A consensus protocol for the recovery of mercury methylation genes from metagenomes
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...
Published in: | Molecular Ecology Resources |
---|---|
Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Linnéuniversitetet, Institutionen för biologi och miljö (BOM)
2023
|
Subjects: | |
Online Access: | http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-116300 https://doi.org/10.1111/1755-0998.13687 |
id |
ftlinnaeusuniv:oai:DiVA.org:lnu-116300 |
---|---|
record_format |
openpolar |
spelling |
ftlinnaeusuniv:oai:DiVA.org:lnu-116300 2023-05-15T15:08:16+02:00 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 Bjoern, Erik Buck, Moritz Cosio, Claudia Elias, Dwayne A. Gilmour, Cynthia Goni-Urriza, Marisol Gu, Baohua Lin, Heyu Liu, Yu-Rong McMahon, Katherine Moreau, John W. Pinhassi, Jarone Podar, Mircea Puente-Sanchez, Fernando Sanchez, Pablo Storck, Veronika Tada, Yuya Vigneron, Adrien Walsh, David A. Vandewalle-Capo, Marine Bravo, Andrea G. Gionfriddo, Caitlin M. 2023 application/pdf http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-116300 https://doi.org/10.1111/1755-0998.13687 eng eng Linnéuniversitetet, Institutionen för biologi och miljö (BOM) Linnéuniversitetet, Vatten CSIC, Spain;Swedish University of Agricultural Sciences, Sweden Univ Wisconsin, USA Colorado State Univ, USA New Mexico Inst Min & Technol, USA;Natl Cave & Karst Res Inst, USA CSIC, Spain Univ Montreal, Canada Swedish University of Agricultural Sciences, Sweden Umeå University, Sweden Univ Reims, France Elias Consulting LLC, USA Smithsonian Environm Res Ctr, USA Univ Pau & Pays Adour, France Oak Ridge Natl Lab, USA Univ Melbourne, Australia Huazhong Agr Univ, China Univ Glasgow, UK Natl Inst Minamata Dis, Japan Concordia Univ, Canada Molecular Ecology Resources, 1755-098X, 2023, 23:1, s. 190-204 orcid:0000-0001-5290-9142 orcid:0000-0002-3157-3544 orcid:0000-0002-0340-3249 orcid:0000-0001-8570-2738 orcid:0000-0002-6405-1347 http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-116300 doi:10.1111/1755-0998.13687 PMID 35839241 ISI:000836019100001 Scopus 2-s2.0-85135534585 info:eu-repo/semantics/openAccess bioinformatics hg methylation hgcAB genes hg-MATE marky-coco mercury metagenomics Bioinformatics and Systems Biology Bioinformatik och systembiologi Ecology Ekologi Article in journal info:eu-repo/semantics/article text 2023 ftlinnaeusuniv https://doi.org/10.1111/1755-0998.13687 2023-02-22T23:33:16Z 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 Linnaeus University Kalmar Växjö: Publications (DiVA) Arctic Molecular Ecology Resources 23 1 190 204 |
institution |
Open Polar |
collection |
Linnaeus University Kalmar Växjö: Publications (DiVA) |
op_collection_id |
ftlinnaeusuniv |
language |
English |
topic |
bioinformatics hg methylation hgcAB genes hg-MATE marky-coco mercury metagenomics Bioinformatics and Systems Biology Bioinformatik och systembiologi Ecology Ekologi |
spellingShingle |
bioinformatics hg methylation hgcAB genes hg-MATE marky-coco mercury metagenomics Bioinformatics and Systems Biology Bioinformatik och systembiologi Ecology Ekologi Capo, Eric Peterson, Benjamin D. Kim, Minjae Jones, Daniel S. Acinas, Silvia G. Amyot, Marc Bertilsson, Stefan Bjoern, Erik Buck, Moritz Cosio, Claudia Elias, Dwayne A. Gilmour, Cynthia Goni-Urriza, Marisol Gu, Baohua Lin, Heyu Liu, Yu-Rong McMahon, Katherine Moreau, John W. Pinhassi, Jarone Podar, Mircea Puente-Sanchez, Fernando Sanchez, 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 |
topic_facet |
bioinformatics hg methylation hgcAB genes hg-MATE marky-coco mercury metagenomics Bioinformatics and Systems Biology Bioinformatik och systembiologi Ecology Ekologi |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Capo, Eric Peterson, Benjamin D. Kim, Minjae Jones, Daniel S. Acinas, Silvia G. Amyot, Marc Bertilsson, Stefan Bjoern, Erik Buck, Moritz Cosio, Claudia Elias, Dwayne A. Gilmour, Cynthia Goni-Urriza, Marisol Gu, Baohua Lin, Heyu Liu, Yu-Rong McMahon, Katherine Moreau, John W. Pinhassi, Jarone Podar, Mircea Puente-Sanchez, Fernando Sanchez, Pablo Storck, Veronika Tada, Yuya Vigneron, Adrien Walsh, David A. Vandewalle-Capo, Marine Bravo, Andrea G. Gionfriddo, Caitlin M. |
author_facet |
Capo, Eric Peterson, Benjamin D. Kim, Minjae Jones, Daniel S. Acinas, Silvia G. Amyot, Marc Bertilsson, Stefan Bjoern, Erik Buck, Moritz Cosio, Claudia Elias, Dwayne A. Gilmour, Cynthia Goni-Urriza, Marisol Gu, Baohua Lin, Heyu Liu, Yu-Rong McMahon, Katherine Moreau, John W. Pinhassi, Jarone Podar, Mircea Puente-Sanchez, Fernando Sanchez, 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 |
Linnéuniversitetet, Institutionen för biologi och miljö (BOM) |
publishDate |
2023 |
url |
http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-116300 https://doi.org/10.1111/1755-0998.13687 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic permafrost |
genre_facet |
Arctic permafrost |
op_relation |
Molecular Ecology Resources, 1755-098X, 2023, 23:1, s. 190-204 orcid:0000-0001-5290-9142 orcid:0000-0002-3157-3544 orcid:0000-0002-0340-3249 orcid:0000-0001-8570-2738 orcid:0000-0002-6405-1347 http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-116300 doi:10.1111/1755-0998.13687 PMID 35839241 ISI:000836019100001 Scopus 2-s2.0-85135534585 |
op_rights |
info:eu-repo/semantics/openAccess |
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_ |
1766339654065324032 |