Genomics and Metagenomics of Marine Microbes
Andrew E Allen, J. Craig Venter Institute

Observations concerning the abundance and metabolism of marine bacteria and have led to the realization that most element cycles in the ocean are governed by the activity of planktonic bacteria (Bacterioplankton). Genomics has provided a new set of tools enabling investigation of the genes and biochemical properties that underlie the metabolic activity of bacterioplankton as well phytoplankton (bacterial and eukaryotic obligate photosynthetic microbes). Metagenomics represents a culture-independent method of surveying the genomic repertoire of microbial communities. Together with advances in culturing methods and methodology in single cell genomics, the field of genomics is making significant advances in understanding the biology and ecology of microorganisms that regulate major ocean processes. While the fields of genomics and metagenomics are concerned with the study of an organism’s complete or partial genetic material, bioinformatics refers to the process of computational identification and interpretation of biologically significant information stored in the genetic material. For studies related to oceanic microorganisms genomics and bioinformatics have revolutionized the research landscape through generation of testable hypotheses about novel microbial activities and ecosystem characteristics. Examples include the discovery of a gene from an uncultured marine bacterium encoding a light driven proton pump for generation of ATP as wells findings related to the influence of wide spread oceanic phosphorous and iron limitation on various aspects of microbial genome evolution. More recently, functional genomics approaches such (meta)-transcriptomics and (meta)-proteomics have been coupled with metagenomics to achieve novel insights into microbial physiology and gene function (Moran, Delong, . While metagenomics is concerned with cataloging the diversity and repertoire of genes present within designated microbial populations, metatranscriptomics is based around identification, timing, and dynamics of gene activity within specific populations.

Further Reading :

Azam, F, AZ Worden. 2004. Microbes, molecules, and marine ecosystems. Science 303:1622-1624.
Bowler, C, A Vardi, AE Allen. 2010. Oceanographic and Biogeochemical Insights from Diatom Genomes. Annual Review of Marine Science 2:333-365.

Coleman, ML, SW Chisholm. 2010. Ecosystem-specific selection pressures revealed through comparative population genomics. Proceedings of the National Academy of Sciences of the United States of America 107:18634-18639.

Cuvelier, ML, AE Allen, A Monier, et al. 2010. Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proceedings of the National Academy of Sciences of the United States of America 107:14679-14684.

DeLong, EF. 2009. The microbial ocean from genomes to biomes. Nature 459:200-206.
Gilbert, JA, CL Dupont. 2011. Microbial Metagenomics: Beyond the Genome. Annual Review of Marine Science, Vol 3. Palo Alto: Annual Reviews. p. 347-371.

McCarren, J, JW Becker, DJ Repeta, YM Shi, CR Young, RR Malmstrom, SW Chisholm, EF DeLong. 2010. Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. Proceedings of the National Academy of Sciences of the United States of America 107:16420-16427.

McCarren, J, JW Becker, DJ Repeta, YM Shi, CR Young, RR Malmstrom, SW Chisholm, EF DeLong. 2010.
Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. Proceedings of the National Academy of Sciences of the United States of America 107:16420-16427.

Reisch, CR, MJ Stoudemayer, VA Varaljay, IJ Amster, MA Moran, WB Whitman. 2011. Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria. Nature 473:208-+.

Stepanauskas, R, ME Sieracki. 2007. Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proceedings of the National Academy of Sciences of the United States of America 104:9052-9057.

Worden, AZ, AE Allen. 2010. The voyage of the microbial eukaryote. Current Opinion in Microbiology 13:652-660.

Yoon, HS, DC Price, R Stepanauskas, VD Rajah, ME Sieracki, WH Wilson, EC Yang, S Duffy, D Bhattacharya. 2011. Single-Cell Genomics Reveals Organismal Interactions in Uncultivated Marine Protists. Science 332:714-717.

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