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

Eric Capo, Benjamin D. Peterson, Minjae Kim, Daniel S. Jones, Silvia G. Acinas, Marc Amyot, Stefan Bertilsson, Erik Björn, Moritz Buck, Claudia Cosio, Dwayne A. Elias, Cynthia Gilmour, Marisol Goñi-Urriza, Baohua Gu, Heyu Lin, Yu Rong Liu, Katherine McMahon, John W. Moreau, Jarone Pinhassi, Mircea PodarFernando Puente-Sánchez, Pablo Sánchez, Veronika Storck, Yuya Tada, Adrien Vigneron, David A. Walsh, Marine Vandewalle-Capo, Andrea G. Bravo, Caitlin M. Gionfriddo

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

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.

Original languageEnglish
Pages (from-to)190-204
Number of pages15
JournalMolecular Ecology Resources
Volume23
Issue number1
DOIs
StatePublished - Jan 2023

Bibliographical note

Publisher Copyright:
© 2022 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.

Keywords

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

ASJC Scopus subject areas

  • Biotechnology
  • Ecology, Evolution, Behavior and Systematics
  • Genetics

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