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ISME J. 2015 May;9(5):1152-65. doi: 10.1038/ismej.2014.208. Epub 2014 Oct 24.

Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases.

Author information

  • 11] Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria [2] Austrian Polar Research Institute, Vienna, Austria.
  • 2Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.
  • 3Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
  • 4Department of Biology, University of Konstanz, Konstanz, Germany.

Abstract

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.

PMID:
25343514
PMCID:
PMC4351914
DOI:
10.1038/ismej.2014.208
[PubMed - indexed for MEDLINE]
Free PMC Article
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