Chapter 26
Adaptation to Nutrient Availability in Marine Microorganisms by Gene Gain and Loss
Adam C. Martiny,
Ying Huang,
Weizhong Li,
Adam C. Martiny
University of California, Irvine, California, USA
Search for more papers by this authorYing Huang
University of California, San Diego, La Jolla, California, USA
Search for more papers by this authorWeizhong Li
University of California, San Diego, La Jolla, California, USA
Search for more papers by this authorAdam C. Martiny,
Ying Huang,
Weizhong Li,
Adam C. Martiny
University of California, Irvine, California, USA
Search for more papers by this authorYing Huang
University of California, San Diego, La Jolla, California, USA
Search for more papers by this authorWeizhong Li
University of California, San Diego, La Jolla, California, USA
Search for more papers by this authorBook Editor(s):Frans J. de Bruijn,
Frans J. de Bruijn
Laboratory of Plant Micro-organism Interaction, CNRS-INRA, Castanet Tolosan, France
Search for more papers by this authorSummary
This chapter contains sections titled:
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Introduction
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Methods
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Results and Discussion
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Internet Resources
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References
INTERNET RESOURCES
- CD-HIT (http://weizhong-lab.ucsd.edu/cd-hit/)
- OrthoMCL (http://www.orthomcl.org)
- World Ocean Atlas (http://www.nodc.noaa.gov/OC5/WOA05/woa05data.html)
- CAMERA (http://camera.calit2.net/)
- REFERENCES
- Bonnet S, Guieu C, Bruyant F, Prasil O, Van Wambeke F, et al. 2008. Nutrient limitation of primary productivity in the Southeast Pacific (BIOSOPE cruise). Biogeosciences 5: 215–225.
- Boyer TP, Antonov JI, Garcia HE, Johnson DR, Locarnini RA, et al. 2006. World Ocean Database 2005. Washington, DC: U.S. Goverment Printing Office.
- Coale KH, Fitzwater SE, Gordon RM, Johnson KS, Barber RT. 1996. Control of community growth and export production by upwelled iron in the equatorial Pacific Ocean. Nature 379: 621–624.
- Dufresne A, Ostrowski M, Scanlan DJ, Garczarek L, Mazard S, et al. 2008. Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. Genome Biol. 9: R90.
- Kettler GC, Martiny AC, Huang K, Zucker J, Coleman ML, et al. 2007. Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus. PLoS Genet. 3: e231.
- Li L, Stoeckert CJ, Roos DS. 2003. OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes. Genome Res. 13: 2178– 2189.
- Li W, Godzik A. 2006. Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658– 1659.
- Martiny AC, Coleman ML, Chisholm SW. 2006. Phosphate acquisition genes in Prochlorococcus ecotypes: Evidence for genome-wide adaptation. Proc. Natl. Acad. Sci. USA 103: 12552– 12557.
- Martiny AC, Huang Y, Li WZ. 2009a. Occurrence of phosphate acquisition genes in Prochlorococcus cells from different ocean regions. Environ. Microbiol. 11: 1340– 1347.
- Martiny AC, Kathuria S, Berube PM. 2009b. Widespread metabolic potential for nitrite and nitrate assimilation among Prochlorococcus ecotypes. Proc. Natl. Acad. Sci. USA 106: 10787–10792.
- Mills MM, Moore CM, Langlois R, Milne A, Achterberg E, et al. 2008. Nitrogen and phosphorus co-limitation of bacterial productivity and growth in the oligotrophic subtropical North Atlantic. Limnol. Oceanogr. 53: 824–834.
- Morris RM, Rappe MS, Connon SA, Vergin KL, Siebold WA, et al. 2002. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420: 806– 810.
- Palenik B, Ren QH, Dupont CL, Myers GS, Heidelberg JF, et al. 2006. Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment. Proc. Natl. Acad. Sci. USA 103: 13555– 13559.
- Partensky F, Hess WR, Vaulot D. 1999. Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol. Mol. Biol. Rev. 63: 106– 127.
- Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S et al. 2007. The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol. 5: e77.
- Sanudo-Wilhelmy SA, Kustka AB, Gobler CJ, Hutchins DA, Yang M, et al. 2001. Phosphorus limitation of nitrogen fixation by Trichodesmium in the central Atlantic Ocean. Nature 411: 66–69.
- Tetu SG, Brahamsha B, Johnson DA, Tai V, Phillippy K, et al. 2009. Microarray analysis of phosphate regulation in the marine cyanobacterium Synechococcus sp WH8102. ISME J. 3: 835–849.
- Wambeke F, Bonnet S, Moutin T, Raimbault P, Alarcon G, Guieu C. 2008. Factors limiting heterotrophic bacterial production in the southern Pacific Ocean. Biogeosciences 5: 833–845.
- Wu J, Sunda W, Boyle EA, Karl DM. 2000. Phosphate Depletion in the Western North Atlantic Ocean. Science 289: 759– 762.
