A systematic analysis of marine lysogens and proviruses.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
27 09 2023
27 09 2023
Historique:
received:
21
07
2023
accepted:
13
09
2023
medline:
4
10
2023
pubmed:
28
9
2023
entrez:
27
9
2023
Statut:
epublish
Résumé
Viruses are ubiquitous in the oceans, exhibiting high abundance and diversity. Here, we systematically analyze existing genomic sequences of marine prokaryotes to compile a Marine Prokaryotic Genome Dataset (MPGD, consisting of over 12,000 bacterial and archaeal genomes) and a Marine Temperate Viral Genome Dataset (MTVGD). At least 40% of the MPGD genomes contain one or more proviral sequences, indicating that they are lysogens. The MTVGD includes over 12,900 viral contigs or putative proviruses, clustered into 10,897 viral genera. We show that lysogens and proviruses are abundant in marine ecosystems, particularly in the deep sea, and marine lysogens differ from non-lysogens in multiple genomic features and growth properties. We reveal several virus-host interaction networks of potential ecological relevance, and identify proviruses that appear to be able to infect (or to be transferred between) different bacterial classes and phyla. Auxiliary metabolic genes in the MTVGD are enriched in functions related to carbohydrate metabolism. Finally, we experimentally demonstrate the impact of a prophage on the transcriptome of a representative marine Shewanella bacterium. Our work contributes to a better understanding of the ecology of marine prokaryotes and their viruses.
Identifiants
pubmed: 37758717
doi: 10.1038/s41467-023-41699-4
pii: 10.1038/s41467-023-41699-4
pmc: PMC10533544
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
6013Informations de copyright
© 2023. Springer Nature Limited.
Références
Sci Rep. 2015 Nov 04;5:16074
pubmed: 26530864
BMC Bioinformatics. 2007 Jun 18;8:209
pubmed: 17577412
PLoS One. 2010 Mar 10;5(3):e9490
pubmed: 20224823
Science. 2014 May 16;344(6185):757-60
pubmed: 24789974
Nat Microbiol. 2018 Aug;3(8):870-880
pubmed: 30013236
Bioinformatics. 2012 Dec 1;28(23):3150-2
pubmed: 23060610
ISME J. 2008 Nov;2(11):1112-21
pubmed: 18719614
Nat Biotechnol. 2019 Jan;37(1):29-37
pubmed: 30556814
Nucleic Acids Res. 2021 Jan 8;49(D1):D764-D775
pubmed: 33137183
Environ Microbiol Rep. 2016 Jun;8(3):358-62
pubmed: 26929122
Environ Microbiol. 2021 Jul;23(7):3743-3757
pubmed: 33511765
Science. 2015 May 22;348(6237):1261498
pubmed: 25999515
J Microbiol. 2014 Mar;52(3):235-42
pubmed: 24585054
Nat Biotechnol. 2010 May;28(5):511-5
pubmed: 20436464
ISME J. 2016 Dec;10(12):2787-2800
pubmed: 27482926
PLoS One. 2013;8(2):e57355
pubmed: 23468974
PeerJ. 2015 May 28;3:e985
pubmed: 26038737
Nucleic Acids Res. 2015 Aug 18;43(14):6761-71
pubmed: 26150420
Nat Microbiol. 2017 Oct;2(10):1367-1373
pubmed: 28808230
Nat Biotechnol. 2021 May;39(5):578-585
pubmed: 33349699
Nat Microbiol. 2023 May;8(5):946-957
pubmed: 37024618
Arch Biochem Biophys. 1992 Oct;298(1):226-30
pubmed: 1524431
ISME J. 2015 Mar 17;9(4):871-81
pubmed: 25303713
Nat Biotechnol. 2021 Apr;39(4):499-509
pubmed: 33169036
Environ Microbiol. 2019 Nov;21(11):4212-4232
pubmed: 31418995
FEMS Microbiol Ecol. 2016 Aug;92(8):
pubmed: 27222221
J Biol Chem. 2016 Mar 25;291(13):7183-94
pubmed: 26755730
Nucleic Acids Res. 2012 Sep;40(16):e126
pubmed: 22584627
Trends Microbiol. 2019 Jan;27(1):51-63
pubmed: 30181062
Sci Data. 2022 Jun 17;9(1):305
pubmed: 35715423
Nucleic Acids Res. 2020 Sep 18;48(16):8883-8900
pubmed: 32766782
Bioinformatics. 2018 Sep 1;34(17):i884-i890
pubmed: 30423086
ISME J. 2016 Nov;10(11):2744-2754
pubmed: 27015004
Nucleic Acids Res. 2021 Jan 8;49(D1):D437-D451
pubmed: 33211854
Viruses. 2021 Mar 18;13(3):
pubmed: 33803862
ISME J. 2018 Apr;12(4):1127-1141
pubmed: 29416123
mBio. 2017 Nov 28;8(6):
pubmed: 29184020
Proc Natl Acad Sci U S A. 2021 Mar 23;118(12):
pubmed: 33723043
Nat Methods. 2020 Mar;17(3):261-272
pubmed: 32015543
ISME J. 2021 Oct;15(10):3094-3110
pubmed: 33972725
ISME J. 2008 Jun;2(6):579-89
pubmed: 18521076
Nat Microbiol. 2019 Nov;4(11):1895-1906
pubmed: 31332386
Nature. 2002 Jan 31;415(6871):496
pubmed: 11823851
Nature. 2021 Aug;596(7873):583-589
pubmed: 34265844
ISME J. 2009 Oct;3(10):1164-79
pubmed: 19458652
ISME J. 2020 Apr;14(4):881-895
pubmed: 31896786
Viruses. 2020 Nov 06;12(11):
pubmed: 33172115
Nat Microbiol. 2021 Jul;6(7):960-970
pubmed: 34168315
Nucleic Acids Res. 2021 Jul 2;49(W1):W293-W296
pubmed: 33885785
Microbiome. 2021 Feb 14;9(1):43
pubmed: 33583433
Bioessays. 2017 Dec;39(12):
pubmed: 28983932
Virol J. 2015 Oct 09;12:164
pubmed: 26453042
Nat Rev Microbiol. 2008 Aug;6(8):592-603
pubmed: 18604222
Nucleic Acids Res. 2018 Jul 2;46(W1):W200-W204
pubmed: 29905871
Curr Opin Microbiol. 2003 Aug;6(4):417-24
pubmed: 12941415
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Nucleic Acids Res. 2021 Jan 8;49(D1):D545-D551
pubmed: 33125081
BMC Bioinformatics. 2011 Aug 04;12:323
pubmed: 21816040
ISME J. 2017 Jul;11(7):1511-1520
pubmed: 28291233
mSystems. 2020 Feb 18;5(1):
pubmed: 32071164
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
PLoS One. 2018 Sep 27;13(9):e0204703
pubmed: 30261037
Nature. 2016 Aug 25;536(7617):425-30
pubmed: 27533034
Front Microbiol. 2017 Jul 13;8:1313
pubmed: 28751882
Appl Environ Microbiol. 2013 Nov;79(22):7101-9
pubmed: 24038680
Nat Commun. 2021 Nov 4;12(1):6382
pubmed: 34737280
Nature. 2016 Sep 29;537(7622):689-693
pubmed: 27654921
Curr Opin Microbiol. 2016 Jun;31:161-168
pubmed: 27088500
FEMS Microbiol Rev. 2020 Mar 1;44(2):155-170
pubmed: 31922549
Environ Microbiol. 2020 Dec;22(12):4919-4933
pubmed: 32935433
FEMS Microbiol Rev. 2018 Sep 1;42(5):639-655
pubmed: 29790926
Bioinformatics. 2010 Jan 1;26(1):136-8
pubmed: 19855105
Front Microbiol. 2017 Jun 09;8:1018
pubmed: 28649233
Mol Microbiol. 2014 Oct;94(2):418-33
pubmed: 25171165
Cell. 2019 May 16;177(5):1109-1123.e14
pubmed: 31031001
Nat Microbiol. 2020 Aug;5(8):1011-1015
pubmed: 32424337
Microbiome. 2021 Feb 1;9(1):37
pubmed: 33522966
Nat Rev Microbiol. 2015 Oct;13(10):641-50
pubmed: 26373372
Nature. 2013 Feb 21;494(7437):357-60
pubmed: 23407494
Stand Genomic Sci. 2016 Feb 24;11:17
pubmed: 26918089
ISME J. 2013 Feb;7(2):233-6
pubmed: 23038175
Virol J. 2019 Feb 1;16(1):15
pubmed: 30709355
Int J Syst Evol Microbiol. 2007 Jan;57(Pt 1):60-65
pubmed: 17220442
Curr Opin Microbiol. 2017 Aug;38:66-73
pubmed: 28527384
J Mol Biol. 2016 Feb 22;428(4):726-731
pubmed: 26585406
Genome Res. 2015 Jul;25(7):1043-55
pubmed: 25977477
PLoS Comput Biol. 2018 Jan 26;14(1):e1005944
pubmed: 29373581
Nat Methods. 2015 Jan;12(1):59-60
pubmed: 25402007
Nat Methods. 2015 Apr;12(4):357-60
pubmed: 25751142
J Mol Biol. 2004 Jan 16;335(3):667-78
pubmed: 14687564
J Econ Entomol. 1946 Apr;39:269
pubmed: 20983181
PLoS One. 2011 Feb 24;6(2):e16900
pubmed: 21383980
Patterns (N Y). 2021 Jun 15;2(7):100274
pubmed: 34286299
Nature. 2020 Feb;578(7795):425-431
pubmed: 32051592
Nucleic Acids Res. 2021 Dec 16;49(22):e128
pubmed: 34551431
BMC Bioinformatics. 2010 Mar 08;11:119
pubmed: 20211023
Proc Natl Acad Sci U S A. 2020 Nov 3;117(44):27587-27597
pubmed: 33077589
Nat Commun. 2010;1:147
pubmed: 21266997
Nucleic Acids Res. 2021 Sep 20;49(16):9077-9096
pubmed: 34417604
mBio. 2016 Jul 26;7(4):
pubmed: 27460793
Nature. 2003 Aug 14;424(6950):741
pubmed: 12917674
Nucleic Acids Res. 2017 Jan 9;45(1):39-53
pubmed: 27899557
Bioinformatics. 2019 Nov 15;:
pubmed: 31730192
Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45
pubmed: 26553804
Curr Biol. 2007 May 15;17(10):881-6
pubmed: 17493812
Elife. 2015 Jul 22;4:
pubmed: 26200428
mBio. 2018 Sep 18;9(5):
pubmed: 30228235
iScience. 2021 Feb 18;24(3):102204
pubmed: 33786421
BMC Bioinformatics. 2010 Oct 30;11:538
pubmed: 21034504
Ann Rev Mar Sci. 2016;8:285-309
pubmed: 26195108
Nat Biotechnol. 2019 Jun;37(6):632-639
pubmed: 31061483
Mol Microbiol. 2019 Feb;111(2):495-513
pubmed: 30475408
Sci Rep. 2016 Apr 01;6:23473
pubmed: 27032335
Nucleic Acids Res. 2021 Jan 8;49(D1):D92-D96
pubmed: 33196830
Trends Microbiol. 2016 Oct;24(10):821-832
pubmed: 27395772
ISME J. 2020 Oct;14(10):2527-2541
pubmed: 32661357