A consensus protocol for the recovery of mercury methylation genes from metagenomes
International audience 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 di...
Published in: | Molecular Ecology Resources |
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Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Other Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
HAL CCSD
2022
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Subjects: | |
Online Access: | https://hal-univ-pau.archives-ouvertes.fr/hal-03766637 https://hal-univ-pau.archives-ouvertes.fr/hal-03766637/document https://hal-univ-pau.archives-ouvertes.fr/hal-03766637/file/FULLTEXT01.pdf https://doi.org/10.1111/1755-0998.13687 |
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ftunivnantes:oai:HAL:hal-03766637v1 |
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openpolar |
institution |
Open Polar |
collection |
Université de Nantes: HAL-UNIV-NANTES |
op_collection_id |
ftunivnantes |
language |
English |
topic |
bioinformatics hg methylation hg-MATE hgcAB genes marky-coco mercury metagenomics [CHIM.MATE]Chemical Sciences/Material chemistry [CHIM.POLY]Chemical Sciences/Polymers [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry [CHIM.ANAL]Chemical Sciences/Analytical chemistry |
spellingShingle |
bioinformatics hg methylation hg-MATE hgcAB genes marky-coco mercury metagenomics [CHIM.MATE]Chemical Sciences/Material chemistry [CHIM.POLY]Chemical Sciences/Polymers [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry [CHIM.ANAL]Chemical Sciences/Analytical chemistry Capo, Eric Peterson, Benjamin, Kim, Minjae Jones, Daniel, Acinas, Silvia, Amyot, Marc Bertilsson, Stefan Björn, Erik Buck, Moritz Cosio, Claudia Elias, Dwayne, Gilmour, Cynthia Goñi‐urriza, Marisol Gu, Baohua Lin, Heyu Liu, Yu‐rong Mcmahon, Katherine Moreau, John, Pinhassi, Jarone Podar, Mircea Puente‐sánchez, Fernando Sánchez, Pablo Storck, Veronika Tada, Yuya Vigneron, Adrien Walsh, David, Vandewalle‐capo, Marine Bravo, Andrea, Gionfriddo, Caitlin A consensus protocol for the recovery of mercury methylation genes from metagenomes |
topic_facet |
bioinformatics hg methylation hg-MATE hgcAB genes marky-coco mercury metagenomics [CHIM.MATE]Chemical Sciences/Material chemistry [CHIM.POLY]Chemical Sciences/Polymers [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry [CHIM.ANAL]Chemical Sciences/Analytical chemistry |
description |
International audience 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 |
Institute of Marine Sciences / Institut de Ciències del Mar Barcelona (ICM) Consejo Superior de Investigaciones Científicas Madrid (CSIC) University of Wisconsin-Madison Colorado State University Fort Collins (CSU) National Cave and Karst Research Institute (NCKRI) Groupe de recherche interuniversitaire en limnologie et en environnement aquatique - GRIL (Montréal, Canada) Université de Montréal (UdeM) Swedish University of Agricultural Sciences (SLU) Umeå University Stress Environnementaux et BIOsurveillance des milieux aquatiques (SEBIO) Institut National de l'Environnement Industriel et des Risques (INERIS)-Université de Reims Champagne-Ardenne (URCA)-Université Le Havre Normandie (ULH) Normandie Université (NU)-Normandie Université (NU)-SFR Condorcet Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS) Smithsonian Environmental Research Center (SERC) Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM) Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS) Oak Ridge National Laboratory Oak Ridge (ORNL) UT-Battelle, LLC University of Melbourne Huazhong Agricultural University Wuhan (HZAU) School of Geographical and Earth Sciences, University of Glasgow University of Glasgow Linnaeus University National Institute for Minamata Disease Department of Biology Concordia Concordia University Montreal |
format |
Article in Journal/Newspaper |
author |
Capo, Eric Peterson, Benjamin, Kim, Minjae Jones, Daniel, Acinas, Silvia, Amyot, Marc Bertilsson, Stefan Björn, Erik Buck, Moritz Cosio, Claudia Elias, Dwayne, Gilmour, Cynthia Goñi‐urriza, Marisol Gu, Baohua Lin, Heyu Liu, Yu‐rong Mcmahon, Katherine Moreau, John, Pinhassi, Jarone Podar, Mircea Puente‐sánchez, Fernando Sánchez, Pablo Storck, Veronika Tada, Yuya Vigneron, Adrien Walsh, David, Vandewalle‐capo, Marine Bravo, Andrea, Gionfriddo, Caitlin |
author_facet |
Capo, Eric Peterson, Benjamin, Kim, Minjae Jones, Daniel, Acinas, Silvia, Amyot, Marc Bertilsson, Stefan Björn, Erik Buck, Moritz Cosio, Claudia Elias, Dwayne, Gilmour, Cynthia Goñi‐urriza, Marisol Gu, Baohua Lin, Heyu Liu, Yu‐rong Mcmahon, Katherine Moreau, John, Pinhassi, Jarone Podar, Mircea Puente‐sánchez, Fernando Sánchez, Pablo Storck, Veronika Tada, Yuya Vigneron, Adrien Walsh, David, Vandewalle‐capo, Marine Bravo, Andrea, Gionfriddo, Caitlin |
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 |
HAL CCSD |
publishDate |
2022 |
url |
https://hal-univ-pau.archives-ouvertes.fr/hal-03766637 https://hal-univ-pau.archives-ouvertes.fr/hal-03766637/document https://hal-univ-pau.archives-ouvertes.fr/hal-03766637/file/FULLTEXT01.pdf https://doi.org/10.1111/1755-0998.13687 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic permafrost |
genre_facet |
Arctic permafrost |
op_source |
ISSN: 1755-098X EISSN: 1755-0998 Molecular Ecology Resources https://hal-univ-pau.archives-ouvertes.fr/hal-03766637 Molecular Ecology Resources, 2022, ⟨10.1111/1755-0998.13687⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1111/1755-0998.13687 hal-03766637 https://hal-univ-pau.archives-ouvertes.fr/hal-03766637 https://hal-univ-pau.archives-ouvertes.fr/hal-03766637/document https://hal-univ-pau.archives-ouvertes.fr/hal-03766637/file/FULLTEXT01.pdf doi:10.1111/1755-0998.13687 |
op_rights |
http://creativecommons.org/licenses/by-nc/ info:eu-repo/semantics/OpenAccess |
op_rightsnorm |
CC-BY-NC |
op_doi |
https://doi.org/10.1111/1755-0998.13687 |
container_title |
Molecular Ecology Resources |
_version_ |
1766339551375130624 |
spelling |
ftunivnantes:oai:HAL:hal-03766637v1 2023-05-15T15:08:08+02:00 A consensus protocol for the recovery of mercury methylation genes from metagenomes Capo, Eric Peterson, Benjamin, Kim, Minjae Jones, Daniel, Acinas, Silvia, Amyot, Marc Bertilsson, Stefan Björn, Erik Buck, Moritz Cosio, Claudia Elias, Dwayne, Gilmour, Cynthia Goñi‐urriza, Marisol Gu, Baohua Lin, Heyu Liu, Yu‐rong Mcmahon, Katherine Moreau, John, Pinhassi, Jarone Podar, Mircea Puente‐sánchez, Fernando Sánchez, Pablo Storck, Veronika Tada, Yuya Vigneron, Adrien Walsh, David, Vandewalle‐capo, Marine Bravo, Andrea, Gionfriddo, Caitlin Institute of Marine Sciences / Institut de Ciències del Mar Barcelona (ICM) Consejo Superior de Investigaciones Científicas Madrid (CSIC) University of Wisconsin-Madison Colorado State University Fort Collins (CSU) National Cave and Karst Research Institute (NCKRI) Groupe de recherche interuniversitaire en limnologie et en environnement aquatique - GRIL (Montréal, Canada) Université de Montréal (UdeM) Swedish University of Agricultural Sciences (SLU) Umeå University Stress Environnementaux et BIOsurveillance des milieux aquatiques (SEBIO) Institut National de l'Environnement Industriel et des Risques (INERIS)-Université de Reims Champagne-Ardenne (URCA)-Université Le Havre Normandie (ULH) Normandie Université (NU)-Normandie Université (NU)-SFR Condorcet Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS) Smithsonian Environmental Research Center (SERC) Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM) Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS) Oak Ridge National Laboratory Oak Ridge (ORNL) UT-Battelle, LLC University of Melbourne Huazhong Agricultural University Wuhan (HZAU) School of Geographical and Earth Sciences, University of Glasgow University of Glasgow Linnaeus University National Institute for Minamata Disease Department of Biology Concordia Concordia University Montreal 2022-08-04 https://hal-univ-pau.archives-ouvertes.fr/hal-03766637 https://hal-univ-pau.archives-ouvertes.fr/hal-03766637/document https://hal-univ-pau.archives-ouvertes.fr/hal-03766637/file/FULLTEXT01.pdf https://doi.org/10.1111/1755-0998.13687 en eng HAL CCSD Wiley/Blackwell info:eu-repo/semantics/altIdentifier/doi/10.1111/1755-0998.13687 hal-03766637 https://hal-univ-pau.archives-ouvertes.fr/hal-03766637 https://hal-univ-pau.archives-ouvertes.fr/hal-03766637/document https://hal-univ-pau.archives-ouvertes.fr/hal-03766637/file/FULLTEXT01.pdf doi:10.1111/1755-0998.13687 http://creativecommons.org/licenses/by-nc/ info:eu-repo/semantics/OpenAccess CC-BY-NC ISSN: 1755-098X EISSN: 1755-0998 Molecular Ecology Resources https://hal-univ-pau.archives-ouvertes.fr/hal-03766637 Molecular Ecology Resources, 2022, ⟨10.1111/1755-0998.13687⟩ bioinformatics hg methylation hg-MATE hgcAB genes marky-coco mercury metagenomics [CHIM.MATE]Chemical Sciences/Material chemistry [CHIM.POLY]Chemical Sciences/Polymers [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry [CHIM.ANAL]Chemical Sciences/Analytical chemistry info:eu-repo/semantics/article Journal articles 2022 ftunivnantes https://doi.org/10.1111/1755-0998.13687 2023-03-08T01:28:31Z International audience 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 Université de Nantes: HAL-UNIV-NANTES Arctic Molecular Ecology Resources |