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A consensus protoco...
A consensus protocol for the recovery of mercury methylation genes from metagenomes
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- Capo, Eric (författare)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för vatten och miljö,Department of Aquatic Sciences and Assessment,Institut de Ciències del Mar (ICM-CSIC)
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- Peterson, Benjamin D. (författare)
- Univ Wisconsin, USA,Department of Bacteriology, University of Wisconsin at Madison, WI, Madison, United States
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- Kim, Minjae (författare)
- Colorado State Univ, USA,Natural Resource Ecology Laboratory, Colorado State University, CO, Fort Collins, United States
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- Jones, Daniel S. (författare)
- New Mexico Inst Min & Technol, USA;Natl Cave & Karst Res Inst, USA,Department of Earth and Environmental Science, New Mexico Institute of Mining and Technology, NM, Socorro, United States; National Cave and Karst Research Institute, NM, Carlsbad, United States
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- Acinas, Silvia G. (författare)
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, Spain
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- Amyot, Marc (författare)
- Univ Montreal, Canada,Department of Biological Sciences, University of Montréal, QC, Montréal, Canada
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- Bertilsson, Stefan (författare)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för vatten och miljö,Department of Aquatic Sciences and Assessment
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- Björn, Erik (författare)
- Umeå universitet,Kemiska institutionen,Umeå University, Sweden
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- Buck, Moritz (författare)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för vatten och miljö,Department of Aquatic Sciences and Assessment
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- Cosio, Claudia (författare)
- Univ Reims, France,University of Reims Champagne-Ardenne, UMR-I 02 SEBIO, Reims, France
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- Elias, Dwayne A. (författare)
- Elias Consulting LLC, USA,Elias Consulting, LLC, TN, Knoxville, United States
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- Gilmour, Cynthia (författare)
- Smithsonian Environm Res Ctr, USA,Smithsonian Environmental Research Center, MD, Edgewater, United States
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- Goni-Urriza, Marisol (författare)
- Univ Pau & Pays Adour, France,University of Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
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- Gu, Baohua (författare)
- Oak Ridge Natl Lab, USA,Oak Ridge National Laboratory, TN, Oak Ridge, United States
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- Lin, Heyu (författare)
- Univ Melbourne, Australia,School of Geography, Earth and Atmospheric Sciences, The University of Melbourne, VIC, Parkville, Australia
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- Liu, Yu-Rong (författare)
- Huazhong Agr Univ, China,College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
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- McMahon, Katherine (författare)
- Univ Wisconsin, USA,Department of Bacteriology, University of Wisconsin at Madison, WI, Madison, United States
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- Moreau, John W. (författare)
- Univ Glasgow, UK,School of Geographical and Earth Sciences, University of Glasgow, Glasgow, United Kingdom
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- Pinhassi, Jarone (författare)
- Linnéuniversitetet,Institutionen för biologi och miljö (BOM),Vatten,Ctr Ecol & Evolut Microbial Model Syst EEMiS,Centre for Ecology and Evolution in Microbial Model Systems – EEMiS, Linnaeus University, Kalmar, Sweden
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- Podar, Mircea (författare)
- Oak Ridge Natl Lab, USA,Oak Ridge National Laboratory, TN, Oak Ridge, United States
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- Puente-Sanchez, Fernando (författare)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för vatten och miljö,Department of Aquatic Sciences and Assessment
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- Sanchez, Pablo (författare)
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, Spain
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- Storck, Veronika (författare)
- Univ Montreal, Canada,Department of Biological Sciences, University of Montréal, QC, Montréal, Canada
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- Tada, Yuya (författare)
- Natl Inst Minamata Dis, Japan,Department of Environment and Public Health, National Institute for Minamata Disease, Kumamoto, Japan
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- Vigneron, Adrien (författare)
- Univ Pau & Pays Adour, France,University of Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
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- Walsh, David A. (författare)
- Concordia Univ, Canada,Department of Biology, Concordia University, QC, Montreal, Canada
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- Vandewalle-Capo, Marine (författare)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för vatten och miljö,Department of Aquatic Sciences and Assessment
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- Bravo, Andrea G. (författare)
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, Spain
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- Gionfriddo, Caitlin M. (författare)
- Smithsonian Environm Res Ctr, USA,Smithsonian Environmental Research Center, MD, Edgewater, United States
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(creator_code:org_t)
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- 2022-08-04
- 2023
- Engelska.
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Ingår i: Molecular Ecology Resources. - : John Wiley & Sons. - 1755-098X .- 1755-0998. ; 23:1, s. 190-204
- Relaterad länk:
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https://doi.org/10.1...
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https://lnu.diva-por... (primary) (Raw object)
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https://umu.diva-por... (primary) (Raw object)
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https://pub.epsilon.... (primary) (Raw object) (free)
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https://urn.kb.se/re...
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https://doi.org/10.1...
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https://urn.kb.se/re...
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https://res.slu.se/i...
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Abstract
Ämnesord
Stäng
- 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.
Ämnesord
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Ekologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Ecology (hsv//eng)
- NATURVETENSKAP -- Geovetenskap och miljövetenskap -- Miljövetenskap (hsv//swe)
- NATURAL SCIENCES -- Earth and Related Environmental Sciences -- Environmental Sciences (hsv//eng)
Nyckelord
- bioinformatics
- hg methylation
- hgcAB genes
- hg-MATE
- marky-coco
- mercury
- metagenomics
- Ecology
- Ekologi
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
Hitta via bibliotek
Till lärosätets databas
- Av författaren/redakt...
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Capo, Eric
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Peterson, Benjam ...
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Kim, Minjae
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Jones, Daniel S.
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Acinas, Silvia G ...
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Amyot, Marc
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visa fler...
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Bertilsson, Stef ...
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Björn, Erik
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Buck, Moritz
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Cosio, Claudia
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Elias, Dwayne A.
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Gilmour, Cynthia
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Goni-Urriza, Mar ...
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Gu, Baohua
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Lin, Heyu
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Liu, Yu-Rong
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McMahon, Katheri ...
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Moreau, John W.
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Pinhassi, Jarone
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Podar, Mircea
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Puente-Sanchez, ...
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Sanchez, Pablo
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Storck, Veronika
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Tada, Yuya
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Vigneron, Adrien
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Walsh, David A.
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Vandewalle-Capo, ...
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Bravo, Andrea G.
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Gionfriddo, Cait ...
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visa färre...
- Om ämnet
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- NATURVETENSKAP
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NATURVETENSKAP
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och Biologi
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och Bioinformatik oc ...
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- NATURVETENSKAP
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NATURVETENSKAP
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och Biologi
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och Ekologi
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- NATURVETENSKAP
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NATURVETENSKAP
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och Geovetenskap och ...
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och Miljövetenskap
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Molecular Ecolog ...
- Av lärosätet
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Linnéuniversitetet
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Umeå universitet
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Sveriges Lantbruksuniversitet