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

• Published in: Molecular Ecology Resources
• Main Authors: Capo, Eric, Peterson, Benjamin D., Kim, Minjae, Jones, Daniel S., Acinas, Silvia G., Amyot, Marc, Bertilsson, Stefan, Björn, Erik, Buck, Moritz, Cosio, Claudia, Elias, Dwayne A., Gilmour, Cynthia, Goñi-Urriza, Marisol, Gu, Baohua, Lin, Heyu, Liu, Yu-Rong, McMahon, Katherine D., Moreau, John W., Pinhassi, Jarone, Podar, Mircea, Puente-Sánchez, Fernando, Sánchez, Pablo, Storck, Veronika, Tada, Yuya, Vigneron, Adrien, Walsh, David A., Vandewalle, Marie, Bravo, Andrea G., Gionfriddo, Caitlin M.
• Other Authors: Agencia Estatal de Investigación (España), Swedish Research Council, European Maritime and Fisheries Fund, National Science Foundation (US), Department of Energy (US)
• Format: Article in Journal/Newspaper
• Language: English
• Published: John Wiley & Sons 2023
• Subjects: Bioinformatics; hg methylation; hgcAB genes; hg-MATE; Marky-coco; Mercury; Metagenomics; Arctic; permafrost
• Online Access: http://hdl.handle.net/10261/288946; https://doi.org/10.1111/1755-0998.13687

15 pages, 4 figures, 3 tables, supporting Information https://doi.org/10.1111/1755-0998.13687.-- Data availability statement: All metagenomes analysed in this study are in the public domain as described in Table 2 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 This work was funded by the Severo Ochoa Excellence Programme postdoctoral fellowship awarded in 2021 to Eric Capo (CEX2019-000928-S), the Swedish Research Council Formas (grant 2018-01031), the EMFF-Blue Economy project MER-CLUB (grant 863584). [.]. Benjamin Peterson was funded as a postdoctoral research associate by the National Science Foundation (award 1935173) during the work in this manuscript.[.]. Oak Ridge National ...