Evaluation of fish biodiversity in estuaries using environmental DNA metabarcoding.

Hyojin Ahn,Masaki Miya,Yoh Yamashita,Feng Ye,Manabu Kume,Satoshi Kameyama,Akihide Kasai,Yuki Terashima,Hideyuki Doi

doi:10.1371/journal.pone.0231127

Abstract

Biodiversity is an important parameter for the evaluation of the extant environmental conditions. Here, we used environmental DNA (eDNA) metabarcoding to investigate fish biodiversity in five different estuaries in Japan. Water samples for eDNA were collected from river mouths and adjacent coastal areas of two estuaries with high degrees of development (the Tama and Miya Rivers) and three estuaries with relatively low degrees of development (the Aka, Takatsu, and Sendai Rivers). A total of 182 fish species across 67 families were detected. Among them, 11 species occurred in all the rivers studied. Rare fishes including endangered species were successfully detected in rich natural rivers. Biodiversity was the highest in the Sendai River and lowest in the Tama River, reflecting the degree of human development along each river. Even though nutrient concentration was low in both the Aka and Sendai Rivers, the latter exhibited greater diversity, including many tropical or subtropical species, owing to its more southern location. Species composition detected by eDNA varied among rivers, reflecting the distribution and migration of fishes. Our results are in accordance with the ecology of each fish species and environmental conditions of each river.

Highlights

Threats to biodiversity in aquatic ecosystems have been an issue for decades because of loss of productive habitats [1, 2]
For the Tama River, water samples were taken from a boat because the estuary is located between Haneda Airport and the Kawasaki industrial complex, and we could not reach the area from the shore
A total of 182 species from 67 families were detected in the present environmental DNA (eDNA) survey (S2 Table)

Summary

Introduction

Threats to biodiversity in aquatic ecosystems have been an issue for decades because of loss of productive habitats [1, 2]. Such environmental perturbations are caused mainly by human influences, through both direct damage to aquatic ecosystems and indirect pollution with sediments, excessive nutrients, and other chemicals. Terrestrial pollutants from agriculture, deforestation, and construction flow into coastal areas through the hydrologic system, mainly through rivers [3,4,5]. Humans affect first the estuaries and coastal areas, whose environmental conservation is indicated by the extent of biodiversity. Comprehensive monitoring of biodiversity is essential for conservation of ecosystems. A number of studies on biodiversity have been reported [6, 7], most of them have focused on local areas of ecologic or economic importance to aquaculture [8], unique

Methods

Results

Discussion

Conclusion