Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction.
dsrAB
dissimilatory sulfite reductase
metagenomics
sulfate reduction
sulfur cycle
sulfur oxidation
Journal
FEMS microbiology reviews
ISSN: 1574-6976
Titre abrégé: FEMS Microbiol Rev
Pays: England
ID NLM: 8902526
Informations de publication
Date de publication:
05 09 2023
05 09 2023
Historique:
received:
28
06
2023
revised:
01
10
2023
accepted:
03
10
2023
medline:
26
10
2023
pubmed:
5
10
2023
entrez:
5
10
2023
Statut:
ppublish
Résumé
Sulfate/sulfite-reducing microorganisms (SRM) are ubiquitous in nature, driving the global sulfur cycle. A hallmark of SRM is the dissimilatory sulfite reductase encoded by the genes dsrAB. Based on analysis of 950 mainly metagenome-derived dsrAB-carrying genomes, we redefine the global diversity of microorganisms with the potential for dissimilatory sulfate/sulfite reduction and uncover genetic repertoires that challenge earlier generalizations regarding their mode of energy metabolism. We show: (i) 19 out of 23 bacterial and 2 out of 4 archaeal phyla harbor uncharacterized SRM, (ii) four phyla including the Desulfobacterota harbor microorganisms with the genetic potential to switch between sulfate/sulfite reduction and sulfur oxidation, and (iii) the combination as well as presence/absence of different dsrAB-types, dsrL-types and dsrD provides guidance on the inferred direction of dissimilatory sulfur metabolism. We further provide an updated dsrAB database including > 60% taxonomically resolved, uncultured family-level lineages and recommendations on existing dsrAB-targeted primers for environmental surveys. Our work summarizes insights into the inferred ecophysiology of newly discovered SRM, puts SRM diversity into context of the major recent changes in bacterial and archaeal taxonomy, and provides an up-to-date framework to study SRM in a global context.
Identifiants
pubmed: 37796897
pii: 7291922
doi: 10.1093/femsre/fuad058
pmc: PMC10591310
pii:
doi:
Substances chimiques
Sulfates
0
Sulfites
0
Sulfur
70FD1KFU70
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Austrian Science Fund FWF
ID : P 31996-B
Pays : Austria
Informations de copyright
© The Author(s) 2023. Published by Oxford University Press on behalf of FEMS.
Références
Nat Commun. 2018 Apr 30;9(1):1729
pubmed: 29712903
mBio. 2016 May 03;7(3):
pubmed: 27143384
Anaerobe. 2008 Jun;14(3):145-56
pubmed: 18457966
Environ Microbiol Rep. 2017 Aug;9(4):323-344
pubmed: 28419734
Nat Microbiol. 2021 Jul;6(7):946-959
pubmed: 34155373
Environ Microbiol. 2018 Feb;20(2):862-877
pubmed: 29322618
Appl Environ Microbiol. 2018 Feb 14;84(5):
pubmed: 29247059
mSystems. 2020 Jan 7;5(1):
pubmed: 31911466
ISME J. 2015 May;9(5):1152-65
pubmed: 25343514
Nature. 2001 Mar 1;410(6824):77-81
pubmed: 11242044
Environ Microbiol Rep. 2016 Jun;8(3):413-23
pubmed: 27085098
Environ Microbiol. 2016 Jan;18(1):159-73
pubmed: 26033198
Environ Microbiol. 2019 Jan;21(1):209-225
pubmed: 30307104
Environ Microbiol. 2014 Jan;16(1):304-17
pubmed: 23809230
Front Microbiol. 2019 Jan 09;9:3159
pubmed: 30687241
PeerJ. 2017 Apr 6;5:e3134
pubmed: 28396823
Nat Commun. 2023 Oct 10;14(1):6337
pubmed: 37816749
BMC Genomics. 2018 Jul 31;19(1):561
pubmed: 30064352
Microbiome. 2022 Feb 16;10(1):33
pubmed: 35172890
Nature. 2000 Oct 5;407(6804):623-6
pubmed: 11034209
Nat Biotechnol. 2018 Nov;36(10):996-1004
pubmed: 30148503
Environ Microbiol. 2016 Sep;18(9):2994-3009
pubmed: 26625892
ISME J. 2019 Aug;13(8):2044-2057
pubmed: 30962514
Nature. 2012 Nov 8;491(7423):218-21
pubmed: 23103872
Dig Dis Sci. 2017 Sep;62(9):2241-2257
pubmed: 28766244
Nat Commun. 2020 Apr 20;11(1):1878
pubmed: 32313021
FEMS Microbiol Ecol. 2006 Feb;55(2):186-94
pubmed: 16420627
Int J Syst Evol Microbiol. 2020 Nov;70(11):5972-6016
pubmed: 33151140
Environ Microbiol. 2020 Feb;22(2):783-795
pubmed: 31854015
FEMS Microbiol Ecol. 2002 Apr 1;40(1):47-54
pubmed: 19709210
Environ Microbiol. 2009 Feb;11(2):289-99
pubmed: 18826437
Science. 2015 Dec 18;350(6267):1541-5
pubmed: 26680199
Appl Environ Microbiol. 2007 Aug;73(16):5218-26
pubmed: 17575000
Front Microbiol. 2017 Feb 20;8:222
pubmed: 28265263
Nat Microbiol. 2018 Mar;3(3):328-336
pubmed: 29379208
Nature. 2014 Sep 25;513(7519):530-3
pubmed: 25209667
Nat Microbiol. 2017 Nov;2(11):1533-1542
pubmed: 28894102
FEMS Microbiol Lett. 2006 Aug;261(2):194-202
pubmed: 16907720
Nat Commun. 2020 Dec 15;11(1):6389
pubmed: 33319778
Annu Rev Microbiol. 2009;63:311-34
pubmed: 19575572
Appl Environ Microbiol. 2015 Sep 1;81(17):6003-11
pubmed: 26116678
Nat Microbiol. 2019 Apr;4(4):614-622
pubmed: 30833730
Nat Microbiol. 2019 Apr;4(4):595-602
pubmed: 30833728
Environ Microbiol. 2019 Jan;21(1):360-373
pubmed: 30394641
Water Res. 2019 Mar 1;150:162-181
pubmed: 30508713
ISME J. 2018 Aug;12(8):2096-2099
pubmed: 29805176
Int J Syst Evol Microbiol. 2021 Oct;71(10):
pubmed: 34694987
J Bacteriol. 1998 Jun;180(11):2975-82
pubmed: 9603890
Anaerobe. 2005 Dec;11(6):339-49
pubmed: 16701597
Syst Appl Microbiol. 2023 Jan;46(1):126388
pubmed: 36493506
Nat Rev Microbiol. 2008 Jun;6(6):441-54
pubmed: 18461075
FEMS Microbiol Rev. 2000 Dec;24(5):691-710
pubmed: 11077159
Environ Microbiol. 2009 May;11(5):1278-91
pubmed: 19220398
Science. 2018 Jan 5;359(6371):
pubmed: 29301986
Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):
pubmed: 35064091
Nat Commun. 2016 Oct 24;7:13219
pubmed: 27774985
Annu Rev Microbiol. 2000;54:827-48
pubmed: 11018146
Nat Biotechnol. 2020 Sep;38(9):1079-1086
pubmed: 32341564
Proc Natl Acad Sci U S A. 2013 Aug 13;110(33):13582-7
pubmed: 23898195
Environ Microbiol. 2017 Dec;19(12):4965-4977
pubmed: 29105249
ISME J. 2017 Oct;11(10):2319-2333
pubmed: 28644444
ISME J. 2021 Oct;15(10):3005-3018
pubmed: 33953361
Front Microbiol. 2012 Feb 28;3:72
pubmed: 22403575
Annu Rev Biochem. 2021 Jun 20;90:817-846
pubmed: 33823652
Nat Commun. 2017 Oct 6;8(1):789
pubmed: 28986518
ISME J. 2022 Jan;16(1):307-320
pubmed: 34331018
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
Int J Syst Evol Microbiol. 2014 Jul;64(Pt 7):2346-2352
pubmed: 24744017
Environ Microbiol Rep. 2016 Dec;8(6):1003-1015
pubmed: 27701830
Genome Res. 2015 Jul;25(7):1043-55
pubmed: 25977477
Environ Microbiol. 2017 Feb;19(2):459-474
pubmed: 27112493
ISME J. 2021 Nov;15(11):3159-3180
pubmed: 33981000
Adv Microb Physiol. 2015;66:55-321
pubmed: 26210106
Front Microbiol. 2011 Apr 19;2:69
pubmed: 21747791
Nucleic Acids Res. 2019 May 21;47(9):4442-4448
pubmed: 31081040
Glob Chang Biol. 2016 Apr;22(4):1481-9
pubmed: 26666217
Int J Syst Evol Microbiol. 2009 Jun;59(Pt 6):1405-15
pubmed: 19502325
Microorganisms. 2015 Nov 12;3(4):866-89
pubmed: 27682122
FEMS Microbiol Ecol. 2018 Apr 1;94(4):
pubmed: 29528404
Proc Natl Acad Sci U S A. 2019 Sep 17;116(38):19116-19125
pubmed: 31427514
Nature. 2018 Aug;560(7716):49-54
pubmed: 30013118
Microb Genom. 2021 Jul;7(7):
pubmed: 34241589
PLoS One. 2012;7(7):e40785
pubmed: 22815818
ISME J. 2020 May;14(5):1233-1246
pubmed: 32042102
J Bacteriol. 2005 Mar;187(6):2203-8
pubmed: 15743970
Microbiome. 2022 Apr 19;10(1):64
pubmed: 35440042
Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):13278-83
pubmed: 26446670
Environ Microbiol. 2021 Jun;23(6):2834-2857
pubmed: 33000514
mBio. 2017 Jul 18;8(4):
pubmed: 28720728
ISME J. 2019 Jun;13(6):1546-1559
pubmed: 30783213
Science. 2008 Aug 15;321(5891):926-9
pubmed: 18703733
ISME J. 2018 Jun;12(7):1715-1728
pubmed: 29467397
Front Microbiol. 2019 Feb 13;10:247
pubmed: 30814991
PLoS One. 2015 Apr 02;10(4):e0123455
pubmed: 25837676
Science. 2010 Dec 3;330(6009):1375-8
pubmed: 21071631
Science. 2011 Sep 2;333(6047):1296-300
pubmed: 21885783
ISME J. 2018 Jun;12(7):1729-1742
pubmed: 29476143
Front Microbiol. 2012 Apr 23;3:137
pubmed: 22536198
ISME J. 2021 Sep;15(9):2779-2791
pubmed: 33790426
Front Microbiol. 2019 Apr 24;10:849
pubmed: 31105660
Mol Ecol Resour. 2022 Oct;22(7):2758-2774
pubmed: 35579058
J Bacteriol. 2001 Oct;183(20):6028-35
pubmed: 11567003