Detection and Quantification of Environmental DNA (e-DNA) as a Tool for Aquatic Ecosystem Monitoring

Abstract

Environmental Deoxyribonucleic acid -(e-DNA) has emerged as a non-invasive and powerful tool for monitoring biodiversity in aquatic ecosystems. The present study is aimed at detecting and quantifying e-DNA in water samples using spectrophotometric analysis and electrophoretic separation following Polymerase Chain Reaction (PCR) amplification. Water samples were collected from three different locations of a highly polluted Hussainsagar lake and analyzed for e-DNA concentration with results expressed as mean ± standard error, the concentrations ranged from 0.35 to 0.60 mg/L. PCR amplification confirmed the presence of DNA fragments, as visualized through electropherograms. The extracted e-DNA was preserved for future sequencing and species identification, particularly focusing on fish species due to their ecological significance. The present findings demonstrate the feasibility of using e-DNA for ecological monitoring and contribute to the development of sustainable, non-invasive biodiversity assessment methods, study of interactions of species as well as ecosystem dynamics.

Introduction

Assessing biodiversity in aquatic environments is vital for monitoring ecosystem health, conservation, and resource management. Traditional methods like sampling and visual surveys are often invasive, laborious, and limited by environmental factors. Advances in molecular techniques, particularly environmental DNA (e-DNA) analysis, offer a sensitive, non-invasive, and efficient alternative. e-DNA refers to genetic material organisms release into the environment, detectable in water, soil, or air. Compared to conventional methods, e-DNA can identify elusive or low-abundance species and estimate their relative abundance using spectrophotometry and PCR.

This study focused on detecting and analyzing e-DNA from water samples collected from polluted Hussainsagar lake sediments, where DNA tends to concentrate. e-DNA was extracted via filtration and chemical lysis, quantified spectrophotometrically, and amplified using PCR with universal primers targeting aquatic vertebrates, primarily fish. Electrophoresis confirmed the presence of amplifiable DNA, which was preserved for future sequencing and taxonomic identification.

Results showed measurable e-DNA concentrations across samples with some variability. The electrophoretic analysis validated DNA quality suitable for further analysis. This supports e-DNA as a promising tool for aquatic biodiversity monitoring, providing insights into species presence, ecosystem dynamics, and environmental conditions without disturbing organisms. The study highlights e-DNA’s potential in conservation biology, especially for fish species that serve as ecological indicators.

Conclusion

The study successfully demonstrated the presence and amplifiability of e-DNA in water samples using spectrophotometry and PCR-based electrophoresis. The varying concentrations of e-DNA across samples suggest differences in biological activity or species distribution within the water body. These results support the utility of e-DNA as a reliable, non-invasive tool for aquatic biodiversity assessment. The stored DNA samples is a valuable resource for our future genetic analysis and species identification studies

References

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Copyright

Copyright © 2025 Dr. K.Y. Chitra. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.