title: Marine metagenomics: new tools for the study and exploitation of marine microbial metabolism.
abstract: The marine environment is extremely diverse, with huge variations in pressure and temperature. Nevertheless, life, especially microbial life, thrives throughout the marine biosphere and microbes have adapted to all the divergent environments present. Large scale DNA sequence based approaches have recently been used to investigate the marine environment and these studies have revealed that the oceans harbor unprecedented microbial diversity. Novel gene families with representatives only within such metagenomic datasets represent a large proportion of the ocean metagenome. The presence of so many new gene families from these uncultured and highly diverse microbial populations represents a challenge for the understanding of and exploitation of the biology and biochemistry of the ocean environment. The application of new metagenomic and single cell genomics tools offers new ways to explore the complete metabolic diversity of the marine biome.
authors.affiliation: Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland. jonathan.kennedy@ucc.ie
authors.forename: Jonathan
authors.initials: J
authors.lastname: Kennedy
authors.forename: Burkhardt
authors.initials: B
authors.lastname: Flemer
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Jackson
authors.forename: David P H
authors.initials: DP
authors.lastname: Lejon
authors.forename: John P
authors.initials: JP
authors.lastname: Morrissey
authors.forename: Fergal
authors.initials: F
authors.lastname: O'Gara
authors.forename: Alan D W
authors.initials: AD
authors.lastname: Dobson
mesh_terms: D001419:Bacteria / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism*; D001709:Biotechnology; D057225:Data Mining; D008386:Marine Biology; D056186:Metagenomics / Q000379:methods; D012623:Seawater / Q000382:microbiology*; D014871:Water Microbiology
references.citation: Science. 2006 Jan 27;311(5760):496-503
references.pmid: 16439655
references.citation: Appl Environ Microbiol. 2006 Nov;72(11):7406-9
references.pmid: 16950897
references.citation: Environ Microbiol. 2002 Jul;4(7):401-13
references.pmid: 12123476
references.citation: Chem Rev. 2009 Jul;109(7):3012-43
references.pmid: 19422222
references.citation: Appl Environ Microbiol. 2009 Sep;75(17):5695-9
references.pmid: 19561181
references.citation: Bioinformatics. 2009 Aug 1;25(15):1849-55
references.pmid: 19515961
references.citation: Environ Microbiol. 2010 Aug;12(8):2070-82
references.pmid: 21966903
references.citation: Science. 2005 Aug 19;309(5738):1242-5
references.pmid: 16109880
references.citation: Environ Microbiol. 2008 Jul;10(7):1888-902
references.pmid: 18430018
references.citation: Science. 2004 Apr 2;304(5667):66-74
references.pmid: 15001713
references.citation: BMC Bioinformatics. 2009 Nov 29;10:391
references.pmid: 19943962
references.citation: J Biol Chem. 2002 Sep 20;277(38):35133-9
references.pmid: 12089151
references.citation: Microbiol Rev. 1996 Sep;60(3):512-38
references.pmid: 8840785
references.citation: Science. 1985 Mar 15;227(4692):1345-7
references.pmid: 2983423
references.citation: Proc Natl Acad Sci U S A. 2008 Jul 29;105(30):10583-8
references.pmid: 18650394
references.citation: Extremophiles. 2006 Feb;10(1):79-82
references.pmid: 16133657
references.citation: Protein Expr Purif. 2007 Apr;52(2):340-7
references.pmid: 17126562
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D260-4
references.pmid: 17151080
references.citation: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W101-5
references.pmid: 19429689
references.citation: Science. 1963 Jun 21;140(3573):1339-40
references.pmid: 17802177
references.citation: Biotechnol Lett. 2007 Mar;29(3):465-72
references.pmid: 17203343
references.citation: Genome Biol. 2005;6(2):R14
references.pmid: 15693943
references.citation: Appl Microbiol Biotechnol. 2004 Nov;65(6):720-6
references.pmid: 15365646
references.citation: PLoS Biol. 2007 Mar;5(3):e16
references.pmid: 17355171
references.citation: Electrophoresis. 2008 Jun;29(12):2603-16
references.pmid: 18494036
references.citation: PLoS Biol. 2007 Mar;5(3):e77
references.pmid: 17355176
references.citation: Proc Natl Acad Sci U S A. 2007 May 22;104(21):9052-7
references.pmid: 17502618
references.citation: J Biotechnol. 2007 Jan 20;127(4):575-92
references.pmid: 16963141
references.citation: Extremophiles. 2008 Mar;12(2):255-62
references.pmid: 18087672
references.citation: Nat Rev Microbiol. 2007 Oct;5(10):770-81
references.pmid: 17828281
references.citation: Org Lett. 2000 Aug 10;2(16):2401-4
references.pmid: 10956506
references.citation: Gene. 2006 Jun 21;375:87-94
references.pmid: 16690231
references.citation: Appl Biochem Biotechnol. 2010 Oct;162(3):625-40
references.pmid: 19711200
references.citation: BMC Bioinformatics. 2008 Sep 19;9:386
references.pmid: 18803844
references.citation: Bioinformatics. 2010 Feb 15;26(4):568-9
references.pmid: 20007739
references.citation: PLoS One. 2008 Aug 22;3(8):e3042
references.pmid: 18725995
references.citation: Microb Cell Fact. 2005 Mar 25;4(1):8
references.pmid: 15790425
references.citation: J Bacteriol. 2001 Mar;183(5):1773-9
references.pmid: 11160110
references.citation: Microbiol Mol Biol Rev. 2004 Dec;68(4):669-85
references.pmid: 15590779
references.citation: Microb Cell Fact. 2008 Aug 21;7:27
references.pmid: 18717988
references.citation: Science. 2009 Oct 9;326(5950):252-7
references.pmid: 19815770
references.citation: BMC Genomics. 2006 Mar 20;7:57
references.pmid: 16549033
references.citation: Bioinformatics. 2006 Jul 15;22(14):e359-67
references.pmid: 16873494
references.citation: Appl Environ Microbiol. 2004 Apr;70(4):2452-63
references.pmid: 15066844
references.citation: Biochem J. 2004 Dec 1;384(Pt 2):247-53
references.pmid: 15287848
references.citation: Proc Natl Acad Sci U S A. 2008 Mar 11;105(10):3805-10
references.pmid: 18316740
references.citation: Appl Environ Microbiol. 2009 Dec;75(23):7391-8
references.pmid: 19820158
references.citation: Environ Microbiol. 2009 Dec;11(12):3132-9
references.pmid: 19659500
references.citation: Appl Environ Microbiol. 2004 Jun;70(6):3724-32
references.pmid: 15184179
references.citation: Appl Environ Microbiol. 1999 Jun;65(6):2553-7
references.pmid: 10347042
references.citation: Lett Appl Microbiol. 2007 Oct;45(4):418-20
references.pmid: 17897385
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D534-8
references.pmid: 17932063
references.citation: FEMS Microbiol Ecol. 2006 Jun;56(3):389-405
references.pmid: 16689872
references.citation: Nature. 2001 Nov 29;414(6863):495, 497-8
references.pmid: 11734832
references.citation: Nat Protoc. 2008;3(7):1202-12
references.pmid: 18600226
references.citation: Environ Microbiol. 2004 Sep;6(9):948-58
references.pmid: 15305920
references.citation: Science. 1997 Oct 24;278(5338):631-7
references.pmid: 9381173
references.citation: Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12115-20
references.pmid: 16880384
references.citation: Antonie Van Leeuwenhoek. 2008 Aug;94(2):245-55
references.pmid: 18340544
references.citation: Environ Microbiol. 2008 Jan;10(1):75-86
references.pmid: 18211268
references.citation: Nat Biotechnol. 2005 Jan;23(1):88-93
references.pmid: 15608629
references.citation: Proc Natl Acad Sci U S A. 1996 Jul 23;93(15):7979-84
references.pmid: 8755588
references.citation: Appl Environ Microbiol. 2008 Mar;74(5):1453-63
references.pmid: 18192407
references.citation: Appl Microbiol Biotechnol. 2007 Nov;77(1):107-15
references.pmid: 17712554
references.citation: Extremophiles. 2003 Aug;7(4):335-7
references.pmid: 12910392
references.citation: Environ Microbiol. 2007 Nov;9(11):2707-19
references.pmid: 17922755
references.citation: PLoS One. 2009;4(4):e5299
references.pmid: 19390573
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D281-8
references.pmid: 18039703
references.citation: Science. 1994 Feb 11;263(5148):802-5
references.pmid: 8303295
references.citation: BMC Bioinformatics. 2009 Dec 18;10:430
references.pmid: 20021646
references.citation: Appl Environ Microbiol. 2009 Mar;75(6):1667-73
references.pmid: 19151184
references.citation: Environ Microbiol. 2007 Sep;9(9):2289-97
references.pmid: 17686025
references.citation: Appl Environ Microbiol. 2007 Dec;73(23):7785-8
references.pmid: 17933945
references.citation: Curr Opin Microbiol. 2007 Oct;10(5):481-9
references.pmid: 17951101
references.citation: Environ Microbiol. 2009 Jan;11(1):111-25
references.pmid: 18783384
references.citation: PLoS One. 2007 Sep 19;2(9):e914
references.pmid: 17878949
references.citation: Environ Microbiol. 2008 Apr;10(4):978-87
references.pmid: 18093161
references.citation: Nat Biotechnol. 2003 Nov;21(11):1266-7
references.pmid: 14595348
references.citation: Genome Res. 2007 Mar;17(3):377-86
references.pmid: 17255551
references.citation: Appl Environ Microbiol. 2004 Oct;70(10):5955-62
references.pmid: 15466538
references.citation: Appl Microbiol Biotechnol. 2008 Sep;80(4):615-25
references.pmid: 18600322
references.citation: Environ Microbiol. 2005 Dec;7(12):1917-26
references.pmid: 16309390
references.citation: PLoS Biol. 2007 Mar;5(3):e75
references.pmid: 17355175
references.citation: Gene. 2008 Mar 15;410(2):234-40
references.pmid: 18242884
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D468-72
references.pmid: 19906710
references.citation: J Biotechnol. 2008 Feb 1;133(3):277-86
references.pmid: 18055055
references.citation: FEMS Microbiol Ecol. 2007 Feb;59(2):524-34
references.pmid: 17328767
references.citation: J Mol Microbiol Biotechnol. 2009;16(1-2):109-23
references.pmid: 18957866
references.citation: Extremophiles. 2008 May;12(3):311-23
references.pmid: 18437283
references.citation: Mar Biotechnol (NY). 2009 May-Jun;11(3):307-16
references.pmid: 18814017
references.citation: Appl Environ Microbiol. 2007 Jun;73(11):3669-76
references.pmid: 17435000
references.citation: Appl Microbiol Biotechnol. 2007 May;75(1):11-20
references.pmid: 17318533
references.citation: Microbiology (Reading). 2006 Feb;152(Pt 2):505-517
references.pmid: 16436438
references.citation: Extremophiles. 2005 Feb;9(1):53-64
references.pmid: 15583965
references.citation: Extremophiles. 1999 Jan;3(1):3-9
references.pmid: 10086839
references.citation: Appl Microbiol Biotechnol. 2009 Jan;81(5):865-74
references.pmid: 18773201
references.citation: Bioinformation. 2009 Aug 20;4(1):46-9
references.pmid: 20011152
references.citation: Environ Microbiol. 2004 Sep;6(9):911-20
references.pmid: 15305916
references.citation: Mar Biotechnol (NY). 2008 Mar-Apr;10(2):190-7
references.pmid: 18040741
references.citation: Chem Biol. 2005 Aug;12(8):895-904
references.pmid: 16125101
references.citation: Proc Natl Acad Sci U S A. 2005 Jun 28;102(26):9306-10
references.pmid: 15967984
references.citation: Microbiol Rev. 1995 Mar;59(1):143-69
references.pmid: 7535888
references.citation: Proc Natl Acad Sci U S A. 1998 Jun 9;95(12):6578-83
references.pmid: 9618454