Aerobic methane oxidizing bacteria (methanotrophs) are a fascinating group of bacteria that have the unique ability to grow on methane as their sole carbon and energy source. They appear to be widespread in nature and have been isolated from a number of different environments. There are now 14 recognized genera of methanotrophs belong to two phyla, Proteobacteria and thermoacidiphilic Verrucomicrobia.The former was well studied and separated into two classes, TypeⅠ and TypeⅡ methanotrophs, which belong to Alpha and Gamma Proteobacteria. Extremely thermophilic, acidophilic methanotrophs from the phylum Verrucomicrobia have been isolated, thus expanding both the taxonomic diversity and physiological range of aerobic methanotrophy.
The discovery of the facultative methanotroph Methylocella silvestris has changed the view that methanotrophs were obligate organism. They can cooxidize a considerable number of organic compounds and also have considerable potential in biotechnology. A wide variety of methanotrophic symbionts in and on the mosses were recently detected, and showing the global prevalence of this symbiosis. Traditional way used cultivation to enrichment or isolation to study methanotrophs in the environment. Molecular ecology techniques applied in the last few decades have greatly expanded our knowledge of methanotroph ecology. The most obvious marker for detecting methanotrophs in various environments is the 16S rRNA gene, due to the large database of sequences available. Primers and probes targeting different genera or species have been designed and used extensively in combination with polymerase chain reaction (PCR) based clone library analysis, denaturing gradient gel electrophoresis (DGGE) analysis, and fluorescent in situ hybridization (FISH) analysis. Several functional genes have also been used for the detection of methanotrophs in environmental samples, including pmoA (encoding the key subunits of particulate methane monooxygenase), mmoX (encoding the key subunits of soluble methane monooxygenase), mxaF (encoding the key subunits of methanol dehydrogenase), nifH (encoding the dinitrogenase reductase), and genes involved in C1 transfer pathways. To understand the active community of methanotrophs in the environment, stable isotope probing (SIP) techniques have been developed, including DNA-SIP, RNA-SIP, mRNA-SIP, and phospholipid fatty acid (PLFA)-SIP. SIP has also been combined with metagenomics to discover novel methanotrophs. Other very powerful molecular techniques have been developed in the last few years, including microautoradiography (MAR)-FISH, isotope array, Raman-FISH, nano-secondary ion mass spectrometry (NanoSIMS), and microfluidic digital PCR, these techniques can now be used in the analyses of methanotrophs. Both cultivation and cultivation independent molecular methods have been used intensively in last few decades to study the diversity, distribution, and abundance in environments of methanotrophs, such as soils, freshwater, marine sediments, acid peat bogs, hot springs, seawater and extreme environments. In the microcosm of soil, the growth and diversity of methanotrophs are also influenced by several environmental factors. This review highlights recent progress in the research of the taxonomy, of the discovery of novel aerobic methanotrophs, of the biochemistry, of the molecular techniques and the environment impacts on methanotrophs, we also emphasize deficiencies and issues need to be solved in future studies. This review will provide theoretical foundation for future methanotrophic ecology study and explain the key role methanotrophs play in carbon cycle.