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Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases
The energy metabolism of essential microbial guilds in the biogeochemical sulfur cycle is based on a DsrAB-type dissimilatory (bi)sulfite reductase that either catalyzes the reduction of sulfite to sulfide during anaerobic respiration of sulfate, sulfite and organosulfonates, or acts in reverse duri...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351914/ https://www.ncbi.nlm.nih.gov/pubmed/25343514 http://dx.doi.org/10.1038/ismej.2014.208 |
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author | Müller, Albert Leopold Kjeldsen, Kasper Urup Rattei, Thomas Pester, Michael Loy, Alexander |
author_facet | Müller, Albert Leopold Kjeldsen, Kasper Urup Rattei, Thomas Pester, Michael Loy, Alexander |
author_sort | Müller, Albert Leopold |
collection | PubMed |
description | The energy metabolism of essential microbial guilds in the biogeochemical sulfur cycle is based on a DsrAB-type dissimilatory (bi)sulfite reductase that either catalyzes the reduction of sulfite to sulfide during anaerobic respiration of sulfate, sulfite and organosulfonates, or acts in reverse during sulfur oxidation. Common use of dsrAB as a functional marker showed that dsrAB richness in many environments is dominated by novel sequence variants and collectively represents an extensive, largely uncharted sequence assemblage. Here, we established a comprehensive, manually curated dsrAB/DsrAB database and used it to categorize the known dsrAB diversity, reanalyze the evolutionary history of dsrAB and evaluate the coverage of published dsrAB-targeted primers. Based on a DsrAB consensus phylogeny, we introduce an operational classification system for environmental dsrAB sequences that integrates established taxonomic groups with operational taxonomic units (OTUs) at multiple phylogenetic levels, ranging from DsrAB enzyme families that reflect reductive or oxidative DsrAB types of bacterial or archaeal origin, superclusters, uncultured family-level lineages to species-level OTUs. Environmental dsrAB sequences constituted at least 13 stable family-level lineages without any cultivated representatives, suggesting that major taxa of sulfite/sulfate-reducing microorganisms have not yet been identified. Three of these uncultured lineages occur mainly in marine environments, while specific habitat preferences are not evident for members of the other 10 uncultured lineages. In summary, our publically available dsrAB/DsrAB database, the phylogenetic framework, the multilevel classification system and a set of recommended primers provide a necessary foundation for large-scale dsrAB ecology studies with next-generation sequencing methods. |
format | Online Article Text |
id | pubmed-4351914 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-43519142015-05-01 Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases Müller, Albert Leopold Kjeldsen, Kasper Urup Rattei, Thomas Pester, Michael Loy, Alexander ISME J Original Article The energy metabolism of essential microbial guilds in the biogeochemical sulfur cycle is based on a DsrAB-type dissimilatory (bi)sulfite reductase that either catalyzes the reduction of sulfite to sulfide during anaerobic respiration of sulfate, sulfite and organosulfonates, or acts in reverse during sulfur oxidation. Common use of dsrAB as a functional marker showed that dsrAB richness in many environments is dominated by novel sequence variants and collectively represents an extensive, largely uncharted sequence assemblage. Here, we established a comprehensive, manually curated dsrAB/DsrAB database and used it to categorize the known dsrAB diversity, reanalyze the evolutionary history of dsrAB and evaluate the coverage of published dsrAB-targeted primers. Based on a DsrAB consensus phylogeny, we introduce an operational classification system for environmental dsrAB sequences that integrates established taxonomic groups with operational taxonomic units (OTUs) at multiple phylogenetic levels, ranging from DsrAB enzyme families that reflect reductive or oxidative DsrAB types of bacterial or archaeal origin, superclusters, uncultured family-level lineages to species-level OTUs. Environmental dsrAB sequences constituted at least 13 stable family-level lineages without any cultivated representatives, suggesting that major taxa of sulfite/sulfate-reducing microorganisms have not yet been identified. Three of these uncultured lineages occur mainly in marine environments, while specific habitat preferences are not evident for members of the other 10 uncultured lineages. In summary, our publically available dsrAB/DsrAB database, the phylogenetic framework, the multilevel classification system and a set of recommended primers provide a necessary foundation for large-scale dsrAB ecology studies with next-generation sequencing methods. Nature Publishing Group 2015-05 2014-10-24 /pmc/articles/PMC4351914/ /pubmed/25343514 http://dx.doi.org/10.1038/ismej.2014.208 Text en Copyright © 2015 International Society for Microbial Ecology http://creativecommons.org/licenses/by-nc-sa/3.0/ This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ |
spellingShingle | Original Article Müller, Albert Leopold Kjeldsen, Kasper Urup Rattei, Thomas Pester, Michael Loy, Alexander Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases |
title | Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases |
title_full | Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases |
title_fullStr | Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases |
title_full_unstemmed | Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases |
title_short | Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases |
title_sort | phylogenetic and environmental diversity of dsrab-type dissimilatory (bi)sulfite reductases |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351914/ https://www.ncbi.nlm.nih.gov/pubmed/25343514 http://dx.doi.org/10.1038/ismej.2014.208 |
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