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Research article - Peer-reviewed, 2023

A consensus protocol for the recovery of mercury methylation genes from metagenomes

Capo, Eric; Peterson, Benjamin D.; Kim, Minjae; Jones, Daniel S.; Acinas, Silvia G.; Amyot, Marc; Bertilsson, Stefan; Bjoern, Erik; Buck, Moritz; Cosio, Claudia; Elias, Dwayne A.; Gilmour, Cynthia; Goni-Urriza, Marisol; Gu, Baohua; Lin, Heyu; Liu, Yu-Rong; McMahon, Katherine; Moreau, John W.; Pinhassi, Jarone; Podar, Mircea;
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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.


bioinformatics; hg methylation; hgcAB genes; hg-MATE; marky-coco; mercury; metagenomics

Published in

Molecular Ecology Resources
2023, volume: 23, number: 1, pages: 190-204
Publisher: WILEY

Authors' information

Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment
Institut de Ciències del Mar (ICM-CSIC)
Peterson, Benjamin D.
University of Wisconsin Madison
Kim, Minjae
Colorado State University
Jones, Daniel S.
New Mexico Institute of Mining Technology
Acinas, Silvia G.
CSIC - Instituto de Ciencias del Mar (ICM)
Amyot, Marc
Universite de Montreal
Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment
Bjoern, Erik
Umea University
Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment
Cosio, Claudia
Universite de Reims Champagne-Ardenne
Elias, Dwayne A.
Elias Consulting LLC
Gilmour, Cynthia
Smithsonian Environmental Research Center
Goni-Urriza, Marisol
Universite de Pau et des Pays de l'Adour
Gu, Baohua
Oak Ridge National Laboratory
Lin, Heyu
University of Melbourne
Liu, Yu-Rong
Huazhong Agricultural University
McMahon, Katherine
University of Wisconsin Madison
Moreau, John W.
University of Glasgow
Pinhassi, Jarone
Linnaeus University
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