title: Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction.
abstract: Marine and estuary sediments contain a variety of uncultured archaea whose metabolic and ecological roles are unknown. De novo assembly and binning of high-throughput metagenomic sequences from the sulfate-methane transition zone in estuary sediments resulted in the reconstruction of three partial to near-complete (2.4-3.9 Mb) genomes belonging to a previously unrecognized archaeal group. Phylogenetic analyses of ribosomal RNA genes and ribosomal proteins revealed that this group is distinct from any previously characterized archaea. For this group, found in the White Oak River estuary, and previously registered in sedimentary samples, we propose the name 'Thorarchaeota'. The Thorarchaeota appear to be capable of acetate production from the degradation of proteins. Interestingly, they also have elemental sulfur and thiosulfate reduction genes suggesting they have an important role in intermediate sulfur cycling. The reconstruction of these genomes from a deeply branched, widespread group expands our understanding of sediment biogeochemistry and the evolutionary history of Archaea.
authors.affiliation: Department of Marine Science, University of Texas Austin, Marine Science Institute, Port Aransas, TX, USA.
authors.forename: Kiley W
authors.initials: KW
authors.lastname: Seitz
authors.affiliation: Department of Marine Sciences, University of North Carolina, Chapel Hill, NC, USA.|MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.|Department of Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Dornburger Straße 159, Jena, Germany.
authors.forename: Cassandre S
authors.initials: CS
authors.lastname: Lazar
authors.affiliation: MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
authors.forename: Kai-Uwe
authors.initials: KU
authors.lastname: Hinrichs
authors.affiliation: Department of Marine Sciences, University of North Carolina, Chapel Hill, NC, USA.
authors.forename: Andreas P
authors.initials: AP
authors.lastname: Teske
authors.affiliation: Department of Marine Science, University of Texas Austin, Marine Science Institute, Port Aransas, TX, USA.
authors.forename: Brett J
authors.initials: BJ
authors.lastname: Baker
mesh_terms: D001105:Archaea / Q000235:genetics*; D063366:Estuaries; D020745:Genome, Archaeal / Q000235:genetics*; D023281:Genomics; D019015:Geologic Sediments / Q000382:microbiology*; D008697:Methane / Q000378:metabolism*; D010802:Phylogeny; D045483:Rivers; D013455:Sulfur / Q000378:metabolism*
chemical_list: D013455:Sulfur; D008697:Methane
references.citation: PeerJ. 2014 Jan 09;2:e243
references.pmid: 24482762
references.citation: Nucleic Acids Res. 2004 Feb 25;32(4):1363-71
references.pmid: 14985472
references.citation: ISME J. 2014 Jul;8(7):1452-63
references.pmid: 24621521
references.citation: Nature. 2015 May 14;521(7551):173-9
references.pmid: 25945739
references.citation: J Bacteriol. 2012 Jan;194(2):475-85
references.pmid: 22081391
references.citation: Front Microbiol. 2012 Jan 13;2:284
references.pmid: 22347874
references.citation: Nature. 2013 Apr 11;496(7444):215-8
references.pmid: 23535597
references.citation: Environ Microbiol. 2015 Jul;17(7):2228-38
references.pmid: 25331558
references.citation: Microbiology. 2004 Nov;150(Pt 11):3527-46
references.pmid: 15528644
references.citation: Genome Biol. 2009;10(8):R85
references.pmid: 19698104
references.citation: Bioinformatics. 2012 Jun 1;28(11):1420-8
references.pmid: 22495754
references.citation: ISME J. 2012 Oct;6(10):1949-65
references.pmid: 22551871
references.citation: Genome Biol. 2007;8(1):R10
references.pmid: 17224063
references.citation: J Bacteriol. 1995 May;177(10):2813-20
references.pmid: 7751291
references.citation: Science. 1990 Jul 13;249(4965):152-4
references.pmid: 17836966
references.citation: Ann Rev Mar Sci. 2011;3:123-45
references.pmid: 21329201
references.citation: Proc Natl Acad Sci U S A. 2010 May 11;107(19):8806-11
references.pmid: 20421484
references.citation: Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
references.pmid: 15034147
references.citation: Appl Environ Microbiol. 1982 Dec;44(6):1270-6
references.pmid: 16346144
references.citation: Microbiol Mol Biol Rev. 2014 Mar;78(1):89-175
references.pmid: 24600042
references.citation: Environ Microbiol. 2011 Sep;13(9):2548-64
references.pmid: 21806748
references.citation: Science. 2012 Sep 28;337(6102):1661-5
references.pmid: 23019650
references.citation: Nucleic Acids Res. 2014 Jan;42(Database issue):D490-5
references.pmid: 24270786
references.citation: ISME J. 2014 Jul;8(7):1534-43
references.pmid: 24553469
references.citation: Trends Microbiol. 2011 Dec;19(12):580-7
references.pmid: 22018741
references.citation: Bioinformatics. 2014 May 1;30(9):1312-3
references.pmid: 24451623
references.citation: Proc Natl Acad Sci U S A. 1993 Jun 1;90(11):5341-4
references.pmid: 8389482
references.citation: Appl Environ Microbiol. 2012 Aug;78(16):5520-8
references.pmid: 22660713
references.citation: Microbiome. 2015 Apr 13;3:14
references.pmid: 25922666
references.citation: Front Microbiol. 2012 Jan 31;3:22
references.pmid: 22319520
references.citation: Curr Biol. 2015 Mar 16;25(6):690-701
references.pmid: 25702576
references.citation: Eur J Biochem. 1997 Mar 1;244(2):561-7
references.pmid: 9119024
references.citation: Proc Natl Acad Sci U S A. 2006 Mar 7;103(10):3846-51
references.pmid: 16505362
references.citation: Microbiome. 2013 Aug 05;1(1):22
references.pmid: 24450983
references.citation: Front Microbiol. 2013 Nov 08;4:327
references.pmid: 24265628
references.citation: Environ Sci Technol. 2008 Dec 15;42(24):9072-8
references.pmid: 19174873
references.citation: ISME J. 2014 Mar;8(3):650-9
references.pmid: 24108328
references.citation: Nat Commun. 2013;4:2120
references.pmid: 23979677
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D115-22
references.pmid: 22194640
references.citation: Mol Biol Evol. 2015 Jan;32(1):268-74
references.pmid: 25371430
references.citation: Nature. 2013 Jul 25;499(7459):431-7
references.pmid: 23851394
references.citation: Nature. 2013 Dec 5;504(7478):61-70
references.pmid: 24305149
references.citation: BMC Evol Biol. 2010 Jul 13;10:210
references.pmid: 20626897
references.citation: Biochim Biophys Acta. 2008 Dec;1784(12):1873-98
references.pmid: 18801467
references.citation: Genome Res. 2015 Jul;25(7):1043-55
references.pmid: 25977477
references.citation: Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7545-50
references.pmid: 12792025
references.citation: Environ Microbiol. 2011 Dec;13(12):3219-34
references.pmid: 21895908
references.citation: ISME J. 2013 Mar;7(3):555-67
references.pmid: 23096400
references.citation: Science. 2007 Nov 30;318(5855):1449-52
references.pmid: 17947550
references.citation: Genome Biol. 2011;12(5):R44
references.pmid: 21595876
references.citation: Microbiology. 2002 Nov;148(Pt 11):3631-8
references.pmid: 12427953