Ocean microbial metagenomics

Deep-Sea Research Part II: Topical Studies in Oceanography

Volumn 56, Issue 19-20, 2009, Pages 1824-1829

  Kerkhof, Lee J ^a   Goodman, Robert M ^b  

^a RUTGERS UNIVERSITY   (United States)

^b The State University of New Jersey   (United States)

Author keywords

Metagenomics; Ocean microbiology

Indexed keywords

ENVIRONMENTAL MICROBIOLOGY; ENVIRONMENTAL SAMPLE; GENOMIC DNA; METAGENOMICS; MICROBIAL DIVERSITY; OCEAN MICROBIOLOGY;

NUCLEIC ACIDS; OCEANOGRAPHY;

MICROORGANISMS;

BIODIVERSITY; BIOLOGICAL OCEANOGRAPHY; DNA; GENOMICS; META-ANALYSIS; MICROBIAL COMMUNITY; MICROBIOLOGY; TECHNOLOGICAL DEVELOPMENT;

EID: 69949124390     PISSN: 09670645     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dsr2.2009.05.005     Document Type: Article

References (44)

1. Abby S., and Daubin V. Comparative genomics and the evolution of prokaryotes. Trends in Microbiology 15 (2007) 135-141
2. Allen E.E., and Banfield J.F. Community genomics in microbial ecology and evolution. Nature Reviews Microbiology 3 (2005) 489-498
3. 2 concentrating mechanism. Journal of Experimental Botany 57 (2006) 249-265
4. Bansal A.K. Bioinformatics in microbial biotechnology-a mini review. Microbial Cell Factories (2005) 4
5. Beja O., Suzuki M.T., Koonin E.V., Aravind L., Hadd A., Nguyen L.P., Villacorta R., Amjadi M., Garrigues C., Jovanovich S.B., Feldman R.A., and DeLong E.F. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environmental Microbiology 2 (2000) 516-529
6. Biddle J.F., Fitz-Gibbon S., Schuster S.C., Brenchley J.E., and House C.H. Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. Proceedings of the National Academy of Sciences of the United States of America 105 (2008) 10583-10588
7. Brinkhoff T., Giebel H.-A., and Simon M. Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Archives of Microbiology 189 (2008) 531-539
8. Chen F., Wang K., Stewart J., and Belas R. Induction of multiple prophages from a marine bacterium: a genomic approach. Applied and Environmental Microbiology 72 (2006) 4995-5001
9. Cottrell M.T., and Kirchman D.L. Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization. Applied and Environmental Microbiology 66 (2000) 5116-5122
10. DeLong E.F., and Karl D.M. Genomic perspectives in microbial oceanography. Nature 437 (2005) 336-342
11. DeLong E.F., Preston C.M., Mincer T., Rich V., Hallam S.J., Frigaard N.U., Martinez A., Sullivan M.B., Edwards R., Brito B.R., Chisholm S.W., and Karl D.M. Community genomics among stratified microbial assemblages in the ocean's interior. Science 311 (2006) 496-503
12. Devereux R., Rublee P., Paul J.H., Field K.G., and Santo Domingo J.W. Development and applications of microbial ecogenomic indicators for monitoring water quality: report of a workshop assessing the state of the science, research needs and future directions. Environmental Monitoring and Assessment 116 (2006) 459-479
13. Dower W.J., Miller J.F., and Ragsdale C.W. High-efficiency transformation of Escherichia coli by high-voltage electroporation. Nucleic Acids Research 16 (1988) 6127-6145
14. Dunlap W.C., Jaspars M., Hranueli D., Battershill C.N., Peric-Concha N., Zucko J., Wright S.H., and Long P.F. New methods for medicinal chemistry-universal gene cloning and expression systems for production of marine bioactive metabolites. Current Medicinal Chemistry 13 (2006) 697-710
15. Fieseler L., Quaiser A., Schleper C., and Hentschel U. Analysis of the first genome fragment from the marine sponge-associated, novel candidate phylum Poribacteria by environmental genomics. Environmental Microbiology 8 (2006) 612-624
16. Foerstner K.U., von Mering C., Hooper S.D., and Bork P. Environments shape the nucleotide composition of genomes. Embo Reports 6 (2005) 1208-1213
17. Frias-Lopez J., Shi Y., Tyson G.W., Coleman M.L., Schuster S.C., Chisholm S.W., and DeLong E.F. Microbial community gene expression in ocean surface waters. Proceedings of the National Academy of Sciences of the United States of America 105 (2008) 3805-3810
18. Giovannoni S.J., Bibbs L., Cho J.C., Stapels M.D., Desiderio R., Vergin K.L., Rappe M.S., Laney S., Wilhelm L.J., Tripp H.J., Mathur E.J., and Barofsky D.F. Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature 438 (2005) 82-85
19. Grzymski J.J., Carter B.J., DeLong E.F., Feldman R.A., Ghadiri A., and Murray A.E. Comparative genomics of DNA fragments from six Antarctic marine planktonic bacteria. Applied and Environmental Microbiology 72 (2006) 1532-1541
20. Grzymski J.J., Murray A.E., Campbell B.J., Kaplarevic M., Gao G.R., Lee C., Daniel R., Ghadiri A., Feldman R.A., and Cary S.C. Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility. Proceedings of the National Academy of Sciences of the United States of America 105 (2008) 17516-17521
21. Hanahan D. Studies on tranformation in Escherichia coli with plasmids. Journal of Molecular Biology 166 (1983) 557-580
22. Jensen P.R., and Lauro F.M. An assessment of actinobacterial diversity in the marine environment. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology 94 (2008) 51-62
23. Kagan J., Sharon I., Beja O., and Kuhn J.C. The tryptophan pathway genes of the Sargasso Sea metagenome: new operon structures and the prevalence of non-operon organization. Genome Biology (2008) 9
24. Kerkhof L., Santoro M., and Garland J. Response of soybean rhizosphere communities to human hygiene water addition as determined by community level physiological profiling (CLPP) and terminal restriction fragment length polymorphism (TRFLP) analysis. Fems Microbiology Letters 184 (2000) 95-101
25. Kettler G.C., Martiny A.C., Huang K., Zucker J., Coleman M.L., Rodrigue S., Chen F., Lapidus A., Ferriera S., Johnson J., Steglich C., Church G.M., Richardson P., and Chisholm S.W. Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. Plos Genetics 3 (2007) 2515-2528
26. Krupovic M., and Bamford D.H. Putative prophages related to lytic tailless marine dsDNA phage PM2 are widespread in the genomes of aquatic bacteria. Bmc Genomics (2007) 8
27. Liu W., Zhao Y., Liu Z., Zhang Y., Lian Z., and Li N. Construction of a 7-fold BAC library and cytogenetic mapping of 10 genes in the giant panda (Ailuropoda melanoleuca). BMC Genomics 7 (2006) 294
28. Martinez A., Bradley A.S., Waldbauer J.R., Summons R.E., and DeLong E.F. Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host. Proceedings of the National Academy of Sciences of the United States of America 104 (2007) 5590-5595
29. McDonald A.E., and Vanlerberghe G.C. Alternative oxidase and plastoquinol terminal oxidase in marine prokaryotes of the Sargasso Sea. Gene 349 (2005) 15-24
30. Medini D., Serruto D., Parkhill J., Relman D.A., Donati C., Moxon R., Falkow S., and Rappuoli R. Microbiology in the post-genomic era. Nature Reviews Microbiology 6 (2008) 419-430
31. Monier A., Claverie J.M., and Ogata H. Taxonomic distribution of large DNA viruses in the sea. Genome Biology (2008) 9
32. Moran M.A., Belas R., Schell M.A., Gonzdlez J.M., Sun F., Sun S., Binder B.J., Edmonds J., Ye W., Orcutt B., Howard E.C., Meile C., Palefsky W., Goesmann A., Ren Q., Paulsen I., Ulrich L.E., Thompson L.S., Saunders E., and Buchanlo A. Ecological genomics of marine Roseobacters. Applied and Environmental Microbiology 73 (2007) 4559-4569
33. Moore B.S., Kalaitzis J.A., and Xiang L.K. Exploiting marine actinomycete biosynthetic pathways for drug discovery. Antonie van Leeuwenhoek 87 (2005) 49-57
34. Mou X.Z., Sun S.L., Edwards R.A., Hodson R.E., and Moran M.A. Bacterial carbon processing by generalist species in the coastal ocean. Nature 451 (2008) 708-714
35. Palenik B., Ren Q.H., Dupont C.L., Myers G.S., Heidelberg J.F., Badger J.H., Madupu R., Nelson W.C., Brinkac L.M., Dodson R.J., Durkin A.S., Daugherty S.C., Sullivan S.A., Khouri H., Mohamoud Y., Halpin R., and Paulsen I.T. Genome sequence of Synechococcus CC9311: insights into adaptation to a coastal environment. Proceedings of the National Academy of Sciences of the United States of America 103 (2006) 13555-13559
36. Phelps C.D., Kerkhof L.J., and Young L.Y. Molecular characterization of a sulfate-reducing consortium which mineralizes benzene. FEMS Microbiology Ecology 27 (1998) 269-279
37. Rusch D.B., Halpern A.L., Sutton G., Heidelberg K.B., Williamson S., Yooseph S., Wu D.Y., Eisen J.A., Hoffman J.M., Remington K., Beeson K., Tran B., Smith H., Baden-Tillson H., Stewart C., Thorpe J., Freeman J., Andrews-Pfannkoch C., Venter J.E., Li K., Kravitz S., Heidelberg J.F., Utterback T., Rogers Y.H., Falcon L.I., Souza V., Bonilla-Rosso G., Eguiarte L.E., Karl D.M., Sathyendranath S., Platt T., Bermingham E., Gallardo V., Tamayo-Castillo G., Ferrari M.R., Strausberg R.L., Nealson K., Friedman R., Frazier M., and Venter J.C. The Sorcerer II global ocean sampling expedition: northwest Atlantic through eastern tropical pacific. Plos Biology 5 (2007) 398-431
38. Sogin M.L., Morrison H.G., Huber J.A., Mark Welch D., Huse S.M., Neal P.R., Arrieta J.M., and Herndl G.J. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedings of the National Academy of Sciences of the United States of America 103 (2006) 12115-12120
39. Stein J.L., Marsh T.L., Wu K.Y., Shizuya H., and DeLong E.F. Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment front a planktonic marine Archaeon. Journal of Bacteriology 178 (1996) 591-599
40. Stepanauskas R., and Sieracki M.E. 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 (2007) 9052-9057
41. Tringe S.G., and Rubin E.M. Metagenomics: DNA sequencing of environmental samples. Nature Reviews Genetics 6 (2005) 805-814
42. Tyson G.W., Chapman J., Hugenholtz P., Allen E.E., Ram R.J., Richardson P.M., Solovyev V.V., Rubin E.M., Rokhsar D.S., and Banfield J.F. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428 (2004) 37-43
43. Venter J.C., Remington K., Heidelberg J.F., Halpern A.L., Rusch D., Eisen J.A., Wu D.Y., Paulsen I., Nelson K.E., Nelson W., Fouts D.E., Levy S., Knap A.H., Lomas M.W., Nealson K., White O., Peterson J., Hoffman J., Parsons R., Baden-Tillson H., Pfannkoch C., Rogers Y.H., and Smith H.O. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304 (2004) 66-74
44. Vetriani C., Tran H.V., and Kerkhof L.J. Fingerprinting microbial assemblages from the oxic/anoxic chemocline of the Black Sea. Applied and Environmental Microbiology 69 (2003) 6481-6488