A consensus protocol for the recovery of mercury methylation genes from metagenomes
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...
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Online Access: | http://dx.doi.org/10.1111/1755-0998.13687 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13687 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.13687 |
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crwiley:10.1111/1755-0998.13687 2024-09-09T19:25:55+00:00 A consensus protocol for the recovery of mercury methylation genes from metagenomes 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 Moreau, John W. Pinhassi, Jarone Podar, Mircea Puente‐Sánchez, Fernando Sánchez, Pablo Storck, Veronika Tada, Yuya Vigneron, Adrien Walsh, David A. Vandewalle‐Capo, Marine Bravo, Andrea G. Gionfriddo, Caitlin M. U.S. Department of Energy Oak Ridge National Laboratory Smithsonian Institution National Science Foundation Svenska Forskningsrådet Formas 2022 http://dx.doi.org/10.1111/1755-0998.13687 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13687 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.13687 en eng Wiley http://creativecommons.org/licenses/by-nc-nd/4.0/ Molecular Ecology Resources volume 23, issue 1, page 190-204 ISSN 1755-098X 1755-0998 journal-article 2022 crwiley https://doi.org/10.1111/1755-0998.13687 2024-08-22T04:15:40Z 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. Article in Journal/Newspaper Arctic permafrost Wiley Online Library Arctic Molecular Ecology Resources 23 1 190 204 |
institution |
Open Polar |
collection |
Wiley Online Library |
op_collection_id |
crwiley |
language |
English |
description |
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. |
author2 |
U.S. Department of Energy Oak Ridge National Laboratory Smithsonian Institution National Science Foundation Svenska Forskningsrådet Formas |
format |
Article in Journal/Newspaper |
author |
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 Moreau, John W. Pinhassi, Jarone Podar, Mircea Puente‐Sánchez, Fernando Sánchez, Pablo Storck, Veronika Tada, Yuya Vigneron, Adrien Walsh, David A. Vandewalle‐Capo, Marine Bravo, Andrea G. Gionfriddo, Caitlin M. |
spellingShingle |
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 Moreau, John W. Pinhassi, Jarone Podar, Mircea Puente‐Sánchez, Fernando Sánchez, Pablo Storck, Veronika Tada, Yuya Vigneron, Adrien Walsh, David A. Vandewalle‐Capo, Marine Bravo, Andrea G. Gionfriddo, Caitlin M. A consensus protocol for the recovery of mercury methylation genes from metagenomes |
author_facet |
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 Moreau, John W. Pinhassi, Jarone Podar, Mircea Puente‐Sánchez, Fernando Sánchez, Pablo Storck, Veronika Tada, Yuya Vigneron, Adrien Walsh, David A. Vandewalle‐Capo, Marine Bravo, Andrea G. Gionfriddo, Caitlin M. |
author_sort |
Capo, Eric |
title |
A consensus protocol for the recovery of mercury methylation genes from metagenomes |
title_short |
A consensus protocol for the recovery of mercury methylation genes from metagenomes |
title_full |
A consensus protocol for the recovery of mercury methylation genes from metagenomes |
title_fullStr |
A consensus protocol for the recovery of mercury methylation genes from metagenomes |
title_full_unstemmed |
A consensus protocol for the recovery of mercury methylation genes from metagenomes |
title_sort |
consensus protocol for the recovery of mercury methylation genes from metagenomes |
publisher |
Wiley |
publishDate |
2022 |
url |
http://dx.doi.org/10.1111/1755-0998.13687 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13687 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.13687 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic permafrost |
genre_facet |
Arctic permafrost |
op_source |
Molecular Ecology Resources volume 23, issue 1, page 190-204 ISSN 1755-098X 1755-0998 |
op_rights |
http://creativecommons.org/licenses/by-nc-nd/4.0/ |
op_doi |
https://doi.org/10.1111/1755-0998.13687 |
container_title |
Molecular Ecology Resources |
container_volume |
23 |
container_issue |
1 |
container_start_page |
190 |
op_container_end_page |
204 |
_version_ |
1809895629337395200 |