A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
20 09 2023
20 09 2023
Historique:
received:
16
02
2023
accepted:
09
08
2023
medline:
22
9
2023
pubmed:
21
9
2023
entrez:
20
9
2023
Statut:
epublish
Résumé
Viruses are abundant, ubiquitous members of soil communities that kill microbial cells, but how they respond to perturbation of soil ecosystems is essentially unknown. Here, we investigate lineage-specific virus-host dynamics in grassland soil following "wet-up", when resident microbes are both resuscitated and lysed after a prolonged dry period. Quantitative isotope tracing, time-resolved metagenomics and viromic analyses indicate that dry soil holds a diverse but low biomass reservoir of virions, of which only a subset thrives following wet-up. Viral richness decreases by 50% within 24 h post wet-up, while viral biomass increases four-fold within one week. Though recent hypotheses suggest lysogeny predominates in soil, our evidence indicates that viruses in lytic cycles dominate the response to wet-up. We estimate that viruses drive a measurable and continuous rate of cell lysis, with up to 46% of microbial death driven by viral lysis one week following wet-up. Thus, viruses contribute to turnover of soil microbial biomass and the widely reported CO
Identifiants
pubmed: 37730729
doi: 10.1038/s41467-023-40835-4
pii: 10.1038/s41467-023-40835-4
pmc: PMC10511743
doi:
Substances chimiques
Soil
0
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
Pagination
5835Informations de copyright
© 2023. Springer Nature Limited.
Références
ISME J. 2022 Apr;16(4):972-982
pubmed: 34743175
Proc Natl Acad Sci U S A. 2012 Jul 3;109(27):10931-6
pubmed: 22715291
Quant Biol. 2020 Mar;8(1):64-77
pubmed: 34084563
Front Microbiol. 2020 May 25;11:925
pubmed: 32528430
Nat Rev Microbiol. 2014 Jul;12(7):519-28
pubmed: 24931044
Nat Microbiol. 2018 Aug;3(8):870-880
pubmed: 30013236
Environ Microbiol. 2016 May;18(5):1403-14
pubmed: 26271760
FEMS Microbiol Ecol. 2011 Oct;78(1):17-30
pubmed: 21470255
ISME J. 2020 Jun;14(6):1520-1532
pubmed: 32203117
Microbiome. 2021 Jun 28;9(1):150
pubmed: 34183048
ISME J. 2015 Jun;9(6):1352-64
pubmed: 25635642
Nat Commun. 2016 Feb 03;7:10613
pubmed: 26837824
Appl Environ Microbiol. 2008 Jan;74(2):495-502
pubmed: 17993550
Appl Environ Microbiol. 2019 Jul 1;85(14):
pubmed: 31076430
Nat Commun. 2016 Apr 13;7:11257
pubmed: 27071849
Ecology. 2014 May;95(5):1162-72
pubmed: 25000748
Environ Microbiol. 2013 May;15(5):1428-40
pubmed: 22845467
Nature. 2016 Mar 24;531(7595):466-70
pubmed: 26982729
Bioinformatics. 2007 May 15;23(10):1282-8
pubmed: 17379688
Science. 2015 May 22;348(6237):1261498
pubmed: 25999515
Commun Biol. 2021 Aug 26;4(1):992
pubmed: 34446837
Nucleic Acids Res. 2021 Mar 18;49(5):2655-2673
pubmed: 33590101
Microbiome. 2020 Jun 10;8(1):90
pubmed: 32522236
Viruses. 2016 Mar 01;8(3):66
pubmed: 26938550
Nat Microbiol. 2018 Jul;3(7):836-843
pubmed: 29807988
PeerJ. 2015 May 28;3:e985
pubmed: 26038737
mSphere. 2021 Oct 27;6(5):e0008521
pubmed: 34468166
Bioinformatics. 2015 May 15;31(10):1674-6
pubmed: 25609793
Nat Rev Microbiol. 2022 Jul;20(7):415-430
pubmed: 35228712
BMC Bioinformatics. 2007 Jun 18;8:209
pubmed: 17577412
Environ Microbiol. 2016 Jun;18(6):2064-77
pubmed: 26914534
Nat Rev Microbiol. 2011 Feb;9(2):119-30
pubmed: 21233850
mBio. 2017 Sep 19;8(5):
pubmed: 28928211
Nat Rev Microbiol. 2021 Aug;19(8):501-513
pubmed: 33762712
ISME J. 2020 Jan;14(1):202-216
pubmed: 31611655
Microb Ecol. 1994 Sep;28(2):237-43
pubmed: 24186450
Nat Methods. 2014 Nov;11(11):1144-6
pubmed: 25218180
ISME J. 2017 Dec;11(12):2864-2868
pubmed: 28742071
Nat Commun. 2019 Jun 24;10(1):2770
pubmed: 31235780
Nucleic Acids Res. 2020 Sep 18;48(16):8883-8900
pubmed: 32766782
ISME J. 2014 Apr;8(4):816-29
pubmed: 24196323
ISME J. 2015 Mar 17;9(4):946-57
pubmed: 25314319
ISME Commun. 2022 Oct 13;2(1):100
pubmed: 37938790
mBio. 2017 Nov 28;8(6):
pubmed: 29184020
PeerJ. 2019 May 09;7:e6902
pubmed: 31119088
Appl Environ Microbiol. 2009 Nov;75(22):7142-52
pubmed: 19783745
Nat Methods. 2020 Mar;17(3):261-272
pubmed: 32015543
Bioinformatics. 2010 Oct 1;26(19):2460-1
pubmed: 20709691
ISME J. 2015 Nov;9(11):2386-99
pubmed: 25848873
Nat Microbiol. 2019 Nov;4(11):1895-1906
pubmed: 31332386
Appl Microbiol Biotechnol. 2014 Apr;98(7):2841-51
pubmed: 24442504
Nat Microbiol. 2020 Feb;5(2):265-271
pubmed: 31819214
Microb Ecol. 2008 Oct;56(3):437-47
pubmed: 18322729
Nature. 2017 Sep 20;549(7672):E1-E3
pubmed: 28933438
Nucleic Acids Res. 2020 Dec 2;48(21):e121
pubmed: 33045744
Microbiol Mol Biol Rev. 2013 Sep;77(3):342-56
pubmed: 24006468
mSystems. 2019 May 28;4(3):
pubmed: 31138723
Nat Rev Microbiol. 2020 Jan;18(1):35-46
pubmed: 31586158
Nat Microbiol. 2016 Dec 19;2:16242
pubmed: 27991881
ISME J. 2017 Jul;11(7):1511-1520
pubmed: 28291233
Microorganisms. 2013 Dec 24;2(1):1-10
pubmed: 27694773
Appl Environ Microbiol. 2000 Apr;66(4):1328-33
pubmed: 10742207
Nature. 2016 Aug 25;536(7617):425-30
pubmed: 27533034
New Microbiol. 2006 Apr;29(2):111-9
pubmed: 16841551
Nature. 2016 Sep 29;537(7622):689-693
pubmed: 27654921
Proc Natl Acad Sci U S A. 2022 Nov 08;119(45):e2209132119
pubmed: 36322723
mSystems. 2022 Dec 20;7(6):e0041722
pubmed: 36300946
Appl Environ Microbiol. 2015 Nov;81(21):7570-81
pubmed: 26296731
Nucleic Acids Res. 1999 Jan 1;27(1):29-34
pubmed: 9847135
Microbiome. 2022 Nov 25;10(1):199
pubmed: 36434737
Microbiome. 2021 Feb 1;9(1):37
pubmed: 33522966
Microbiome. 2014 Aug 01;2:26
pubmed: 25136443
mSystems. 2019 May 14;4(4):
pubmed: 31098394
Database (Oxford). 2011 Mar 29;2011:bar009
pubmed: 21447597
Nature. 2020 Feb;578(7795):425-431
pubmed: 32051592
Appl Environ Microbiol. 2007 May;73(10):3189-95
pubmed: 17369331
Front Microbiol. 2021 May 25;12:670799
pubmed: 34113331
Trends Microbiol. 2018 Aug;26(8):649-662
pubmed: 29306554
BMC Bioinformatics. 2010 Mar 08;11:119
pubmed: 20211023
Environ Microbiol Rep. 2011 Apr;3(2):195-202
pubmed: 21572525
ISME Commun. 2022 Mar 16;2(1):24
pubmed: 37938672
Soil Biol Biochem. 2016 Oct;101:1-5
pubmed: 27698513
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Nature. 2005 Sep 15;437(7057):356-61
pubmed: 16163346
mBio. 2021 Dec 21;12(6):e0259521
pubmed: 34724822
Appl Environ Microbiol. 2005 Jun;71(6):3119-25
pubmed: 15933010
ISME J. 2016 Feb;10(2):437-49
pubmed: 26296067
Bioinformatics. 2019 Nov 15;:
pubmed: 31730192
Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45
pubmed: 26553804
Genome Biol. 2013 Nov 07;14(11):R123
pubmed: 24200126
Annu Rev Virol. 2017 Sep 29;4(1):201-219
pubmed: 28961409
ISME J. 2013 Nov;7(11):2229-41
pubmed: 23823489
PeerJ. 2016 May 17;4:e1999
pubmed: 27231649
mSystems. 2021 Aug 31;6(4):e0120520
pubmed: 34402646
mSystems. 2022 Apr 26;7(2):e0008422
pubmed: 35323045
mBio. 2015 Aug 04;6(4):e00746
pubmed: 26242625
Appl Environ Microbiol. 2007 Apr;73(8):2541-6
pubmed: 17322324
Microbiome. 2018 Sep 15;6(1):158
pubmed: 30219103
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Appl Environ Microbiol. 2013 May;79(10):3294-302
pubmed: 23524666
Environ Microbiol. 2007 Oct;9(10):2563-74
pubmed: 17803780
Sci Rep. 2017 Mar 22;7:45142
pubmed: 28327667
Proc Natl Acad Sci U S A. 2018 Sep 25;115(39):9791-9796
pubmed: 30209211
PeerJ. 2015 Aug 27;3:e1165
pubmed: 26336640
ISME J. 2022 Jan;16(1):296-306
pubmed: 34321619
Proc Natl Acad Sci U S A. 2014 May 20;111(20):7486-91
pubmed: 24799689