A first insight into the Polish Bochnia Salt Mine metagenome

The Bochnia Salt Mine is one of the oldest mines in Europe. It was established in the thirteenth century, and actively operated until 1990. The mine has been placed on the UNESCO World Heritage List. Previous research describing Polish salt mines has been focused on bioaerosol characteristics and the identification of microorganisms potentially important for human health. The use of Polish salt mines as inhalation chambers for patients of health resorts has also been investigated. Nevertheless, the biodiversity of salt mines associated with biotechnological potential has not been well characterized. The present study paper examines the biodiversity of microorganisms in the Bochnia Salt Mine based on 16S rRNA gene and shotgun sequencing. Biodiversity studies revealed a significantly higher relative abundance of Chlamydiae at the first level of the mine (3.5%) compared to the other levels (< 0.1%). Patescibacteria microorganisms constituted a high percentage (21.6%) in the sample from site RA6. Shotgun sequencing identified 16 unique metagenome-assembled genomes (MAGs). Although one was identified as Halobacterium bonnevillei, the others have not yet been assigned to any species; it is possible that these species may be undescribed. Preliminary analyses of the biotechnological and pharmaceutical potential of microorganisms inhabiting the mine were also performed, and the biosynthetic gene cluster (BGC) profiles and antimicrobial peptide (AMP) coding genes in individual samples were characterized. Hundreds of BGCs and dozens of AMP coding genes were identified in metagenomes. Our findings indicate that Polish salt mines are promising sites for further research aimed at identifying microorganisms that are producers of potentially important substances with biotechnological and pharmaceutical applications. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11356-023-25770-7.