Detection of methanotrophs with highly divergent pmoA genes from Arctic soils

• Published in: FEMS microbiology letters 2002-04, Vol.209 (2), p.313-319
• Main Authors: Pacheco-Oliver, M, McDonald, I.R, Groleau, D, Murrell, J.C, Miguez, C.B
• Format: Article
• Language: English
• Subjects: 16S rRNA; Agronomy. Soil science and plant productions; amino acid sequences; Amino acids; Arctic Regions; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Bacteriology; Biochemistry and biology; Biodegradation, Environmental; Biological and medical sciences; Chemical, physicochemical, biochemical and biological properties; Deoxyribonucleic acid; DNA; Fundamental and applied biological sciences. Psychology; Gene sequencing; Genes; Genetics; Hydrocarbons - metabolism; Methane; Methane monooxygenase; Methane monooxygenase gene; Methanotroph; Methanotrophic bacteria; methanotrophs; Methylococcaceae - enzymology; Methylococcaceae - genetics; Methylococcaceae - isolation & purification; Methylocystis; Methylosinus; Microbiology; Microorganisms; Molecular Sequence Data; Naphthalene; nucleotide sequences; Oxidation; Oxygenases - genetics; Oxygenases - metabolism; Phylogeny; Physics, chemistry, biochemistry and biology of agricultural and forest soils; Plating; pmoA gene; PmoA protein; Polymerase chain reaction; ribosomal RNA; RNA, Ribosomal, 16S - genetics; rRNA 16S; Sequence Homology, Amino Acid; Soil Microbiology; Soil microorganisms; soil sampling; Soil science; Soils; Tundra; tundra soils
• ISSN: 0378-1097; 1574-6968
• DOI: 10.1111/j.1574-6968.2002.tb11150.x

Tundra soil samples from the Canadian Arctic community, Kuujjuaq, were analyzed for the presence of the soluble (sMMO) and particulate (pMMO) methane monooxygenase genes. Total genomic DNA extracted from these soils was used as template for PCR using sMMO- and pMMO-specific primers, mmoX1-mmoX2 and A189-A682, respectively. pMMO and sMMO genes were detected in the Kuujjuaq soil samples. Isolation of sMMO-possessing methanotrophic microorganisms from the three soils, as determined by the colony naphthalene oxidation assay, was carried out using direct plating (5 degrees C) and methane enrichment studies (5 degrees C and 25 degrees C). Direct plating did not yield sMMO-possessing methanotrophic bacteria, whereas methane enrichments yielded isolates possessing and expressing sMMO activity. Analysis of derived amino acid sequences of pmoA genes and partial 16S rRNA genes obtained by PCR, using DNA isolated directly from this environment and from isolates, revealed the presence of highly divergent PmoA/AmoA sequences and 16S rRNA sequences that cluster closely with but are distinct from the genes from the genera Methylosinus and Methylocystis.