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Marine Pollution Bulletin
Volume 171, 2021, 112786

Environmental DNA reveals aquatic biodiversity of an urban backwater area, southeast coast of India

Vignesh KumarBalasubramanian, Midhuna Immaculate Joseph Maran, Darwin Ramteke, Deepak Samuel Vijaykumar, Abhilash Kottarathail Rajendran, Purvaja Ramachandran, Ramesh Ramachandran

Conservation of Coastal and Marine Resources Division (CMR), National Centre for Sustainable Coastal Management (NCSCM), India.

Abstract

Strong conservation management needs comprehensive data on biodiversity. Rapid methods that document aquatic biodiversity or assess the health condition of an ecosystem remain scarce. Herein, we have performed a metagenomics study on environmental DNA (eDNA) collected from an urban backwater area - Muttukadu, located in the southeast coast of India. Shotgun metagenomics approach using Illumina®NextSeq500 sequencing yielded 88.4 million raw reads. The processed data was assigned as 80% prokaryotes, 0.4% eukaryotes, ~2% viruses, and ~17% remain unknown. This approach has the potential to identify small micro-eukaryote, unseen species from both estuarine and marine environments. We have identified 156 eukaryote organisms represented from 21 phyla and 112 families, including those that are of conservational significance and ecological importance. Furthermore, our data also demonstrated the presence of pathogenic microorganisms due to sewage mixing with the backwaters. Given its sensitivity, we suggest this approach for an initial assessment of biodiversity structure in an ecosystem for the biomonitoring program.

Keywords: Biodiversity, Environmental DNA (eDNA), Muttukadu backwaters, NGS, Shotgun metagenomics, Illumina.

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