Genomic and metabolic adaptations of biofilms to ecological windows of opportunity in glacier-fed streams.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
20 04 2022
20 04 2022
Historique:
received:
08
10
2021
accepted:
07
04
2022
entrez:
21
4
2022
pubmed:
22
4
2022
medline:
23
4
2022
Statut:
epublish
Résumé
In glacier-fed streams, ecological windows of opportunity allow complex microbial biofilms to develop and transiently form the basis of the food web, thereby controlling key ecosystem processes. Using metagenome-assembled genomes, we unravel strategies that allow biofilms to seize this opportunity in an ecosystem otherwise characterized by harsh environmental conditions. We observe a diverse microbiome spanning the entire tree of life including a rich virome. Various co-existing energy acquisition pathways point to diverse niches and the exploitation of available resources, likely fostering the establishment of complex biofilms during windows of opportunity. The wide occurrence of rhodopsins, besides chlorophyll, highlights the role of solar energy capture in these biofilms while internal carbon and nutrient cycling between photoautotrophs and heterotrophs may help overcome constraints imposed by oligotrophy in these habitats. Mechanisms potentially protecting bacteria against low temperatures and high UV-radiation are also revealed and the selective pressure of this environment is further highlighted by a phylogenomic analysis differentiating important components of the glacier-fed stream microbiome from other ecosystems. Our findings reveal key genomic underpinnings of adaptive traits contributing to the success of complex biofilms to exploit environmental opportunities in glacier-fed streams, which are now rapidly changing owing to global warming.
Identifiants
pubmed: 35444202
doi: 10.1038/s41467-022-29914-0
pii: 10.1038/s41467-022-29914-0
pmc: PMC9021309
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2168Informations de copyright
© 2022. The Author(s).
Références
Bioscience. 2017 Oct 1;67(10):897-911
pubmed: 29599537
Appl Environ Microbiol. 2010 Apr;76(7):2304-12
pubmed: 20154119
Bioinformatics. 2018 Sep 1;34(17):i884-i890
pubmed: 30423086
Proc Natl Acad Sci U S A. 2021 Mar 23;118(12):
pubmed: 33723043
Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6
pubmed: 23193283
CRC Crit Rev Plant Sci. 2016;35(2):81-105
pubmed: 28966438
Nature. 2015 Jun 4;522(7554):98-101
pubmed: 26017307
J Photochem Photobiol B. 2002 Aug;68(1):23-32
pubmed: 12208033
ISME J. 2020 Jun;14(6):1369-1383
pubmed: 32071394
Nature. 2003 Nov 27;426(6965):439-42
pubmed: 14647381
Nat Microbiol. 2017 Jun 26;2:17100
pubmed: 28650444
PeerJ. 2019 Jul 26;7:e7359
pubmed: 31388474
Appl Environ Microbiol. 2012 Jan;78(2):549-59
pubmed: 22081564
Front Microbiol. 2020 Nov 19;11:591465
pubmed: 33329472
Commun Biol. 2019 Aug 29;2:323
pubmed: 31482142
Front Microbiol. 2014 Aug 20;5:425
pubmed: 25191307
Mol Ecol. 2010 Mar;19 Suppl 1:21-31
pubmed: 20331767
Microbiome. 2020 Jun 10;8(1):90
pubmed: 32522236
Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):10913-8
pubmed: 16043709
Nat Microbiol. 2018 Jul;3(7):836-843
pubmed: 29807988
Microbiome. 2022 Feb 16;10(1):33
pubmed: 35172890
Nucleic Acids Res. 2007 Jan;35(Database issue):D61-5
pubmed: 17130148
Bioinformatics. 2015 May 15;31(10):1674-6
pubmed: 25609793
PLoS Comput Biol. 2012;8(9):e1002687
pubmed: 23028285
Biol Lett. 2018 Oct 10;14(10):
pubmed: 30305460
Front Microbiol. 2019 Jul 17;10:1571
pubmed: 31379764
Environ Microbiol. 2010 Oct;12(10):2658-76
pubmed: 20482592
PLoS One. 2013;8(2):e55045
pubmed: 23405110
Antonie Van Leeuwenhoek. 2002 Aug;81(1-4):61-72
pubmed: 12448706
Bioinformatics. 2016 Feb 15;32(4):605-7
pubmed: 26515820
EMBO Rep. 2014 May;15(5):508-17
pubmed: 24671034
Microbiome. 2020 Apr 3;8(1):48
pubmed: 32245390
Nat Biotechnol. 2021 May;39(5):578-585
pubmed: 33349699
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Nat Commun. 2020 Sep 2;11(1):4403
pubmed: 32879312
Appl Environ Microbiol. 2009 Nov;75(22):7189-95
pubmed: 19767473
Sci Total Environ. 2020 May 15;717:137101
pubmed: 32065887
Genome Biol. 2014;15(12):550
pubmed: 25516281
Gigascience. 2021 Jun 2;10(6):
pubmed: 34076241
Sci Total Environ. 2021 Mar 1;758:143581
pubmed: 33223169
NPJ Biofilms Microbiomes. 2017 Apr 19;3:10
pubmed: 28649411
PLoS Comput Biol. 2015 May 07;11(5):e1004226
pubmed: 25950956
Nat Rev Microbiol. 2018 May;16(5):263-276
pubmed: 29398704
Proc Natl Acad Sci U S A. 2021 Jun 8;118(23):
pubmed: 34074785
Nature. 2021 May;593(7860):553-557
pubmed: 33911286
Biofilm. 2019 Dec 06;2:100016
pubmed: 33447802
Elife. 2016 Nov 18;5:
pubmed: 27855786
PeerJ. 2020 Oct 27;8:e9973
pubmed: 33194372
Methods Mol Biol. 2019;1962:227-245
pubmed: 31020564
Proc Natl Acad Sci U S A. 2019 Sep 3;116(36):17690-17695
pubmed: 31427515
Bioinformatics. 2019 Oct 15;35(20):4162-4164
pubmed: 30865266
ISME J. 2018 Jun;12(7):1861-1866
pubmed: 29523891
Front Biosci (Schol Ed). 2011 Jan 01;3(2):416-27
pubmed: 21196386
PLoS Comput Biol. 2011 Oct;7(10):e1002195
pubmed: 22039361
Genome Res. 2018 Apr;28(4):569-580
pubmed: 29496730
Aquat Sci. 2019;81(3):45
pubmed: 31057304
Appl Microbiol Biotechnol. 2019 Mar;103(6):2537-2549
pubmed: 30719551
FEMS Microbiol Ecol. 2007 Feb;59(2):307-17
pubmed: 17313580
ISME J. 2013 Jun;7(6):1211-26
pubmed: 23389107
Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):8239-44
pubmed: 24843170
Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):9770-9778
pubmed: 28874558
PLoS Comput Biol. 2017 Feb 21;13(2):e1005404
pubmed: 28222096
Life (Basel). 2018 Mar 13;8(1):
pubmed: 29534000
ISME J. 2022 Mar;16(3):666-675
pubmed: 34522009
Genome Res. 2015 Jul;25(7):1043-55
pubmed: 25977477
Bioinformatics. 2009 Aug 1;25(15):1972-3
pubmed: 19505945
Nat Microbiol. 2016 Oct 10;2:16180
pubmed: 27723761
Sci Rep. 2017 Oct 4;7(1):12668
pubmed: 28978929
Curr Biol. 2016 Apr 25;26(8):R319-21
pubmed: 27115686
PLoS One. 2010 Mar 10;5(3):e9490
pubmed: 20224823
Nat Microbiol. 2016 Apr 11;1:16048
pubmed: 27572647
ISME J. 2016 Mar;10(3):655-64
pubmed: 26296066
Environ Microbiome. 2021 Dec 14;16(1):24
pubmed: 34906246
BMC Bioinformatics. 2010 Mar 08;11:119
pubmed: 20211023
Bioinformatics. 2019 Nov 15;:
pubmed: 31730192
Environ Microbiol. 2006 Apr;8(4):732-40
pubmed: 16584484
Nat Rev Microbiol. 2007 Jan;5(1):76-81
pubmed: 17170748
Microb Ecol. 1982 Oct;8(2):115-26
pubmed: 24225806
Nature. 2009 Dec 10;462(7274):795-8
pubmed: 20010687
Genome Biol. 2020 Sep 10;21(1):244
pubmed: 32912302
Proc Natl Acad Sci U S A. 2021 Jan 12;118(2):
pubmed: 33419920
Microorganisms. 2020 Nov 27;8(12):
pubmed: 33260993
Genome Biol. 2019 Nov 28;20(1):257
pubmed: 31779668
PeerJ. 2015 Oct 08;3:e1319
pubmed: 26500826
Genome Biol. 2016 Dec 16;17(1):260
pubmed: 27986083
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Nature. 2005 Nov 3;438(7064):90-3
pubmed: 16267554
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
pubmed: 15034147
Oecologia. 2020 Dec;194(4):541-554
pubmed: 32803339
Nat Microbiol. 2020 Aug;5(8):1026-1039
pubmed: 32451471
Nat Microbiol. 2017 May 30;2:17065
pubmed: 28555622
Nat Biotechnol. 2019 Aug;37(8):852-857
pubmed: 31341288
PLoS One. 2015 Dec 15;10(12):e0145353
pubmed: 26671564
J Photochem Photobiol B. 2001 Sep 1;62(1-2):35-42
pubmed: 11693365
Nat Rev Microbiol. 2016 Apr;14(4):251-63
pubmed: 26972916
Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314
pubmed: 30418610
ISME J. 2021 Jun;15(6):1844-1857
pubmed: 33452478