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

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

doi:10.1111/1755-0998.13687

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

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

Research output: Contribution to journal › Article › peer-review

28 Scopus citations

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.

Original language	English
Pages (from-to)	190-204
Number of pages	15
Journal	Molecular Ecology Resources
Volume	23
Issue number	1
DOIs	https://doi.org/10.1111/1755-0998.13687
State	Published - Jan 2023

Bibliographical note

Publisher Copyright:
© 2022 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.

Funding

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). Caitlin Gionfriddo was a Robert and Arlene Kogod Secretarial Scholar with the Smithsonian Environmental Research Center while conducting work described in this manuscript. Benjamin Peterson was funded as a postdoctoral research associate by the National Science Foundation (award 1935173) during the work in this manuscript. The computations were performed on resources provided by SNIC through Uppsala Multidisciplinary Centre for Advanced Computational Science (UPPMAX) using the compute project SNIC 2021/5-53. Some of the computations for compiling the Hg-MATE database were conducted on the Smithsonian High Performance Cluster (SI/HPC), Smithsonian Institution. https://doi.org/10.25572/SIHPC. Oak Ridge National Laboratory is managed by UT-Battelle, LLC under contract no. DE-AC05-00OR22725 with the U.S. Department of Energy (DOE). The authors are thankful to an anonymous reviewer and the associate editor Lucie Zinger for their insightful comments, the members of the Meta-Hg working group (https://ercapo.wixsite.com/meta-hg) and of the Mersorcium network (https://mersorcium.github.io/). 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). Caitlin Gionfriddo was a Robert and Arlene Kogod Secretarial Scholar with the Smithsonian Environmental Research Center while conducting work described in this manuscript. Benjamin Peterson was funded as a postdoctoral research associate by the National Science Foundation (award 1935173) during the work in this manuscript. The computations were performed on resources provided by SNIC through Uppsala Multidisciplinary Centre for Advanced Computational Science (UPPMAX) using the compute project SNIC 2021/5‐53. Some of the computations for compiling the Hg‐MATE database were conducted on the Smithsonian High Performance Cluster (SI/HPC), Smithsonian Institution. https://doi.org/10.25572/SIHPC . Oak Ridge National Laboratory is managed by UT‐Battelle, LLC under contract no. DE‐AC05‐00OR22725 with the U.S. Department of Energy (DOE). The authors are thankful to an anonymous reviewer and the associate editor Lucie Zinger for their insightful comments, the members of the Meta‐Hg working group ( https://ercapo.wixsite.com/meta‐hg ) and of the Mersorcium network ( https://mersorcium.github.io/ ).

Funders	Funder number
Oak Ridge National Laboratory
Smithsonian Institution
U.S. Department of Energy
Mersorcium network
Smithsonian Environmental Research Center
UT Battelle LLC	DE-AC05-00OR22725
National Science Foundation Arctic Social Science Program	SNIC 2021/5-53, 1935173
UK Industrial Decarbonization Research and Innovation Centre	53706
Svenska Forskningsrådet Formas	2018‐01031, 863584

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 14 Life Below Water
SDG 15 Life on Land

Keywords

bioinformatics
hg methylation
hg-MATE
hgcAB genes
marky-coco
mercury
metagenomics

ASJC Scopus subject areas

Biotechnology
Ecology, Evolution, Behavior and Systematics
Genetics

Access to Document

10.1111/1755-0998.13687

Cite this

Capo, E., Peterson, B. D., Kim, M., Jones, D. S., Acinas, S. G., Amyot, M., Bertilsson, S., Björn, E., Buck, M., Cosio, C., Elias, D. A., Gilmour, C., Goñi-Urriza, M., Gu, B., Lin, H., Liu, Y. R., McMahon, K., Moreau, J. W., Pinhassi, J., ... Gionfriddo, C. M. (2023). A consensus protocol for the recovery of mercury methylation genes from metagenomes. Molecular Ecology Resources, 23(1), 190-204. https://doi.org/10.1111/1755-0998.13687

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title = "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 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.",

keywords = "bioinformatics, hg methylation, hg-MATE, hgcAB genes, marky-coco, mercury, metagenomics",

author = "Eric Capo and Peterson, \{Benjamin D.\} and Minjae Kim and Jones, \{Daniel S.\} and Acinas, \{Silvia G.\} and Marc Amyot and Stefan Bertilsson and Erik Bj{\"o}rn and Moritz Buck and Claudia Cosio and Elias, \{Dwayne A.\} and Cynthia Gilmour and Marisol Go{\~n}i-Urriza and Baohua Gu and Heyu Lin and Liu, \{Yu Rong\} and Katherine McMahon and Moreau, \{John W.\} and Jarone Pinhassi and Mircea Podar and Fernando Puente-S{\'a}nchez and Pablo S{\'a}nchez and Veronika Storck and Yuya Tada and Adrien Vigneron and Walsh, \{David A.\} and Marine Vandewalle-Capo and Bravo, \{Andrea G.\} and Gionfriddo, \{Caitlin M.\}",

note = "Publisher Copyright: {\textcopyright} 2022 The Authors. Molecular Ecology Resources published by John Wiley \& Sons Ltd.",

year = "2023",

month = jan,

doi = "10.1111/1755-0998.13687",

language = "English",

volume = "23",

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Capo, E, Peterson, BD, Kim, M, Jones, DS, Acinas, SG, Amyot, M, Bertilsson, S, Björn, E, Buck, M, Cosio, C, Elias, DA, Gilmour, C, Goñi-Urriza, M, Gu, B, Lin, H, Liu, YR, McMahon, K, Moreau, JW, Pinhassi, J, Podar, M, Puente-Sánchez, F, Sánchez, P, Storck, V, Tada, Y, Vigneron, A, Walsh, DA, Vandewalle-Capo, M, Bravo, AG & Gionfriddo, CM 2023, 'A consensus protocol for the recovery of mercury methylation genes from metagenomes', Molecular Ecology Resources, vol. 23, no. 1, pp. 190-204. https://doi.org/10.1111/1755-0998.13687

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T1 - A consensus protocol for the recovery of mercury methylation genes from metagenomes

AU - Capo, Eric

AU - Peterson, Benjamin D.

AU - Kim, Minjae

AU - Jones, Daniel S.

AU - Acinas, Silvia G.

AU - Amyot, Marc

AU - Bertilsson, Stefan

AU - Björn, Erik

AU - Buck, Moritz

AU - Cosio, Claudia

AU - Elias, Dwayne A.

AU - Gilmour, Cynthia

AU - Goñi-Urriza, Marisol

AU - Gu, Baohua

AU - Lin, Heyu

AU - Liu, Yu Rong

AU - McMahon, Katherine

AU - Moreau, John W.

AU - Pinhassi, Jarone

AU - Podar, Mircea

AU - Puente-Sánchez, Fernando

AU - Sánchez, Pablo

AU - Storck, Veronika

AU - Tada, Yuya

AU - Vigneron, Adrien

AU - Walsh, David A.

AU - Vandewalle-Capo, Marine

AU - Bravo, Andrea G.

AU - Gionfriddo, Caitlin M.

PY - 2023/1

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AB - 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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KW - hg methylation

KW - hg-MATE

KW - hgcAB genes

KW - marky-coco

KW - mercury

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

Abstract

Bibliographical note

Funding

UN SDGs

Keywords

ASJC Scopus subject areas

Access to Document

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