Diversity and Functional Characterization of Endophytes in Two Contrasting Cultivars of Ocimum sanctum: Insights from Culture-Based and Metagenomic Approaches

In this study, a comparative evaluation was conducted on two different cultivars of Ocimum sanctum to determine the diversity of bacterial and fungal endophytes in root and shoot tissues. This assessment utilized both culture-based and culture-independent high-throughput sequencing approaches. Phylum and subsequently genus level information of bacteria and fungi revealed contrasting differences in the shoot tissue. CIM-Ayu cultivar was dominated by Firmicutes with Bacillus as most abundant genera, while Proteobacteria dominated the CIM-Angana cultivar that had major abundance of Pseudomonas. Overall, the operational taxonomic units (OTUs) information indicated dominance of Pseudomonas, Bacillus, Stenotrophomonas, and Flavobacterium genera in both the shoot and root samples of O. sanctum. Likewise, in case of fungal endophytes CIM-Ayu shoot was specifically enriched with Ascomycota while CIM-Angana was dominated by Basidiomycota. Notably, Saitozyma, Xenomyrothecium, and Cladosporium were the abundant fungal genera in shoot samples of CIM-Ayu while Fusarium, Corynespora, and Kazachstania dominated the root tissues. In total, 45 endophytes were discerned from the above- and belowground tissues of both O. sanctum cultivars through the implementation of a culture-dependent method. Further investigation of these isolates through the application of 16S rRNA and ITS gene sequencing substantiated that Bacillus and Pseudomonas were the prevailing genera. Furthermore, when all the isolates were screened for their plant growth promotion activity, Lysinibacillus irui An29 significantly enhanced the biomass, oil yield, and eugenol content. Overall, the amalgamation of metagenomics and culture-dependent techniques has furnished significant insights concerning potential bacterial endophytes that can be effectively employed in the field to facilitate growth promotion and enhance secondary metabolites in planta in forthcoming investigations.