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

• Published in: Molecular Ecology Resources
• Main Authors: Capo, Eric, Peterson, Benjamin, Kim, Minjae, Jones, Daniel, Acinas, Silvia, Amyot, Marc, Bertilsson, Stefan, Björn, Erik, Buck, Moritz, Cosio, Claudia, Elias, Dwayne, Gilmour, Cynthia, Goñi‐urriza, Marisol, Gu, Baohua, Lin, Heyu, Liu, Yu‐rong, Mcmahon, Katherine, Moreau, John, Pinhassi, Jarone, Podar, Mircea, Puente‐sánchez, Fernando, Sánchez, Pablo, Storck, Veronika, Tada, Yuya, Vigneron, Adrien, Walsh, David, Vandewalle‐capo, Marine, Bravo, Andrea, Gionfriddo, Caitlin
• Other Authors: Institute of Marine Sciences / Institut de Ciències del Mar Barcelona (ICM), Consejo Superior de Investigaciones Científicas Madrid (CSIC), University of Wisconsin-Madison, Colorado State University Fort Collins (CSU), National Cave and Karst Research Institute (NCKRI), Groupe de recherche interuniversitaire en limnologie et en environnement aquatique - GRIL (Montréal, Canada), Université de Montréal (UdeM), Swedish University of Agricultural Sciences (SLU), Umeå University, Stress Environnementaux et BIOsurveillance des milieux aquatiques (SEBIO), Institut National de l'Environnement Industriel et des Risques (INERIS)-Université de Reims Champagne-Ardenne (URCA)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Normandie Université (NU)-SFR Condorcet, Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Smithsonian Environmental Research Center (SERC), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Oak Ridge National Laboratory Oak Ridge (ORNL), UT-Battelle, LLC, University of Melbourne, Huazhong Agricultural University Wuhan (HZAU), School of Geographical and Earth Sciences, University of Glasgow, University of Glasgow, Linnaeus University, National Institute for Minamata Disease, Department of Biology Concordia, Concordia University Montreal
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2022
• Subjects: bioinformatics; hg methylation; hg-MATE; hgcAB genes; marky-coco; mercury; metagenomics; [CHIM.MATE]Chemical Sciences/Material chemistry; [CHIM.POLY]Chemical Sciences/Polymers; [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry; [CHIM.ANAL]Chemical Sciences/Analytical chemistry; Arctic; permafrost
• Online Access: https://hal-univ-pau.archives-ouvertes.fr/hal-03766637; https://hal-univ-pau.archives-ouvertes.fr/hal-03766637/document; https://hal-univ-pau.archives-ouvertes.fr/hal-03766637/file/FULLTEXT01.pdf; https://doi.org/10.1111/1755-0998.13687

International audience 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.