Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment

Appl Environ Microbiol. 2002 Oct;68(10):5064-81. doi: 10.1128/aem.68.10.5064-5081.2002.

Abstract

For cultivation-independent detection of sulfate-reducing prokaryotes (SRPs) an oligonucleotide microarray consisting of 132 16S rRNA gene-targeted oligonucleotide probes (18-mers) having hierarchical and parallel (identical) specificity for the detection of all known lineages of sulfate-reducing prokaryotes (SRP-PhyloChip) was designed and subsequently evaluated with 41 suitable pure cultures of SRPs. The applicability of SRP-PhyloChip for diversity screening of SRPs in environmental and clinical samples was tested by using samples from periodontal tooth pockets and from the chemocline of a hypersaline cyanobacterial mat from Solar Lake (Sinai, Egypt). Consistent with previous studies, SRP-PhyloChip indicated the occurrence of Desulfomicrobium spp. in the tooth pockets and the presence of Desulfonema- and Desulfomonile-like SRPs (together with other SRPs) in the chemocline of the mat. The SRP-PhyloChip results were confirmed by several DNA microarray-independent techniques, including specific PCR amplification, cloning, and sequencing of SRP 16S rRNA genes and the genes encoding the dissimilatory (bi)sulfite reductase (dsrAB).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Nucleic Acid Hybridization
  • Oligonucleotide Array Sequence Analysis / methods*
  • Oligonucleotide Probes / genetics
  • Phylogeny
  • RNA, Bacterial / chemistry
  • RNA, Ribosomal, 16S / analysis*
  • RNA, Ribosomal, 16S / genetics
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Sequence Analysis, DNA
  • Sulfates / metabolism*
  • Sulfur-Reducing Bacteria / classification*
  • Sulfur-Reducing Bacteria / genetics
  • Sulfur-Reducing Bacteria / metabolism
  • Tooth / microbiology

Substances

  • Oligonucleotide Probes
  • RNA, Bacterial
  • RNA, Ribosomal, 16S
  • Sulfates