Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance.
antibiotic resistance
extrachromosomal DNA
groundwater
metal resistance
phage
plasmidome
viral genome
viral host
viral sequences
virus
Journal
mSystems
ISSN: 2379-5077
Titre abrégé: mSystems
Pays: United States
ID NLM: 101680636
Informations de publication
Date de publication:
29 Jun 2021
29 Jun 2021
Historique:
entrez:
29
6
2021
pubmed:
30
6
2021
medline:
30
6
2021
Statut:
aheadofprint
Résumé
Viruses are ubiquitous microbiome components, shaping ecosystems via strain-specific predation, horizontal gene transfer and redistribution of nutrients through host lysis. Viral impacts are important in groundwater ecosystems, where microbes drive many nutrient fluxes and metabolic processes; however, little is known about the diversity of viruses in these environments. We analyzed four groundwater plasmidomes (the entire plasmid content of an environment) and identified 200 viral sequences, which clustered into 41 genus-level viral clusters (approximately equivalent to viral genera) including 9 known and 32 putative new genera. We used publicly available bacterial whole-genome sequences (WGS) and WGS from 261 bacterial isolates from this groundwater environment to identify potential viral hosts. We linked 76 of the 200 viral sequences to a range of bacterial phyla, the majority associated with
Identifiants
pubmed: 34184913
doi: 10.1128/mSystems.00537-21
pmc: PMC8269241
doi:
Types de publication
Journal Article
Langues
eng
Pagination
e0053721Subventions
Organisme : NCI NIH HHS
ID : P30 CA014051
Pays : United States
Références
Nucleic Acids Res. 2019 Jan 8;47(D1):D427-D432
pubmed: 30357350
Nat Biotechnol. 2019 Jan;37(1):29-37
pubmed: 30556814
Front Microbiol. 2014 Jul 24;5:355
pubmed: 25104950
Environ Microbiol. 2019 Jan;21(1):152-163
pubmed: 30289197
RNA Biol. 2013 May;10(5):817-27
pubmed: 23492433
ISME J. 2019 Mar;13(3):618-631
pubmed: 30315316
Infect Genet Evol. 2014 Aug;26:132-8
pubmed: 24859088
PeerJ. 2017 May 3;5:e3243
pubmed: 28480138
Microb Ecol. 2018 Feb;75(2):375-386
pubmed: 28825127
Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14250-5
pubmed: 12384570
ISME J. 2017 Jan;11(1):7-14
pubmed: 27420028
PeerJ. 2015 May 28;3:e985
pubmed: 26038737
PLoS Biol. 2007 Mar;5(3):e16
pubmed: 17355171
mBio. 2016 Apr 05;7(2):e02234-15
pubmed: 27048805
Science. 2008 May 23;320(5879):1047-50
pubmed: 18497291
BMC Bioinformatics. 2007 Jun 18;8:209
pubmed: 17577412
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
FEMS Microbiol Rev. 2016 Mar;40(2):258-72
pubmed: 26657537
Nat Rev Microbiol. 2005 Jun;3(6):504-10
pubmed: 15886693
Adv Virus Res. 2018;101:1-38
pubmed: 29908587
Mol Biol Evol. 2008 Apr;25(4):762-77
pubmed: 18234706
PLoS One. 2009 Sep 29;4(9):e7264
pubmed: 19787045
Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6
pubmed: 23193283
Environ Microbiol. 2020 Sep;22(9):4000-4013
pubmed: 32761733
Nature. 2009 May 14;459(7244):207-12
pubmed: 19444207
Science. 1996 Jun 28;272(5270):1910-4
pubmed: 8658163
Nat Commun. 2013;4:2420
pubmed: 24036533
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Mol Microbiol. 1999 Oct;34(2):217-26
pubmed: 10564466
Infect Genet Evol. 2016 Apr;39:304-316
pubmed: 26873065
Appl Environ Microbiol. 1983 Sep;46(3):549-52
pubmed: 6416164
Nature. 2016 Sep 29;537(7622):689-693
pubmed: 27654921
PLoS Comput Biol. 2011 Oct;7(10):e1002195
pubmed: 22039361
Bioinformatics. 2012 Jun 1;28(11):1420-8
pubmed: 22495754
Sci Total Environ. 2019 Mar 15;656:1413-1426
pubmed: 30625669
J Comput Biol. 2012 May;19(5):455-77
pubmed: 22506599
Nat Rev Microbiol. 2015 Mar;13(3):147-59
pubmed: 25639680
Nucleic Acids Res. 2014 Jan;42(Database issue):D633-42
pubmed: 24288368
Nat Commun. 2018 Nov 19;9(1):4881
pubmed: 30451857
Front Microbiol. 2015 Sep 15;6:960
pubmed: 26441894
BMC Bioinformatics. 2004 Aug 19;5:113
pubmed: 15318951
Genome Res. 2015 Jul;25(7):1043-55
pubmed: 25977477
Nat Microbiol. 2018 Jul;3(7):754-766
pubmed: 29867096
PLoS One. 2012;7(3):e33641
pubmed: 22432038
Bioinformatics. 2011 Mar 15;27(6):764-70
pubmed: 21217122
Sci Data. 2018 Jul 03;5:180114
pubmed: 29969110
Mol Biol Evol. 2016 Jul;33(7):1870-4
pubmed: 27004904
Trends Microbiol. 2018 Nov;26(11):955-965
pubmed: 29937307
ISME J. 2010 May;4(5):660-72
pubmed: 20182523
PLoS Genet. 2013;9(12):e1003987
pubmed: 24348267
Appl Environ Microbiol. 2013 Jun;79(12):3822-8
pubmed: 23584787
Sci Adv. 2015 Jun 19;1(5):e1400127
pubmed: 26601189
PLoS One. 2016 Feb 29;11(2):e0150361
pubmed: 26927795
Elife. 2015 Jul 22;4:
pubmed: 26200428
Nucleic Acids Res. 2007;35(9):3100-8
pubmed: 17452365
Virol J. 2018 Apr 10;15(1):66
pubmed: 29636072
Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5452-7
pubmed: 22431592
mBio. 2019 Feb 26;10(1):
pubmed: 30808697