Publications

2015

  • Fuhrman, Jed A, Jacob Cram, David Needham. (2015). Marine microbial dynamics and their ecological interpretation. Nature Reviews Microbiology, in press
  • 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. (2015). A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes. ISME Journal, in press.

2014

  • 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_721-3
  • Cram, J. A., C. E. T. Chow, R. Sachdeva, D. M. Needham, A. E. Parada, J. A. Steele, and J. A. Fuhrman. (2014). Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years. ISME Journal.
  • Chow,  C. E. T., D. Y. Kim, R. Sachdeva, D. A. Caron, and J. A. Fuhrman. (2014). Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists. ISME Journal. 8 (4): 816-829

2013 

  • Chow, C. E. T., R. Sachdeva, J. A. Cram, J. A. Steele, D. M. Needham, A. Patel, A. E. Parada, and J. A. Fuhrman. (2013). Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight. ISME Journal. 7 (12): 2259-2273
  • 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.
  • Hatosy, S. M., Martiny, J. B., Sachdeva, R., Steele, J., Fuhrman, J. A., & Martiny, A. C. (2013). Beta-diversity of marine bacteria depends on temporal scale. Ecology.
  • Needham, D. M., Chow, C. E. T., Cram, J. A., Sachdeva, R., Parada, A., & Fuhrman, J. A. (2013). Short-term observations of marine bacterial and viral communities: patterns, connections and resilience. The ISME journal. 7:1274;1285
  • Fuhrman, J., Follows, M., & Forde, S. (2013). Applying “‐omics” Data in Marine Microbial Oceanography. Eos, Transactions American Geophysical Union94(27), 241-241.
  • Chow, C. E. T., Sachdeva, R., Cram, J. A., Steele, J. A., Needham, D. M., Patel, A., ... & Fuhrman, J. A. (2013). Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight. The ISME journal.
  • Xia, L. C., Ai, D., Cram, J., Fuhrman, J. A., & Sun, F. (2013). Efficient statistical significance approximation for local similarity analysis of high-throughput time series data. Bioinformatics29(2), 230-237.
  • Riedel, T., Gómez-Consarnau, L., Tomasch, J., Martin, M., Jarek, M., González, J. M., ... & Wagner-Döbler, I. (2013). Genomics and Physiology of a Marine Flavobacterium Encoding a Proteorhodopsin and a Xanthorhodopsin-Like Protein. PloS one8(3), e57487.
  • Harwood, V. J., Boehm, A. B., Sassoubre, L. M., Vijayavel, K., Stewart, J. R., Fong, T. T., ... & Wicki, M. (2013). Performance of viruses and bacteriophages for fecal source determination in a multi-laboratory, comparative study. Water research.

2012

  • Fuhrman, J. A. (2012). Metagenomics and its connection to microbial community organization. F1000 biology reports4.
  • Amend, A. S., Oliver, T. A., Amaral‐Zettler, L. A., Boetius, A., Fuhrman, J. A., Horner‐Devine, M. C., ... & Martiny, J. B. (2012). Macroecological patterns of marine bacteria on a global scale. Journal of Biogeography.
  • Hanson, C. A., Fuhrman, J. A., Horner-Devine, M. C., & Martiny, J. B. (2012). Beyond biogeographic patterns: processes shaping the microbial landscape. Nature Reviews Microbiology10(7), 497-50
  • Knight, R., Jansson, J., Field, D., Fierer, N., Desai, N., Fuhrman, J. A., ... & Gilbert, J. A. (2012). Unlocking the potential of metagenomics through replicated experimental design. Nature biotechnology30(6), 513-520.
  • Chow, C. E. T., & Fuhrman, J. A. (2012). Seasonality and monthly dynamics of marine myovirus communities. Environmental Microbiology14(8), 2171-2183.
  • Freitas, S., Hatosy, S., Fuhrman, J. A., Huse, S. M., Welch, D. B. M., Sogin, M. L., & Martiny, A. C. (2012). Global distribution and diversity of marine Verrucomicrobia. The ISME Journal6(8), 1499-1505.
  • Brown, M. V., Lauro, F. M., DeMaere, M. Z., Muir, L., Wilkins, D., Thomas, T., ... & Cavicchioli, R. (2012). Global biogeography of SAR11 marine bacteria. Molecular systems biology8(1).

2011

  • 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.2235
  • Fuhrman, J. A. (2011). Oceans of Crenarchaeota: a Personal History Describing This Paradigm Shift. Microbe6(12), 531-537.
  • Romero, I. C., Jacobson, M., Fuhrman, J. A., Fogel, M., & Capone, D. G. (2011). Long-term nitrogen and phosphorus fertilization effects on N2 fixation rates and nifH gene community patterns in mangrove sediments. Marine Ecology, Advanced Online Publication. doi:10.1111/j.1439-0485.2011.00465.x
  • Gilbert, J. A., J. A. Steele, J. G. Caporaso, L. Steinbrück, J. Reeder, B. Temperton, S. Huse, A. C. McHardy, R. Knight, I. Joint, P. Somerfield, J. A. Fuhrman, and D. Field. 2011. Defining seasonal marine microbial community dynamics. The ISME Journal 1-11,
  • Xia, L. C., Cram, J. A., Chen, T., Fuhrman, J. A., & Sun, F. (2011). Accurate Genome Relative Abundance Estimation Based on Shotgun Metagenomic Reads. (E. Dias-Neto, Ed.)PLoS ONE6(12), e27992. doi:10.1371/journal.pone.0027992
  • Xia, Li C., Steele, Joshua A., Cram, Jacob A., Cardon, Zoe G., Simmons, Sheri L., Vallino, Josepth J., Fuhrman Jed A., Sun, F. (2011). Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates.pdf. BMC Systems Biology5(Suppl 2), S15
  • Yilmaz, P., et al. 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.1823
  • Zinger, L., L. a. Amaral-Zettler, J. a. Fuhrman, M. C. Horner-Devine, S. M. Huse, D. B. M. Welch, J. B. H. Martiny, M. Sogin, A. Boetius, and A. Ramette. 2011. Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems J.A. Gilbert [ed.]. PLoS ONE 6: e24570, doi:10.1371/journal.pone.0024570
  • 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.

2010

  • 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.

Selected Publications Prior to 2010

  •  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.