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

Jayanath Gopi, Applied Research Center for Environment and Marine Studies, King Fahd University of Petroleum & Minerals, Dhahran 31261, Kingdom of Saudi Arabia
Bhavya Kachiprath, Dept. of Marine Science, College of Natural Sciences, Incheon National University, Incheon 22012, Republic of Korea
Solly Solomon, Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Kochi 682016, Kerala, India AND Fishery Survey of India, Cochin Zonal Base, Kochangadi Road, Kochi 682005, Kerala, India
Sowmya P. Mohandas, National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi 682016, Kerala, India
Sajan C. Raju, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, NO-0316, Oslo, Norway
Rosamma Philip, Dept. of Marine Biology, Microbiology & AND Biochemistry, Cochin University of Science and Technology, Kochi 682016, Kerala, IndiaFollow

Abstract

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.

First Page

227

Last Page

237

Recommended Citation

Gopi, Jayanath; Kachiprath, Bhavya; Solomon, Solly; Mohandas, Sowmya P.; Raju, Sajan C.; and Philip, Rosamma (2025) "Preprocessing Improves the eDNA Quality for 16S rRNA Metabarcoding of Sediment Samples of Solar Salterns," Journal of King Abdulaziz University: Marine Science: Vol. 35: No. 2, Article 10.