title: Community structure and function of planktonic Crenarchaeota: changes with depth in the South China Sea.
abstract: Marine Crenarchaeota represent a widespread and abundant microbial group in marine ecosystems. Here, we investigated the abundance, diversity, and distribution of planktonic Crenarchaeota in the epi-, meso-, and bathypelagic zones at three stations in the South China Sea (SCS) by analysis of crenarchaeal 16S rRNA gene, ammonia monooxygenase gene amoA involved in ammonia oxidation, and biotin carboxylase gene accA putatively involved in archaeal CO(2) fixation. Quantitative PCR analyses indicated that crenarchaeal amoA and accA gene abundances varied similarly with archaeal and crenarchaeal 16S rRNA gene abundances at all stations, except that crenarchaeal accA genes were almost absent in the epipelagic zone. Ratios of the crenarchaeal amoA gene to 16S rRNA gene abundances decreased ~2.6 times from the epi- to bathypelagic zones, whereas the ratios of crenarchaeal accA gene to marine group I crenarchaeal 16S rRNA gene or to crenarchaeal amoA gene abundances increased with depth, suggesting that the metabolism of Crenarchaeota may change from the epi- to meso- or bathypelagic zones. Denaturing gradient gel electrophoresis profiling of the 16S rRNA genes revealed depth partitioning in archaeal community structures. Clone libraries of crenarchaeal amoA and accA genes showed two clusters: the "shallow" cluster was exclusively derived from epipelagic water and the "deep" cluster was from meso- and/or bathypelagic waters, suggesting that niche partitioning may take place between the shallow and deep marine Crenarchaeota. Overall, our results show strong depth partitioning of crenarchaeal populations in the SCS and suggest a shift in their community structure and ecological function with increasing depth.
authors: State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, People's Republic of China.
authors: Anyi
authors: A
authors: Hu
authors: Nianzhi
authors: N
authors: Jiao
authors: Chuanlun L
authors: CL
authors: Zhang
references: Trends Microbiol. 2010 Aug;18(8):331-40
references: 20598889
references: Appl Environ Microbiol. 2006 Oct;72(10):6773-9
references: 17021230
references: Environ Microbiol. 2005 Dec;7(12):1985-95
references: 16309395
references: FEMS Microbiol Ecol. 2007 Dec;62(3):242-57
references: 17991018
references: ISME J. 2008 Apr;2(4):429-41
references: 18200070
references: Environ Microbiol. 2010 Mar;12(3):679-88
references: 20002133
references: Environ Microbiol. 2001 Jan;3(1):72-8
references: 11225725
references: Biol Rev Camb Philos Soc. 2006 May;81(2):259-91
references: 16573844
references: Nat Rev Microbiol. 2005 Jun;3(6):479-88
references: 15931166
references: Annu Rev Microbiol. 2001;55:485-529
references: 11544365
references: Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14683-8
references: 16186488
references: Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6513-8
references: 19366673
references: Science. 2004 Apr 2;304(5667):66-74
references: 15001713
references: Nature. 1994 Oct 20;371(6499):695-7
references: 7935813
references: Appl Environ Microbiol. 2005 Mar;71(3):1501-6
references: 15746353
references: Nature. 1992 Mar 12;356(6365):148-9
references: 1545865
references: Nature. 2006 Aug 17;442(7104):806-9
references: 16915287
references: Environ Microbiol. 2008 Mar;10(3):810-8
references: 18205821
references: Proc Natl Acad Sci U S A. 1992 Jun 15;89(12):5685-9
references: 1608980
references: Nucleic Acids Res. 2004 Feb 25;32(4):1363-71
references: 14985472
references: Environ Microbiol. 2009 Jul;11(7):1658-71
references: 19236445
references: Environ Microbiol. 2009 Sep;11(9):2434-45
references: 19601959
references: Science. 2008 Jul 18;321(5887):342; author reply 342
references: 18635779
references: Proc Natl Acad Sci U S A. 2010 May 11;107(19):8818-23
references: 20421470
references: ISME J. 2011 Jun;5(6):945-61
references: 21209665
references: Nat Rev Microbiol. 2008 Mar;6(3):245-52
references: 18274537
references: PLoS Biol. 2006 Apr;4(4):e95
references: 16533068
references: Environ Microbiol. 2005 Mar;7(3):337-47
references: 15683394
references: Environ Microbiol. 2007 May;9(5):1162-75
references: 17472632
references: Mol Ecol. 2000 Jul;9(7):935-48
references: 10886656
references: ISME J. 2009 Feb;3(2):147-58
references: 18818711
references: Nature. 2008 Dec 11;456(7223):788-91
references: 19037244
references: Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6442-7
references: 16614070
references: Nature. 2005 Sep 22;437(7058):543-6
references: 16177789
references: Nature. 2001 Jan 25;409(6819):507-10
references: 11206545
references: Environ Microbiol. 2008 Nov;10(11):2966-78
references: 18707610
references: Appl Environ Microbiol. 1997 Dec;63(12):4704-12
references: 9406389
references: Appl Environ Microbiol. 2005 May;71(5):2303-9
references: 15870315
references: ISME J. 2007 Dec;1(8):743-55
references: 18059497
references: Appl Environ Microbiol. 2010 Nov;76(22):7575-87
references: 20870784
references: Bioinformatics. 2003 Aug 12;19(12):1572-4
references: 12912839
references: Microb Biotechnol. 2010 Sep;3(5):595-606
references: 21255356
references: Environ Microbiol. 2010 Jul;12(7):1989-2006
references: 20345944
references: Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12317-22
references: 16894176
references: FEMS Microbiol Ecol. 2000 Mar 1;31(3):231-239
references: 10719204
references: FEMS Microbiol Ecol. 2010 Jun;72(3):370-85
references: 20402778
references: Appl Environ Microbiol. 2009 Aug;75(16):5345-55
references: 19542347
references: Environ Microbiol. 2008 Oct;10(10):2527-36
references: 18557770
references: Appl Environ Microbiol. 2000 Dec;66(12):5368-82
references: 11097916
references: J Appl Microbiol. 2009 May;106(5):1482-93
references: 19187134
references: Appl Environ Microbiol. 2004 Feb;70(2):781-9
references: 14766555
references: Appl Environ Microbiol. 1997 Sep;63(9):3367-73
references: 9292986
references: Environ Microbiol. 2009 Apr;11(4):971-80
references: 19077007
references: Appl Environ Microbiol. 2000 May;66(5):1777-87
references: 10788339
references: Science. 2007 Dec 14;318(5857):1782-6
references: 18079405
references: Environ Microbiol. 2010 May;12(5):1282-92
references: 20192962
references: Appl Environ Microbiol. 2007 Sep;73(17):5642-7
references: 17586663