Scientists of the Joint Institute together with colleagues from the Institute for Nuclear Research of RAS (INR RAS) have extracted a new species of extremophilic bacteria from subsurface water in an unused tunnel of the Baksan Neutrino Observatory of INR RAS. The species is able to withstand high concentrations of heavy metals and to grow using C1 compounds as a carbon source. In the long term, this bacterial species can be used to purify soils and wastewater from heavy metals and also to recover biomass using an inexpensive carbon source methanol.

Photo of expedition members. From left to right: Albert Gangapshev (BNO INR RAS), Mikhail Zarubin, Kirill Tarasov, Elena Kravchenko (SMGC DLNP JINR)

During two expeditions to the Baksan Neutrino Observatory of the Institute for Nuclear Research of the Russian Academy of Sciences (BNO INR RAS), biologists from the Sector of Molecular Genetics of the Cell of the Dzhelepov Laboratory of Nuclear Problems of the Joint Institute for Nuclear Research (SMGC DLNP JINR) took water samples and brought them frozen to JINR. Part of the water containing microorganisms was examined using a chemical analysis. Another part was put onto the nutrient medium, which resulted in growth of bacterial clumps. These bacteria were reproduced and further analysed ― the complete genome sequencing of DNA of the bacterium was performed, biochemical and chemotaxonomic tests were conducted, its ability to grow at a high concentration of heavy metals and to use methanol as a carbon source was estimated.

“We learned about the hot spring at BNO when investigating the effect of reducing the natural radiation background on model organisms in the special low-background laboratory of INR RAS,” Kirill Tarasov, bioinformatician at the SMGC DLNP JINR, says. “And we wondered whether it was possible to isolate something new and interesting from this water.”

Remote part of an unused tunnel at the Baksan Neutrino Observatory. Location of sample collection

As a result of the study, the bacterium was assigned to a new species Cytobacillus pseudoceanisediminis. A large number of genes responsible for metal resistance have been found in the genome of the bacterium. The inoculation of media containing a line of concentrations of four metals (cadmium, zinc, lead, copper) allowed determining maximum concentrations of these metals at which the bacterium is able to survive. It turned out that the bacterium belongs to the most lead-tolerant microorganisms known at present. In addition, genes of enzymes were found responsible for using C1 compounds in metabolism. It is quite unusual that there are two pathways of carbon assimilation from C1 compounds in this bacterium. Methylotrophic bacteria most often have only one of the pathways. This feature can be of value for a more precise tuning of biochemical pathways of a producer based on this bacterium using genetically engineered methods. The ability to grow at considerable concentrations of methanol was also observed during this study.

“This is by no means the only bacterium inhabiting the underground spring at BNO. We have identified other new interesting microorganisms in the samples, and the study of their metagenome will allow describing all this extremophilic community,” head of SMGC DLNP, Candidate of Biological Sciences Elena Vladimirovna Kravchenko says.

One of the endemic bacteria isolated from extremophilic community at BNO of INR RAS

The scientists are going to investigate in more detail the possibility of purifying water and soils from heavy metals with the already isolated bacterium.

Extremophiles are organisms inhabiting environments remarkably different from those considered standard by humans. They have always been of interest to scientists, because they have unique systems of adaptation to extreme habitats. Studying such systems helps to understand the laws of evolution, as well as to provide biotechnology industry with necessary enzymes that can work in various conditions. Thermostable enzymes extracted from bacteria inhabiting hot springs are currently widely used in molecular biology and medicine, for example, for PCR (polymerase chain reaction). Extremophiles are also model objects for astrobiology. Scientists look for conditions on Earth that would be similar to those on other planets and study the organisms living there to understand how extraterrestrial life could evolve. That is why scientists from JINR working at the Baksan Neutrino Observatory of INR RAS on a completely different experiment decided to collect water samples from a saline spring located at a depth of 1,700 meters under Mount Andyrchi thus to determine whether there are living organisms. And if there are some, what kind of adaptation mechanisms they have.

“The unique underground infrastructure of BNO of INR of RAS aimed at solving problems in particle physics, neutrino physics and astrophysics also allows conducting studies in interdisciplinary areas of science, such as geophysics, geology, radiogenetics and ecology. Some localities of underground structures of BNO of INR of RAS are a habitat of unique microorganisms, extremophiles,” Deputy Head for Science of BNO INR RAS, Candidate of Physics and Mathematics Albert Gangapshev commented on the results of work.

The results of the research have been published in Current Microbiology journal.