Identification of Methanotrophs by Molecular Markers

The aim of this review is to evaluate the molecular markers used to identify and study the diversity of methanotrophs in different environments. Methanotrophs have been divided into two taxonomic groups: type I and type II. Type I represents following ten genera: Methylomonas, Methylobacter, Methylomicrobium, Methylosarcina, Methylosphaera, Methylosoma, Methylohalobium, Methylococcus, Methylocaldum and Methylothermus, which belong to the gamma subdivision of the Proteobacteria. The type II is represented by only four genera (Methylosinus, Methylocystis, Methylocella and Methylocapsa) of the alpha subdivision of the Proteobacteria. The 16S rRNA gene is structurally and functionally the most conserved in prokaryotes. Due to availability of the large database of sequences, the one obvious marker for the methanotrophs is 16S rRNA gene. A complementary option of molecular marker is a functional gene that is unique to the physiology and metabolism of the organisms being studied. For the methanotrophs, two genes, pmoA and mmoX, are of particular use in molecular ecology studies. pmoA genes have been sequenced from a considerable number of methanotrophs and a large data set of partial sequences is also available in GenBank from a number of different environmental studies, however, the data set of mmoX sequences available still remains relatively small. Both pmoA and mmoX have been shown to produce phylogenies largely congruent with the 16S rRNA phylogenies of the same organisms. Other functional gene markers which are not unique to the methanotrophs such as mxaF (coding for the large subunit of methanol dehydrogenase), nifH (which encodes dinitrogen reductase) and fhcD (which encodes the D subunit of the formyltransferase/hydrolase complex) have been used to identify methanotrophs in environmental samples. It has been observed that the comparison between housekeeping gene and functional gene is a better method of study than individual gene. If positive correlations can be made between 16S rRNA gene sequences and the presence or absence of functional genes, then 16S rRNA surveys of environmental samples can be used to understand the functional potential of the community.