Rapid enumeration of sulphate-reducing bacteria from aquatic environments using real-time PCR

• Kondo Ryuji

  Department of Marine Bioscience, Fukui Prefectural University

• Shigematsu Kotaro

  Graduate School of Bioscience and Biotechnology, Fukui Prefectural University

• Butani Junki

  Graduate School of Bioscience and Biotechnology, Fukui Prefectural University

Abstract

We describe a rapid and simple enumeration method for sulphate-reducing bacteria (SRB) from aquatic environments using a quantitative real-time PCR (qPCR) in combination with a rapid DNA isolation method. Enumeration of SRB in the sediment and water samples was performed by quantifying the copy number of the dsrA gene coding for the α-subunit of the dissimilatory sulphite reductase using real-time PCR with the SYBR Green I assay. Using dsrA-specific primers, we demonstrated that quantification of SRB in known numbers of SRB assemblages can be achieved. We compared DNA isolation methods using commercial DNA extraction kits and a published technique. We found two commercial kits were of advantage for extraction of DNA from water or sediment samples, where a large number of samples could be processed at the same time. We showed this newly developed qPCR technique targeting dsrA is rapid, simple and reproducible for the quantification of SRB numbers in situ and is superior to the use of culture-dependent techniques.

Journal

• Plankton and Benthos Research

  Plankton and Benthos Research 3 (3), 180-183, 2008

  The Plankton Society of Japan, The Japanese Association of Benthology

Keywords

• dissimilatory sulphite reductase
• DNA extraction
• real-time PCR

Details

• CRID: 1390282680242084096
• NII Article ID: 10021907601
• NII Book ID: AA12130745
• DOI: 10.3800/pbr.3.180
• ISSN: 1882627X
• ISSN: 18808247
• NDL BIB ID: 9638127
• Web Site: https://ndlsearch.ndl.go.jp/books/R000000004-I9638127
• Text Lang: en
• Data Source:
  • JaLC
  • NDL
  • Crossref
  • CiNii Articles
• Abstract License Flag: Disallowed