title: Genomic properties of Marine Group A bacteria indicate a role in the marine sulfur cycle.
abstract: Marine Group A (MGA) is a deeply branching and uncultivated phylum of bacteria. Although their functional roles remain elusive, MGA subgroups are particularly abundant and diverse in oxygen minimum zones and permanent or seasonally stratified anoxic basins, suggesting metabolic adaptation to oxygen-deficiency. Here, we expand a previous survey of MGA diversity in O2-deficient waters of the Northeast subarctic Pacific Ocean (NESAP) to include Saanich Inlet (SI), an anoxic fjord with seasonal O2 gradients and periodic sulfide accumulation. Phylogenetic analysis of small subunit ribosomal RNA (16S rRNA) gene clone libraries recovered five previously described MGA subgroups and defined three novel subgroups (SHBH1141, SHBH391, and SHAN400) in SI. To discern the functional properties of MGA residing along gradients of O2 in the NESAP and SI, we identified and sequenced to completion 14 fosmids harboring MGA-associated 16S RNA genes from a collection of 46 fosmid libraries sourced from NESAP and SI waters. Comparative analysis of these fosmids, in addition to four publicly available MGA-associated large-insert DNA fragments from Hawaii Ocean Time-series and Monterey Bay, revealed widespread genomic differentiation proximal to the ribosomal RNA operon that did not consistently reflect subgroup partitioning patterns observed in 16S rRNA gene clone libraries. Predicted protein-coding genes associated with adaptation to O2-deficiency and sulfur-based energy metabolism were detected on multiple fosmids, including polysulfide reductase (psrABC), implicated in dissimilatory polysulfide reduction to hydrogen sulfide and dissimilatory sulfur oxidation. These results posit a potential role for specific MGA subgroups in the marine sulfur cycle.
authors.affiliation: Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Jody J
authors.initials: JJ
authors.lastname: Wright
authors.affiliation: Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Keith
authors.initials: K
authors.lastname: Mewis
authors.affiliation: Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Niels W
authors.initials: NW
authors.lastname: Hanson
authors.affiliation: Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Kishori M
authors.initials: KM
authors.lastname: Konwar
authors.affiliation: Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Kendra R
authors.initials: KR
authors.lastname: Maas
authors.affiliation: 1] Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada [2] Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Hallam
mesh_terms: D059001:Aquatic Organisms / Q000145:classification / Q000235:genetics / Q000378:metabolism; D001419:Bacteria / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D044822:Biodiversity; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics; D008969:Molecular Sequence Data; D010100:Oxygen / Q000032:analysis; D010140:Pacific Ocean; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012623:Seawater / Q000737:chemistry
chemical_list: D012336:RNA, Ribosomal, 16S; D010100:Oxygen
references.citation: Science. 2009 Oct 23;326(5952):578-82
references.pmid: 19900896
references.citation: Front Microbiol. 2011 May 24;2:116
references.pmid: 21833341
references.citation: BMC Bioinformatics. 2004 Oct 26;5:163
references.pmid: 15507136
references.citation: Appl Environ Microbiol. 1993 May;59(5):1294-302
references.pmid: 7685997
references.citation: Nucleic Acids Res. 2001 Jan 1;29(1):22-8
references.pmid: 11125040
references.citation: BMC Bioinformatics. 2010 Mar 08;11:119
references.pmid: 20211023
references.citation: Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):506-10
references.pmid: 22203982
references.citation: Int J Syst Evol Microbiol. 2010 Sep;60(Pt 9):2120-2123
references.pmid: 19854873
references.citation: Environ Microbiol. 2009 Aug;11(8):2078-93
references.pmid: 19453607
references.citation: J Bacteriol. 2000 Dec;182(24):6964-74
references.pmid: 11092857
references.citation: Appl Environ Microbiol. 1996 Apr;62(4):1171-7
references.pmid: 8919778
references.citation: Environ Microbiol. 2008 May;10(5):1244-59
references.pmid: 18294206
references.citation: ISME J. 2013 Feb;7(2):256-68
references.pmid: 23151638
references.citation: Proc Natl Acad Sci U S A. 2006 Nov 28;103(48):18296-301
references.pmid: 17114289
references.citation: Genome Biol. 2004;5(2):R12
references.pmid: 14759262
references.citation: Nat Rev Microbiol. 2012 May 14;10(6):381-94
references.pmid: 22580367
references.citation: Nature. 2012 Nov 22;491(7425):541-6
references.pmid: 23135396
references.citation: Appl Environ Microbiol. 2006 Jul;72(7):5069-72
references.pmid: 16820507
references.citation: BMC Bioinformatics. 2005 Jul 02;6:167
references.pmid: 15992409
references.citation: Science. 2006 Jan 27;311(5760):496-503
references.pmid: 16439655
references.citation: Nucleic Acids Res. 2001 Jan 1;29(1):137-40
references.pmid: 11125071
references.citation: Int J Syst Evol Microbiol. 2003 Jan;53(Pt 1):323-329
references.pmid: 12656191
references.citation: J Vis Exp. 2009 Jun 17;(28):
references.pmid: 19536065
references.citation: J Vis Exp. 2009 Sep 18;(31):
references.pmid: 19767717
references.citation: BMC Bioinformatics. 2005 Jan 05;6:2
references.pmid: 15634352
references.citation: Mol Microbiol. 2002 Apr;44(2):479-88
references.pmid: 11972784
references.citation: Eur J Biochem. 1995 Jun 1;230(2):601-6
references.pmid: 7607234
references.citation: Nat Struct Biol. 1996 Jun;3(6):539-46
references.pmid: 8646540
references.citation: J Vis Exp. 2009 Jun 18;(28):
references.pmid: 19543200
references.citation: Appl Environ Microbiol. 2001 Apr;67(4):1663-74
references.pmid: 11282619
references.citation: Environ Microbiol. 2004 Sep;6(9):938-47
references.pmid: 15305919
references.citation: Genome Res. 2009 Sep;19(9):1639-45
references.pmid: 19541911
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):56-9
references.pmid: 10592180
references.citation: IUBMB Life. 2007 Feb;59(2):51-9
references.pmid: 17454295
references.citation: Environ Microbiol. 2011 Jan;13(1):116-134
references.pmid: 20695878
references.citation: Nat Struct Mol Biol. 2008 Jul;15(7):730-7
references.pmid: 18536726
references.citation: PLoS One. 2009;4(4):e5299
references.pmid: 19390573
references.citation: IUBMB Life. 2008 May;60(5):287-300
references.pmid: 18421771
references.citation: BMC Bioinformatics. 2013 Jun 21;14:202
references.pmid: 23800136
references.citation: Nucleic Acids Res. 1999 Jan 1;27(1):29-34
references.pmid: 9847135
references.citation: Science. 2008 May 2;320(5876):655-8
references.pmid: 18451300
references.citation: Microb Ecol. 2004 Nov;48(4):473-88
references.pmid: 15696381
references.citation: Appl Environ Microbiol. 2002 Feb;68(2):505-18
references.pmid: 11823184
references.citation: J Biol Chem. 2001 Dec 28;276(52):48915-20
references.pmid: 11677230
references.citation: Nature. 2004 Jul 29;430(6999):551-4
references.pmid: 15282603
references.citation: Curr Opin Microbiol. 2012 Oct;15(5):613-20
references.pmid: 23026140
references.citation: Environ Microbiol. 2010 Jan;12(1):172-91
references.pmid: 19788414
references.citation: Int J Syst Evol Microbiol. 2004 Jan;54(Pt 1):33-39
references.pmid: 14742456
references.citation: Ann Rev Mar Sci. 2010;2:199-229
references.pmid: 21141663
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W394-9
references.pmid: 16845035
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W557-9
references.pmid: 15980534
references.citation: Science. 2010 Dec 3;330(6009):1375-8
references.pmid: 21071631
references.citation: Eur J Biochem. 1992 Jun 1;206(2):503-10
references.pmid: 1597189
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
references.pmid: 15034147
references.citation: Science. 2011 Sep 2;333(6047):1296-300
references.pmid: 21885783