Methane-eating relative of tuberculosis bacteria found in Romanian cave

Previously unknown microbes live on important greenhouse gas

Bacteria living on the walls of a cave in Romania use methane as their only source of food. Researchers from Utrecht University and national and international colleagues describe the previously unknown microbes in a paper in Nature Microbiology. Knowledge about the new species might contribute to the development of new techniques that reduce the concentration of methane in the atmosphere. As the bacteria are closely related to the pathogens that cause tuberculosis and leprosy, insights from the bacteria could also support the development of new methods to fight these two diseases. 

Extreme environment 

Inside the cave, which is located in eastern Transylvania, volcanic gases meet the Earth’s atmosphere. The concentration of methane is high, and the surfaces of the cave wall are extremely acidic. When speleologists, safe inside their protective suits, took samples from these surfaces, nobody really expected to find many living things there. Yet, the cave wall turned out to be full of life.  

Speleologist Serban M. Sarbu collects samples in the cave. Image: Jean-François Flot/Sherban A. Sarbu

Utrecht University researcher and data scientist Chrats Melkonian: “We found a lot of diversity on the cave wall. When we analysed the DNA in the samples, microorganisms like archaea and even viruses turned up. Most surprisingly, we discovered that a certain type of bacterium, a Mycobacterium, was very abundant there. Mycobacteria are usually not very abundant in nature, let alone in such an environment.” 

Methane for food 

Melkonian, who was responsible for several data analyses, continues: “We were obviously very interested in these bacteria and wanted to know how they were living in such an extreme environment. As a first step, we analysed their DNA and mapped what proteins the bacteria were producing. This is how we found that they were producing a full set of proteins that are known to make it possible to live on methane.” 

Chrats Melkonian in the supercomputer server room of Theoretical Biology and Bioinformatics (a collaboration with ITS-UU-networking)

To conclusively show that the bacteria were able to grow on methane, Utrecht University researcher Lubos Polerecky then provided them with methane in the lab. By using a technique that allowed the researcher to track the carbon in the methane, Polerecky demonstrated that the bacteria use the gas as their only source for carbon and energy.

Greenhouse gas 

Methane is a very important greenhouse gas that contributes to global warming. The Romanian cave bacteria are not the first microorganism or bacteria known to live on methane, but it is the first in a certain group of bacteria, the Actinobacteria. According to Melkonian, methane-eating microbes do influence methane concentrations in the atmosphere by lowering emissions that originate from gases released by the earth, such as the volcanic gases in the Romanian cave.  

Farms of methane-eating organisms could be used to take out the methane and produce something that we can use later, like biomass.

By collecting samples from locations surrounding the cave, the researchers found that the bacteria they discovered are abundant in acidic environments with high methane concentrations in the region. Melkonian: “This might mean that these bacteria are also key players of breaking down methane worldwide. But at the moment we do not have direct evidence for this.” 

Knowledge about methane-eating microorganisms might lead to new approaches to reduce levels of methane in the atmosphere. Melkonian: “Farms of methane-eating organisms could for example be used to take out the methane and produce something that we can use later, like biomass. But right now this is still science fiction. Yet, you first have to know what organisms are able to live on methane and how the mechanisms work.” 


Melkonian and his colleagues also established that the newly discovered microbes are closely related to the bacteria that cause tuberculosis and leprosy. Melkonian: “All these bacteria are Mycobacteria. Current treatments do not work well against some of the defense mechanisms of these pathogens. It is important to know more about these organisms and their relatives and how they live in an ecological context. Understanding what evolutionary steps are needed to go from one way of life to another might help to find new approaches to fight these pathogens.” 

International collaboration 

The paper is the result of an international collaboration between researchers from Utrecht University, Vrije Universiteit Amsterdam, Amsterdam University Medical Centers, Netherlands Institute of Ecology, King Abdullah University of Science and Technology (Saudi Arabia), the Institute of Speleology (Romania), Université libre de Bruxelles (Belgium), University of Amsterdam and the California State University (USA). The research was led by Wilbert Bitter and Rob J. M. van Spanning. 


Methanotrophy by a Mycobacterium species that dominates a cave microbial ecosystem

Rob J. M. van Spanning, Qingtian Guan, Chrats Melkonian, James Gallant, Lubos Polerecky, Jean-François Flot, Bernd W. Brand, Martin Braster, Paul Iturbe Espinoza, Joost W. Aerts, Marion M. Meima-Franke, Sander R. Piersma, Catalin M. Bunduc, Roy Ummels, Arnab Pain, Emily J. Fleming, Nicole N. van der Wel, Vasile D. Gherman, Serban M. Sarbu, Paul L. E. Bodelie, Wilbert Bitter

Nature Microbiology, 3 November 2022, DOI: 10.1038/s41564-022-01252-3