Biodiversity Hotspots in Salt-Saturated Environments: Unravelling Microbial Communities from the Great Rann of Kachchh and Saltpans

Hypersaline environments exhibit extreme physiochemical conditions yet support diverse microbial communities. These communities are not only ecologically important but also possess substantial potential for biotechnological exploitation. In this study, we employed a comparative metagenomic approach to assess microbial diversity using two distinct methodologies: (1) direct DNA extraction from raw sediment, and (2) DNA extraction following halophilic enrichment in selective media. Sediment samples were collected from multiple sites and pooled together within the Rann of Kachchh and close-by saltpans and were analysed using 16S rRNA sequencing coupled with bioinformatics pipelines. The results revealed pronounced differences in microbial community composition between the two approaches. Raw sediment samples exhibited significantly higher alpha diversity, with dominant taxa including Halobacterota, Cyanobacteria, and Desulfobacterota, with a substantial proportion of unclassified genera. In contrast, enriched samples were dominated by fast-growing, culturable genera such as Halobacterium , Alkalibacillus , and Candidatus haloredivivus . Principal coordinate analysis (PCoA) of beta diversity demonstrated distinct clustering between raw and enriched communities, even within samples from the same sites, underscoring the selective bias introduced by enrichment procedures. These findings emphasise that the methodological choice strongly influences the observed microbial diversity. Direct metagenomic analysis captures the native community structure, whereas enrichment techniques favour proliferation of specific taxa that may outcompete others under laboratory conditions due to differential growth rates and nutrient availability. By integrating both direct and enriched-based metagenomic approaches, a more comprehensive understanding of microbial community structure in hypersaline environments can be achieved.