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Background  Natural gas contains methane and the gaseous alkanes ethane, propane and butane, which collectively influence atmospheric chemistry and cause global warming. Methane-oxidising bacteria, methanotrophs, are crucial in mitigating emissions of methane as they oxidise most of the methane produced in soils and the subsurface before it reaches the atmosphere. Methanotrophs are usually obligate, i.e. grow only on methane and not on longer chain alkanes. Bacteria that grow on the other gaseous alkanes in natural gas such as propane have also been characterised, but they do not grow on methane. Recently, it was shown that the facultative methanotroph  Methylocella silvestris  grew on ethane and propane, other components of natural gas, in addition to methane. Therefore, we hypothesised that  Methylocella  may be prevalent at natural gas seeps and might play a major role in consuming all components of this potent greenhouse gas mixture before it is released to the atmosphere.    Results  Environments known to be exposed to biogenic methane emissions or thermogenic natural gas seeps were surveyed for methanotrophs. 16S rRNA gene amplicon sequencing revealed that  Methylocella  were the most abundant methanotrophs in natural gas seep environments. New  Methylocella -specific molecular tools targeting  mmoX  (encoding the soluble methane monooxygenase) by PCR and Illumina amplicon sequencing were designed and used to investigate various sites. Functional gene-based assays confirmed that  Methylocella  were present in all of the natural gas seep sites tested here. This might be due to its ability to use methane and other short chain alkane components of natural gas. We also observed the abundance of  Methylocella  in other environments exposed to biogenic methane, suggesting that  Methylocella  has been overlooked in the past as previous ecological studies of methanotrophs often used  pmoA  (encoding the alpha subunit of particulate methane monooxygenase) as a marker gene.    Conclusion  New biomolecular tools designed in this study have expanded our ability to detect, and our knowledge of the environmental distribution of  Methylocella , a unique facultative methanotroph. This study has revealed that  Methylocella  are particularly abundant at natural gas seeps and may play a significant role in biogeochemical cycling of gaseous hydrocarbons.    Electronic supplementary material  The online version of this article (10.1186/s40168-018-0500-x) contains supplementary material, which is available to authorized users.

Facultative methanotrophs are abundant at terrestrial natural gas seeps