Evaluation of fish biodiversity in estuaries using environmental DNA metabarcoding

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.

Fig 1. Sampling stations.

Location of (a) the five rivers surveyed in this study. Maps showing the location of sampling stations RM (river mouth), L1 (left 500 m), L2 (left 1 km), R1 (right 500 m), and R2 (right 1 km) of (b) Aka River, (c) Tama River, (d) Miya River, (e) Takatsu River, and (f) Sendai River. The satellite photos from (b) to (f) were provided by Geospatial Information Authority of Japan. Scale bar = 1 km.

Fig 2. Species richness.

Number of species present in (a) all five rivers and at each station, (b) Aka River, (c) Tama River, (d) Miya River, (e) Takatsu River, and (f) Sendai River. HT: river mouth at high tide; LT: river mouth at low tide; L1: left 500 m; L2: left 1 km; R1: right 500 m; R2: right 1 km; S: seawater species; B: brackish water species having a wide range of salinity tolerance including migrating fishes; F: freshwater species.

Fig 3. Human effects.

Nutrients (mean ± SD) including (a) total nitrogen [mg/L] and (b) total phosphorus [mg/L] of the five rivers based on 2016 data obtained from the Ministry of the Environment, Japan (https://water-repo.env.go.jp/water-repo/). (c) Revetment rate [%] of the five rivers calculated using Google Earth Pro (2018 Google Image Landsat/Copernicus, US Dept of State Geographer Data SIO, NOAA, U. S. Navy, NGA, GEBCO). Bars show standard deviations.