Journal
JOURNAL OF MICROBIOLOGICAL METHODS
Volume 70, Issue 1, Pages 103-111Publisher
ELSEVIER SCIENCE BV
DOI: 10.1016/j.mimet.2007.03.015
Keywords
denaturing gradient gel electrophoresis (DGGE); dissimilatory (bi)sulfite reductase (DSR); sulfate-reducing prokaryotes (SRP); soil; sediment; Bolboschoenus (Scirpus) maritimus
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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. (C) 2007 Elsevier B.V All rights reserved.
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