Jed Fuhrman

Tenure Track Appointments

• Department Chair, Biological Sciences, University of Southern California, 01/01/1994 – 01/01/1996
• Professor Of Biological Sciences, University of Southern California, 01/01/1992 –
• Associate Professor of Biological Sciences, University of Southern California, 01/01/1988 – 01/01/1992
• Associate Professor of Oceanography, State University of New York, Stony Brook, 01/01/1986 – 01/01/1988
• Assistant Professor of Oceanography, State University of New York, Stony Brook, 01/01/1981 – 01/01/1986

Summary Statement of Research Interests

Professor Fuhrman researches the roles of microorganisms in natural marine ecosystems and the cycling of matter in the ocean, from the microscopic scale to the global scale. He also measures human pathogenic viruses at recreational beaches as a potential health hazard, and works on innovative ways to make such measurements relatively easy and inexpensive. Professor Fuhrman is currently exploring global marine microbial biodiversity with molecular biological techniques, which has enabled him to identify major new taxonomic groups and make better estimates of the total diversity found in these communities and its role in ecosystem function. His team has discovered a major new group of Archaea inhabiting the deep sea and other novel microbial groups in coral reefs and other ocean habitats. Recently, his lab has determined patterns in diversity that help show how the microorganisms interact as a complex network. In the public health realm, his team has helped to link cases of illness to exposure to microbial and viral pathogens in the coastal zone.

Detailed Statement of Research Interests

My research has focused on several related areas. These include the following: Aquatic microbial ecology and biological oceanography; functioning of microbial systems – particularly, roles of  bacteria, archaea, and viruses in natural systems; microbial biodiversity and identification of nonculturable bacteria and archaea and their functions; 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; use of sytems biology and network analysis to assess marine microbial systems; connections to global cycles; 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.

Students interested in becoming a graduate student in my lab should apply at college.usc.edu/bisc/marine/graduate/admissions.cfm

Book Chapter

• Hewson, I., Fuhrman, J. A. (2008). Viruses, bacteria and the microbial loop. Nitrogen in the marine environment, Elsevier.
• Fuhrman, J. A., Hagström, Å. (2008). Bacterial and archaeal community structure and its patterns. 2nd pp. 45-90. Microbial Ecology of the Oceans, Wiley.

Journal Article

• 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 data sets vary widely in sensitivity and precision. ISME J/International Society for Microbial Ecology.
• Cram, J. A., Parada, A. E., Fuhrman, J. A. (2016). Dilution reveals how viral lysis and grazing shape microbial communities. Limnol. Oceanogr. online 8 February 2016, doi 10.1002/lno.10259.
• Needham, D. M., Fuhrman, J. A. (2016). Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom. Nature Microbiology/Macmillan Publishers Limited. pp. 16005.
• 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 data sets vary widely in sensitivity and precision. ISME J/International Society for Microbial Ecology.
• Parada, A., Needham, D., Fuhrman, J. A. (2015). Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time-series and global field samples. Envir. Microbiol.. Vol. in press
• Fuhrman, J. A., Cram, J., Needham, D. (2015). Marine microbial dynamics and their ecological interpretation. Nature Reviews Microbiology. Vol. in press
• Fuhrman, J. A., Cram, J. A., Needham, D. M. (2015). Marine microbial community dynamics and their ecological interpretation. Nat Rev Micro/Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.. Vol. 13 (3), pp. 133-146.
• Gomez-Consarnau, L., Gonzalez, J. M., Riedel, T., Jaenicke, S., Wagner-Dobler, I., Sanudo-Wilhelmy, S. A., Fuhrman, J. A. (2015). Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria. ISME J/International Society for Microbial Ecology.
• Parada, A., Needham, D. M., Fuhrman, J. A. (2015). Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time-series and global field samples. Environ Microbiol. (2015/08/15)
• Walters, W., Hyde, E. R., Berg-Lyons, D., Ackermann, G., Humphrey, G., Parada, A., Gilbert, J. A., Jansson, J. K., Caporaso, J. G., Fuhrman, J. A., Apprill, A., Knight, R. (2015). Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys. mSystems. Vol. 1 (1)
• Weitz, J. S., Stock, C. A., Wilhelm, S. W., Bourouiba, L., Coleman, M. L., Buchan, A., Follows, M. J., Fuhrman, J. A., Jover, L. F., Lennon, J. T., Middelboe, M., Sonderegger, D. L., Suttle, C. A., Taylor, B. P., Frede Thingstad, T., Wilson, W. H., Eric Wommack, K. (2015). A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes. ISME J. Vol. 9 (62015/01/31), pp. 1352-64.
• Xia, L. C., Ai, D. M., Cram, J. A., Liang, X. Y., Fuhrman, J. A., Sun, F. Z. (2015). Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains. Bmc Bioinformatics. Vol. 16
• Gomez-Consarnau, L., Gonzalez, J. M., Riedel, T., Jaenicke, S., Wagner-Dobler, I., Sanudo-Wilhelmy, S. A., Fuhrman, J. A. (2015). Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria. ISME J/International Society for Microbial Ecology.
• Parada, A., Needham, D. M., Fuhrman, J. A. (2015). Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time-series and global field samples. Environ Microbiol. (2015/08/15)
• Walters, W., Hyde, E. R., Berg-Lyons, D., Ackermann, G., Humphrey, G., Parada, A., Gilbert, J. A., Jansson, J. K., Caporaso, J. G., Fuhrman, J. A., Apprill, A., Knight, R. (2015). Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys. mSystems. Vol. 1 (1)
• Weitz, J. S., Stock, C. A., Wilhelm, S. W., Bourouiba, L., Coleman, M. L., Buchan, A., Follows, M. J., Fuhrman, J. A., Jover, L. F., Lennon, J. T., Middelboe, M., Sonderegger, D. L., Suttle, C. A., Taylor, B. P., Frede Thingstad, T., Wilson, W. H., Eric Wommack, K. (2015). A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes. ISME J. Vol. 9 (62015/01/31), pp. 1352-64.
• Xia, L. C., Ai, D. M., Cram, J. A., Liang, X. Y., Fuhrman, J. A., Sun, F. Z. (2015). Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains. Bmc Bioinformatics. Vol. 16
• Cram, J. A., Chow, C. T., Sachdeva, R., Needham, D. M., Parada, A. E., Steele, J. A., Fuhrman, J. A. (2014). Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years. ISME J/International Society for Microbial Ecology.
• Chow, C. E., Sachdeva, R., Cram, J. A., Steele, J. A., Needham, D. M., Patel, A., Parada, A. E., Fuhrman, J. A. (2013). Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight. Isme Journal. Vol. 7 (12), pp. 2259-2273.
• Chow, C. T., Kim, D. Y., Sachdeva, R., Caron, D. A., Fuhrman, J. A. (2013). Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists. ISME Journal. Vol. 8, pp. 816-829.
• Needham, D. M., Chow, C. E., Cram, J. A., Sachdeva, R., Parada, A., Fuhrman, J. A. (2013). Short-term observations of marine bacterial and viral communities: patterns, connections and resilience. Isme Journal. Vol. 7 (7), pp. 1274-1285.
• Fuhrman, J. A., Chow, C. E. (2012). Seasonality and Monthly Dynamics of Marine Myovirus Communities. Envir. Microbiol.. Vol. 14, pp. 2171.
• Hanson, C., Horner-Devine, C., Fuhrman, J. A., Martiny, J. B. (2012). Beyond biogeographic patterns: evolutionary and ecological processes that shape the microbial landscape. Nature Reviews Microbiology.. Vol. 10, pp. 497-506.
• Brown, M. V., Lauro, F. M., DeMaere, M. Z., Muir, L., Wilkins, D., Thomas, T., Riddle, M. J., Fuhrman, J. A., Andrews-Pfannkoch, C., Hoffman, J. M., McQuaid, J. B., Allen, A., Rintoul, S. R., Cavicchioli, R. (2012). Global biogeography of SAR11 marine bacteria. Molecular Systems Biology. Vol. 8
• Chow, C. E., Fuhrman, J. A. (2012). Seasonality and monthly dynamics of marine myovirus communities. Environ Microbiol. (2012/04/18)
• Steele, J. A., Countway, P. D., Xia, L., Vigil, P. D., Beman, J. M., Kim, D. Y., Chow, C. E., Sachdeva, R., Jones, A. C., Schwalbach, M. S., Rose, J. M., Hewson, I., Patel, A., Sun, F., Caron, D. A., Fuhrman, J. A. (2011). Marine bacterial, archaeal and protistan association networks reveal ecological linkages. ISME J. Vol. 5 (9), pp. 1414-1425.
• Danovaro, R., Corinaldesi, C., Dell’Anno, A., Fuhrman, J. A., Middelburg, J. J., Noble, R. T., Suttle, C. A. (2011). Marine viruses and global climate change. Fems Microbiology Reviews. Vol. 35 (6), pp. 993-1034.
• Perrings, C., Naeem, S., Ahrestani, F. S., Bunker, D. E., Burkill, P., Canziani, G., Elmqvist, T., Fuhrman, J. A., Jaksic, F. M., Kawabata, Z., Kinzig, A., Mace, G. M., Mooney, H., Prieur-Richard, A. H., Tschirhart, J., Weisser, W. (2011). Ecosystem services, targets, and indicators for the conservation and sustainable use of biodiversity. Frontiers in Ecology and the Environment. Vol. 9 (9), pp. 512-520.
• Beman, J. M., Chow, C. E., King, A. L., Feng, Y. Y., Fuhrman, J. A., Andersson, A., Bates, N. R., Popp, B. N., Hutchins, D. A. (2011). Global declines in oceanic nitrification rates as a consequence of ocean acidification. Proceedings of the National Academy of Sciences of the United States of America. Vol. 108 (1), pp. 208-213.
• Beman, J. M., Chow, C. T., Popp, B. N., Fuhrman, J. A., Andersson, A., Feng, Y., King, A. L., Hutchins, D. A. (2010). Global declines in ammonia oxidation as a consequence of ocean acidification. Proc Nat Acad Sci USA. Vol. 108, pp. 208-213.
• Perrings, C., Naeem, S., Arestani, F., Bunker, D. E., Burkill, D. E., Canziani, G., Elmqvist, T., Ferrari, R., Fuhrman, J. A., Jasic, 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. Vol. 330, pp. 323-324.
• Beman, J. M., Sachdeva, R., Fuhrman, J. A. (2010). Population ecology of nitrifying Archaea and Bacteria in the Southern California Bight. Envir. Microbiol.. Vol. 12, pp. 1282-1292.
• Brown, M. V., Philip, G. K., Bunge, J. A., Smith, M. C., Bissett, A., Lauro, F. M., Fuhrman, J. A., Donachie, S. P. (2009). Microbial community structure in the North Pacific Ocean. ISME Journal. Vol. doi: 10.1038/ismej.2009.86
• Fuhrman, J. A. (2009). Microbial community structure and its functional implications. Nature. Vol. 459, pp. 193-199.
• Fuhrman, J. A., Steele, J. A. (2008). Community structure of marine bacterioplankton: patterns, networks, and relationships to function. Aquat Microb Ecol.. Vol. 53, pp. 69-81.
• Fuhrman, J. A., Schwalbach, M. S., Stingl, U. (2008). Proteorhodopsins: an array of physiological roles?. Nature Rev Microbiol. Vol. 6, pp. 488-494.
• Fuhrman, J. A., Steele, J. A., Hewson, I., Schwalbach, M. S., Brown, M. V., Green, J. L., Brown, J. H. (2008). A latitudinal diversity gradient in planktonic marine bacteria. Proceedings of the National Academy of Sciences of the United States of America. Vol. 105 (22), pp. 7774-7778.
• Patel, A. R., Nobel, T., Steele, J. A., Schwalbach, M. S., Hewson, I., Fuhrman, J. A. (2007). Virus and prokaryote enumeration from planktonic marine environments. epifluorescence microscopy with SYBR? Green I. Nature Protocols. Vol. 2, pp. 269-276.
• Fuhrman, J. A., Hewson, I., Schwalbach, M., Steele, J., Brown, M. V., Naeem, S. (2006). Annually reoccurring bacterial communities are predictable from ocean conditions. Proc. Natl. Acad. Sci. USA. Vol. 103, pp. 13104-13109.
• Martiny, J. H., Bohannan, B., Brown, J. H., Colwell, R., Fuhrman, J. A., Green, J., Horner-Devine, M. C., Kane, M., Krumins, J. A., Kuske, C. R., Morin, P., Naeem, S., Øvreås, L., Reysenbach, A., Smith, V., Staley, J. (2006). Microbial biogeography: Putting microorganisms on the map. Nature Reviews Microbiology/Nature Publishing Group. Vol. 4, pp. 102-112.
• Ruan, Q., Dutta, D., Schwalbach, M., Steele, J., Fuhrman, J. A., Sun, F. (2006). Local Similarity Analysis Reveals Unique Associations Among Marine Bacterioplankton Species and Environmental Factors. Bioinformatics. Vol. 20, pp. 2532-2538. PMID: 16882654.
• Hewson, I., Fuhrman, J. A. (2006). Improved strategy for comparing community fingerprints. Microbial Ecology. Vol. 51, pp. 147-153.
• Hewson, I., Capone, D. G., Steele, J., Fuhrman, J. A. (2006). Influence of Amazon and Orinoco offshore surface water plumes on oligotrophic bacterioplankton diversity in the West Tropical Atlantic. Aquat. Microb. Ecol. Vol. 43, pp. 11-22.
• Brown, M. V., Schwalbach, M., Hewson, I., Fuhrman, J. A. (2005). Coupling 16S-ITS rDNA clone libraries and ARISA to show marine microbial diversity; development and application to a time series. Environmental Microbiology. Vol. 7, pp. 1466-1479.
• Fuhrman, J. A., Schwalbach, M., Brown, M. V. (2005). Impact of light on marine bacterioplankton community structure. Aquat. Microb. Ecol. Vol. 39, pp. 235-245.
• Brown, M. V., Fuhrman, J. A. (2005). Marine bacterial microdiversity as revealed by internal transcribed spacer analysis. Aquat. Microb. Ecol. pp. p.41.
• Fuhrman, J. A. (1999). Marine viruses and their biogeochemical and ecological effects(6736):541-8. Nature.. Vol. 399, pp. 541-8.

• Sustaining Fellow (Inaugural class), Assoc for the Sciences of Limnology and Oceanography , 2015
• American Academy of Arts and Sciences Fellow, 2013
• Gordon and Betty Moore Foundation Marine Microbiology Initiative Investigator, 2013
• USC Raubenheimer Outstanding Senior Faculty Award, 2006
• Fellow, American Academy of Microbiology, 2004
• ISI Highly Cited Researcher, 2002
• Fellow, American Association for the Advancement of Science, 1997
• McCulloch-Crosby Chair in Marine Biology, 1995/09/01
• USC Associates Award For Creativity In Research And Scholarship, 2015-2016
• Hutchinson Medal, American Society of Limnology and Oceanography, 2006

Editorships and Editorial Boards

• Editorial Board Member, The ISME Journal”, 2007 –
• Editorial Board Member, Environmental Microbiology”, 2005 –
• Subject Editor, Aquatic Microbial Ecology”, 1995 –
• Contributing Editor, Marine Ecology – Progress Series”, 1997 – 2003