Unique cave bacterium discovered thriving on methane

A team led by Vrije Universiteit Amsterdam in the Netherlands extracted and analysed the bacteria's DNA in the extremely acidic (pH 1) biofilm covering the cave walls. They found that the most abundant species in the biofilm belongs to the Mycobacterium genus, which has great metabolic diversity, and includes the bacteria responsible for tuberculosis and leprosy. 

Scientists at King Abdullah University of Science and Technology (KAUST) in Saudi Arabia reconstructed the genome of this Mycobacterium from the DNA sample of the biofilm. This data was then used to study the proteins found in the same biofilm sample. The team identified key enzymes these bacteria require for their metabolism to convert methane into carbon dioxide. The researchers proposed this species be called Candidatus Mycobacterium methanotrophicum. 

“When our Romanian speleologist collaborators took samples from the walls of the cave, no one really believed they would find something alive in there. The discovery of a novel methanotrophic Mycobacterium was really surprising,” says Wilbert Bitter from Vrije Universiteit Amsterdam. 

Bacteria known to lower the concentration of methane released by the earth in the presence of air have been found in two phyla, but this is the first case of methane-utilising bacteria in the Actinobacteria phylum. “This example will be impetus for further discoveries. It also reminds us to constantly look out for the unexpected, and challenge the conventional wisdom,” comments microbiologist, Adrian Ho, of Leibniz University Hannover in Germany, who was not involved in this study.

The team also grew Candidatus M. methanotrophicum in the laboratory, mimicking the cave’s gas composition, and confirmed that these bacteria can survive on methane only. Electron microscopy revealed other differences between this species and other mycobacteria. For example, they are double in width compared to M. tuberculosis and have a thick cell wall that could protect them against the acidic pH. 

Finally, a bioinformatics analysis suggested that other species closely related to Candidatus M. methanotrophicum are widespread in other low-pH, high-methane environments, such as basalts, lava beds and concrete sewer systems. “These bacteria may well be key players of breaking down methane worldwide,” says Rob van Spanning from Vrije Universiteit Amsterdam.

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