Abstract
In this study we evaluated a high resolution PCR-DGGE strategy for the characterization of complex sulfate-reducing microbial communities inhabiting natural environments. dsrB fragments were amplified with a two-step nested PCR protocol using combinations of primers targeting the dissimilatory (bi)sulfite reductase genes. The PCR-DGGE conditions were initially optimized using a dsrAB clone library obtained from a vegetated intertidal riparian soil along the river Rhine (Rozenburg, the Netherlands). Partial dsrB were successfully amplified from the same environmental DNA extracts used to construct the library, DGGE-separated and directly sequenced. The two approaches were in good agreement: the phylogenetic distribution of clones and DGGE-separated dsrB was comparable, suggesting the presence of sulfate-reducing prokaryotes (SRP) belonging to the families 'Desulfobacteraceae,' 'Desulfobulbaceae' and 'Syntrophobacteraceae,' and to the Desulfomonile tiedjei- and Desulfobacterium anilini-groups. The nested PCR-DGGE was also used to analyze sediment samples (Appels, Belgium) from a series of microcosms subjected to a tidal flooding regime with water of different salinity, and proved to be a valid tool also to monitor the SRP community variation over time and space as a consequence of environmental changes.
Publication types
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Evaluation Study
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Research Support, Non-U.S. Gov't
MeSH terms
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Biodiversity
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DNA, Bacterial / chemistry
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DNA, Bacterial / genetics*
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Deltaproteobacteria / classification*
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Deltaproteobacteria / genetics
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Deltaproteobacteria / isolation & purification*
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Electrophoresis, Polyacrylamide Gel / methods*
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Geologic Sediments / microbiology*
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Hydrogensulfite Reductase / genetics
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Molecular Sequence Data
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Nucleic Acid Denaturation
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Phylogeny
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Polymerase Chain Reaction / methods*
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Sequence Analysis, DNA
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Soil Microbiology*
Substances
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DNA, Bacterial
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Hydrogensulfite Reductase
Associated data
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GENBANK/AM181062
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GENBANK/AM181063
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GENBANK/AM181064
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GENBANK/AM181065
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