A consensus protocol for the recovery of mercury methylation genes from metagenomes.
bioinformatics
hg methylation
hg-MATE
hgcAB genes
marky-coco
mercury
metagenomics
Journal
Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604
Informations de publication
Date de publication:
Jan 2023
Jan 2023
Historique:
revised:
24
06
2022
received:
14
03
2022
accepted:
08
07
2022
pubmed:
16
7
2022
medline:
7
12
2022
entrez:
15
7
2022
Statut:
ppublish
Résumé
Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.
Identifiants
pubmed: 35839241
doi: 10.1111/1755-0998.13687
pmc: PMC10087281
doi:
Substances chimiques
Mercury
FXS1BY2PGL
Soil
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
190-204Subventions
Organisme : Severo Ochoa Excellence Program Post-doctoral Fellowship
ID : CEX2019-000928-S
Organisme : U.S. Department of Energy
Organisme : LLC
ID : DE-AC05-00OR22725
Organisme : Oak Ridge National Laboratory
Organisme : Smithsonian Institution
Organisme : Smithsonian High Performance Cluster (SI/HPC)
Organisme : Uppsala Multidisciplinary Centre for Advanced Computational Science (UPPMAX)
ID : SNIC 2021/5-53
Organisme : National Science Foundation
ID : 1935173
Organisme : EMFF-Blue Economy project MER-CLUB
ID : 863584
Organisme : Swedish Research Council Formas
ID : 2018-01031
Informations de copyright
© 2022 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.
Références
Mol Biol Evol. 2018 Jun 1;35(6):1547-1549
pubmed: 29722887
Front Microbiol. 2020 Sep 22;11:574080
pubmed: 33072037
Cell. 2019 Nov 14;179(5):1068-1083.e21
pubmed: 31730850
Nat Biotechnol. 2021 Apr;39(4):499-509
pubmed: 33169036
Appl Environ Microbiol. 2011 Jun;77(12):3938-51
pubmed: 21515733
Sci Adv. 2015 Oct 09;1(9):e1500675
pubmed: 26601305
Mol Ecol Resour. 2023 Jan;23(1):190-204
pubmed: 35839241
Environ Sci Technol. 2019 Aug 6;53(15):8649-8663
pubmed: 31260289
mBio. 2018 Apr 10;9(2):
pubmed: 29636434
Nat Microbiol. 2016 Apr 11;1:16048
pubmed: 27572647
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
mSystems. 2020 Aug 18;5(4):
pubmed: 32817383
Environ Sci Technol. 2018 Sep 4;52(17):9758-9767
pubmed: 30037219
Bioinformatics. 2014 Apr 1;30(7):923-30
pubmed: 24227677
NPJ Biofilms Microbiomes. 2021 Nov 19;7(1):83
pubmed: 34799579
ISME J. 2012 Jan;6(1):81-93
pubmed: 21716304
Front Microbiol. 2021 Oct 04;12:741523
pubmed: 34675906
Nucleic Acids Res. 2007 Jan;35(Database issue):D260-4
pubmed: 17151080
Nature. 2017 Nov 23;551(7681):457-463
pubmed: 29088705
Nat Methods. 2017 Nov;14(11):1063-1071
pubmed: 28967888
ISME J. 2019 Dec;13(12):3126-3130
pubmed: 31388130
Science. 2013 Mar 15;339(6125):1332-5
pubmed: 23393089
Bioinformatics. 2015 May 15;31(10):1674-6
pubmed: 25609793
Syst Appl Microbiol. 2019 Jan;42(1):30-40
pubmed: 30528276
ISME J. 2019 Jul;13(7):1659-1675
pubmed: 30809010
Sci Total Environ. 2021 Jun 20;774:145686
pubmed: 33609815
Bioinformatics. 2014 Mar 1;30(5):629-35
pubmed: 24123672
Environ Microbiol. 2020 Sep;22(9):3685-3699
pubmed: 32558127
BMC Genomics. 2017 Jul 10;18(1):521
pubmed: 28693474
Mol Biol Evol. 2008 Jul;25(7):1307-20
pubmed: 18367465
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37
pubmed: 21593126
Nat Microbiol. 2016 Aug 01;1(10):16127
pubmed: 27670112
BMC Genomics. 2019 Dec 10;20(1):960
pubmed: 31823721
Genome Biol. 2015 Mar 25;16:51
pubmed: 25853934
Bioinformatics. 2018 Sep 1;34(17):i884-i890
pubmed: 30423086
Front Microbiol. 2020 Oct 06;11:541554
pubmed: 33123100
Sci Data. 2018 Jul 31;5:180146
pubmed: 30063227
Stand Genomic Sci. 2017 Jan 19;12:9
pubmed: 28127419
ISME J. 2021 Jun;15(6):1810-1825
pubmed: 33504941
Environ Microbiol Rep. 2020 Jun;12(3):277-287
pubmed: 32090489
Environ Sci Technol. 2020 Dec 15;54(24):15840-15851
pubmed: 33228362
BMC Genomics. 2018 Apr 20;19(1):274
pubmed: 29678163
Environ Sci Technol. 2016 Sep 6;50(17):9177-86
pubmed: 27461938
Appl Environ Microbiol. 2018 Nov 15;84(23):
pubmed: 30242005
Nature. 2022 Jul;607(7917):111-118
pubmed: 35732736
Nucleic Acids Res. 2019 Jul 2;47(W1):W256-W259
pubmed: 30931475
Appl Environ Microbiol. 2006 Dec;72(12):7919-21
pubmed: 17056699
Mol Ecol Resour. 2023 Jan;23(1):16-40
pubmed: 35108459
Microbiome. 2022 May 6;10(1):72
pubmed: 35524337
Appl Environ Microbiol. 2015 May 1;81(9):3205-17
pubmed: 25724962
Commun Biol. 2020 Jun 19;3(1):320
pubmed: 32561885
Appl Environ Microbiol. 1985 Aug;50(2):498-502
pubmed: 16346866
Environ Sci Technol. 2013 Oct 15;47(20):11810-20
pubmed: 24024607
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Environ Sci Technol. 2022 Sep 20;56(18):13119-13130
pubmed: 36069707
J Mol Biol. 2001 Jan 19;305(3):567-80
pubmed: 11152613
Appl Environ Microbiol. 2006 Jan;72(1):457-64
pubmed: 16391078
Commun Biol. 2021 Nov 18;4(1):1302
pubmed: 34795375
BMC Bioinformatics. 2010 Mar 08;11:119
pubmed: 20211023
Bioinformatics. 2019 Nov 15;:
pubmed: 31730192
Bioinformatics. 2016 Apr 1;32(7):1088-90
pubmed: 26614127
Environ Sci Technol. 2011 Sep 15;45(18):7693-700
pubmed: 21875053
Environ Sci Technol. 2018 Nov 20;52(22):13110-13118
pubmed: 30335986
BMC Bioinformatics. 2010 Oct 30;11:538
pubmed: 21034504
Front Microbiol. 2020 Jul 03;11:1369
pubmed: 32719662
Limnol Oceanogr. 2020 May;65(5):1010-1027
pubmed: 32612306