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Methane-eating relative of tuberculosis bacteria found in cave

4 November 2022
An international team of scientists discovered new unique bacteria living on the walls of a cave in Romania, using methane as their only source of food.

The researchers describe this previously unknown methanotrophic Mycobacterium in a paper in Nature Microbiology. The paper is the result of an international research collaboration, led by VU scientists Wilbert Bitter and Rob van Spanning.

Knowledge about this new species might contribute to the development of new approaches to reduce the concentration of methane in the atmosphere. And as the bacteria are closely related to pathogenic Mycobacteria that cause tuberculosis and leprosy, insights from this benign Mycobacterium could also support the development of new treatments to combat these two diseases.

Toxic volcanic gases
In the so-called Sulphur Cave in eastern Transylvania in Romania, toxic volcanic gases are emitted from the bed rock in the lower layer and only slowly mix with the Earth’s atmospheric air on top of that. As such, these two layers form a relatively stable gaseous chemocline. Exactly at the interface of these layers is a 10 cm thick greyish film on the cave wall. Romanian speleologists noted that the volcanic gas contained high concentrations of carbon dioxide and lower concentrations of methane and hydrogen sulphide. They also found that the grey film was extremely acidic with a pH lower than 1. When they took samples from that film for further inspection, no one really believed to find something alive in there.

The Romanian speleologists had a long-term collaboration with scientists from VU Amsterdam and contacted them for the analyses of the grey film. The VU researchers analysed the DNA from the film and found that it contained a small microbial community in which microorganisms like bacteria, archaea and even viruses turned up. Most surprisingly, they discovered that a Mycobacterium species was very abundant in the acidic biofilm. They then asked the question what these bacteria use for food as the cave is minimally exposed to light, has no contact with external sources of organic carbon or fixed nitrogen, and its only source of liquid water is the condensation of atmospheric water vapour. One plausible theory was that the Mycobacterium uses a source of food from the lower volcanic layer, perhaps methane, and metabolizes that with oxygen from the upper layer. Further research, together with national and international colleagues, proved this theory right. Key insights came from Paul Bodelier (NIOO, physiology), Chrats Melkonian (UU, bioinformatics), and Lubos Polerecky (UU, methane assimilation).

Greenhouse gas
These newly discovered bacteria may well be key players of breaking down methane worldwide. Methane is a very important greenhouse gas that contributes to global warming. This is not the first microorganism or bacteria known to live on methane, but it is the first in a certain group of bacteria, called the Actinobacteria. Methanotrophic microbes affect 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. Knowledge about methanotrophic microorganisms may lead to new approaches to reduce levels of methane in the atmosphere. Farms of methanotrophic organisms could for example be used to consume the methane and produce biomass.

The researchers also established that the newly discovered Mycobacterium is closely related to those causing tuberculosis and leprosy, all of which slow growing 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 which evolutionary steps are needed to switch from one lifestyle to another might help to find new approaches to combat these pathogens.

Photo: Romanian speleologist Serban Sarbu collects samples in the cave. Image: Jean-François Flot/ Serban Sarbu.