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2007 Papers |
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1. Anand Patel, Rachel T Noble, Joshua A Steele, Michael S Schwalbach, Ian Hewson, and Jed A Fuhrman. 2007. Virus and prokaryote enumeration from planktonic aquatic environments by epifluourescence microscopy with SYBR Green I. Nature Protocols 2: 269-276. (Download
PDF)
2. 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.
3. 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 Øvreas, Anna-Louise Reysenbach, and Val H. Smith. 2007. A comparison of taxon co-occurrence patterns for macro- and microorganisms. Ecology 88:1345-1353. (Download
PDF)
4. 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.2007.02.003. (Download
PDF)
5. 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: 923–933. (Download
PDF)
6. Hewson, I. and J.A. Fuhrman. 2007. Characterization of lysogens in bacterioplankton assemblages of the Southern California Borderland. Microbial Ecology, in press (Download
PDF)
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Year
2006 Papers |
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1. Hughes
Martiny, Jennifer B. , Brendan J.M. Bohannan, James H.
Brown, Robert Colwell, Jed A. Fuhrman, Jessica Green,
M. Claire Horner-Devine, Matthew Kane, Jennifer Adams
Krumins, Cheryl R. Kuske, Peter Morin, Shahid Naeem, Lise
Øvreås, Anna-Louise Reysenbach, Val Smith,
James Staley. 2006. Microbial
biogeography: putting microorganisms on the map.
Nature Reviews Microbiology 4:102-112 (Download
PDF)
2.
Ian Hewson, Jed A. Fuhrman. 2006.
Spatial and vertical biogeography of coral reef sediment
bacterial and diazotroph communities.
Marine Ecology Progress Series 306:79-86
(Download
PDF)
3. Ian
Hewson, Jed A. Fuhrman. 2006. Improved
strategy for Comparing Microbial Assemblage Fingerprints. Microbial
Ecology. 51: 147-153 DOI: 10.1007/s00248-005-0144-9
(Download
PDF)
4. Hewson
Ian, Danielle M. Winget, Kurt E.Williamson, Jed A. Fuhrman
and K. Eric Wommack. 2006.Viral
and bacterial assemblage covariance in oligotrophic
waters of the West Florida Shelf (Gulf of Mexico).
J.
Mar. Biol. Asoc U.K. In Press (Download
PDF)
5. 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: 67-77 (Download
PDF)
6. 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: (Download
PDF)
7. Hewson,
I, J. A. Steele, D.G. Capone , J.A. Fuhrman. In press.
Remarkable heterogeneity
in meso- and bathypelagic bacterioplankton community
composition. Limnol.
Oceanogr. (Download
PDF)
8. Fuhrman,
J.A. Community
Structure: Bacteria and Archaea. 2006.
In: Hurst, C.J., Knudsen, G.R., McInerney, M.J., Stetzenbach,
L.D. and M.V. Walter (eds.). Manual of Environmental
Microbiology, Section IV, ASM Press, Washington, D.C.
9. 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 in press. (Download
PDF)
10. 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. In press. (Download
PDF)
11. Hewson,
Ian, and Jed A. Fuhrman. 2006. Viral
impacts upon marine bacterioplankton assemblage structure.
J. Mar. Biol. Asoc U.K. In press (Download
PDF)
12. Hewson,
I., and J. A. Fuhrman. 2006. Improved
strategy for comparing community fingerprints.
Microbial Ecology. 51: 147-153 DOI: 10.1007/s00248-005-0144-9
(Download PDF)
13. 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
(Download
PDF)
14. 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, 103:13104-13109 (Download
PDF)
15. 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. 31 July. PMID: 16882654 (Download
PDF)
16. Hewson,
I. and J.A. Fuhrman. Characterization
of lysogens in bacterioplankton assemblages of the Southern
California Borderland.
Microbial Ecology, in press |
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Year
2005 Papers |
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1.
Schwalbach, M.S., Brown, M.V. and J.A. Fuhrman. 2005.
Impact
of light on marine bacterioplankton community
structure. Aquat.
Microb. Ecol.39:235-245. (Download PDF)
2. Brown,
M.V., M.S. Schwalbach, I. Hewson and J.A.
Fuhrman. 2005. Coupling
16S-ITS rDNA clone libraries and ARISA to show marine
microbial diversity; development and application to a time
series. Envir.
Microbiol. 7:1466-1479. (Download
PDF)
3.
Schwalbach, M.S. and J. A. Fuhrman. 2005. Wide-ranging
abundances of
Aerobic, Anoxygenic
Phototrophic Bacteria in the world ocean revealed by
epifluorescence
and Quantitative PCR.
Limnol.
Oceanogr. 50:620-628. (Download
PDF)
4.
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. 71:4523-4530. (Download
PDF)
5.
Brown, M.V. and J.A. Fuhrman. 2005. Marine bacterial
microdiversity as revealed
by internal transcribed spacer analysis. Aquat. Microb.
Ecol. (Download
PDF)
6. 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
(Download
PDF)
7.
Steele, J.A., F. Ozis, J.A. Fuhrman, J.S. Devinny. In
Press. Structure of microbial communities in ethanol
biofilters. In press Chemical Engineering Journal.
(Download
PDF)
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Year
2004 Papers |
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1.
Schwalbach, M.S., I. Hewson, and J.A. Fuhrman. 2004. Viral
effects on
bacterial community composition in marine plankton
mesocosms. Aquatic
Microbial Ecology 34:117-127 (Download
PDF)
2.
Ouverney, C. C. and J. A. Fuhrman. In press.
Correlating single-cell count with function in mixed
natural microbial communities through STARFISH.
In: Molecular
Microbial Ecology Manual. Kluwer Academic
Publishers. (Download
PDF)
3.
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 - 8 (Download
PDF)
4.
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): 3425-3433 (Download
PDF)
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Year
2004 Presentations |
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1.
Fuhrman, J., I. Hewson, M. Schwalbach, M.Brown. “Temporal
and geographic patterns
of marine bacterial community composition” Presented at
ASLO Ocean
Sciences Meeting, Honolulu, Febuary 2004
2.
Brown, 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 2004
3.
Steele, 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 2004
4.
Hewson, 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 2004
5.
Govil,
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 2004
6.
Fuhrman, 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.
7.
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.
8.
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.
9.
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.
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Year
2003 |
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1. 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. (Download
PDF)
2.
Boehm, A.B, J.A.Fuhrman, R.D.Mrše, and S. B.Grant. 2003.
A tiered approach for identification 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. (Download
PDF)
3.
Fuhrman, J.A. and M.S. Schwalbach. 2003. Viral
influence on aquatic bacterial communities. Biol.
Bulletin.
204(2):192-195
4.
Gonzalez, J.M., J.S. Covert, W.B. Whitman, J. 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.,
DMSP demethylating bacteria from marine environments.
Int. J. Syst. Evol. Microbiol. I53(5):1261-1269
5.
Hewson I, and J. A. Fuhrman. Viriobenthos
production and virioplankton sorptive scavenging by
suspended sediment particles in coastal and pelagic
waters.
Microbial Ecology. 46:337-347 (Download
PDF)
6.
Hewson,
I.
, G. A. Vargo, and J.A. Fuhrman. Bacterial
diversity in shallow oligotrophic marine benthos and
overlying waters: effects of virus infection, containment,
and nutrient enrichment.
Microbial Ecology. 46:322-336. (Download
PDF)
7.
Breitbart M., Hewson, I.
, Felts, B., Mahaffy, J.M., Nulton, J., Salamon, P., and
Rohwer, F.
Metagenomic Analyses of an Uncultured Viral
Community from Human Feces.
Journal of Bacteriology. 185: 6220-6223 [Abstract]
8.
Katharine G., Eunice C., Linda K., Jed A., John Griffith,
Patricia A., Michael G., Joann Le, Betty Olson and Michael
T. 2003. A
comparative study of culture-independent,
library-independent genotypic methods of fecal source
tracking. (Download
PDF)
9.
Fuhrman J.A. 2003. Genome
Sequences from the Sea. (Download
PDF) |
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Year
2002 |
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1.
Fuhrman, J. A., J. F. Griffith, and M. S. Schwalbach.
2002. Prokaryotic and
viral diversity patterns in marine plankton.
Ecological Research 17 (2): 183-194 (Download
PDF)
2.
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 environmental change,
H.A. Mooney and J.G. Canadell, editors. Wiley & Sons,
Chichester
UK
. pp 421-425
3.
Fuhrman, J.A.2002. Community
structure and function in prokaryotic marine plankton.
Antonie van Leeuwenhoek 81:521-527 [Abstract]
4. Fuhrman,
J.A. 2002. Viruses in
the Marine Environment. In:
Encyclopedia of Environmental Microbiology, G. Bitton,
ed., Wiley & Sons, New York
pages 3300-3310
5. Fuhrman,
J.A, Hewson, I., Schwalbach, M.S. 2002. Viral
and bacterial community shifts at an ocean time series
station. Eos
transactions AGU: Abstract OS1 1I-09
6.
Hewson, I., Fuhrman J.A. Viriobenthos
abundance and production in neretic and basin sediments of
Southern California. Eos
83: OS3 1C-29
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Year
2001 |
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1.
Fuhrman, J.A., and D.G. Capone. 2001. Nifty
nanoplankton.
Nature (London) 412: 593-594 (Download
PDF)
2.
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. (Download
PDF)
3.
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. [Abstract]
4. 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 371-377
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Year
2000 |
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1.
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
2.
Noble, R.T and, J. A. Fuhrman. 2000. Rapid
viral production and removal as measured with
fluorescently labeled viruses as tracers. Appl.
Environ. Microbiol.. 66:3790-3797
3.
Ouverney, C.C. and J.A. Fuhrman. 2000. Marine
planktonic Archaea take up amino acids.
Appl. Environ. Microbiol. 66:4829-4833 (Download
PDF)
4. Fuhrman,
J.A. 2000. Microbial
Contamination.
In: Opportunities for Environmental Applications of Marine
Biotechnology.
National
Academy
Press,
Washington
DC
, pp. 102-111
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Year
1999 |
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1.
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. 65:1746-1752 (Download
PDF)
2.
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. 18:1-13
3.
Fuhrman, J.A. 1999. Marine
viruses and their biogeochemical and ecological effects.
Nature (
London
) 399: 541-548 (Download
PDF)
4.
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 [Abstract]
5. 40. Gasol,
J.M.,U. L. Zweifel, F. Peters, J.A. Fuhrman, and A
Hangstrom. 1999.
Significance
of size and nucleic acid content heterogeneity as measured
by flow cytometry in natural planktonic bacteria. Appl.
Environ. Microbiol. 65:4475-4483 [Abstract]
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Year
1998 |
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1.
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: 113-118 [Abstract]
2.
Fuhrman, J.A. and L. Campbell. 1998. Microbial
microdiversity.
Nature (
London
) 393: 410-411 (Download
PDF)
3. 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: 3-15 (Download
PDF)
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Year
1997 |
|
1.
Noble, R.T., and J.A. Fuhrman. 1997. Virus
decay and its causes in coastal waters. (Download
PDF)
2.
Karner, M. and J.A. Fuhrman. 1997. Determination
of “active” marine bacterioplankton: a comparison of
universal 16S rRNA probes, autoradiography, and nucleoid
staining.
(Download
PDF)
3.
Fuhrman, J.A., and A.A. Davis.1997. Widespread
Archaea and novel Bacteria from the deep sea as shown by
16S rRNA gene sequences. [Abstract]
4. Ouverney,
C.C. and J.A. Fuhrman. 1997. Increase
in
fluorescence Intensity of 16S rRNA in situ hybridization
in natural samples treated with
chloramphenicol. (Download
PDF)
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Year
1995 |
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1. Fuhrman,
J.A. and R.T. Noble. 1995. Viruses
and protists cause similar bacterial mortality in coastal
seawater.
Limnol. Oceanogr. 40: 1236-1242 [Abstract]
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Year
1994 |
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1.
Wilcox, R.M. and J.A. Fuhrman. 1994. Bacterial
viruses in coastal seawater: lytic rather than lysogenic
production.
Mar. Ecol. Prog. Ser. 114: 35-45 [Abstract]
2. 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. 28:133-145 [Abstract] |
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Year
1993 |
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1.
Fuhrman, J.A. 1993. Measuring
marine bacterial growth (Current Contents Citation
Classic).
Current Contents: Agriculture, Biology, and Environmental
Sciences 24: 8 (not reviewed).
2.
Fuhrman, J.A. and C. A. Suttle. 1993. Viruses
in marine plankton. Oceanography
6: 51-63
3.
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 [Abstract]
4. 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: 1294-1302
(Download
PDF) |
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Year 1992 |
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1.
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. 361-383
2. Fuhrman,
J.A., K. McCallum, and A.A. Davis. 1992. Novel
major archaebacterial group from marine plankton. Nature
(
London
) 356: 148-149 (Download
PDF) |
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Year
1991 |
|
1.
Fuhrman, J.A. and D.G. Capone. 1991. Possible
biogeochemical consequences of ocean fertilization.
Limnol. Oceanogr. 36: 1951-1959 [Abstract]
2. 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: 1277-1287 [Abstract] |
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Year
1990 |
|
1.
Fuhrman, J.A. 1990. Dissolved
free amino acid cycling in an estuarine outflow plume.
Mar. Ecol. Prog. Ser. 66: 197-203
2.
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
3.
Lee, S. and J.A. Fuhrman. 1990. DNA
hybridization to compare species compositions of natural
bacterioplankton assemblages.
Appl. Environ. Microbiol. 56: 739-746 (Download
PDF)
4. Proctor,
L.M. and J.A. Fuhrman. 1990. Viral
mortality of marine cyanobacteria and bacteria.
Nature 343: 60-62 |
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Prior to 1990 |
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1.
Fuhrman J.A., Dorothy E. Comeau, Ake Hagstrom and Amy
M. Chan 1988. Extraction
from Natural Planktonic Microorganisms of DNA Suitable
for Molecular Biological Studies.
(Download
PDF)
2.
Sanghoon Lee and Fuhrman J.A. 1987. Relationships
between Biovolume and Biomass of Naturally Derived Marine
Bacterioplankton. (Download
PDF)
3.
Fuhrman J.A., Farooq Azam. 1980. Bacterioplankton
Secondary Production Estimates for Coastal Waters of
British Columbia, Antarctica and California.
(Download
PDF)
4.
For the other publications prior to 1990, please refer to
Jed's (CV) |
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