Bioprospecting and genome mining of culturable bacteria from a quartzite cave

Oligotrophic, aphotic, subterranean environments represent promising habitats for microbiology studies including the discovery of novel microbial metabolic pathways and bioactive molecules. In this work, eighty bacterial strains were isolated from siliceous speleothems collected from the pristine and recently explored orthoquartzite Imawarì Yeuta cave in the Venezuelan tepuis. These isolates were further analyzed for the capacity to solubilize silicates and to produce antimicrobial molecules. Twenty-five isolates were able to generate silica solubilization halos on solid minimal growth medium plates supplied with magnesium trisilicate, whereas four bacterial isolates inhibited the growth of several human pathogens in soft-agar assays. Whole genome sequencing of these four bacterial isolates was performed to get insight into their taxonomy definition (using a phylogenomics approach) and their genomic traits associated with oligotrophic growth and antimicrobials production. These isolates belonged to the genera Paraburkholderia and Sphingomonas, the latter strain representing a novel species. Phenotype Microarray analyses were also performed to assess their metabolic activities in the presence of different carbon sources and stressors (i.e., metals, detergents, antibiotics). These results open new insights into the investigation of quartzite pristine caves as a source of novel metabolic activities and microorganisms able to produce bioactive molecules.