A consensus protocol for the recovery of mercury methylation genes from metagenomes
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- Department of Marine Biology and Oceanography Institute of Marine Sciences, CSIC Barcelona Spain, Department of Aquatic Sciences and Assessment Swedish University of Agricultural Sciences Uppsala Sweden
- Department of Bacteriology University of Wisconsin at Madison Madison Wisconsin USA
- Natural Resource Ecology Laboratory Colorado State University Fort Collins Colorado USA
- Department of Earth and Environmental Science New Mexico Institute of Mining and Technology Socorro New Mexico USA, National Cave and Karst Research Institute Carlsbad New Mexico USA
- Department of Marine Biology and Oceanography Institute of Marine Sciences, CSIC Barcelona Spain
- Department of Biological Sciences University of Montréal Montréal Quebec Canada
- Department of Aquatic Sciences and Assessment Swedish University of Agricultural Sciences Uppsala Sweden
- Department of Chemistry Umeå University Umeå Sweden
- University of Reims Champagne‐Ardenne, UMR‐I 02 SEBIO Reims France
- Elias Consulting, LLC Knoxville Tennessee USA
- Smithsonian Environmental Research Center Edgewater Maryland USA
- University of Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM Pau France
- Oak Ridge National Laboratory Oak Ridge Tennessee USA
- School of Geography, Earth and Atmospheric Sciences, The University of Melbourne Parkville Victoria Australia
- College of Resources and Environment, Huazhong Agricultural University Wuhan China
- School of Geographical and Earth Sciences, University of Glasgow Glasgow UK
- Centre for Ecology and Evolution in Microbial Model Systems – EEMiS Linnaeus University Kalmar Sweden
- Department of Environment and Public Health National Institute for Minamata Disease Kumamoto Japan
- Department of Biology Concordia University Montreal Quebec Canada
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.
- Research Organization:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Organization:
- EMFF-Blue Economy Project; Swedish Research Council (SRC); USDOE
- Grant/Contract Number:
- AC05-00OR22725
- OSTI ID:
- 1879917
- Journal Information:
- Molecular Ecology Resources, Journal Name: Molecular Ecology Resources Journal Issue: 1 Vol. 23; ISSN 1755-098X
- Publisher:
- Wiley-BlackwellCopyright Statement
- Country of Publication:
- United Kingdom
- Language:
- English
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