J A Fuhrman

Summary

Affiliation: University of Southern California
Country: USA

Publications

  1. ncbi request reprint A comparison of taxon co-occurrence patterns for macro- and microorganisms
    M Claire Horner-Devine
    School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington 98195, USA
    Ecology 88:1345-53. 2007
  2. pmc Metagenomics and its connection to microbial community organization
    Jed A Fuhrman
    Department of Biological Sciences, University of Southern California Los Angeles CA 90089 USA
    F1000 Biol Rep 4:15. 2012
  3. pmc Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates
    Li C Xia
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 2910, USA
    BMC Syst Biol 5:S15. 2011
  4. doi request reprint Proteorhodopsins: an array of physiological roles?
    Jed A Fuhrman
    Department of Biological Sciences and Wrigley Institute, University of Southern California, Los Angeles, California 90089 0371, USA
    Nat Rev Microbiol 6:488-94. 2008
  5. ncbi request reprint Viral influence on aquatic bacterial communities
    J A Fuhrman
    University of Southern California, Los Angeles, California 90089 0371, USA
    Biol Bull 204:192-5. 2003
  6. pmc A latitudinal diversity gradient in planktonic marine bacteria
    Jed A Fuhrman
    Wrigley Institute for Environmental Studies and Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 0371, USA
    Proc Natl Acad Sci U S A 105:7774-8. 2008
  7. ncbi request reprint Community structure and function in prokaryotic marine plankton
    Jed A Fuhrman
    Department of Biological Sciences, University of Southern California, Los Angeles 90089 0371, USA
    Antonie Van Leeuwenhoek 81:521-7. 2002
  8. doi request reprint Microbial community structure and its functional implications
    Jed A Fuhrman
    Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
    Nature 459:193-9. 2009
  9. ncbi request reprint Marine viruses and their biogeochemical and ecological effects
    J A Fuhrman
    Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles 90089 0371, USA
    Nature 399:541-8. 1999
  10. pmc Rapid detection of enteroviruses in small volumes of natural waters by real-time quantitative reverse transcriptase PCR
    Jed A Fuhrman
    Department of Biological Sciences and Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA 90089 0371, USA
    Appl Environ Microbiol 71:4523-30. 2005

Collaborators

Detail Information

Publications29

  1. ncbi request reprint A comparison of taxon co-occurrence patterns for macro- and microorganisms
    M Claire Horner-Devine
    School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington 98195, USA
    Ecology 88:1345-53. 2007
    ....
  2. pmc Metagenomics and its connection to microbial community organization
    Jed A Fuhrman
    Department of Biological Sciences, University of Southern California Los Angeles CA 90089 USA
    F1000 Biol Rep 4:15. 2012
    ..However, we don't yet know to what extent such predictions are applicable...
  3. pmc Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates
    Li C Xia
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 2910, USA
    BMC Syst Biol 5:S15. 2011
    ..With replicates, it is possible to understand the variability of local similarity (LS) score and to obtain its confidence interval...
  4. doi request reprint Proteorhodopsins: an array of physiological roles?
    Jed A Fuhrman
    Department of Biological Sciences and Wrigley Institute, University of Southern California, Los Angeles, California 90089 0371, USA
    Nat Rev Microbiol 6:488-94. 2008
    ..This suggests an energetic role for proteorhodopsins. However, results from a growing number of investigations do not readily fit this model, which indicates that proteorhodopsins could have a range of physiological functions...
  5. ncbi request reprint Viral influence on aquatic bacterial communities
    J A Fuhrman
    University of Southern California, Los Angeles, California 90089 0371, USA
    Biol Bull 204:192-5. 2003
    ..Other virus roles, such as in genetic exchange or microbial evolution, have the potential to be extremely important, but we know very little about them...
  6. pmc A latitudinal diversity gradient in planktonic marine bacteria
    Jed A Fuhrman
    Wrigley Institute for Environmental Studies and Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 0371, USA
    Proc Natl Acad Sci U S A 105:7774-8. 2008
    ..The latitudinal gradient in marine bacteria supports the hypothesis that the kinetics of metabolism, setting the pace for life, has strong influence on diversity...
  7. ncbi request reprint Community structure and function in prokaryotic marine plankton
    Jed A Fuhrman
    Department of Biological Sciences, University of Southern California, Los Angeles 90089 0371, USA
    Antonie Van Leeuwenhoek 81:521-7. 2002
    ..This suggests the group is at least partly heterotrophic and able to compete successfully with bacteria for nutrients. Other as-yet uncultivated groups are also amenable to similar studies...
  8. doi request reprint Microbial community structure and its functional implications
    Jed A Fuhrman
    Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
    Nature 459:193-9. 2009
    ..Some microbial systems are found to change predictably, helping us to anticipate how microbial communities and their activities will shift in a changing world...
  9. ncbi request reprint Marine viruses and their biogeochemical and ecological effects
    J A Fuhrman
    Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles 90089 0371, USA
    Nature 399:541-8. 1999
    ..Newly developed fluorescence and molecular techniques leave the field poised to make significant advances towards evaluating and quantifying such effects...
  10. pmc Rapid detection of enteroviruses in small volumes of natural waters by real-time quantitative reverse transcriptase PCR
    Jed A Fuhrman
    Department of Biological Sciences and Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA 90089 0371, USA
    Appl Environ Microbiol 71:4523-30. 2005
    ..The presented filtration-qRT-PCR approach is fast (<8 h from sampling to results), sensitive, and cost efficient and is promising for monitoring viral contamination in environmental water samples...
  11. pmc Combined microautoradiography-16S rRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ
    C C Ouverney
    Department of Biological Sciences, University of Southern California, Los Angeles, California 90089 0371, USA
    Appl Environ Microbiol 65:1746-52. 1999
    ..We suggest a name for our triple-labeling technique, substrate-tracking autoradiographic fluorescent in situ hybridization (STARFISH), which should aid in the "dissection" of microbial communities by type and function...
  12. ncbi request reprint Bacterial diversity in shallow oligotrophic marine benthos and overlying waters: effects of virus infection, containment, and nutrient enrichment
    I Hewson
    Department of Biological Sciences, University of Southern California, USA
    Microb Ecol 46:322-36. 2003
    ....
  13. ncbi request reprint Diversity and biogeography of bacterial assemblages in surface sediments across the San Pedro Basin, Southern California Borderlands
    Ian Hewson
    Department of Biological Sciences and Wrigley Institute for Environmental Studies, University of Southern California, 3616 Trousdale Pkwy AHF 107, Los Angeles, CA 90089 0371, USA
    Environ Microbiol 9:923-33. 2007
    ....
  14. pmc Annually reoccurring bacterial communities are predictable from ocean conditions
    Jed A Fuhrman
    Department of Biological Sciences and Wrigley Institute for Environmental Studies, University of Southern California, 3616 Trousdale Parkway, Los Angeles, 90089, USA
    Proc Natl Acad Sci U S A 103:13104-9. 2006
    ....
  15. pmc Rapid virus production and removal as measured with fluorescently labeled viruses as tracers
    R T Noble
    University of Southern California, Los Angeles, California 90089 0371, USA
    Appl Environ Microbiol 66:3790-7. 2000
    ..This new method can be used to determine rates of virus degradation, production, and turnover in eutrophic, mesotrophic, and oligotrophic waters and will provide important inputs for future investigations of microbial food webs...
  16. ncbi request reprint Improved strategy for comparing microbial assemblage fingerprints
    Ian Hewson
    Department of Biological Sciences, University of Southern California, 3616 Trousdale Pkwy AHF 107, Los Angeles, CA 90089 0371, USA
    Microb Ecol 51:147-53. 2006
    ..We believe this binning technique provides the most accurate and least biased comparison between different microbial fingerprints...
  17. ncbi request reprint Virus and prokaryote enumeration from planktonic aquatic environments by epifluorescence microscopy with SYBR Green I
    Anand Patel
    Marine Environmental Biology Section, University of Southern California, 3616 Trousdale Parkway, AHF 107, Los Angeles, California 90089, USA
    Nat Protoc 2:269-76. 2007
    ..The protocol provides an inexpensive, rapid (30 min) and reliable technique for obtaining counts of viruses and prokaryotes simultaneously...
  18. pmc Richness and diversity of bacterioplankton species along an estuarine gradient in Moreton Bay, Australia
    Ian Hewson
    Department of Biological Sciences, University of Southern California, Los Angeles, 90089 0371, USA
    Appl Environ Microbiol 70:3425-33. 2004
    ..Furthermore, these results contrast with previous reports of spatially homogeneous bacterioplankton communities in other coastal waters...
  19. ncbi request reprint Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors
    Quansong Ruan
    Department of Mathematics, University of Southern California 3620 Vermont Avenue, KAP 108, Los Angeles, CA 90089 2532, USA
    Bioinformatics 22:2532-8. 2006
    ..However, this approach may not be able to capture more complex interactions which occur in situ; thus, alternative analyses were explored...
  20. ncbi request reprint Viriobenthos production and virioplankton sorptive scavenging by suspended sediment particles in coastal and pelagic waters
    I Hewson
    Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 0371, USA
    Microb Ecol 46:337-47. 2003
    ..01% of daily benthic virus production. Calculated mortality rates of benthic bacteria (4-14% h(-1)) suggest viruses may play an important role in sediment carbon cycling...
  21. pmc Marine planktonic archaea take up amino acids
    C C Ouverney
    Department of Biological Sciences, University of Southern California, Los Angeles, California 90089 0371, USA
    Appl Environ Microbiol 66:4829-33. 2000
    ..Bacteria showed a similar proportion of active cells. We concluded that a portion of these Archaea is heterotrophic and also appears to coexist successfully with Bacteria in the same water...
  22. ncbi request reprint A dynamic programming algorithm for binning microbial community profiles
    Quansong Ruan
    Department of Mathematics, University of Southern California 3620 South Vermont Avenue, KAP 108, Los Angeles, California 90089 253, USA
    Bioinformatics 22:1508-14. 2006
    ..We have developed a dynamic programming algorithm based binning method for ARISA data analysis which minimizes the overall differences between replicates from the same sampling location and time...
  23. ncbi request reprint Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series
    Mark V Brown
    Department of Biological Science and Wrigley Institute for Marine Studies, University of Southern California, 3616 Trousdale Parkway, AHF B4, Los Angeles, CA 90089, USA
    Environ Microbiol 7:1466-79. 2005
    ..16S-ITS data allowed high-resolution identification of organisms by ITS sequence analysis, and examination of microdiversity...
  24. ncbi request reprint Population ecology of nitrifying archaea and bacteria in the Southern California Bight
    J Michael Beman
    Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    Environ Microbiol 12:1282-92. 2010
    ..These data capture a dynamic nitrogen cycle in which multiple microbial groups appear to be active participants...
  25. ncbi request reprint Characterization of lysogens in bacterioplankton assemblages of the southern California borderland
    Ian Hewson
    Wrigley Institute for Environmental Studies, University of Southern California, 3616 Trousdale Pkwy AHF 107, Los Angeles, CA 90089 0371, USA
    Microb Ecol 53:631-8. 2007
    ..Because lysogenic OTU may also be resistant to closely related lytic (i.e., free-living) viruses, the impact of lytic virioplankton on assemblages may only be pronounced transiently or when conditions causing lysogenic induction arise...
  26. ncbi request reprint Microbial biogeography: putting microorganisms on the map
    Jennifer B Hughes Martiny
    Department of Ecology and Evolutionary Biology, 80 Waterman Street, Box G W, Brown University, Providence, Rhode Island 02912, USA
    Nat Rev Microbiol 4:102-12. 2006
    ..However, recent studies also dispute the idea that 'everything is everywhere'. We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world...
  27. pmc Multitiered approach using quantitative PCR to track sources of fecal pollution affecting Santa Monica Bay, California
    Rachel T Noble
    University of North Carolina Chapel Hill, Chapel Hill Institute of Marine Sciences, Morehead City, NC 28557, USA
    Appl Environ Microbiol 72:1604-12. 2006
    ..These results indicated the power of using multiple approaches to assess and quantify fecal contamination in freshwater conduits to high-use, high-priority recreational swimming areas...
  28. ncbi request reprint Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments
    Jose M Gonzalez
    Departamento de Microbiologia y Biologia Celular, Facultad de Farmacia, Universidad de La Laguna, 38071 La Laguna, Tenerife, Spain
    Int J Syst Evol Microbiol 53:1261-9. 2003
    ..nov. with strain DSS-3(T) (=ATCC 700808(T)=DSM 15171(T)) as the type strain, and Roseovarius nubinhibens sp. nov. with strain ISM(T) (=ATCC BAA-591(T)=DSM 15170(T)) as the type strain...
  29. ncbi request reprint Tiered approach for identification of a human fecal pollution source at a recreational beach: case study at Avalon Bay, Catalina Island, California
    Alexandria B Boehm
    Department of Civil and Environmental Engineering Stanford University, Stanford, California 94305 4020, USA
    Environ Sci Technol 37:673-80. 2003
    ..Multiple shoreline samples and two subsurface water samples tested positive for human-specific bacteria and enterovirus, suggesting that at least a portion of the FIB contamination is from human sewage...