Capo, Eric
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences
- Institut de Ciències del Mar (ICM-CSIC)
Research article2023Peer reviewedOpen access
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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Abstract
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.
Keywords
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
Bertilsson, Stefan
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences
Buck, Moritz
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences
Puente Sanchez, Fernando
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences
Vandewalle, Marine
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences
SLU Authors
UKÄ Subject classification
Ecology
Publication identifier
DOI: https://doi.org/10.1111/1755-0998.13687
Permanent link to this page (URI)
https://res.slu.se/id/publ/118707