Dynamics of Methane-Consuming Biomes from Wieliczka Formation: Environmental and Enrichment Studies

SIMPLE SUMMARY: Deep subsurfaces such as caves and mines are extreme environments inhabited by specialized microorganisms that are able to cope with the adverse conditions caused by low moisture, and high pressure. Our research confirmed that one such site is the rocks surrounding the salt beds in the Wieliczka Salt Mine, where methane-oxidizing bacteria are present. We demonstrated methanotrophic activity in both natural and mineral-supplemented rock material. In the next stage of our research, we confirmed that the methanotrophic community can be cultured on a mineral substrate, using methane as the sole source of carbon and energy source. The issues addressed in this study contribute to our understanding of the biodiversity of microorganisms inhabiting the extreme subsurface biosphere but also provide insights into changes in biodiversity during the isolation of bacterial communities from this type of ecosystem. This information can be valuable for the acquisition of microorganisms with potential applications in biotechnology. ABSTRACT: The rocks surrounding Wieliczka salt deposits are an extreme, deep subsurface ecosystem that as we studied previously harbors many microorganisms, including methanotrophs. In the presented research bacterial community structure of the Wieliczka Salt Mine was determined as well as the methanotrophic activity of the natural microbiome. Finally, an enrichment culture of methane-consuming methanotrophs was obtained. The research material used in this study consisted of rocks surrounding salt deposits in the Wieliczka Salt Mine. DNA was extracted directly from the pristine rock material, as well as from rocks incubated in an atmosphere containing methane and mineral medium, and from a methanotrophic enrichment culture from this ecosystem. As a result, the study describes the composition of the microbiome in the rocks surrounding the salt deposits, while also explaining how biodiversity changes during the enrichment culture of the methanotrophic bacterial community. The contribution of methanotrophic bacteria ranged from 2.614% in the environmental sample to 64.696% in the bacterial culture. The methanotrophic enrichment culture was predominantly composed of methanotrophs from the genera Methylomonas (48.848%) and Methylomicrobium (15.636%) with methane oxidation rates from 3.353 ± 0.105 to 4.200 ± 0.505 µmol CH(4 mL)(−1) day(−1).