A consensus protocol for the recovery of mercury methylation genes from metagenomes |
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| Authors: | 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 Podar Fernando Puente-Sánchez Pablo Sánchez Veronika Storck Yuya Tada Adrien Vigneron David A Walsh Marine Vandewalle-Capo Andrea G Bravo Caitlin M Gionfriddo |
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| Institution: | 1. Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, Spain;2. Department of Bacteriology, University of Wisconsin at Madison, Madison, Wisconsin, USA;3. Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado, USA;4. Department of Earth and Environmental Science, New Mexico Institute of Mining and Technology, Socorro, New Mexico, USA;5. Department of Biological Sciences, University of Montréal, Montréal, Quebec, Canada;6. Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden;7. Department of Chemistry, Umeå University, Umeå, Sweden;8. University of Reims Champagne-Ardenne, UMR-I 02 SEBIO, Reims, France;9. Elias Consulting, LLC, Knoxville, Tennessee, USA;10. Smithsonian Environmental Research Center, Edgewater, Maryland, USA;11. University of Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France;12. Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA;13. School of Geography, Earth and Atmospheric Sciences, The University of Melbourne, Parkville, Victoria, Australia;14. College of Resources and Environment, Huazhong Agricultural University, Wuhan, China;15. School of Geographical and Earth Sciences, University of Glasgow, Glasgow, UK;16. Centre for Ecology and Evolution in Microbial Model Systems – EEMiS, Linnaeus University, Kalmar, Sweden;17. Department of Environment and Public Health, National Institute for Minamata Disease, Kumamoto, Japan;18. Department of Biology, Concordia University, Montreal, Quebec, Canada |
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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. |
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| Keywords: | bioinformatics hg methylation hgcAB genes hg-MATE marky-coco mercury metagenomics |
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