Open this publication in new window or tab >>Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, Spain.
Department of Biological Sciences, University of Montréal, QC, Montréal, Canada.
Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Umeå University, Faculty of Science and Technology, Department of Chemistry.
Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden.
University of Reims Champagne-Ardenne, UMR-I 02 SEBIO, Reims, France.
Elias Consulting, LLC, TN, Knoxville, United States.
Smithsonian Environmental Research Center, MD, Edgewater, United States.
University of Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
Oak Ridge National Laboratory, TN, Oak Ridge, United States.
School of Geography, Earth and Atmospheric Sciences, The University of Melbourne, VIC, Parkville, Australia.
College of Resources and Environment, Huazhong Agricultural University, Wuhan, China.
Department of Bacteriology, University of Wisconsin at Madison, WI, Madison, United States.
School of Geographical and Earth Sciences, University of Glasgow, Glasgow, United Kingdom.
Centre for Ecology and Evolution in Microbial Model Systems – EEMiS, Linnaeus University, Kalmar, Sweden.
Oak Ridge National Laboratory, TN, Oak Ridge, United States.
Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, Spain.
Department of Biological Sciences, University of Montréal, QC, Montréal, Canada.
Department of Environment and Public Health, National Institute for Minamata Disease, Kumamoto, Japan.
University of Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
Department of Biology, Concordia University, QC, Montreal, Canada.
Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, Spain.
Smithsonian Environmental Research Center, MD, Edgewater, United States.
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2023 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 23, no 1, p. 190-204Article in journal (Refereed) Published
Abstract [en]
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.
Place, publisher, year, edition, pages
John Wiley & Sons, 2023
Keywords
bioinformatics, hg methylation, hg-MATE, hgcAB genes, marky-coco, mercury, metagenomics
National Category
Ecology Environmental Sciences
Identifiers
urn:nbn:se:umu:diva-198622 (URN)10.1111/1755-0998.13687 (DOI)000836019100001 ()35839241 (PubMedID)2-s2.0-85135534585 (Scopus ID)
Funder
Swedish Research Council Formas, 2018-01031
2022-08-152022-08-152022-12-30Bibliographically approved