Metagenomics of carbonate rocks from limestone mines, Udaipur, Rajasthan, India, reveal insight into lithobiontic microbial community and biogeochemical cycling.

Opencast limestone mines, being oligotrophic environments characterized by harsh environmental conditions are considered as challenging habitat for colonization and growth of all life forms. These conditions include elevated temperatures, prolonged exposure to sunlight, and deficiencies in organic matter, moisture, and soil nutrients. In such environments, lithobionts may play an important role as the main sources of primary production and maintaining the ecosystem functioning. Unfortunately, our knowledge regarding the taxonomic diversity, potential functions, and ecology of limestone quarry/mines remains quite limited. Here, we explored the taxonomic composition and metabolic potential of lithobiontic microorganisms dwelling carbonate rocks of a limestone mine in Udaipur, Rajasthan, India by using high-throughput shotgun metagenomic sequencing. Community profile analysis revealed that the lithobiontic community was dominated by bacteria (98.94 %), with a minute fraction of the Eukaryota (0.77 %) and archaeal population (0.23 %). Microbes belonging to Phylum Cyanobacteria (39.74 %), Proteobacteria (35.21 %) and Actinobacteria (10.34 %) were predominant followed by a remarkable share of Chloroflexi (4.77 %) and Firmicutes (2.41 %). Metabolic potential analysis, based on six functional modules of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, revealed that functional genes involved in microbial metabolisms are highly represented in this community (59.68 %). Functional analysis of the carbonate microbiome indicated their capacity to influence carbon, nitrogen, and sulfur cycles. Results suggest that the oxygenic photosynthetic bacteria contribute significantly to primary productivity as well as carbonate precipitation in such arid and oligotrophic environments. Multi-omics level study on isolated cyanobacterial strains is underway to gain deeper insights into habitat adaptation and the functioning of lithobiontic niche of cyanobacteria in carbonate rocks.