Culturable bacterial diversity and genome-encoded metabolic potential in Al Wahbah Crater’s volcanic soils, Saudi Arabia

Abstract

The growing demand for sustainable biotechnological solutions has intensified interest in microorganisms inhabiting understudied and environmentally constrained ecosystems. Volcanic systems create ecological niches shaped by geochemical and physicochemical stressors, yet the culturable bacteria in many remain poorly characterized. Here, we investigated the culturable bacterial fraction in the soils of Al Wahbah Crater (Saudi Arabia), an underexplored volcanic ecosystem, and evaluated its members’ hydrolytic enzyme production and the genome-encoded metabolic potential of the most-promising isolates. Using multiple media and incubation conditions, we isolated bacterial strains from three crater soil types, identifying 65 representative isolates through 16S rRNA gene sequencing. The culture collection was dominated by Bacillota, particularly Bacillus spp., reflecting selective pressures typical of mineral-rich, saline soils. All isolates were screened for six hydrolases: cellulase, xylanase, amylase, protease, lipase, and gelatinase. Twenty-three strains exhibited activities for all six, while only one (Paenibacillus sp. AWC54) showed no detectable enzymatic activity. Cellulase activity was most prevalent (61/65 isolates), followed by xylanase (59/65), amylase (57/65), protease (48/65), lipase (35/65), and gelatinase (31/65). Five high-performing strains, Bacillus spizizenii AWC2, B. cereus AWC16, B. vallismortis AWC57 and AWC81, and B. haynesii AWS14, were selected for whole-genome sequencing and genome mining. Genome annotations revealed diverse carbohydrate-active enzyme repertoires including glycoside hydrolases, glycosyl transferases, and polysaccharide lyases, as well as multiple biosynthetic gene clusters predicted to encode antimicrobial and antifungal metabolites. Together, these findings establish Al Wahbah Crater as a cultivable regional reservoir of metabolically versatile bacteria and provide a curated strain collection and genomic framework for future ecological, evolutionary, and biotechnological investigations of volcanic microbiomes in the Arabian Peninsula.