A comparative whole-genome approach identifies bacterial traits for marine microbial interactions.
Journal
Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179
Informations de publication
Date de publication:
28 03 2022
28 03 2022
Historique:
received:
09
10
2020
accepted:
30
12
2021
entrez:
29
3
2022
pubmed:
30
3
2022
medline:
19
4
2022
Statut:
epublish
Résumé
Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities. We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10% of genomes), phytohormones (3-8%) and different B vitamins (57-70%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions. Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics.
Identifiants
pubmed: 35347228
doi: 10.1038/s42003-022-03184-4
pii: 10.1038/s42003-022-03184-4
pmc: PMC8960797
doi:
Banques de données
figshare
['10.6084/m9.figshare.16942780']
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
276Subventions
Organisme : Human Frontier Science Program (HFSP)
ID : RGB 0020/2016
Informations de copyright
© 2022. The Author(s).
Références
Front Microbiol. 2016 Sep 07;7:1414
pubmed: 27656176
Nature. 2015 Jun 4;522(7554):98-101
pubmed: 26017307
Environ Pollut. 2018 Jun;237:253-261
pubmed: 29494919
mBio. 2012 Sep 18;3(5):
pubmed: 22991429
Nat Microbiol. 2017 Jun 26;2:17100
pubmed: 28650444
Nat Commun. 2018 Jan 18;9(1):266
pubmed: 29348571
Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):3160-5
pubmed: 14973198
mBio. 2012 May 02;3(2):
pubmed: 22448042
Science. 2007 Feb 16;315(5814):972-6
pubmed: 17218491
J Biol Chem. 1973 Jan 10;248(1):251-64
pubmed: 4144254
Genome Biol Evol. 2018 Sep 1;10(9):2255-2265
pubmed: 30137329
Cell. 1998 Oct 16;95(2):189-98
pubmed: 9790526
ISME J. 2011 Jul;5(7):1125-32
pubmed: 21326334
Nature. 2017 Nov 9;551(7679):242-246
pubmed: 29088696
Fish Shellfish Immunol. 2020 Sep;104:587-591
pubmed: 32470511
Commun Biol. 2019 Aug 2;2:284
pubmed: 31396564
PLoS One. 2020 Jan 28;15(1):e0227864
pubmed: 31990915
Nat Rev Microbiol. 2019 May;17(5):284-294
pubmed: 30923350
Elife. 2016 Apr 07;5:e11888
pubmed: 27054497
Microbiol Mol Biol Rev. 2012 Sep;76(3):667-84
pubmed: 22933565
Proc Natl Acad Sci U S A. 2009 Oct 6;106(40):17071-6
pubmed: 19805106
FEBS J. 2012 Jun;279(11):2036-46
pubmed: 22568782
Appl Environ Microbiol. 1995 Jun;61(6):2439-41
pubmed: 16535058
Front Plant Sci. 2019 Jan 10;9:1945
pubmed: 30687350
Proc Natl Acad Sci U S A. 2013 Jan 15;110(3):1053-8
pubmed: 23277585
Mol Microbiol. 2018 Feb;107(4):455-471
pubmed: 29235173
Front Microbiol. 2017 Apr 19;8:637
pubmed: 28469605
FEMS Microbiol Ecol. 2020 May 1;96(5):
pubmed: 32109282
Nat Rev Microbiol. 2019 Nov;17(11):665-678
pubmed: 31485034
Environ Microbiol. 2018 Feb;20(2):492-505
pubmed: 28967193
Proc Natl Acad Sci U S A. 2013 Jul 16;110(29):12030-5
pubmed: 23818639
Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18260-5
pubmed: 21969545
Proc Natl Acad Sci U S A. 2009 Sep 15;106(37):15527-33
pubmed: 19805210
Biometals. 2012 Feb;25(1):135-47
pubmed: 21894542
Nat Chem. 2011 Apr;3(4):331-5
pubmed: 21430694
J Chem Ecol. 2016 Dec;42(12):1201-1211
pubmed: 27822708
Front Microbiol. 2014 May 27;5:251
pubmed: 24904563
Science. 2012 Apr 6;336(6077):48-51
pubmed: 22491847
Nature. 2017 May 31;546(7656):56-64
pubmed: 28569813
ISME J. 2018 Apr;12(4):981-996
pubmed: 29335641
Proc Natl Acad Sci U S A. 2016 Sep 20;113(38):10451-2
pubmed: 27651473
Nat Rev Microbiol. 2020 Jan;18(1):21-34
pubmed: 31690825
Bioinformatics. 2014 Oct;30(19):2811-2
pubmed: 24930139
ISME J. 2010 Jun;4(6):784-98
pubmed: 20072162
PLoS One. 2015 Dec 16;10(12):e0145035
pubmed: 26673755
J Bacteriol. 2011 Sep;193(18):4790-7
pubmed: 21764915
Eukaryot Cell. 2006 Aug;5(8):1175-83
pubmed: 16896203
Nat Rev Microbiol. 2010 Jan;8(1):15-25
pubmed: 19946288
Cell. 2019 Dec 12;179(7):1623-1635.e11
pubmed: 31835036
Nat Rev Microbiol. 2014 Sep;12(9):635-45
pubmed: 25118885
Theor Popul Biol. 1971 Jun;2(2):174-208
pubmed: 5162686
ISME J. 2020 Feb;14(2):544-559
pubmed: 31685936
IEEE Trans Vis Comput Graph. 2014 Dec;20(12):1983-92
pubmed: 26356912
Plant Physiol. 2011 Jan;155(1):209-21
pubmed: 21081694
Biometals. 2019 Feb;32(1):139-154
pubmed: 30623317
Nat Microbiol. 2019 Oct;4(10):1706-1715
pubmed: 31332382
Bioinformatics. 2016 Sep 15;32(18):2847-9
pubmed: 27207943
Elife. 2016 Nov 18;5:
pubmed: 27855786
Nat Prod Rep. 2019 Mar 20;36(3):458-475
pubmed: 30191940
Front Microbiol. 2017 Oct 12;8:1985
pubmed: 29075248
FEMS Microbiol Ecol. 2004 Mar 1;47(3):387-96
pubmed: 19712327
Science. 2008 May 23;320(5879):1034-9
pubmed: 18497287
ISME J. 2017 Jun;11(6):1434-1446
pubmed: 28186498
Nat Biotechnol. 2020 Sep;38(9):1079-1086
pubmed: 32341564
Appl Environ Microbiol. 2000 Jul;66(7):3044-51
pubmed: 10877804
Front Microbiol. 2018 Apr 20;9:746
pubmed: 29731741
Ann Rev Mar Sci. 2012;4:523-42
pubmed: 22457986
Science. 2008 May 23;320(5879):1081-5
pubmed: 18497299
J Am Chem Soc. 1978 Jan 4;100(1):316-8
pubmed: 618947
Proc Natl Acad Sci U S A. 2015 Jan 13;112(2):453-7
pubmed: 25548163
Proc Natl Acad Sci U S A. 2019 Nov 19;116(47):23609-23617
pubmed: 31685631
Science. 2015 Feb 13;347(6223):1257594
pubmed: 25678667
Sci Adv. 2018 May 16;4(5):eaar4536
pubmed: 29774236
Front Microbiol. 2014 Jun 25;5:311
pubmed: 25009539
Science. 2016 Sep 16;353(6305):1272-7
pubmed: 27634532
ISME J. 2020 May;14(5):1247-1259
pubmed: 32047279
Curr Biol. 2010 Sep 14;20(17):1557-61
pubmed: 20705465
Front Microbiol. 2015 Nov 13;6:1262
pubmed: 26617596
Molecules. 2019 Apr 10;24(7):
pubmed: 30974826
Biometals. 2012 Feb;25(1):181-92
pubmed: 21947474
Appl Environ Microbiol. 2005 Dec;71(12):8531-6
pubmed: 16332844
Annu Rev Biochem. 2009;78:569-603
pubmed: 19348578
Microbiologyopen. 2016 Feb;5(1):106-17
pubmed: 26677108
ISME J. 2018 Oct;12(10):2470-2478
pubmed: 29925880
Crit Rev Microbiol. 2013 Nov;39(4):395-415
pubmed: 22978761
Proc Natl Acad Sci U S A. 2017 Oct 3;114(40):10684-10688
pubmed: 28923945
Genome Res. 2015 Jul;25(7):1043-55
pubmed: 25977477
ISME J. 2017 Jan;11(1):31-42
pubmed: 27623332
Sci Rep. 2019 Mar 29;9(1):5312
pubmed: 30926855
ISME J. 2016 Dec;10(12):2892-2906
pubmed: 27128996
Microbiologyopen. 2018 Oct;7(5):e00599
pubmed: 29573209
Biometals. 2013 Jun;26(3):507-16
pubmed: 23700243
BMC Evol Biol. 2018 Oct 3;18(1):148
pubmed: 30285626
Mol Microbiol. 1991 May;5(5):1251-63
pubmed: 1659649
ISME J. 2014 Dec;8(12):2517-29
pubmed: 25171333
Appl Environ Microbiol. 2003 Jan;69(1):568-76
pubmed: 12514043
Science. 2015 Nov 6;350(6261):aac9323
pubmed: 26542581
Curr Opin Microbiol. 2015 Feb;23:14-22
pubmed: 25461568
Microb Cell Fact. 2017 Jan 30;16(1):15
pubmed: 28137297
Nat Biotechnol. 2013 Sep;31(9):814-21
pubmed: 23975157
Ann Rev Mar Sci. 2009;1:43-63
pubmed: 21141029
Environ Microbiol. 2009 Oct;11(10):2698-709
pubmed: 19659554
PLoS One. 2016 Sep 22;11(9):e0163098
pubmed: 27658251
Nat Genet. 1999 Jan;21(1):108-10
pubmed: 9916801
Microb Biotechnol. 2018 Mar;11(2):369-380
pubmed: 29215194
Nat Rev Microbiol. 2007 Oct;5(10):782-91
pubmed: 17853906
Science. 2015 May 22;348(6237):1261359
pubmed: 25999513
Front Microbiol. 2012 Mar 07;3:43
pubmed: 22408637
Bioinformatics. 2011 Sep 1;27(17):2463-4
pubmed: 21737437
Proc Natl Acad Sci U S A. 1999 Apr 13;96(8):4285-8
pubmed: 10200254
Clin Microbiol Rev. 2010 Jan;23(1):35-73
pubmed: 20065325
Trends Microbiol. 2016 Jan;24(1):51-62
pubmed: 26549582
Bioinformatics. 2019 Nov 15;:
pubmed: 31730192
Nat Rev Microbiol. 2020 Mar;18(3):152-163
pubmed: 31748738
FEMS Microbiol Ecol. 2017 Mar 1;93(3):
pubmed: 28115400
Nat Rev Microbiol. 2013 Feb;11(2):95-105
pubmed: 23268227
PeerJ. 2017 Sep 29;5:e3865
pubmed: 28975058
Appl Environ Microbiol. 2001 Nov;67(11):4975-83
pubmed: 11679315
Bioinformatics. 2014 Jul 15;30(14):2068-9
pubmed: 24642063
Appl Environ Microbiol. 2012 Oct;78(19):6900-7
pubmed: 22820333
Bioinformatics. 2020 Apr 1;36(7):2251-2252
pubmed: 31742321
Nat Microbiol. 2017 May 30;2:17065
pubmed: 28555622
Nat Biotechnol. 2017 Aug 8;35(8):725-731
pubmed: 28787424
J Bacteriol. 2003 Dec;185(23):6938-49
pubmed: 14617658
FEMS Microbiol Ecol. 1999 Dec 1;30(4):285-293
pubmed: 10568837
Bioinformatics. 2018 Jul 15;34(14):2371-2375
pubmed: 29506021
Nucleic Acids Res. 2019 Jul 2;47(W1):W81-W87
pubmed: 31032519
Nat Rev Microbiol. 2015 Jan;13(1):13-27
pubmed: 25435307
Proc Natl Acad Sci U S A. 2012 Aug 28;109(35):14041-5
pubmed: 22826241