Marine DNA Viral Macro- and Microdiversity from Pole to Pole.
community ecology
diversity gradients
marine biology
metagenomics
population ecology
species
viruses
Journal
Cell
ISSN: 1097-4172
Titre abrégé: Cell
Pays: United States
ID NLM: 0413066
Informations de publication
Date de publication:
16 05 2019
16 05 2019
Historique:
received:
31
10
2018
revised:
05
01
2019
accepted:
20
03
2019
pubmed:
30
4
2019
medline:
26
2
2020
entrez:
30
4
2019
Statut:
ppublish
Résumé
Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.
Identifiants
pubmed: 31031001
pii: S0092-8674(19)30341-1
doi: 10.1016/j.cell.2019.03.040
pmc: PMC6525058
mid: NIHMS1525378
pii:
doi:
Substances chimiques
DNA, Viral
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
1109-1123.e14Subventions
Organisme : NIAID NIH HHS
ID : T32 AI112542
Pays : United States
Investigateurs
Silvia G Acinas
(SG)
Marcel Babin
(M)
Peer Bork
(P)
Emmanuel Boss
(E)
Chris Bowler
(C)
Guy Cochrane
(G)
Colomban de Vargas
(C)
Michael Follows
(M)
Gabriel Gorsky
(G)
Nigel Grimsley
(N)
Lionel Guidi
(L)
Pascal Hingamp
(P)
Daniele Iudicone
(D)
Olivier Jaillon
(O)
Stefanie Kandels-Lewis
(S)
Lee Karp-Boss
(L)
Eric Karsenti
(E)
Fabrice Not
(F)
Hiroyuki Ogata
(H)
Stéphane Pesant
(S)
Nicole Poulton
(N)
Jeroen Raes
(J)
Christian Sardet
(C)
Sabrina Speich
(S)
Lars Stemmann
(L)
Matthew B Sullivan
(MB)
Shinichi Sunagawa
(S)
Patrick Wincker
(P)
Commentaires et corrections
Type : CommentIn
Informations de copyright
Copyright © 2019 Elsevier Inc. All rights reserved.
Références
Open Virol J. 2009 Mar 19;3:1-6
pubmed: 19572052
Science. 2016 Sep 30;353(6307):1532-1535
pubmed: 27708102
Annu Rev Microbiol. 2002;56:457-87
pubmed: 12142474
Science. 2006 Jun 23;312(5781):1795-8
pubmed: 16794078
Proc Natl Acad Sci U S A. 2012 Mar 20;109(12):4544-9
pubmed: 22388749
Microbiome. 2017 May 4;5(1):50
pubmed: 28473000
Environ Microbiol. 2009 Nov;11(11):2893-903
pubmed: 19691502
Ecol Lett. 2008 Jun;11(6):609-23
pubmed: 18400018
Bioinformatics. 2015 Mar 15;31(6):926-32
pubmed: 25398609
Ecol Lett. 2016 Aug;19(8):825-38
pubmed: 27250037
Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):6506-6511
pubmed: 29784790
J Microbiol Methods. 2011 Jul;86(1):42-51
pubmed: 21457733
Nat Commun. 2017 Jun 23;8:15892
pubmed: 28643787
PLoS One. 2012;7(8):e41578
pubmed: 22870232
Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17633-8
pubmed: 23045668
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D138-41
pubmed: 14681378
Nat Biotechnol. 2019 Jan;37(1):29-37
pubmed: 30556814
Nature. 2012 Nov 1;491(7422):56-65
pubmed: 23128226
Environ Microbiol. 2016 Nov;18(11):4240-4253
pubmed: 27696643
Mol Ecol. 2010 Mar;19 Suppl 1:81-8
pubmed: 20331772
Science. 2015 May 22;348(6237):1262073
pubmed: 25999517
Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2342-7
pubmed: 23324742
Nature. 2016 Aug 25;536(7617):456-9
pubmed: 27533038
Science. 2015 May 22;348(6237):1261498
pubmed: 25999515
Nucleic Acids Res. 2002 Jan 1;30(1):42-6
pubmed: 11752249
PLoS One. 2013;8(2):e57355
pubmed: 23468974
PeerJ. 2015 May 28;3:e985
pubmed: 26038737
Viruses. 2017 Jun 02;9(6):
pubmed: 28574420
Nat Microbiol. 2017 Jul 10;2:17112
pubmed: 28692019
Genome Biol. 2004;5(2):R12
pubmed: 14759262
Mol Ecol. 2014 Jun;23(12):2890-901
pubmed: 24750409
Trends Microbiol. 2019 Jan;27(1):51-63
pubmed: 30181062
J Virol. 2015 Mar;89(5):2459-61
pubmed: 25540374
Science. 2012 Apr 6;336(6077):48-51
pubmed: 22491847
Nature. 2014 Sep 11;513(7517):242-5
pubmed: 25043051
Nat Ecol Evol. 2018 Aug;2(8):1243-1249
pubmed: 29915345
Nat Commun. 2018 Jan 25;9(1):373
pubmed: 29371626
Am Nat. 2004 Feb;163(2):192-211
pubmed: 14970922
ISME J. 2013 Mar;7(3):672-9
pubmed: 23151645
Bioinformatics. 1998 Jun;14(5):423-9
pubmed: 9682055
Environ Microbiol. 2016 Nov;18(11):3714-3727
pubmed: 26950773
Mol Ecol Resour. 2018 Nov;18(6):1444-1455
pubmed: 30256532
Virus Res. 2018 Jan 2;243:83-90
pubmed: 29111455
Front Microbiol. 2013 May 23;4:131
pubmed: 23734148
Nat Rev Genet. 2008 Apr;9(4):267-76
pubmed: 18319742
Genome Res. 2017 May;27(5):824-834
pubmed: 28298430
Science. 2006 Nov 3;314(5800):787-90
pubmed: 17082450
Open Biol. 2013 Dec 11;3(12):130160
pubmed: 24335607
Curr Opin Microbiol. 2016 Jun;31:161-168
pubmed: 27088500
Science. 2015 May 29;348(6238):1019-23
pubmed: 26023139
Nature. 2018 Jul;559(7714):392-395
pubmed: 29973726
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Science. 2009 Feb 6;323(5915):741-6
pubmed: 19197054
Microbiome. 2017 Jul 6;5(1):69
pubmed: 28683828
J Virol. 2016 Nov 28;90(24):11043-11055
pubmed: 27681128
Nature. 2016 Sep 29;537(7622):689-693
pubmed: 27654921
Nat Rev Microbiol. 2008 Jun;6(6):431-40
pubmed: 18461076
PLoS One. 2011;6(9):e24570
pubmed: 21931760
Science. 2018 Mar 30;359(6383):1542-1545
pubmed: 29599247
Sci Data. 2017 Aug 01;4:170093
pubmed: 28763055
Science. 2015 May 22;348(6237):1261605
pubmed: 25999516
Nat Methods. 2015 Jan;12(1):59-60
pubmed: 25402007
Proc Natl Acad Sci U S A. 2018 Jun 5;115(23):6040-6045
pubmed: 29784828
Bioinformatics. 2001 Sep;17(9):847-8
pubmed: 11590104
Nucleic Acids Res. 2002 Apr 1;30(7):1575-84
pubmed: 11917018
Virus Res. 2018 Jan 15;244:218-229
pubmed: 29055712
PeerJ. 2017 May 3;5:e3243
pubmed: 28480138
Nat Microbiol. 2018 Apr;3(4):456-460
pubmed: 29531366
Nat Rev Microbiol. 2007 Oct;5(10):801-12
pubmed: 17853907
Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13758-63
pubmed: 21825119
Curr Biol. 2017 Jun 5;27(11):R511-R527
pubmed: 28586689
Trends Ecol Evol. 2014 Jan;29(1):42-50
pubmed: 24139126
BMC Bioinformatics. 2010 Mar 08;11:119
pubmed: 20211023
Nat Rev Microbiol. 2007 Oct;5(10):782-91
pubmed: 17853906
Sci Data. 2015 May 26;2:150023
pubmed: 26029378
Nature. 2016 Dec 22;540(7634):539-543
pubmed: 27880757
Science. 2009 Oct 23;326(5952):539
pubmed: 19900890
Science. 2015 May 22;348(6237):1261359
pubmed: 25999513
Cell Host Microbe. 2018 Feb 14;23(2):229-240.e5
pubmed: 29447696
BMC Genomics. 2016 Nov 16;17(1):930
pubmed: 27852226
Nat Commun. 2017 Jun 28;8:16054
pubmed: 28656958
PLoS Biol. 2006 Nov;4(11):e368
pubmed: 17090214
Environ Microbiol. 2014 Sep;16(9):2659-71
pubmed: 24102695
Virus Res. 2018 Jan 15;244:84-89
pubmed: 29138044
mSystems. 2017 Feb 14;2(1):
pubmed: 28217745
PeerJ. 2017 Sep 21;5:e3817
pubmed: 28948103
J Mol Microbiol Biotechnol. 1999 Aug;1(1):45-50
pubmed: 10941783
Environ Microbiol Rep. 2017 Apr;9(2):55-70
pubmed: 28185400
Nat Commun. 2018 Nov 8;9(1):4698
pubmed: 30409965
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Nature. 2016 Apr 28;532(7600):465-470
pubmed: 26863193
PLoS Biol. 2012 Feb;10(2):e1001265
pubmed: 22363207
Nat Biotechnol. 2019 Jun;37(6):632-639
pubmed: 31061483
Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2567-72
pubmed: 15701695
Appl Environ Microbiol. 2007 Sep;73(18):5937-44
pubmed: 17644642
Nature. 2013 Jan 3;493(7430):45-50
pubmed: 23222524