Preprocessing Improves the eDNA Quality for 16S rRNA Metabarcoding of Sediment Samples of Solar Salterns

The present study examines the efficacy of pre- processing of sediment samples prior to DNA isolation to obtain high-quality eDNA for metagenomic analyses from crystallizer saltern pond in Goa during the salt harvesting phase. The quality of the extracted eDNA were confirmed through spectrophotometric analysis and PCR amplification of the 16S rRNA gene. The study showed that method 2 and 3 incorporating preprocessing of the sediment samples yielded better quality eDNA compared to the direct isolation protocol (method1). By adopting the best method i.e., preprocessing by sediment suspension- filtration, followed by DNA isolation, the eDNA was procured and subjected to 16S rRNA metabarcoding using Illumina MiSeq platform. Taxonomic profiling at the domain level indicated that 96% of the sequences belonged to bacteria with Proteobacteria (27%) as the dominant phyla followed by Bacteroidetes (15%), Firmicutes (8%), and Actinobacteria (2%). Archaea represented 1% of the sequences, with Euryarchaeota as the dominant phylum. Major bacterial genera observed were Hymenobacter, Halomonas, Salinibacter, Marinobacter and Halanaerobium, while the key archaeal genera included Halorubrum, Natronorubum, Haloferax, Haloarcula and Halobacterium. This study provides a quality DNA isolation protocol for solar salterns apart from giving a baseline profile of the microbial community composition in a hypersaline environment.