Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick.
Journal
ISME communications
ISSN: 2730-6151
Titre abrégé: ISME Commun
Pays: England
ID NLM: 9918205372406676
Informations de publication
Date de publication:
18 Sep 2023
18 Sep 2023
Historique:
received:
27
07
2023
accepted:
06
09
2023
medline:
19
9
2023
pubmed:
19
9
2023
entrez:
18
9
2023
Statut:
epublish
Résumé
Visible surface films, termed slicks, can extensively cover freshwater and marine ecosystems, with coastal regions being particularly susceptible to their presence. The sea-surface microlayer (SML), the upper 1-mm at the air-water interface in slicks (herein slick SML) harbors a distinctive bacterial community, but generally little is known about SML viruses. Using flow cytometry, metagenomics, and cultivation, we characterized viruses and bacteria in a brackish slick SML in comparison to non-slick SML as well as seawater below slick and non-slick areas (subsurface water = SSW). Size-fractionated filtration of all samples distinguished viral attachment to hosts and particles. The slick SML contained higher abundances of virus-like particles, prokaryotic cells, and dissolved organic carbon compared to non-slick SML and SSW. The community of 428 viral operational taxonomic units (vOTUs), 426 predicted as lytic, distinctly differed across all size fractions in the slick SML compared to non-slick SML and SSW. Specific metabolic profiles of bacterial metagenome-assembled genomes and isolates in the slick SML included a prevalence of genes encoding motility and carbohydrate-active enzymes (CAZymes). Several vOTUs were enriched in slick SML, and many virus variants were associated with particles. Nine vOTUs were only found in slick SML, six of them being targeted by slick SML-specific clustered-regularly interspaced short palindromic repeats (CRISPR) spacers likely originating from Gammaproteobacteria. Moreover, isolation of three previously unknown lytic phages for Alishewanella sp. and Pseudoalteromonas tunicata, abundant and actively replicating slick SML bacteria, suggests that viral activity in slicks contributes to biogeochemical cycling in coastal ecosystems.
Identifiants
pubmed: 37723220
doi: 10.1038/s43705-023-00307-8
pii: 10.1038/s43705-023-00307-8
pmc: PMC10507051
doi:
Types de publication
Journal Article
Langues
eng
Pagination
97Subventions
Organisme : Deutsche Forschungsgemeinschaft (German Research Foundation)
ID : RA3432/1-1
Organisme : Deutsche Forschungsgemeinschaft (German Research Foundation)
ID : 34509606
Organisme : Deutsche Forschungsgemeinschaft (German Research Foundation)
ID : 451574234
Organisme : Deutsche Forschungsgemeinschaft (German Research Foundation)
ID : 451574234
Organisme : Crafoordska Stiftelsen (Crafoord Foundation)
ID : CR2019-0034
Organisme : Crafoordska Stiftelsen (Crafoord Foundation)
ID : CR2019-0034
Organisme : Vetenskapsrådet (Swedish Research Council)
ID : 2018-05973
Informations de copyright
© 2023. ISME Publications B.V.
Références
Appl Environ Microbiol. 2019 Aug 29;85(18):
pubmed: 31324626
Nucleic Acids Res. 2018 Jul 2;46(W1):W246-W251
pubmed: 29790974
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Front Microbiol. 2019 Jun 04;10:1204
pubmed: 31214143
Environ Microbiol. 2021 Aug;23(8):4576-4594
pubmed: 34190387
Viruses. 2019 Feb 22;11(2):
pubmed: 30813345
PeerJ. 2019 Jul 26;7:e7359
pubmed: 31388474
Protein Sci. 2022 Jan;31(1):47-53
pubmed: 34423492
Microbiome. 2014 May 05;2:15
pubmed: 24910773
Microbiome. 2020 Jun 10;8(1):90
pubmed: 32522236
Front Microbiol. 2022 Jul 05;13:834675
pubmed: 36212867
Nucleic Acids Res. 2020 Jan 8;48(D1):D454-D458
pubmed: 31612915
Nat Commun. 2018 Nov 30;9(1):5114
pubmed: 30504855
Nat Microbiol. 2018 Jul;3(7):836-843
pubmed: 29807988
ISME J. 2022 Jun;16(6):1627-1635
pubmed: 35236926
Bioinformatics. 2020 Aug 15;36(14):4126-4129
pubmed: 32413137
Nat Commun. 2019 Mar 4;10(1):1014
pubmed: 30833550
Bioinformatics. 2015 May 15;31(10):1674-6
pubmed: 25609793
Microbiome. 2022 Dec 5;10(1):212
pubmed: 36464731
PLoS One. 2013 Apr 22;8(4):e61217
pubmed: 23630581
Viruses. 2020 Jan 30;12(2):
pubmed: 32019073
Nat Microbiol. 2023 May;8(5):946-957
pubmed: 37024618
Nat Commun. 2023 Oct 10;14(1):6354
pubmed: 37816747
PeerJ. 2021 May 5;9:e11111
pubmed: 33996275
Appl Environ Microbiol. 2005 Sep;71(9):5282-9
pubmed: 16151115
Nat Biotechnol. 2016 Dec;34(12):1256-1263
pubmed: 27819664
FEMS Microbiol Ecol. 2019 May 1;95(5):
pubmed: 31055603
FEMS Microbiol Ecol. 2017 May 1;93(5):
pubmed: 28369320
Nat Methods. 2014 Nov;11(11):1144-6
pubmed: 25218180
ISME J. 2017 Dec;11(12):2864-2868
pubmed: 28742071
Nucleic Acids Res. 2020 Sep 18;48(16):8883-8900
pubmed: 32766782
Environ Microbiol. 2023 Jun;25(6):1077-1083
pubmed: 36764661
FEMS Microbiol Ecol. 2021 Mar 31;97(4):
pubmed: 33625484
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W182-5
pubmed: 17526522
Nat Rev Microbiol. 2020 Jan;18(1):21-34
pubmed: 31690825
ISME J. 2022 Feb;16(2):555-568
pubmed: 34475519
Appl Environ Microbiol. 1998 Feb;64(2):575-80
pubmed: 9464396
Environ Microbiol. 2009 Nov;11(11):2775-7
pubmed: 19519870
PLoS One. 2018 Aug 20;13(8):e0202636
pubmed: 30125317
Appl Environ Microbiol. 2007 Nov;73(21):6730-9
pubmed: 17766444
Viruses. 2020 Nov 06;12(11):
pubmed: 33172115
Int J Microbiol. 2009;2009:701735
pubmed: 20016676
Bioinformatics. 2017 Aug 01;33(15):2379-2380
pubmed: 28379287
Biotechnol Adv. 2010 Jul-Aug;28(4):436-50
pubmed: 20172021
PLoS One. 2008 Sep 24;3(9):e3252
pubmed: 18813346
Brief Bioinform. 2023 Jan 19;24(1):
pubmed: 36464489
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Bioinformatics. 2012 Jun 15;28(12):1647-9
pubmed: 22543367
Genome Res. 2017 May;27(5):824-834
pubmed: 28298430
Environ Microbiol. 2016 Nov;18(11):3949-3961
pubmed: 27235779
Mol Microbiol. 2000 Apr;36(1):244-6
pubmed: 10760181
Microorganisms. 2021 Feb 04;9(2):
pubmed: 33557117
Nat Commun. 2014 Jul 24;5:4399
pubmed: 25056268
PeerJ. 2017 Sep 7;5:e3788
pubmed: 28894651
Mar Drugs. 2009 Nov 12;7(4):576-88
pubmed: 20098599
Microbiome. 2021 Feb 1;9(1):37
pubmed: 33522966
Sci Rep. 2021 Feb 4;11(1):3197
pubmed: 33542255
Phage (New Rochelle). 2021 Dec 1;2(4):214-223
pubmed: 36159887
Mar Pollut Bull. 2004 Jun;48(11-12):1016-30
pubmed: 15172807
Genome Res. 2015 Jul;25(7):1043-55
pubmed: 25977477
Geophys Res Lett. 2018 May 16;45(9):4230-4237
pubmed: 29937608
Sci Rep. 2016 Jan 12;6:19123
pubmed: 26753514
Nat Biotechnol. 2021 Jun;39(6):727-736
pubmed: 33462508
Science. 1977 Nov 11;198(4317):575-80
pubmed: 918656
Nature. 2003 Aug 28;424(6952):1047-51
pubmed: 12944965
Appl Environ Microbiol. 2022 May 24;88(10):e0031522
pubmed: 35499326
PeerJ. 2017 May 3;5:e3243
pubmed: 28480138
BMC Bioinformatics. 2010 Mar 08;11:119
pubmed: 20211023
Proc Natl Acad Sci U S A. 2014 May 20;111(20):7202-7
pubmed: 24733921
Environ Microbiol Rep. 2011 Apr;3(2):195-202
pubmed: 21572525
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Bioinformatics. 2021 Aug 25;37(16):2473-2475
pubmed: 33459763
Nat Rev Microbiol. 2019 Apr;17(4):247-260
pubmed: 30760902
Nucleic Acids Res. 2017 Jan 9;45(1):39-53
pubmed: 27899557
Bioinformatics. 2019 Nov 15;:
pubmed: 31730192
Nat Methods. 2012 Jul;9(7):671-5
pubmed: 22930834
PeerJ. 2017 Sep 21;5:e3817
pubmed: 28948103
Biologicals. 1997 Sep;25(3):289-97
pubmed: 9324997
Proc Math Phys Eng Sci. 2020 Feb;476(2234):20190763
pubmed: 32201480
mSystems. 2022 Oct 26;7(5):e0074122
pubmed: 36069454
Nucleic Acids Res. 2021 Jul 2;49(W1):W29-W35
pubmed: 33978755
Nucleic Acids Res. 2018 Jul 2;46(W1):W95-W101
pubmed: 29771380