Methanotrophy by a Mycobacterium species that dominates a cave microbial ecosystem

So far, only members of the bacterial phyla Proteobacteria and Verrucomicrobia are known to grow methanotrophically under aerobic conditions. Here we report that this metabolic trait is also observed within the Actinobacteria. We enriched and cultivated a methanotrophic Mycobacterium from an extremely acidic biofilm growing on a cave wall at a gaseous chemocline interface between volcanic gases and the Earth's atmosphere. This Mycobacterium, for which we propose the name Candidatus Mycobacterium methanotrophicum, is closely related to well-known obligate pathogens such as M. tuberculosis and M. leprae. Genomic and proteomic analyses revealed that Candidatus M. methanotrophicum expresses a full suite of enzymes required for aerobic growth on methane, including a soluble methane monooxygenase that catalyses the hydroxylation of methane to methanol and enzymes involved in formaldehyde fixation via the ribulose monophosphate pathway. Growth experiments combined with stable isotope probing using 13C-labelled methane confirmed that Candidatus M-. m-et-ha-no-tr-op-hicum can grow on methane as a sole carbon and energy source. A broader survey based on 16S metabarcoding suggests that species closely related to Candidatus M. methanotrophicum may be abundant in low-pH, high-methane environments.

Automated summary

A study has found a methanotrophic Mycobacterium within the Actinobacteria, a group of bacteria not previously known to grow on methane under aerobic conditions. This Mycobacterium, named Candidatus Mycobacterium methanotrophicum, is closely related to well-known pathogens like M. tuberculosis and M. leprae. Genomic and proteomic analyses showed that Candidatus M. methanotrophicum possesses all the necessary enzymes for aerobic growth on methane. Stable isotope probing confirmed that this bacterium can use methane as its sole carbon and energy source.