planes ?Serge, Scholin ?Chris, Vogler P Alfried, Gates D Ruth, Toonen ?Rob, Berteaux-Lecellier ?Véronique, Barbier ?Michèle, Barker ?Katherine, Bertilsson ?Stefan, Bicak ?Mesude, Bietz J Matthew, Bobe ?Jason, Bodrossy ?Levente, Borja ?Angel, Coddington ?Jonathan, Fuhrman ?Jed, Gerdts ?Gunnar, Gillespie ?Rosemary, Goodwin ?Kelly, Hanson C Paul, Hero ?Jean-Marc, Hoekman ?David, Jansson ?Janet, Jeanthon ?Christian, Kao ?Rebecca, Klindworth ?Anna, Knight ?Rob, Kottmann ?Renzo, Koo S Michelle, Kotoulas ?Georgios, Lowe J Andrew, Marteinsson Thór Viggó, Meyer ?Folker, Morrison ?Norman, Myrold D David, Pafilis ?Evangelos, Parker ?Stephanie, Parnell Jacob John, Polymenakou N Paraskevi, Ratnasingham ?Sujeevan, Roderick K George, Rodriguez-Ezpeleta ?Naiara, Schonrogge ?Karsten, Simon ?Nathalie, Valette-Silver J Nathalie, Springer ?Yuri, Stone N Graham, Stones-Havas ?Steve, Sansone ?Susanna-Assunta, Thibault M Kate, Wecker ?Patricia, Wichels ?Antje, Wooley C John, Yahara ?Tetsukazu, Zingone ?Adriana. 2014. The founding charter of the Genomic Observatories Network., GigaScience. 2014, 3:2. DOI: 10.1186/2047-217X-3-2.URL:? Kopf, Mesude Bica, Renzo Kottmann, Julia Schnetzer,, Ivaylo Kostadinov, Katja Lehmann, Antonio Fernandez-Guerra,, Christian Jeanthon, Eyal Rahav, Matthias Ullrich, Antje Wichels, Gunnar Gerdts, Paraskevi Polymenakou, Giorgos Kotoulas, Rania Siam, Rehab Z Abdallah, Eva C Sonnenschein, Thierry Cariou, Fergal O’Gara,, Stephen Jackson, Sandi Orlic, Michael Steinke, Julia Busch, Bernardo Duarte, Isabel Ca?ador, Jo?o Canning-Clode,, Oleksandra Bobrova, Viggo Marteinsson, Eyjolfur Reynisson, Clara Magalh?es Loureiro, Gian Marco Luna, Grazia Marina Quero, Carolin R L?scher, Anke Kremp, Marie E DeLorenzo, Lise ?vre?s, Jennifer Tolman, Julie LaRoche, Antonella Penna, Marc Frischer, Timothy Davis, Barker Katherine, Christopher P Meyer, Sandra Ramos, Catarina Magalh?es, Florence Jude-Lemeilleur, Ma Leopoldina Aguirre-Macedo, Shiao Wang, Nicole Poulton, Scott Jones,Rachel Collin, Jed A Fuhrman, Pascal Conan, Cecilia Alonso, Noga Stambler,, Kelly GoodwinMichael M Yakimov, Federico Baltar, Levente Bodrossy, Jodie Van De Kamp, Dion MF Frampton,Martin Ostrowski, Paul Van Ruth, Paul Malthouse, Simon Claus, Klaas Deneudt, Jonas Mortelmans,Sophie Pitois, David Wallom, Ian Salter,, Rodrigo Costa, Declan C Schroeder, Mahrous M Kandil,Valentina Amaral, Florencia Biancalana, Rafael Santana, Maria Luiza Pedrotti, Takashi Yoshida,Hiroyuki Ogata, Tim Ingleton,, Kate Munnik, Naiara Rodriguez-Ezpeleta, Veronique Berteaux-Lecellier,Patricia Wecker, Ibon Cancio, Daniel Vaulot, Christina Bienhold,, Hassan Ghazal,, Bouchra Chaouni,, Soumya Essayeh, Sara Ettamimi,, El Houcine Zaid, Noureddine Boukhatem, Abderrahim Bouali,Rajaa Chahboune,, Said Barrijal, Mohammed Timinouni, Fatima El Otmani, Mohamed Bennani,Marianna Mea, Nadezhda Todorova, Ventzislav Karamfilov, Petra ten Hoopen, Guy Cochrane,Stephane L’Haridon, Kemal Can Bizsel, Alessandro Vezzi, Federico M Lauro, Patrick Martin,Rachelle M Jensen, Jamie Hinks, Susan Gebbels, Riccardo Rosselli, Fabio De Pascale, Riccardo Schiavon,Antonina dos Santos, Emilie Villar, Stéphane Pesant, Bruno Cataletto, Francesca Malfatti, Ranjith Edirisinghe, Jorge A Herrera Silveira, Michele Barbier, Valentina Turk, Tinkara Tinta,Wayne J Fuller, Ilkay Salihoglu, Nedime Serakinci, Mahmut Cerkez Ergoren, Eileen Bresnan, Juan Iriberri,Paul Anders Fronth Nyhus, Edvardsen Bente, Hans Erik Karlsen, Peter N Golyshin, Josep M Gasol,Snejana Moncheva, Nina zhembekova, Zackary Johnson, Christopher David Sinigalliano,Maribeth Louise Gidley,, Adriana Zingone, Roberto Danovaro,, George Tsiamis, Melody S Clark,Ana Cristina Costa, Monia El Bour, Ana M Martins,, R Eric Collins, Anne-Lise Ducluzeau, Jonathan Martinez, Mark J Costello, Linda A Amaral-Zettler,, Jack A Gilbert,,,, Neil Davies, ,Dawn Field, and Frank Oliver Gl?ckner. The ocean sampling day consortium. GigaScience (2015) 4:27. DOI 10.1186/s13742-015-0066-5Television interview for Xploration Awesome Planet, Season 3, Episode 14 “Microscopic World.” Originally aired 17 December 2016. Available on Amazon or Hulu.Online 2019 Video about Fuhrman Lab San Pedro Ocean Time Series, Smithsonian Press Release regarding Red Queen Dynamics, December 2019. ABSTRACTS AND PRESENTATIONS Fuhrman, J.A. "Accumulation of silicon by Platymonas, a marine alga with no apparent silicon requirement." 1978 Annual Meeting of the American Society of Limnology and Oceanography, Victoria, British ColumbiaFuhrman, J.A. and F. Azam. "Trophic dynamics of bacterioplankton in an enclosed marine water column: Controlled Ecosystem Population Experiment." 1979 Annual Meeting of the American Society for Microbiology, Los Angeles, CaliforniaAzam, F., J.T. Hollibaugh, J.A. Fuhrman, J.W. Ammerman, A.B. Carruthers and E.I. Mousalli. "Population dynamics of bacterioplankton in natural and polluted pelagic marine environments: studies in enclosed experimental ecosystems." Symposium on Enclosed Marine Experimental Ecosystems, Sidney, British Columbia,1980Azam, F. and J.A. Fuhrman. "Measurements of bacterial biomass and secondary production in pelagic marine environments." Second International Symposium on Microbial Ecology, University of Warwick, U.K., 1980 Fuhrman, J.A. "Patterns of bacterioplankton production in the Southern California Bight." American Society for Microbiology Annual Meeting, Atlanta, 1982Fuhrman, J.A. "Diel studies of bacteria, phytoplankton, and related chemical parameters in the Southern California Bight. Marine Microbial Ecology Symposium on Major Element Flow in Pelagic and Benthic Environments. Univ. of Copenhagen, Sept. 1982Fuhrman, J.A., F. Azam, R.W. Eppley, A. Hagstrom." Diel variations of phytoplankton, bacterioplankton, and related parameters in the Southern California Bight". Winter Meeting of the American Society of Limnology and Oceanography, San Francisco, 1982 (in EOS 63:946)Ammerman, J.W., J.A. Fuhrman, A. Hagstrom, and F. Azam. Growth characteristics of bacteria grown in "seawater cultures". Third International Symposium on Microbial Ecology, Lansing, Michigan, 1983Fuhrman, J.A., J. Mitchell, and J. Bauer." Bacterioplankton abundance and production in Long Island Sound: Seasonal cycle and implications regarding grazing". Third International Symposium on Microbial Ecology, Lansing, Michigan, 1983Fuhrman, J.A. "Close coupling between uptake and release of amino acids in seawater." Winter meeting of the American Society of Limnology and Oceanography, New Orleans, 1984 (in EOS 64:1095)McManus, G.B. and J.A. Fuhrman. "Do bacteria-sized eukaryotes consume significant bacterial production?" Winter meeting of the American Society of Limnology and Oceanography, New Orleans, 1984 (in EOS 64:1095) Fuhrman, J.A. " Are small unseen eukaryotes important in marine ecosystems?" Annual Meeting of the American Association for the Advancement of Science, New York, 1984Fuhrman, J.A. " Biological considerations in the measurement of dissolved free amino acids in seawater: implications for chemical and microbiological studies." Winter ASLO/AGU Meeting, San Francisco, 1984 (in EOS 65:926)McManus, G.B., J.A. Fuhrman, and D.G. Capone. "Bactivory in seawater studied with the use of inert fluorescent particles." Winter AGU/ASLO Meeting, San Francisco, 1984 (in EOS 65:926)Mitchell, J.G., A. Okubo, and J.A. Fuhrman. "Microzones and phycospheres, their size, nutrient concentration, and location in the water." Winter AGU/ASLO Meeting, San Francisco, 1984 (in EOS 65:925)Ferguson, R.L., J.A. Fuhrman, and A.V. Palumbo. "Response of coastal bacterioplankton to chronic dumping of wastewater sludge." Winter AGU/ASLO Meeting, San Francisco, 1984 (in EOS 65:926)Fuhrman, J.A., S.G. Horrigan, J.G. Mitchell, and D.G. Capone."Bacterial and algal uptake of ammonium from seawater studied with short- lived and stable isotopes of nitrogen" Winter AGU/ASLO Meeting, New Orleans, 1986 (in EOS 66:1334)McManus, G.B. and J.A. Fuhrman. "Field estimates of bacterivory in the plume of the Chesapeake Bay." Winter AGU/ASLO Meeting, New Orleans, 1986 (in EOS 66:1314)Malone, T.C., W.C. Boicourt, H.W. Ducklow, M.R. Roman, J.A. Fuhrman, G.B. McManus, C. Garside, and P.M. Glibert. "Hydrography and plankton dynamics in a coastal estuarine plume." Winter AGU/ASLO Meeting, New Orleans, 1986 (in EOS 66:1268)Fuhrman, J.A. and J.A. McDaniel. "Utilization of dissolved proteins by marine bacteria". Am. Soc. for Microbiology annual meeting, Washington DC, 1986Fuhrman, J.A. and J.A. McDaniel. "Temporal patterns of amino acid uptake and regeneration in estuarine plumes". ASLO/PSA Joint Meeting, Univ. of Rhode Island, 1986McManus, G.B. and J.A. Fuhrman. "Chloroplasts and pigments in the ciliate Laboea strobila Lohmann". ASLO/PSA Joint Meeting, Univ. of Rhode Island, 1986Lee, S. and J.A. Fuhrman. "Conversion of marine bacterial biovolume to carbon and nitrogen biomass". ASLO/PSA Joint Meeting, Univ. of Rhode Island, 1986Mitchell, J.G. and J.A. Fuhrman. "A search for microzones and phycospheres in steep pycnoclines". ASLO/PSA Joint Meeting, Univ. of Rhode Island, 1986Fuhrman, J.A. and G.B. McManus. "Control of natural bacterioplankton populations". Fourth International Congress of Ecology, Syracuse, NY, 1986Fuhrman, J.A. and G.B. McManus. "Carbon and nitrogen exchanges among microbial populations of estuarine outflows: pathways of material flux to and from bacteria". Fourth International Symposium on Microbial Ecology, Ljubljana, Yugoslavia, 1986Roman, M.R., H.W. Ducklow, P.M. Glibert, T.C. Malone, J.A. Fuhrman, G.B. McManus, and C. Garside. "Copepods can jump through the microbial loop." Winter AGU/ASLO Meeting, San Francisco, 1986 (in EOS 67: 968)McManus, G.B., W.T. Peterson, and J.A. Fuhrman. "Bacterial production at a nearshore station during coastal upwelling." Winter AGU/ASLO Meeting, San Francisco, 1986, (in EOS 67: 976)Fuhrman, J.A., S. Lee, J. Mitchell, M. Legier, G.B. McManus, and S.G. Horrigan. "Seasonal and interannual variations of bacterial and phytoplankton parameters at a temperate coastal station." Winter AGU/ASLO Meeting, San Francisco, 1986 (in EOS 67: 976)Mitchell, J.G., J.A. Fuhrman, and A. Okubo. "A new mechanism for microscale heterogeneity of plankton." Winter AGU/ASLO Meeting, San Francisco, 1986 (in EOS 67: 977)Ducklow, H.W., T.C. Malone, M.R. Roman, J.A. Fuhrman, and G.B. McManus. "Planktonic carbon fluxes and community structure in the outflow plume of Chesapeake Bay." Winter AGU/ASLO Meeting, San Francisco, 1986 (in EOS 67: 997) Fuhrman, J.A., D.E. Comeau, A.M. Chan, and A. Hagstrom. "DNA extraction, genomic library development, and molecular phylogenetic characterization of mixed planktonic microbial communities." Winter AGU/ASLO Meeting, New Orleans, 1988 (in EOS 68: 1677)Mitchell, J.G., J.A. Fuhrman, and A. Okubo. "The contribution of plankton to ocean density gradients." Winter AGU/ASLO Meeting, New Orleans, 1988 (in EOS 68: 1696)Glibert, P.M., J.A. Fuhrman, C. Garside, and M.R. Roman. "Comparison of inorganic and organic nitrogen fluxes in the Chesapeake Bay Plume." Winter AGU/ASLO Meeting, New Orleans, 1988 (in EOS 68: 1704)McManus, G.B., J.A. Fuhrman, M.R. Roman, and H.W. Ducklow. "Growth and mortality of heterotrophic microflagellates in the Chesapeake Bay outflow plume." Winter AGU/ASLO Meeting, New Orleans, 1988 (in EOS 68: 1704)Fuhrman, J.A., T. Sleeter, and C. Carlson. "Oligotrophic ocean biomass is dominated by nonphotosynthetic bacteria, even in the euphotic zone." Winter AGU/ASLO Meeting, New Orleans, 1988 (in EOS 68: 1729)Suttle, C.A., and J.A. Fuhrman. "Amino acid uptake rates and turnover times in oligotrophic oceanic water near Bermuda." Winter AGU/ASLO Meeting, New Orleans, 1988 (in EOS 68: 1740)Suttle, C.A., J.A. Fuhrman, and D.G. Capone. "Rapid ammonium turnover times and concentration dependent resource partitioning in planktonic communities measured using 13N." Winter AGU/ASLO Meeting, New Orleans, 1988 (in EOS 68: 1761)Fuhrman, J.A. "Rapid turnover of dissolved organic nutrients by estuarine microorganisms." Gordon Research Conference on Estuarine Processes: Regulatory Mechanisms, Ventura CA, 1988Lee, S., and J.A. Fuhrman. "A quantitative comparison of natural bacterioplankton population similarities by total DNA hybridization." Fall AGU/ASLO Meeting, San Francisco, 1988 (in EOS 69: 1088)McManus, G.B., J.A. Fuhrman, and C.W. Sullivan. "Heterotrophic nanoflagellate abundance in relation to marine mesoscale features: the Cheasapeake plume and the Bering Sea ice edge." Fall AGU/ASLO Meeting, San Francisco, 1988 (in EOS 69: 1091)Suttle, C.A., L.M. Proctor, A.M. Chan, and J.A. Fuhrman. "Do phytoplankton incorporate amino acids at ambient concentrations in Sargasso Seawater?" Fall AGU/ASLO Meeting, San Francisco, 1988 (in EOS 69: 1097)Proctor, L.M., J.A. Fuhrman, and M.C. Ledbetter. "Marine bacteriophages and bacterial mortality." Fall AGU/ASLO Meeting, San Francisco, 1988. EOS 69: 1111-1112, DOI:?10.1029/88EO01175Fuhrman, J.A. and S. Lee "Natural microbial species variations studied at the DNA level." Invited talk at Fifth International Symposium on Microbial Ecology, Kyoto, Japan 1989 (published in symposium volume)Proctor, L.M. and J.A. Fuhrman. "Bacteriophage-infected bacteria in the sea." Fifth International Symposium on Microbial Ecology, Kyoto, Japan 1989Lee, S. and J.A. Fuhrman. "Spatial and temporal variation of species compositions of natural bacterioplankton communities studied at the DNA level." Winter AGU/ASLO Meeting, New Orleans, 1990 (in EOS 71: 186)Proctor, L.M. and J.A. Fuhrman. "Phage replication rates and generation times of marine vibrios". Annual ASM National Meeting. Anaheim, CA. 1990Lee, S.H. and J.A. Fuhrman. " The unique species composition of natural bacterial communities from a Bermuda coral reef lagoon studied by community DNA hybridization." Annual ASM National Meeting, Dallas, Texas. 1991Masuchi, Y. and J.A. Fuhrman. " Natural bacterial communities in marine environments" Annual ASM National Meeting, Dallas, Texas. 1991Fuhrman, J.A. "Bacterial production in relation to primary production." Brookhaven National Laboratory Symposium entitled Primary Productivity and Biogeochemical Bycles in the Sea. 1991.Fuhrman, J.A. " Virus abundance and potential roles." Fifth International Workshop on the Measurement of Microbial Activities in the Carbon Cycle in Aquatic Environments. Helsing?r, Denmark . 1991Fuhrman, J.A., R.T. Noble, and R.M. Wilcox. "Fates of viruses in seawater." ASLO Aquatic Sciences Meeting. Santa Fe, New Mexico. 1992.Fuhrman, J.A., K. McCallum, and A.A. Davis. "Novel bacteria in marine plankton as studied by 16S rRNA genes cloned from biomass." ASM Annual Meeting. New Orleans. 1992Noble, R.T., R.M. Wilcox, and J.A. Fuhrman. "Degradation of viruses in seawater." ASM Annual Meeting. New Orleans. 1992Fuhrman, J.A. "Bacteriophage roles in marine food webs." International Symposium on Microbial Ecology. Barcelona, Spain. 1992.Fuhrman, J.A. "Characterization of marine microbial communities via DNA and RNA." Microbial Loop Symposium, University of Georgia, October 1993.Fuhrman, J.A. and A.A. Davis. "Novel prokaryotic phylogenetic groups from marine plankton" ASM Annual Meeting. Las Vegas. 1994.Noble, R.T., R.M. Wilcox, and J.A. Fuhrman. "Viral and bacterial dynamics in Santa Monica Bay seawater mesocosms." ASM Annual Meeting. Las Vegas. 1994.Fuhrman, J.A. "What is out there? Strange and unexpected microbes in marine plankton." Sixth International Workshop on the Measurement of Microbial Activities in the Cycling of Matter in Aquatic Environments. Konstanz, Germany. April 1995.Fuhrman, J.A. "Viruses and protists cause similar bacterial mortality in coastal seawater." Invited seminar at University of Konstanz (Germany) Limnological Institute. April 1995.Nobel, R.T. and J.A. Fuhrman. "Dynamics of the marine microbial food web in ocean mesocosms." ASM Annual Meeting. Washington, D.C. May 1995.Davis, A.A. and J.A. Fuhrman. " Rapid screening for novel organisms by RNA colony blot." ASM Annual Meeting. Washington, D.C. May 1995.Fuhrman, J.A. "Diversity of marine microbes." Invited speaker at the Gordon Research Conference on Applied and Environmental Microbiology. New Hampton School, New Hampshire. July 1995. Noble, R.T. and J.A. Fuhrman."Anthropogenic influences on the microbiology of the urban ocean of Los Angeles. AGU/ASLO Ocean Sciences Meeting, San Diego, February 1996. In EOS 76(3): OS14Fuhrman, J.A. and A.A. Davis. " Microbial biodiversity of antarctic and coral reef plankton by 16S rRNA cloning and sequencing. AGU/ASLO Ocean Sciences Meeting, San Diego, February 1996. In EOS 76(3): OS160-OS161Fuhrman, J.A. "What is out there? Biodiversity patterns in marine plankton." Scripps Institution of Oceanography Marine Biology Seminar. 16 February 1996 Fuhrman, J.A. "Microbes in the Sea: Changing Paradigms." Lecture at Princeton University, 11 March 1996Noble, R.T. and J.A. Fuhrman. “Comparison between decay of infectivity and macromolecular fates of viruses in Santa Monica Bay.” ASM Annual Meeting, New Orleans, May 1996Karner, M. and J.A. Fuhrman. “Fluorescent 16S rRNA probe marine bacterial counts match or exceed counts obtained by autoradiography, nucleoid staining, or 5-Cyano-2,3-ditolyl tetrazolium chloride staining.” ASM Annual Meeting, New Orleans, May 1996Fuhrman, J.A. “Paradigms Lost: Changes in Our View of Marine Microbes” Seminar given at California Institute of Technology, 20 November 1996Fuhrman, J.A. “Two decades of change in marine microbiology” Seminar given at Texas A&M University, 21 April 1997Fuhrman, J.A. “Changing views of marine prokaryotes” Seminar given at UC Santa Cruz, May 1997Noble, R.T. and J.A. Fuhrman, "Breakdown and Microbial Uptake of Marine Viruses" ASM National Meeting, Miami Beach, FL, May 1997. Fuhrman, J.A. “Molecular approaches in the study of marine microbial diversity” Symposium at Royal Dutch Academy of Sciences, Amsterdam, 11 June 1997Fuhrman, J.A. “Changing views of marine microbes” Seminar given at the Netherlands Institute for Sea Research, Texel, 12 June 1997.Fuhrman, J.A. “Changing ideas in marine microbiology” Seminar given at the Marine Biology Laboratory of Trieste University, Trieste, Italy, 1 July 1997.Fuhrman, J.A. “Changing views of aquatic prokaryotes” Symposium at the Max Planck Institute for Terrestrial Microbiology, Marburg, Germany, 2 July 1997. Fuhrman, J.A. “Marine microbes in a global context.” Seminar given at the Jet Propulsion Lab, California Institute of Technology, Pasadena, 22 July 1997Noble, R.T., J.G. Griffith, and J. A. Fuhrman, "Detection of human pathogenic viruses in Santa Monica Bay seawater: Any correlation to presence and numbers of fecal coliforms?" Conference: Coastal Zone 1997. Boston, MA, 24 July 1997.Fuhrman, J.A., “Shifting paradigms about marine microorganisms.” Seminar given at the Institute of Marine Sciences, Barcelona, Spain, 2 October 1997.Fuhrman, J.A. “Our changing view of marine microbes.” Seminar given at University of Murcia, Spain, 6 October 1997.Fuhrman, J.A. “Qualitative and quantitative analysis of marine microbial diversity.” Keynote address given at University of Georgia, 8 December 1997.Fuhrman, J.A. “Changing perspectives of marine microbes.” Seminar given at Georgia Institute of Technology, 27 January 1998.Fuhrman, J.A. and R.T. Noble “Potential Roles of Viruses in Regulating Marine Carbon Flux.” ASLO/AGU Ocean Sciences Meeting, San Diego, February 1998Ouverney, C.C. and J.A. Fuhrman “Determining in Situ Nutrient Uptake by Specific Prokaryotic Groups in a Mixed Marine Community.” ASLO/AGU Ocean Sciences Meeting, San Diego, February 1998Noble, R.T. and J.A. Fuhrman. “Estimates of Production and Loss of Viruses in Seawater From Tracer Studies” ASLO/AGU Ocean Sciences Meeting, San Diego, February 1998Thingstad, T.F., G.-A. Fonnes, C. Marrasé, F.Peters, J. Gasol , M. Sala, M.Vidal, U.L. Zweifel, F. Rassoulzadegan, and J.A. Fuhrman. “Microbial affinity for orthophosphate studied in microcosms with natural plankton communities from western Mediterranean.” Sixth European Marine Microbiology Symposium, Sitges, Spain, May 1998Fuhrman, J.A. and R.T. Noble. “Causative agents of bacterial mortality and the consequences to marine food webs.” Eighth International Symposium on Microbial Ecology. Halifax, Canada, August 1998Noble, R.T. and J.A. Fuhrman. “Estimates of virus production and removal rates: implications to bacterial mortality in the marine environment.” Eighth International Symposium on Microbial Ecology. Halifax, Canada, August 1998Fuhrman, J.A. “Biodiversity.” Keynote address at Salzau Workshop of Kiel Institut fur Meereskunde, Salzau, Germany, September 1998Fuhrman, J.A. “Changing views of marine microbes.” Seminar given at Kiel Institute fur Meereskunde, Kiel, Germany, September 1998. Rossi, P., M. Karner, C. Ouverney, J.A. Fuhrman, M. Aragno. “Mise en évidence de la biodiversité microbienne en milieux océaniques à l’aide de sondes oligonucléotides fluorescentes et de l’hydridation in situ de l’ARN 16S.” Atelier du Riseau Biodiversiti et Ecologie Microbienne, Aussois, France, December 1998 Fuhrman, J.A. “Changing perspectives on marine microorganisms” Seminar given at University of Paris VI, December 1998Fuhrman, J.A. “Which microbes are active and what kinds are they?” American Society of Limnology and Oceanography Meeting, Santa Fe, New Mexico, February 1999Ouverney, C.C. and J.A. Fuhrman “Simultaneous in situ measurements of specific nutrient uptake by specific marine bacterioplankton cells. ”American Society of Limnology and Oceanography Meeting, Santa Fe, New Mexico, February 1999Carr, L., C.C. Ouverney, and J.A. Fuhrman “Comparisons of bacterial and archaeal concentrations between nearshore and open ocean depth profiles off Southern California.”American Society of Limnology and Oceanography Meeting, Santa Fe, New Mexico, February 1999Noble, R.T., J.A. Fuhrman, and A. Michaels “Detection of indicator viruses in effluent-impacted coastal waters of the Southern California Bight.”American Society of Limnology and Oceanography Meeting, Santa Fe, New Mexico, February 1999Fuhrman, J.A. and C.C. Ouverney. “Marine bacterioplankton identification and activity assays with 16S rRNA probes and microautoradiography.” 143rd Meeting of the Society for General Microbiology, University of Edinburgh, Scotland, April 1999Noble, R.T. and J.A. Fuhrman. “Detection of human enteric viruses in the Southern California Bight: any relation to bacteriological water quality?” Coastal Zone Meeting, San Diego, July 1999Fuhrman, J.A. “Microbial Contamination.” National Research Council Workshop on Opportunities for Advancement of Environmental Marine Biotechnology. Washington, D.C. October 1999 Fuhrman, J.A. “Virus-caused mortality of marine microbes.” Invited. American Geophysical Union/ American Society of Limnology and Oceanography Meeting. San Antonio. January 2000.Fuhrman, J.A. “Breaking open the black box of marine prokaryotes.” Invited. Microbial Genomics and Molecular Ecology Workshop of the Natural Environment Research Council, Warwick University, U.K. May 2000Fuhrman, J.A. “Marine viruses and their biogeochemical and ecological effects.” Invited. Microbial Genomics and Molecular Ecology Workshop of the Natural Environment Research Council, Warwick University, U.K. May 2000Griffith, J.F., J.A. Fuhrman, and A.A. Davis. “Temporal variation in bacterial and viral communities.” American Society for Microbiology Annual Meeting, Los Angeles, May, 2000Fuhrman, J.A. “ Marine viruses and their ecological and biogeochemical effects.” Steinbach Scholar lecture, Woods Hole Oceanographic Institution, July 2000Fuhrman, J.A. “Breaking open the “black box” of marine prokaryotes.” Steinbach Scholar lecture, Woods Hole Oceanographic Institution, July 2000Fuhrman, J.A. “Bacterial diversity patterns and viruses in marine plankton.” Food Web Conference, Kyoto Japan, December 2000Griffith, J.F. A.A. Davis, and J.A. Fuhrman “Relating prokaryotic and viral diversity in marine waters.” American Society for Limnology and Oceanography Aquatic Sciences Meeting, Albuquerque, February 2001Fuhrman, J.A. “Two decades of change in marine microbiology.” Seminar at University of Pennsylvania, May 2001Fuhrman, J.A. “Community structure and function in prokaryotic marine plankton.” 9th International Symposium on Microbial Ecology, Amsterdam, August 2001Griffith, J.F. and J.A. Fuhrman. “Temporal change in marine prokaryotic and viral diversity in nutrient amended mesocosms.” 9th International Symposium on Microbial Ecology, Amsterdam, August 2001Fuhrman, J.A. “Marine viruses and bacterial diversity - are they connected?” Society for General Microbiology Annual Meeting, Univ. of East Anglia, UK, September 2001Fuhrman, J.A. “Two decades of change in marine microbiology.” Opening lecture, Annual Meeting of the Spanish Society for Microbiology, Alicante, Spain. September 2001.Fuhrman, J.A. “ Activity and diversity of marine microorganisms.” Seminar at Scripps Institution of Oceanography, October 2001Fuhrman, J.A., I. Hewson, and M. Schwalbach. “Viral and Bacterial Community Shifts at an Ocean Time Series Station.” AGU/ASLO Meeting, Honolulu, February 2002 StationFuhrman, J.A. and M. Schwalbach “Interactions between genomes of bacteria and bacteriophages in an environmental context.” Outcomes of Genome-Genome Interactions Workshop, NASA, Woods Hole, May 2002Fuhrman, J.A. “Bacteria and viruses in Southern California waters.” Santa Monica Bay Science Workshop, Los Angeles, May 2002.Fuhrman, J.A., I. Hewson, and M. Schwalbach. “Relationships between viral and bacterial community composition in marine plankton. Inernational Union of Microbiological Societies Meeting, Paris, August 2002.Fuhrman, J., D. Caron, M. Brown, P. Countway, I. Hewson, X. Hernandez, X. Liang, M. Schwalbach, A. Schnetzer, R. Schaffner, , and M. Travao. “The USC Microbial Observatory” NSF Workshop on Microbial Observatories and Life in Extreme Environments, Arlington, Virginia, September 2002.Fuhrman, J. “ Two decades of change in marine microbiology” Seminar at UC Santa Barbara, January 2003 Fuhrman, J. “Marine bacterial diversity: dynamics and controlling factors “ Seminar at University of British Columbia, January 2003Hewson, I, And J. Fuhrman “Virus effects on bacterial communities in shallow coastal benthos.” Presented at ASLO Ocean Sciences Meeting, Salt Lake City. February 2003Schwalbach, M.S.. I Hewson, and J. Fuhrman. “Aerobic anoxygenic phototrophs: quantification in California coastal waters and possible ecological roles in marine bacterioplankton.” Presented at ASLO Ocean Sciences Meeting, Salt Lake City. February 2003 Fuhrman, J. “Changing paradigms in marine microbiology” Seminar at Oceanographic Observatory, Villefranche-sur-Mer, France, February 2003Fuhrman, J. “Marine viruses and their effects on bacteria” Seminar at University of Barcelona, April 2003Fuhrman, J. “Patterns of narine bacterial and viral diversity” Seminar at University of Paris VI Marine station in Banyuls, France. April 2003Fuhrman, J. “Two decades of change in marine microbiology” Seminar at University of Barcelona, April 2003.Fuhrman, J. “Human pathogens in the marine environment” Invited talk at The Oceanography Society National Meeting , New Orleans June 2003Fuhrman, J. "How Marine Biology Concerns Us All", Lecture at Temple Beth Hillel, Studio City CA June 2003Featured interview on ‘The Osgood File’ (CBS Radio), August 2003 osgood/osgood_story_216112839.htmFuhrman, J. “Our changing view of marine microbiology” Seminar at Scripps Institution of Oceanography, UCSD, September 2003Fuhrman, J. “Our changing view of marine microbiology” Seminar at Cornell University, October 2003Fuhrman, J., I. Hewson, M. Schwalbach, M.Brown. “Temporal and geographic patterns of marine bacterial community composition” Presented at ASLO Ocean Sciences Meeting, Honolulu, Febuary 2004Brown, M.V., I. Hewson, J. Fuhrman. “Tracking temporal patterns of microbial biodiversity, microdiversity and community structure at various depths in the San Pedro Channel, California.” Presented at ASLO Ocean Sciences Meeting, Honolulu, Febuary 2004Steele, J. A., Hewson, I., Capone, D. G., Fuhrman, J. A. “ Effects of inorganic iron, phosphorus, and dust addition on prokaryote community dynamics in the North Pacific subtropical gyre.” Presented at ASLO Ocean Sciences Meeting, Honolulu, Febuary 2004Hewson, I., JA. Steele, DG. Capone, JA. Fuhrman . “Viral influence on bacterial communities in the North Pacific Gyre” Presented at ASLO Ocean Sciences Meeting, Honolulu, Febuary 2004Govil, S., Hewson, I., Capone, D.,Carpenter, E., Fuhrman, J.”Cyanophage may play important roles in Trichodesmium spp. ecology in the oligotrophic ocean..” Presented at ASLO Ocean Sciences Meeting, Honolulu, Febuary 2004Fuhrman, J.S., I. Hewson, M Brown, M Schwalbach, J. Steele, A Patel. “ Microbial biogeography and temporal patterns in marine plankton.” Presented at Tenth International Symposium on Microbial Ecology, Cancun. August 2004.Hewson, I., T.E. Gunderson, D.G. Capone, and J.A. Fuhrman, Viral effects on diazotrophic bacteria in the oligotrophic oceans.” Presented at Tenth International Symposium on Microbial Ecology, Cancun. August 2004.Fuhrman, J..A. “Evolving ideas on marine microbial systems, from the microbial loop and viruses to genomics, biogeography, and global change.” Presented at Tenth International Symposium on Microbial Ecology, Cancun. August 2004.Schwalbach, M.S. and J.A. Fuhrman. “Global QPCR survey of planktonic aerobic anoxygenic phototrophs and insights from light manipulation experiments.” Presented at Tenth International Symposium on Microbial Ecology, Cancun. August 2004.Fuhrman, J.A. “ Changing views of marine microbes.” Invited seminar at University of Miami (FL). November 2004Fuhrman, J.A. “Human pathogens in the marine environment.” Invited workshop pressentation at the Pew Fellows Annual Meeting, Key Largo, Florida. November 2004.Fuhrman, J.A., I. Hewson, M. Schwalbach. "Interactions Between Marine Viral and Bacterial Community Composition." Invited presentation at First European Workshop on Aquatic Phage Ecology, Thonon-les-Bains, France, January 2005.Schwalbach, M.S. and J.A Fuhrman. Factors controlling bacterial phototrophs in seawater. ASLO Aquatic Sciences Meeting, Salt Lake City. February 2005Fuhrman, J.A., I. Hewson, M. Schwalbach, J. Steele, M. Brown, and A. Patel. Biogeographic patterns in marine bacterioplankton. ASLO Aquatic Sciences Meeting, Salt Lake City. February 2005Steele. J.A., A Patel, I. Hewson, and J.A. Fuhrman. “Stability in marine bacterial communities on hour-day time scales and kilometer spatial scales in the San Pedro Basin, California.” ASLO Aquatic Sciences Meeting, Salt Lake City. February 2005Fuhrman, J.A. “Evolving ideas on marine microbial systems, from the microbial loop and viruses to genomics, biogeography, and global change.” Plenary Lecture at Dutch Society for Microbiology, Arnhem, The Netherlands. April 2005Fuhrman, J.A. "The power of molecular genetics in biological oceanography." Invited Plenary Lecture, Annual Meeting of The Oceanography Society at UNESCO, Paris, June 2005.Fuhrman, J.A. "Microbial genomics, biogeography and global change" Invited talk at the International Union of Microbiological Societies Joint Meeting, San Francisco, July 2005.Fuhrman, J.A. " Cyanophages and oceanic cyanobacteria." Invited talk at the Marine Cyanobacteria Symposium, Wenner Gren Foundation, Stockholm, Sweden. August 2005.Fuhrman, J.A. “ Changing perspectives on marine microbes.” Invited seminar at Stanford University, January 2006Fuhrman, J.A. “New ideas on microbes in the sea.” Invited seminar at Jet Propulsion Laboratory, January 2006.Caron, D.A. and J.A. Fuhrman. “Ecological Insights from Studies of Microbial Diversity: Examples from a Microbial Observatory.” ASLO/AGU/TOS Ocean Sciences Meeting, Honolulu, February 2006Fuhrman, J.A. “Metagenomics is not the only fruit.” Invited speaker, Society for General Microbiology workshop on Environmental Genomics. Warwick, U.K., April 2006.Fuhrman, J.A. “Changing perspectives on marine microbes.” Invited Seminar at Monterey Bay Aquarium Research Institute. April 2006.Fuhrman, J.A. “Archaea and 'New' Phototrophs in the Sea: Just What Are They Up To?” Invited Symposium, American Society for Microbiology annual meeting, Orlando, Florida. May 2006Fuhrman, J.A. “Marine microbes keep surprising us.” Hutchinson Award lecture, Americal Society for Limnology and Oceanography annual meeting, Victoria, British Columbia, June 2006.Fuhrman, J.A. “Phototrophy and other interesting functional genes from seawater” Invited seminar speaker, Catalina Geobiology Course Symposium on Functional Genes, July 2006Fuhrman, J.A. “Top down and bottom up controls of marine bacterial abundance and diversity.” Invited speaker, Gordon Conference on Marine Microbes, Biddeford, Maine, July 2006Fuhrman, J.A. “ How do viruses influence of marine bacterial assemblage structure?” Invited speaker, Int. Soc. For Microbial Ecology, Vienna Austria, August 2006Patel, A. and J.A. Fuhrman. Water column and sediment marine biofilms: a temporal succession and comparative study of microbial diversity using DNA fingerprinting. Poster. Int. Soc. For Microbial Ecology, Vienna Austria, August 2006B?er, S.I., A. Ramette, J.E. van Beusekom, J.A. Fuhrman, and A. Boetius. Linking spatial and seasonal variations in bacterial activities and community structure: a case study in coastal sandy sediments. Poster. Int. Soc. For Microbial Ecology, Vienna Austria, August 2006Fuhrman, J.A. Metagenomics in the study of biogeochemistry. Invited presentation at Metagenomics 2006 conference, La Jolla CA, October 2006.Steele, J. A., Countway, P. D., Schwalbach, M. S., Rose, J. M., Vigil, P. D., O’Brien, S. G., Hewson, I., Brown, M. V., Jones, A. C., Patel, A., Ruan, Q., Huang, J., Sun, F., Caron, D. A., Fuhrman, J. A.: Bacterial and protistan cooccurrence and interactions at the San Pedro Ocean Time Series in the San Pedro Channel, California. Am. Soc. Limnol. Oceanogr. Meeting, Santa Fe NM, February 2007B?er, S. I., Ramette, A., Volkenborn, N., Fuhrman, J.A., Boetius, A.: Does bioturbation influence bacterial community structure in intertidal sands? Results from a large scale lugworm exclusion experiment in the German Wadden Sea. Am. Soc. Limnol. Oceanogr. Meeting, Santa Fe NM, February 2007Steele, J. A., Countway, P. D., Schwalbach, M. S., Rose, J. M., Vigil, P. D., O’Brien, S. G., Hewson, I., Brown, M. V., Jones, A. C., Patel, A., Kakajiwala, M., Chow, C., Ruan, Q., Huang, J., Sun, F., Caron, D. A., Fuhrman, J. A.: Bacterial and protistan interactions at the USC Microbial Observatory. NSF Microbial Observatory Workshop, Washington DC March 2007.Fuhrman, J.A. “From viruses to protists - drawing together the diffuse strands of marine microbial ecology.” Presentation at the “Sequencing the Seas” Symposium, Royal Society, London April, 2007.Steele, Joshua A., Peter D Countway, Michael S Schwalbach, Julie M Rose, Patrick D Vigil, Sheila G O'Brien, Ian Hewson, Mark V Brown, Adriane C Jones, Anand Patel, Quansong Ruan, Jerry Huang, Mahira Z Kakajiwala, Cheryl-Emiliane T Chow, Fengzhu Sun, Shahid Naeem, David A Caron, Jed A Fuhrman. Bacterial and protistan interactions at the USC Microbial Observatory. Poster Presentation at the “Sequencing the Seas” Symposium, Royal Society, London April, 2007.Fuhrman, J.A. and J. M. Beman. Marine Crenarchaea: discovery, diversity, distribution, and activity. Divisional Lecture, American Society of Microbiology Annual Meeting, Toronto, May 2007.Fuhrman, J.A. Marine Metagenomics: discoveries and future directions. Keynote address, Metagenomics 2007 Conference, UC San Diego, July 2007.Fuhrman, J.A. Changing perspectives on marine microbes. Hopkins Marine Laboratory, Stanford University, July 2007.Fuhrman, J.A. Linking microbial diversity to function. Keynote Lecture, 10th Symposium on Aquatic Microbial Ecology, Faro Portugal Sept. 2007Bertics, V. J., Sohm, J. A., Treude, T., Chow, C. T., Fuhrman, J. A., Capone, D. G., Ziebis, W. Linked nitrogen fixation and sulfate reduction in a benthic system heavily influenced by bioturbation. ASLO/AGU Ocean Sciences Meeting Orlando March 2008Chow, C. T., Steele, J. A., Patel, A., Kakajiwala, M., Sachdeva, R., Fuhrman, J. A. Connecting bacterial identity with function by response to enrichment. ASLO/AGU Ocean Sciences Meeting Orlando March 2008B?er, S. I., Ramette, A., Hedtkamp, S. I., Beusekom van, J., Fuhrman, J. A., Boetius, A.. Which factors shape bacterial community structure in coastal permeable sediments? ASLO/AGU Ocean Sciences Meeting Orlando March 2008Steele, J. A., Countway, P. D., Huang, J., Jones, A. C., Beman, J. M., Schwalbach, M. S., Vigil, P. D., Rose, J. M., O’Brien, S. G., Hewson, I., Brown, M. V., Patel, A., Ruan, Q., Sun, F., Caron, D. A., Fuhrman, J. A., Ecological relationships of marine microbes described through interaction networks at the San Pedro Channel, California. ASLO/AGU Ocean Sciences Meeting Orlando March 2008Romero, I.C., J.A. Fuhrman, M .Jacobsen, M.L. Fogel, J.A. Steele, D.G. Capone. Interactions between diazotrophic bacteria and mangrove roots under different nutrient conditions. ASLO/AGU Ocean Sciences Meeting Orlando March 2008Fuhrman, J.A. Combining marine metagenomics and spatial/temporal patterns to infer system function. Invited at: Genomes to Systems Conference (The Consortium for Post-Genome Science). Manchester, UK. March 2008Fuhrman, J.A. Marine microbial diversity and its impact on global biogeochemical cycles. Invited at: Colloquium on “ Assessing marine microbial diversity: problems and solutions.” Royal Academy of Arts and Sciences, Amsterdam, May 2008.Fuhrman, J.A. Changing views of marine microbes. Hopkins Marine Laboratory, Stanford University, June 2008. Marine Microbiology Course lecture.Fuhrman, J.A. Marine viruses: historical perspective and future directions. Invited Keynote Speaker. Aquatic Virus Workshop, Vancouver BC July 2008. Fuhrman J.A. Taking the long view: time-series data for understanding microbial communitiesInvited Workshop speaker. Twelfth Annual Meeting of the International Society for Microbial Ecology. Cairns Australia, August 2008.nd microbial community ecology in the seaBeman, J. M., Joshua Steele, and Jed Fuhrman.Variability of marine Crenarchaeota in relation to ammonia oxidation rates and abundant marine bacterial lineages: implications for nitrogen biogeochemistry and microbial community ecology in the sea. Twelfth Annual Meeting of the International Society for Microbial Ecology. Cairns Australia, August 2008.Chow, C.T., Anand Patel, J. Michael Beman, and Jed A. Fuhrman. Bacterial and Archaeal Community Shifts as a Response to Ammonium and Nitrite Enrichments in Seawater. Twelfth Annual Meeting of the International Society for Microbial Ecology. Cairns Australia, August 2008.Fuhrman, J.A. Joshua Steele, Peter Countway, David Caron, Fengzhu Sun. Inferring marine microbial system function from temporal and spatial patterns. Invited Talk. Twelfth Annual Meeting of the International Society for Microbial Ecology. Cairns Australia, August 2008.Patel, A. and J.A. Fuhrman. Exploring phage diversity in marine biofilms using major capsid protein as a phylogenetic marker. Twelfth Annual Meeting of the International Society for Microbial Ecology. Cairns Australia, August 2008.Fuhrman, J.A., Joshua Steele, Peter Countway, David Caron, Fengzhu Sun. Changing perspectives on marine microbes: inferring system function from pattern. Invited talk, SCOPE Workshop on Microbial Environmental Genomics, Changsha, China September 2008Fuhrman, J.A. Making the Leap from DNA to Microbial Community Association Networks . Invited Seminar, Scripps Institution of Oceanography, February 2009Fuhrman, J.A. Association network analysis shows potential marine food web interactions. Invited Speaker, American Society for Limnology and Oceanography Ocean Sciences Meeting, Nice, February 2009.Fuhrman, J.A. Patterns in Marine Microbes and Microbial Association Networks . Invited Lecture, University of South Florida, March 2009Fuhrman, J.A. Changing views of marine microbes (Marine Microbiology Course lecture). Hopkins Marine Laboratory, Stanford University, June 2009.Fuhrman, J.A. Practical implications of microbial community structure. Invited talk, Gordon Research Conference on Microbial Population Biology, Andover NH, July 2009Fuhrman JA. Networks of microbes. Invited talk, ICoMM Workshop, Amsterdam. September 2009Fuhrman, J. A. Roles of viruses in marine systems. Invited seminar at Caltech. Feb 2010Chow, C.E. , J.A. Steele, R. Sachdeva, J. Cram, J.A. Fuhrman. Viral connections in a diverse microbial community. ASLO Meeting Portland OR February 2010Fuhrman, J.A., B. H. Jones, J. Griffith, R. Noble, J. A. Steele. Microbial contamination of the coastal zone: experience linking research to policy (Invited). ASLO Meeting Portland OR, February 2010? Fuhrman, JA. Marine bacterioplankton diversity along spatial and temporal gradients. Invited talk, Society for General Microbiology, Edinburgh, Scotland, March 2010.Fuhrman, JA. Changing perspectives on marine microbes. Plenary Lecture, Southern California Academy of Sciences Annual Meeting. Cal State Univ. Los Angeles, May 2010.Fuhrman, JA. Oceans of Crenarchaeota. Invited Lecture, American Society for Microbiology Annual Meeting, San Diego, May 2010Fuhrman, JA. Marine microbes, the nitrogen cycle, and global change. Invited Lecture (last minute replacement for ill colleague), American Society for Microbiology Annual Meeting, San Diego, May 2010Fuhrman, JA and J Steele. Roseobacters in the context of the broader microbial community. Invited Lecture at a symposium entitled, “Ecology, Physiology, and Molecular Biology of the Roseobacter clade” Hanse Institute for Advanced Studies, Delmhorst Germany. June 1010.Fuhrman, JA. Changing perspectives on marine microbes. Invited Seminar, Oldenburg Universty. June 2010.Fuhrman, JA. A long term perspective on marine microbes. Invited Seminar, Max Planck Institute for Marine Microbiology, Bremen Germany. June 2010.Fuhrman, JA. Marine Plankton Microbes. Invited Lecture (Marine Microbiology Course), Hopkins Marine Station of Stanford University. July 2010.Steele , Joshua A., Peter D. Countway, Li Xia, Patrick D. Vigil, J. Michael Beman, Diane Y.Kim, Cheryl-Emiliane T. Chow, Rohan Sachdeva, Adriane C. Jones, Michael S. Schwalbach, Julie M. Rose, Ian Hewson, Anand Patel, Fengzhu Sun, David A. Caron, Jed A. FuhrmanThree-domain marine microbial association networks reveal ecological linkages. Poster presentation, Gordon Research Conference, Tilton NH. July 2010.Chow, C, Sachdeva, R, Fuhrman, J. Monthly variation of marine viral communities at the san pedro ocean time series. ISME Meeting, Seattle WA, August 2010Cram, J, Sachadeva, R, Steele, J, Capone, D, Fuhrman, J. Microbial associations across the North Pacific gyre and Amazon river plume. ISME Meeting, Seattle WA, August 2010Sachdeva, R, Shaw, A, Fuhrman, J, Horner-Devine, M. Temporal scaling of marine bacterioplankton assemblage composition . ISME Meeting, Seattle WA, August 2010Steele, J, Xia, L, Amaral-Zettler, L ,Mark Welch, D, Gilbert, J, Neal, P, Huse, S, Zinger, L, Pommier,T, Field, D, Caron, D., Herndl, G, Sogin, M, Sun, F, Fuhrman, J. Microbial-environmental networks among bacteria and archaea from the ICOMM database. ISME Meeting, Seattle WA, August 2010 Patel, A , Fuhrman J., Ziebis, W. Bacterial and viral colonizers of native carbonate minerals at deep-sea methane seeps. ISME Meeting, Seattle WA, August 2010Zinger, L, Amaral-Zettler, L, Fuhrman, J, Herndl, G, Horner-Devine, M, Huse, S, Mark Welch, D, Martiny, J, Neal, P, Pommier, T, Sogin, M, Boetius, A, Ramette, A. Global-scale analysis of water column and sediment bacterial communities indicates contrasting beta-diversity patterns. ISME Meeting, Seattle WA, August 2010Fuhrman, J, Steele, J, Xia, L, Amaral-Zettler, L ,Mark Welch, D, Gilbert, J, Neal, P, Huse, S, Zinger, L, Pommier,T, Field, D, Caron, D., Herndl, G, Sogin, M, Sun, F. Temporal patterns and association networks in a time-series from the ICOMM database. Invited talk, ICOMM Satellite Meeting, Seattle WA Aug 2010Fuhrman, J. A., J. A. Steele, L. A. Amaral-Zettler, D. B. Mark Welch, P. Neal, S. M. Huse, A. Boetius, A. Ramette, L. Zinger, G. Herndl, T. Pommier, C. Pedrós-Alió, L. Xia, F. Sun, M. L. Sogin. Global Patterns of Marine Microbial Communities. Presented at Census of Marine Life Conference, London, October 2010.Fuhrman, J.A. Integrating molecular and environmental data to evaluate community patterns. Invited talk. Keystone Symposium: Microbial communities as drivers of ecosystem complexity. Breckenridge, Colorado. March 2011Fuhrman, J.A. Long-Term perspective on marine microbes. Invited Seminar UC Irvine. April 2011.Needham, D. M., C. E. Chow, R. Sachdeva, J. A. Cram, A. Parada, J. A. Fuhrman. Day-to-day Dynamics of Bacterial and Myoviral Communities of the Surface Ocean. Am. Soc. for Microbiology Annual Meeting, New Orleans May 2011.Fuhrman, J.A. The aquatic EMP: Building on the most characterized environmental ecosystem. Invited talk. First International Earth Microbiome Project Conference. Shenzhen China, June 2011.Fuhrman, J.A., S. Weisberg, J. Griffith, R. Noble. Invited presentation. Urban Stresses on the Coastal Ocean in Los Angeles: The Microbial Component. Meeting of the Ocean Studies Board of the National Academy of Sciences, Beckman Center, Irvine CA, July 2011.Fuhrman, J., Griffith, J., Noble, R., Sirimanne,R., and Witheridge,A. "Southern California Coastal Water Research Project A Microbial Source Identification Title: Project in the Lower San Luis Rey River and the Next Steps toward the Bacteria Phase I TMDL in Region 9," California Stormwater Quality Association (CASQA) Stormwater Conference, Monterey Bay, CA, Hyatt Regency 2011.Fuhrman, J.A. Aquatic Microbial Ecology: where have we been and where might we be going? Keynote Address (invited), Society for Aquatic Microbial Ecology Meeting, Rostock, Germany, August 2011Needham DM, Chow CE, Sachdeva R, Cram JA, Parada A, Fuhrman JA. "Day-to-Day dynamics of bacterial and myoviral communities of the surface ocean". Oral presentation at 6th Aquatic Virus Workshop at the Royal Netherlands Institute of Sea Research in Den Burg (Texel), The Netherlands. October 31, 2011.?Chow, CET and JA Fuhrman Seasonality and Monthly Dynamics of Marine Myovirus Communities by Capsid Gene Sequences at the San Pedro Ocean Time-Series. Talk presented at the 6th Aquatic Virus Workshop, Texel, The Netherlands, November 2011.Chow, CET, R Sachdeva, JA Cram, and JA Fuhrman. Viral control of autotrophic vs. heterotrophic bacteria in the surface ocean: ecological networks linking viruses and bacteria. Talk presented at ASLO AGU Ocean Sciences Meeting, Salt Lake City Feb 2012Fuhrman, JA. Three decades of discovery in marine microbiology. Van Niel Lecture, Hopkins Marine Station of Stanford University, May 2012Fuhrman, JA. Time series of diversity patterns: what do they tell us? (Invited Talk) American Society for Microbiology Annual Meeting, San Francisco, June 2012Fuhrman, JA. Omics should supplement, not replace, traditional microbiological oceanographic approaches. Invited. Gordon Research Conference on Marine Microbes, Barga Italy, June 2012Gomez-Consarnau, L. L. Cutter, J.A. Cram, D. Needham, G Salazar, J.A. Fuhrman. Diel cycles of dissolved B-vitamins in the coastal ocean. Poster, Gordon Research Conference on Marine Microbes, Barga Italy, June 2012Cram, J., R. Sachdeva, C. Chow, L. Xia, J, Steele, D. Needham, A. Parada, J. Fuhrman. Bacterial community variability across ten years and five depths at the San Pedro Ocean Time Series. Poster. ISME 14, Copenhagen, August 2012.Fuhrman, J.A. Three-domain (+ virus) microbial association networks at the San Pedro Ocean Time series. Invited. ISME 14, Copenhagen, August 2012.Gomez-Consarnau, L. L. Cutter, J.A. Cram, D. Needham, G Salazar, J.A. Fuhrman. Diel cycles of dissolved B-vitamins in the coastal ocean. Poster, ISME 14, Copenhagen, August 2012.Fuhrman, J.A. Three decades of discovery in marine microbial ecology. Invited Lecture, University of Paris and CNRS Oceanological Observatory, Banyuls-sur-mer, France. September 2012. Fuhrman, J.A. Temporal and spatial patterns of microbial communities: what do they tell us about genomes? Invited Plenary talk, Cross Disciplinary Genomics Symposium, University of Pierre and Marie Curie, Paris, France. October 2012.Fuhrman, J.A. Three-domain (+ virus) microbial association networks from time series. CSIC Barcelona, Spain, November 2012.Fuhrman, J. A. Needham, D., Cram, J., Chow, C. “ Microbial Interactions and networks.” Invited talk, ASLO Ocean Sciences, New Orleans Febuary 2013.Fuhrman, J.A. “Omics and Biogeochemical models: Challenges and promises.” Invited talk, in workshop entitled “Merging complex “-omic” data and computational ecosystem models,” sponsored by the Gordon and Betty Moore Foundation. Miami Beach FL, March 2013. Fuhrman, J.A. “Three decades of discovery in marine microbiology.” Invited seminar, Duke University Marine Lab, April 2013.Fuhrman, J.A. “Interactions and association networks from time series studies of microbial metagenomes.” American Society For Microbiology annual meeting Invited Lecture in Workshop on Metagenomic Approaches: Frontiers of Annotation?and Assembly, Networking and Discovery. Denver, May 2013.Cram, J. A., L. Xia, D. Needham, R. Sachdeva, C-E. Chow, A. E. Parada, J. Steele, J. A. FuhrmanInter-depth Associations Between Marine Bacterial Communities in a Ten Year Time Series. American Society For Microbiology annual meeting. Denver, May 2013.Needham, David M., C-E. T. Chow, J. A. Cram, R. Sachdeva, A. Parada, J. A. Fuhrman Daily-to-decadal Community And Co-variation Patterns Of Marine Microbial Communities. American Society For Microbiology annual meeting. Denver, May 2013.Parada, A. E., C. Chow, D. Needham, D. Caron, J.A. Fuhrman. Surface to Sea Floor Time Series of All Three Domains Via rRNA Tag Sequences. American Society For Microbiology annual meeting. Denver, May 2013.Fuhrman, J.A. Analyzing microbial diversity patterns. Invited Lecture at EU-US Marine Bioinformatics Course, University of Delaware. June 2013.Fuhrman, J.A. Microbes in aquatic habitats. Invited, Gordon Research Conference on Applied and Environmental Microbiology, Mt. Holyoke College, July 2013.Fuhrman J.A. A long term perspective on recent discoveries in marine microbiology. Invited Lecture, Stazione Zoologica, Naples Italy, September 2013.Needham, David M , Bella Nguyen and Jed A Fuhrman. Poster. Assessment and application of molecular methods to study in-situ bacteria and T4-like-virus dynamics. Aquatic Virus Ecology annual workshop, University of South Florida, October 2013Mayali, X.; Gomez-Consarnau, L.; Needham, D. M.; Weber, P. K.; Fuhrman, J. Light effects on marine microbial carbon incorporation analyzed with stable isotope probing, RNA microarrays and nanosims. Ocean Sciences Meeting (ASLO AGU), Honolulu February 2014 Cram, J. A.; Parada, A. E.; Fuhrman, J. A.: Response of microbial communities to relief of top down pressure by viruses and grazers via dilution. Ocean Sciences Meeting (ASLO AGU), Honolulu February 2014Gomez-Consarnau, L.; Gonzalez, J. M.; Riedel, T.; Wagner-Dobler, I.; Fuhrman, J. A. A transcriptome approach to understanding the function of proteorhodopsin in the marine genus Dokdonia. Ocean Sciences Meeting (ASLO AGU), Honolulu February 2014Needham, D. M.; Sachdeva, R.; Fuhrman, J. A.: Strain level day-to-day variation of SAR11 revealed by high throughput its sequencing. Ocean Sciences Meeting (ASLO AGU), Honolulu February 2014Fuhrman J.A. Working Group panelist on microbial association networks and on distilling ecological information from big data.Also invited seminar, “A long term perspective on recent discoveries in marine microbiology,” University of Michigan, April 2014.Needham DM and Fuhrman JA. Daily time-series off Southern California reveal dynamics and potential successional patterns of bacteria, archaea, protists, and viruses. Invited Oral Presentation .American Society of Limnology and Oceanography Joint Aquatic Sciences Meeting. Portland, OR. May 19-23, 2014.Cram, Jacob, Cheryl-Emiliane T. Chow,Rohan Sachdeva, David M.Needham, Alma E. Parada, Joshua A. Steele, Jed A.Fuhrman. Seasonal and interannual dynamics of microbial heterotrophic productivity and community structure throughout the water column. Poster presentation, Gordon Research Conference on Marine Microbes, Waltham MA July 2014.Parada, Alma, David Needham, Jed Fuhrman. Long term temporal and spatial dynamics of Euryarchaea Marine Group II and Thaumarchaea Marine Group I examined through rRNA tag sequencing. Poster presentation, Gordon Research Conference on Marine Microbes, Waltham MA July 2014.Fuhrman JA .Towards a holistic perspective on microbial interactions. The Gordon and Betty Moore Foundation Marine Microbiology Initiative Investigator Symposium. Palo Alto CA July 2014.Fuhrman JA. Inferring interactions among bacteria, archaea, protists, and viruses via association networks. Invited talk, International Symposium for Microbial Ecology, Seoul Korea August 2014.Fuhrman, J.A. How Marine Viruses Entered the Mainstream: A Historical Perspective. Invited plenary lecture, Year of the Phage Conference, San Diego. January 2015.Gomez Consarnau, L.; Sachdeva, R.; Gifford, S. M.; Cutter, L. S.; Fuhrman, J. A.; Sa?udo-Wilhelmy, S. A.; Moran, M. A.: B-vitamin exchange as a central nexus of the microbial community in a coastal environment. ASLO Aquatic Sciences Meeting, Granada Spain February 2015Parada, A. E.; Needham, D. M.; Ahlgren, N. A.; Fuhrman, J. A.: Time-series and surface to seafloor analysis of marine archaeal diversity through 16s rDNA and metagenomic sequencing. ASLO Aquatic Sciences Meeting, Granada Spain February 2015Sieradzki, E.; Sachdeva, R.; Fichot, E.; Fuhrman, J.: Human impact on marine microbial community composition. ASLO Aquatic Sciences Meeting, Granada Spain February 2015Needham, D. M.; Fuhrman, J. A.: Daily successional patterns of marine virus, bacteria, archaea, and protistan communities following a diatom bloom via marker genes and shotgun metagenomics. ASLO Aquatic Sciences Meeting, Granada Spain February 2015Fuhrman, J.A. “Benefits of higher phylogenetic resolution in marine microbial ecology.” Invited talk, High Resolution Microbiome Informatics Conference. Marine Biological Lab, Woods Hole March 2015Fuhrman, J.A.,David Needham, Alma Parada, Cheryl Chow, Nathan Ahlgren. Invited Talk, “Microbial diversity patterns and interactions at an ocean time series.” CIFAR (Canadian Institute for Advanced Research)Integrated Microbial Biodiversity Program Meeting, Victoria BC May 2015Fuhrman, J.A. Invited Talk. Microbial Ecology in the 21st Century, current trends and predictions. The Science of Tara Oceans Symposium. Paris, June 2015Fuhrman, J.A. David Needham, Alma Parada, Nathan Ahlgren. Invited Talk. Bacteria, Archaeal, Viral and Protistan association networks reveal many levels of connectivity in marine plankton. Jacques Monod Conference on Eco-Systems Biology, Roscoff France June 2015.Fuhrman, J.A, David Needham, Alma Parada, Nathan Ahlgren, Lyria Berdjeb, Interactions among Bacteria, Archaea, Viruses, and Protists. Gordon and Betty Moore Foundation Marine Microbiology Initiative Investigators’ Meeting, San Francisco, July 2015.Fuhrman, J.A. “A long term perspective on recent discoveries in marine microbiology.” Invited lecture, Harvard University, Oct 2015Fuhrman, J.A. “A long term perspective on recent discoveries in marine microbiology.” Invited lecture, Bigelow Laboratory, Boothbay Harbor Maine, October 2015Berdjeb, Lyria, Alma E. Parada, David M. Needham, Jed A. Fuhrman. Marine protist network revealed by high frequency temporal survey in the San Pedro Ocean Time-Series station. Symposium on a New Age of Discovery for Aquatic Microeukaryotes, Heidelberg Germany January 2016Dekas, Anne E., Alma Parada1,Xavier Mayali, Peter K. Weber, Jed Fuhrman, and Jennifer Pett-Ridge. Single-cell measurement of archaeal and bacterial carbon assimilation in dark Pacific Ocean waters. ASLO AGU Ocean Sciences Meeting, New Orleans February 2016Parada, A E, N Ahlgren, J A Fuhrman. Genome and metagenome enabled analyses reveal new insight into the global biogeography and potential urea utilization in marine Thaumarchaeota. ASLO AGU Ocean Sciences Meeting, New Orleans February 2016Ahlgren, N, A E Parada, J A Fuhrman. The complete genome of a new marine Thaumarchaea strain contains evidence of previous virus infection and a possible defense mechanism from infection. ASLO AGU Ocean Sciences Meeting, New Orleans February 2016Gómez-Consarnau L, NM Levine, LS Cutter, D Wang, B Seegers, XA Salgado, J Arístegui, JA Fuhrman, JM Gasol and SA Sa?udo-Wilhelmy. Quantifying Proteorhodopsin in the Sea. ISME Montreal Aug 2016Needham, David M., Rohan Sachdeva, Jed A. Fuhrman. Taxon-by-taxon microdiversity and eco-genomics of phytoplankton bloom-associated marine phytoplankton, bacteria, archaea and virus populations. ISME Montreal Aug 2016Ahlgren, Nathan, Jessie Perelman, Jed Fuhrman. Viruses control fine-scale genotypes within marine cyanobacterial ecotypes while seasonal bottom-up factors drive ecotype level community structure. ISME Montreal Aug 2016Fuhrman, J.A., Nathan Ahlgren, Lyria Berdjeb, David Caron, Erin Fichot, Julio Cesar Ignacio Espinoza, David Needham, Alma Parada, Ella Sieradzki, Yi-Chun Yeh. Holistic marine microbial community networks and theory assessed with three-domain plus virus analysis via amplicons and ‘omics. ISME Montreal Aug 2016Sieradzki, Ella and Jed Fuhrman. Biodegradation of polycyclic aromatic hydrocarbons in naturally occurring marine microbial communities. ISME Montreal Aug 2016Fuhrman, J.A. From the microbial loop to ‘omics: three decades of marine microbial ecology. Lectures at Hjort Center summer course in marine microbial ecology. Bergen Norway August 2016.Fuhrman, J.A. Advances over three decades in marine microbial ecology. Invited seminar at German National Culture Collection (DSMZ), Braunschweig, Germany. September 2016.Fuhrman. J.A. From the microbial loop to ‘omics: three decades of marine microbial ecology. Distinguished visitor series invited seminar, Oklahoma University. September 2016Yang Lu, Jinchi Lv, Jed Fuhrman and Fengzhu Sun. Heterogeneity Rescaling Pursuit: Enhanced Clustering and Classification in Integrative Genomics. RECOMB 2017Jie Ren, Fengzhu Sun, Nathan A Ahlgren, Jed A Fuhrman and Yang Young Lu. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. RECOMB 2017Connell, Paige E., Michael R. Stukel, Thomas B. Kelly, Jed A. Fuhrman, Doug E. Hammond, & David A. Caron. Microbial carbon fluxes at a coastal ocean site: an inverse ecosystem modeling analysis. ASLO Ocean Sciences, Honolulu Feb 2017Fuhrman, Jed A, David Needham, Ella Sieradzki, Nathan Ahlgren, Julio Cesar Ignacio Espinoza, Lyria Berdjeb, Jie Ren, Yang Lu, Yi-Chun Yeh Fengzhu Sun. Assessing potential interactions among viruses, bacteria, archaea, and protists via ‘omics and high resolution time series. ASLO Ocean Sciences, Honolulu Feb 2017Fuhrman, J.A. Three decades of advances in marine microbial ecology. Invited seminar at Johns Hopkins University, March 2017Fuhrman, J.A. A long term perspective on recent advances in marine microbial ecology. Invited seminar at UC Santa Cruz, April 2017Fuhrman, J.A. Where marine microbiology is going and how to get there” Invited talk at Gordon Research Seminar on Marine Molecular Ecology, Hong Kong July 2017.Fuhrman, J.A. “Assessing potential interactions among viruses, bacteria, archaea, and protists via ‘omics and high resolution time series ” Invited talk at Gordon Research Conference on Marine Molecular Ecology, Hong Kong July 2017.Fuhrman, J.A. “From the microbial loop to ‘omics. Three decades of marine microbial ecology.” Invited Seminar, CIIMAR Porto Portugal. September 2017Dekas, A E, A E Parada, X Mayali, J A Fuhrman, P K Weber, Pett-Ridge. Investigating Organic Substrate Utilizationby Marine Thaumarchaeota Using Metatranscriptomics and FISHNanoSIMS. ASLO AGU Ocean Sciences Meeting, Portalnd OR, February 2018Levine, N M, E Teel, X Liu, J A Cram, J A Fuhrman. Impact of a Dynamic Heterotrophic Bacterial Community on Biogeochemical Cycling. ASLO AGU Ocean Sciences Meeting, Portalnd OR, February 2018Yeh, Y C, D Needham, J A Fuhrman Warming and other effects on the free-living prokaryotic community at the San Pedro Ocean Time-series over 16 years. ASLO AGU Ocean Sciences Meeting, Portalnd OR, February 2018Ahlgren, N, C A Fuchsman, G Rocap, J A Fuhrman Discovery of many novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode nitrifying genes: ASLO AGU Ocean Sciences Meeting, Portland OR, February 2018Needham, D, R Sachdeva, J A Fuhrman Microdiversity following a phytoplankton bloom: marker genes and metagenomics reveals ecologically-relevant dynamics at strain-level ASLO AGU Ocean Sciences Meeting, Portalnd OR, February 2018Fuhrman, J.A. Biodiversity: a Narrative Tapestry on Life. Harman Academy for Polymathic Studies, USC, Feb 2018.Fuhrman, J.A. Julio Cesar Ignacio Espinoza, Yi-chun Yeh, David Needham, Lyria Berdjeb, Nathan Ahlgren. Integrating prokaryotic, viral, and protistan processes on scales ranging from days to years via 'omics and other approaches. ASLO Annual Meeting, Victoria B.C. June 2018.Fuhrman, J.A. Marine microbial ecological and biogeochemical processes: integration of classic and omics approachesInvited lecture, Ramon Margalef Summer Colloquium. Barcelona, July 2018 Fuhrman, Jed, Julio Cesar Ignacio Espinoza, Yi-chun Yeh, David Needham, Lyria Berdjeb, Ella Sieradzki, Nathan Ahlgren, Andrew Long, Yuxuan Zou and Jesse McNichol. Assessing marine prokaryotic, protistan, and viral processes from diel to interannual scales via 'omics and other approaches. ISME 17, Leipzig Germany. August 2018.J Cesar Ignacio Espinoza, Yuxuan Zou, Erin Fichot, David Needham, Jed Fuhrman. Metagenomic and metatranscriptomic time series reveals a highly dynamic virus-host interaction landscape. ISME 17, Leipzig Germany. August 2018.Ignacio Espinoza, J.; Alhgren, N.; Yeh, Y.; Fuhrman, J. Long-term virus community stability facilitated by ‘red queen’ dynamics.ASLO Aquatic Sciences Meeting, San Juan February 2019Aleman, M.; Ignacio Espinoza, J.; Long, A.; Fuhrman, J. Dynamics of viruses analyzed metagenomically in relation to other plankton during an algal bloom. ASLO Aquatic Sciences Meeting, San Juan February 2019Long, A.; Ignacio Espinoza, J.; Fuhrman, J.: Estimating marine bacterial growth rates using metagenomics and metatranscriptomics. ASLO Aquatic Sciences Meeting, San Juan February 2019Mayali, X.; Gomez-Consarnau, L.; Needham, D.; Fuhrman, J.; Weber, P.: Light influences taxon-specific bacterial degradation of phytodetrital particles. ASLO Aquatic Sciences Meeting, San Juan February 2019Fuhrman, Jed. Integrating classic and omics approaches to study marine microbial systems, three domains plus viruses. Invited Seminar, MIT March 2019Fuhrman, Jed. Marine microbes. Annual Investigator Meeting, Gordon and Betty Moore Foundation, Half Moon Bay July 2019Yi-Chun Yeh and Jed Fuhrman. Long-term dynamics of free-living and particle-associated prokaryotic communities at the San Pedro Ocean Time-series . GRC Marine Molecular Biology Hong Kong July 2019 Fuhrman, JA. Marine microbial community patterns and interactions. Plenary speaker. Symposium: Marine Microbiota - Ecology, Interactions and Systems Biology, Oldenburg Germany August 2019Sanchez, Selene, Felix Milke, Jesse McNichol, Hui Wang, Johannes Mansky, Helena Sztajer, Jed Fuhrman, Meinhard Simon, and Irene Wagner-D?bler Atlantic and Pacific Ocean bacterioplankton diversity. Symposium: Marine Microbiota - Ecology, Interactions and Systems Biology, Oldenburg Germany August 2019Fuhrman, J.A. J. Cesar Ignacio Espinoza, Nathan Ahlgren, Yi-chun Yeh. Stability, seasonality, and red queen-like dynamics in a 5-year virome from the San Pedro Ocean Time series. Invited. Fall AGU Meeting, San Francisco December 2019 Yi-Chun Yeh and Jed A Fuhrman, Long-term dynamics of phytoplankton, protistan, and prokaryotic communities at the San Pedro Ocean Time-series. AGU ASLO Ocean Sciences Meeting San Diego Feb 2020Emily Dart, Julio Cesar Ignacio Espinoza, Jed A Fuhrman and Nathan Ahlgren, Cyanophage Dynamics at the San Pedro Ocean Time Series: Generalists, Specialists, and One-shot-wonders . AGU ASLO Ocean Sciences Meeting San Diego Feb 2020Delaney Nolin, David Needham, Julio Cesar Ignacio Espinoza, Shengwei Hou, Erin Biers Fichot, Colette Fletcher-Hoppe, Melody Aleman and Jed A Fuhrman. In Situ Viral Dynamics off the Coast of Southern California using Transcriptomes from Automated High-Frequency Sampling AGU ASLO Ocean Sciences Meeting San Diego Feb 2020Colette Fletcher-Hoppe, Yi-Chun Yeh and Jed A Fuhrman Temporal Dynamics of the Diazotroph UCYN-A and its Known and Possible Hosts over 10 Years at the San Pedro Ocean Time-series (SPOT), AGU ASLO Ocean Sciences Meeting San Diego Feb 2020Jesse McNichol, Paul Berube, Steven Biller, Sallie W Chisholm and Jed A Fuhrman. Testing model predictions and revealing basin-scale biogeography with whole-community PCR amplicons from GEOTRACES, AGU ASLO Ocean Sciences Meeting San Diego Feb 2020Felix Milke, Selene Sanchez, Jesse McNichol, Jed A Fuhrman, Irene Wagner-D?bler and Meinhard Simon. Atlantic and Pacific Ocean bacterioplankton diversity, AGU ASLO Ocean Sciences Meeting San Diego Feb 2020Jed Fuhrman. Marine microbial community patterns and interactions. Invited seminar at University of Technology Sydney, Australia. March 2020. RESEARCH GRANTS AWARDED (as sole Principal Investigator unless otherwise noted), currentSponsor Title Amount Period $ Research Importance of Bacterio- 2,775 4/82-4/84 Foundation plankton Production inof SUNY Long Island SoundNSF Dissolved Free Amino Acid 79,279 7/82-7/84 Chem. Formation in Seawater and Oceanogr. its Coupling to Uptake Renewal 191,851 7/84-7/87 Second renewal 284,000 10/87-11/91NSF Bacterioplanktivores: 96,217 1/83-1/85 Identification and Elucidation of Their Roles in Marine Food WebsNSF Couplings between 169,105 11/84-11/87 nutrients, bacteria, and bacteriovores in estuarine plumes (a component of MECCAS, a multi-institution, multi-disciplinary project) one-year renewal 42,000 11/87-11/88 Hudson Bacterioplankton in the 29,879 7/85-7/86River lower Hudson: biomass, Found'n growth, and interactions with hazardous pollutants NSF Use of the Short-lived Assoc. 1986-88 isotope, 13-N, in marine Investigator nitrogen cycle studiesNSF Characterization of 355,400 12/87-10/92 culturable and nonculturable marine bacteria: a 16S rRNA sequence approachSea Viruses in the ocean 127,000 10/91-10/94Grant near Los AngelesNSF Novel marine archaebacteria: 49,964 2/92-2/93 potential contribution to mid- water biomass and activity NSF Survey of prokaryotic marine 152,699 7/92-7/94 plankton Renewal 299,315 7/94 - 7/97 Research Experiences for Undergraduates (Supplement) 20,000 7/95 - 7/97 Renewal 245,917 6/97 -1/01 Research Experiences for Undergraduates (Supplement) 10,000 6/98 - 5/00Santa Enteric virus detection in Santa 34,169 6/95-5/96Monica Monica BayBayRestorationFoundationNSF Viruses in marine food webs 285,000 11/92 - 11/96 Renewal 320,375 10/96 -9/99 Renewal 390,000 8/99 – 7/02 Renewal 402,139 2/03 –1/07Sea Viruses in the ocean 110,582 10/96-3/99Grant near Los Angeles Renewal 150,104 3/99 – 3/02NSF Discovery and characterization 1,049,654 9/00-9/06 of marine bacteria, archaea, and protisa from the San Pedro Channel time series (D. Caron, co PI) (Microbial Observatory) NSF Survey of marine prokaryotes 149,998 11/00-10/02Sea An integrated approach to 152,034 3/01 – 8/03Grant understanding nearshore processes and microbial beach contamination in an urban coastal region (B. Jones and D. Sherman co-PIs)Sea Molecular assays of human 100, 228 3/02-2/04 Grant pathogenic viruses in the coastal zoneSea Factors Affecting Dispersion 105,532 3 /04 –2/07Grant of Pathogenic Microorganisms in Coastal Waters ( B. Jones Co-PI)NSF Relating MicrobialBiodiversity 553,151 9/05-10/09 to Biological Oceanographic Processes (D. Capone Co-PI)NASA Detection of airborne viruses 150,000 11/05-11/06(JPLSubcontract)NSF Biogeochemical roles 257,392 8/06- 9/09 of planktonic archaeaSea Stormwater, Pathogens, 58,821 3/07-3/08Grant and Particles – Presence and Transport from an Urban Watershed (Burton Jones, PI)NSFExperimentally linking 330,000 3/07 – 2/11identification and function of marine bacteria CICEET Assessment of microbial 55,890 5/07-4/08(UNC contaminants pertinent toSub- swimming related illnessescontract) at Doheny BeachNSFAssembly of marine 1,200,000 8/07 -8/13microbial communities(with 1 yr no-cost extension)(Microbial Observatory)(co-PI with D. Caron)Sea High Resolution Remote 162, 406 2/10-1/12Grant Sensing of Coastal Discharge Algal Blooms in the Southern California Bight (Burton Jones, PI)NSF Marine viral dynamics and 565,955 10/10-9/14 incorporation into microbial (with 1 yr no-cost extension) association networks NSF ATD: Computational Analysis 608,732 2/11-2/14 of Metagenomic Sequencing Data ($74,546 to JAF) (co-PI with T. Chen and F. Sun)NSF Dimensions: Pattern and process 1,999,577 10/11 – 3/17 in marine bacterial, archaeal, and +116,000 + 4008 supplements protistan diversity, and effects of (no-cost extended from 9/16) human impacts.Co-PIs: D. Caron, J. Heidelberg, W. Nelson, F. Sun, T. Chen. GordonSupport Marine Microbial 2,302,300 7/13-10/20& BettyEcology Research(with 2 yr extension)Moore FoundationNSF Environmental regulation of 827,621 8/2013-8/2017 retinal and bacteriochlorophyll no-cost extended biosynthesis (Co-PI with Sergio Sa?udo-Wilhelmy) NSF Inference of Markovian Properties 600,000 9/2015-8/2019 of Molecular Sequences Using Shotgun (with 1 yr no-cost extension) Reads and Applications (Co-PI with Fengzhu Sun and Michael Waterman)NIHComputational Studies of Virus-host 1,624,622 4/2017-3/2021 Interactions Using Metagenomics Data and Applications (R01)(Co-PI with Fengzhu Sun, Michael Waterman, Stacey Finley, Nathan Ahlgren)NSF Daily to decadal patterns of archaea, 1,530,487 7/2017 – 7/2021 bacteria, protists, and viruses at the San Pedro Ocean Time Series (Co-PI: D. Caron)Simons Simons Collaboration on 1,999,578 7/2017-6/2022Foundation Computational Biogeochemical Modeling of Marine Ecosystems (SCBIOMES): Microbial growth, interactions, and biogeographies from ‘omics data.Consulting ProjectsMicrobial contamination of beaches in Avalon Harbor, Santa Catalina Island, Califonia 2001. Supported by State of California. Focus on human-based sources. Result was that the beach appeared to be contaminated by leaking sewer pipes, which were then slip-lined, this reduced the contamination considerably.Microbial contamination of beaches in Huntington Beach, California, with a focus on the contribution of a power plant, 2002. Supported by California Energy Commission. Result was that the plant did not appear to be a significant source of human-based contamination.Microbial contamination of Topanga Creek watershed, California, 2003-2004. Supported by State of California. Measurement of airborne human pathogenic viruses (Varicella zoster, Coronavirus, Epstein-Barr, Influenza, Respiratory Syncytial Virus, Adenovirus) in enclosed public places (2005-2006). (subcontracted by JPL, TSA project) Microbial testing of Southern California waters, 2002-. Supported by State of California as well as various local agencies and NGOs (often coordinated through Southern California Coastal Water Research Project). Numerous studies including development of new field tests for a variety of viral pathogens and human bacterial source indicators, improvement of these tests to be faster and less expensive, and laboratory inter-calibrations. Also includes performing the tests as a service (fee-based).Evaluation of microbial complications and impacts of proposed desalination plant in Orange County, CA 2012Review and constructive improvement recommendations for proposals to Genome Canada for Genome Quebec, 2015, 2016. Science advisory committee to that funded project 2017- Students Advised and their ProjectsMarianne Legier (M.S. 1985)- Copepod chemo- and mechanoreceptionJohn Hudak (M.S. 1985) - Bacterial interactions with organic pollutants: effects on productivity, detoxification, and implications for the ecosystem as a wholeGeorge McManus (Ph.D. 1986) - Quantitative ecology of marine bacterivorous nanoplanktonJames Mitchell (Ph.D. 1987) - Small-scale (micrometer to meter) ecology of marine bacteria and phytoplankton, with particular reference to fluid dynamics.SangHoon Lee (M.S. 1986, Ph.D. 1990) - Conversion from biovolume to carbon and nitrogen content in "seawater cultures" of naturally-derived bacteria (M.S. work). Molecular genetic analysis of natural microbial species composition and diversity.Lita Proctor (Ph.D. 1991)- Bacteriophage infection in marine systems. Robin Wilcox (M.S. 1993) Lysogeny vs. lytic growth of marine viruses Stefanie Gehret (M.S. 1998 ). Microbial biodiversity - experimental approachesRachel Noble (Ph.D. 1998). Fates of viruses in marine systemsAlison Davis (M.S.). Probing of rRNA from colony blots to identify bacteria.Cleber Ouverney (Ph. D. 2000). Quantitative microbial biodiversity/activity studies with fluorescent rRNA-targeted probes, also combination with microautoradiographyIan Hewson (Ph.D. 2005). Virus in benthic and coastal systems, effects on bacterial diversityXiaolin Liang (M.S. 2005) Microbial contamination of coastal watersJohn Griffith (Ph.D. 2006). Human enteric viruses and indicator bacteria in the coastal zone, molecular methods intercomparisons and verification, microbial contamination source trackingMichael Schwalbach (Ph.D. 2006). Viral ecological effects / Phototrophic bacteriaJoshua Steele (Ph.D. 2010) Microbial community composition patterns and sea surface filmsAnand Patel (Ph.D. 2010) Marine biofilms, viruses and archaeaCheryl Chow (Ph.D. 2012. NSF Fellow). Bacterial and viral diversity time series and relationshipsJacob Cram (Ph.D. 2014). Bacterial diversity time series and depth patternsDavid Needham (Ph.D. 2015, NSF Fellow). Marine viral effects on biogeochemical cyclesAlma Parada (Ph.D. 2016, NSF Fellow). Archaeal diversity time series and depth patternsElla Sieradzki (Ph.D 2017, USC Provost’s Fellow). Marine archaea and human impacts Yi-Chun Yeh (Ph.D. student, USC Global Fellow). Application of ecological theory to marine microbial systemsColette Fletcher-Hoppe (Ph.D. student). Omics and other analyses of N fixation at SPOTMelody Aleman (Ph.D. student). Linking viruses and hosts from natural samplesDelaney Nolin (Ph.D. student). Microbial distribution patternsAlexandra Santora (Ph.D. student). Microbial distribution patterns(Also served on numerous M.S. and Ph.D. committees)Postdoctoral Researchers SupervisedCurtis Suttle (1986-88) - Nitrogen (organic and inorganic) and phosphorus cycling by marine planktonYaeko Masuchi (1989-90) - 16S rRNA sequencing of marine bacterial oligotroph cultures, search for "representative" cultures by DNA-DNA hybridization, direct sequencing of PCR-amplified 16S rRNA genesKirk McCallum (1990) - cloning and sequencing of PCR-amplified 16S rRNA genes from natural marine microbial assemblagesMarkus Karner (1995-96) - single cell molecular probes and relation to native bacterial activitiesPierre Rossi (1996-97) - microbial biodiversity patterns by single cell probes and DNA reassociation kineticsRachel Noble (1998-2001, in cooperation with Wrigley Institute for Environmental Studies and Southern California Coastal Water Resources Project) - coastal monitoring of native and contaminant bacteria and viruses in relation to water quality issues.Mark Brown (2002- 2004)- intensive studies of microbial diversity at the San Pedro Time Series / Microbial Observatory site. J. Michael Beman (2006-2008) – roles of marine archaea in N cyclingLaura Gomez-Consarnau (2010- 13, 2014-15) - proteorhodopsin roles in microbial ecology; microbial ecology of vitamins; impact of ocean acidifaction on marine bacteriaLyria Berdjeb (2014-16) – integration of growth and grazing on the control of marine microbial populationsNathan Ahlgren (2013-16) – Single cell marine genomics, marine archaeal genomics, viral genomics, and interactions among bacteria, archaea, and protistsDavid Needham (2015-17) – High frequency molecular genetic studies of bacteria, viruses, and microbial eukaryotesAndrew Long (2017- 19) – Microbial growth via ‘omics, and microbial interactions. Experimental and informatic approachesJulio Cesar Ignacio Espinoza (2015-2018)– Bioinformatic analysis of marine viral and microbial communities, and interactions among those communitiesJesse McNichol (2018-) – Microbial global biogeography, genome distributions, and incorporation of microbial processes into basin-scale modelsShengwei Hou (2018- ) – Metatranscriptomic and metagenomic analysis of microbial properties and activities, incorporation into models Sarah Laperriere (2019- ) – Microbial interactions and biogeographies in biological oceanographic and computational modeling contextsJake Weissman (2020- ) – Microbial defenses against viruses, and their global ocean distribution. Statistical interpretation of metagenomic and related data.Outside (non USC) Student CommitteesLaura Gomez-Consarnau – Kalmar University, Sweden. Served as “Opponent” in Ph.D. defense, June 2009.Tom Delmont – University of Lyon, France. Served as outside PhD committee member, December 2011Sachia Jo Traving – Copenhagen University, outside PhD committee member, June 2016Selene Sanchez and Felix Milke – Oldenburg University and HZI, outside PhD committee member 2019 Courses TaughtEnvironmental Microbiology (undergraduate)Introduction to Microbiology (undergraduate)Marine Microbiology and Microbial Ecology (both graduate and undergraduate level)Biological Oceanography (undergraduate, at Santa Catalina Island)Advanced Biological Oceanography (graduate)Oceanography (undergraduate, primarily for nonscience majors - taught biological portion)Special Topics in Marine Microbiology (seminar-type courses, versions include a focus on molecular biological approaches to diversity and function) Seminar in Ecology (various topics - usually related to pelagic ecology)Environmental Biology (General Education, topic - ozone depletion)Summer Course in Marine Microbial Ecology at Bermuda Biological Station (summer 1987, with D. Capone, 1991 with B. Taylor)Summer Course in Protozoology at University of Copenhagen Marine Laboratory, Helsing?r, Denmark (1988 with T. Fenchel and B. Finlay)Advanced General Biology: Organismal Biology and Evolution (undergraduate – Honors version)Molecular Methods in Microbial Ecology (undergraduate, Santa Catalina Island; graduate seminar)STAMPS (Strategies and Techniques for Analyzing Microbial Population Structure) Course Lecturer, marine Biological Lab, Woods Hole, August 2011 and August 2012Committees, Panels and Service, At USC:HIMS Director Search Committee (88-89)Committee for development of R/V Osprey (88-89)Marine Biology Comprehensive Exam Committee (88-91)Marine Biology Committee on Graduate Studies (88-91)Marine Biology Screening Exam Committee (88-93, 99-07)Neurobiology Senior Faculty Search Committee (89-91)Chair of Catalina Postdoc Fellowship Search Committee (89-90)Ship Committee (R/V Vickers) 90-91Hancock Institute of Marine Studies Advisory Committee (90-95)Hancock Institute of Marine Studies Executive Committee (95-97)Department Instructional Committee (91-94)Department Executive Committee (91-94, 96-99)Ship Users Committee (91-93)CRESPE Committee on microbiology (91-93)University-wide Radiation Safety Committee (member 91-96, Chair 92-96)Promotion Committees (Prof. Ko, Prof. McFall-Ngai) 1992-93Department Curriculum Revision Committee (93-96)Department of Biological Sciences Chair (94-97)Ad Hoc Committee of Natural Sciences Chairs on General Education (94-96)Search for Wrigley Chair and associated junior faculty (Chair 96-98)Provost’s Research Committee (97-99)Search for 2nd Wrigley Chair (Co-Chair 98-00)College of Letters, Arts, and Sciences Personnel Committee for Natural Sciences & Mathematics (98- 00, 02-04, Chair 03-06)Provost’s Initiative on Urban Sustainability (00-01)Center for Electron Microscopy and Microanalysis Advisory Committee (01- 08)Biology Website update committee (focus on Graduate Recruitment) (02-03)Search Committee for Microbiologist, USC School of Dentistry (02-03)Search Committee for Physiological Ecologist (03-04)Marine Environmental Biology cluster hire dossier committee (05-06)Department self-study committee, headed section on quality assessment (08)Wrigley Oversight and Resources Committee (08-10)Wrigley Strategic Planning Advisory Committee (08-10)Discovery Scholar Prize Panel (08-11) USC College Faculty Council (08-12)Vice-chair, Research Caucus of Faculty Council (08-09)USC College Dean’s Research Excellence Advisory Board (08-10)College award advisory committee (08, 09)Director of Marine Environmental Biology Program, Dept. of Biological Sci., (09-12)Chair, Research Caucus of College Faculty Council (09-12)NTT faculty search committee (2014)Biological Sciences Self Study Committee (2014-15)NTT faculty evaluation committee (2015-17)Geobiology faculty search committee (2015-2017)Interviewer for Presidential/Trustee Scholarship Candidates (07-)National Fellowship advisory group (USC Graduate School, school-wide) (2012-)Marine Biology Graduate Admissions Committee (88-93, 99-03, 16-17, Chair 03-10, 10-17)Provost’s Research Collaboration fund review (2016-17)Marine and Environmental Biology Faculty Search Committee (Chair 2017-8)Marine and Environmental Biology Faculty Merit Review Committee (2009-2013, 2017-18,Chair 2017)Peaks and Professors faculty participant (2017-19)Undergraduate student awards committee (2018-)Faculty Award ad hoc committee, USC Provost’s Office (2018-9)Department Promotion Committee, chair, 2019Department Merit Review Committee 2018, 2019Consultative Committee for selection of new Chair of Biological Sciences 2020Building Space Committee - Freezer Farm evaluation and upgrade 2020National / International/ Regional: (current)NSF Biological Oceanography Review Panels 1990, 2000DOE Subsurface Biology Advisory Panel 1992NSF Advisory Panel reviewing JGOFS 1993NSF Biotic Surveys and Inventories Review Panel 1996NSF Biotic Surveys and Inventories Workshop 1996NSF Marine Biodiversity Workshop, Denver, 1993 NASA Planetary Protection Workshop, JPL 1997 NSF Workshop on future of Biological Oceanography (OEUVRE), Keystone, CO, 1998NSF Conference on Biodiversity Observation Networks (later NEON) , San Francisco, 1999NSF Workshop on Environmental Determinants of Carbon Cycling, 1999Visiting Committee to evaluate future of Univ. of Kiel Marine Science Research 1999 National Sea Grant Press Briefing, microbiological safety of marine waters, 1999National Research Council Ocean Studies Board Workshop on Opportunities for Environmental Applications of Marine Biotechnology, Washington DC, 1999ASM Microbiological Diversity Meeting Plenary Roundtable 1999NSF/NIEHS Panel on Oceans and Human Health, Research Triangle Park, NC, 2001Co-Convener for Marine Microbiology in DIVERSITAS (sponsored by IUBS, SCOPE, UNESCO, IUMS, ICSU, IGPB) 1998- 2014Project Leader, Discovery of New Microbial Kingdoms, International Biodiversity Observation Year (2000-2002)Scientific Committee of DIVERSITAS-Core Project 2, called EcoSERVICES, 2003-14 and Marine Biology Working Group 2005-2014SCOR Working Group 126 on Role of Viruses in Marine Ecosystems 2005-10American Academy Of Microbiology Colloquium participant, "Marine Microbial Diversity: The Key to Earth's Habitability" 2005Working Group on Microbial Diversity, National Center for Ecological Analysis and Synthesis 2004-2006Advisory Committee for SCCWRP Water Quality and Epidemiology Study of Dana Point, Surfrider Site visit team, NSF Center for Coastal Margin Observation and Prediction, 2011-12 Experts Panel, SOCOD Desalination Plant Pilot Study, Orange County, CA 2012Advisory Panel to American Association for the Advancement of Science to evaluate the Moore Foundation Marine Microbiology Initiative 2012Beach, Avalon 2006-ASLO Awards Committee 2011-2014Working Group on Ocean Viral Dynamics at the National Institute for Mathematical and Biological Synthesis, 2012-2014DOE Joint Genome Institute Microbial Genomics & Metagenomics Program User Advisory Committee 2010-15 (Regional) Topanga Watershed Advisory Committee, and ad hoc advisory group for local water quality issues (1998- )Steering Committee, Earth Microbiome Project 2010~2015Science Advisory Board, Tara Oceans 2010- 2015, Chair 2011-12Genome Canada/Quebec advisory committee (2015-16)Genome Quebec Research Oversight Committee (2016-)Euromarine Open Science Exploration (EMOSE) Organizer (2017-)Science Advisory Board Tara Oceans Global Ocean Systems Ecology and Evolution (2019- )Simons Foundation early career award evaluation committee (2018- ) ................
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