Detection of novel marine methanotrophs using phylogenetic and functional gene probes after methane enrichment

A. J. Holmes, N. J.P. Owens, J. Colin Murrell

Research output: Contribution to journalArticlepeer-review

Abstract

A major limitation of rRNA-targeted group-specific probes is that they may cross-react with organisms of other physiological, or even phylogenetic groups when applied to environmental samples containing unknown sequences. We have exploited the restricted physiology of methane-oxidizing bacteria to assess the specificity and efficiency of probes for this physiological type which target the 16S rRNA or genes involved in methanotroph physiology. Seawater samples were enriched for methanotrophs by addition of methane and essential nutrients. The changes in composition of the bacterial population were monitored by analysis of 16S rRNA gene libraries. Methanotroph group-specific probes failed to give a signal with samples from these enrichments even though a methanol dehydrogenase structural gene was detected. A 16S rDNA sequence that was abundant only after methane addition was recovered and found to show a close phylogenetic relationship to Methylomonas. Organisms containing this sequence were observed in enrichments by in situ hybridization. The combination of enrichment on methane and screening with the broad specificity methanol dehydrogenase probe allowed detection of novel methanotrophs that were not detected with the original suite of methanotroph group-specific probes.

Original languageEnglish
Pages (from-to)1947-1955
Number of pages9
JournalMicrobiology
Volume141
Issue number8
DOIs
Publication statusPublished - 1 Aug 1995

Keywords

  • 16S ribosomal RNA
  • Marine methane-oxidizing bacteria
  • Oligonucleotide probe

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