Diversity and biotechnological potential of actinobacteria from the Krem Dam Cave, Meghalaya, India

Abstract

This study aimed to explore the cultivable actinobacterial diversity in Krem Dam cave, Meghalaya, India, and to evaluate their biotechnological potential through antimicrobial activity, plant growth-promoting traits, and metabolic pathway prediction. Sediment samples were collected from five locations within the cave, pretreated, and cultured on selective media to isolate actinobacteria. Isolates were characterized morphologically, physiologically, and chemotaxonomically, followed by 16S rDNA sequencing for molecular identification. The PAPRICA pipeline was used to predict metabolic pathways from 16S rDNA sequences. Antimicrobial activity was assessed against Gram-positive, Gram-negative bacteria, and Candida species using cross-streak and agar-well diffusion methods, while biosynthetic gene clusters (PKS-I, PKS-II, and NRPS) were screened via polymerase chain reaction (PCR). Plant growth-promoting (PGP) traits, including IAA production, phosphate solubilization, siderophore activity, and nitrogen fixation were evaluated, along with antagonism against phytopathogens and seedling vigor in tomato. Forty-eight isolates were identified, predominantly Streptomyces thermocarboxydus-related strains, with one Amycolatopsis species. Seventy-seven percent harbored at least one biosynthetic gene cluster, and significant antimicrobial activity was observed, particularly against Gram-positive bacteria. Several isolates exhibited multiple PGP traits, and two (KD-21, KD-29) enhanced tomato seedling vigor. The study concludes that Krem Dam cave harbors diverse, bioactive actinobacteria with promising applications in pharmaceuticals and sustainable agriculture, warranting further metabolomic and genomic investigations.

Keywords: Meghalaya; actinobacteria; antimicrobial; plant growth promotion; sandstone cave.