Evaluation of fish biodiversity in estuaries using environmental DNA metabarcoding

RESEARCH ARTICLE Evaluation of fish biodiversity in estuaries using environmental DNA metabarcoding Hyojin AhnID1,2*, Manabu Kume1, Yuki Terashima1, Feng Ye1,3, Satoshi Kameyama3, Masaki Miya4, Yoh Yamashita1, Akihide Kasai2 1 Connectivity of Hills, Humans and Oceans Unit, Kyoto University, Kyoto, Japan, 2 Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan, 3 Center for Environmental Biology and Ecosystem, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan, 4 Department of Ecology and Environmental Sciences, National History Museum and Institute, Chiba, Japan * ahn.hyojin.4a@kyoto-u.ac.jp Abstract Biodiversity is an important parameter for the evaluation of the extant environmental condi- tions. Here, we used environmental DNA (eDNA) metabarcoding to investigate fish biodiver- sity 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 subtropi- cal 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. 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 sedi- ments, excessive nutrients, and other chemicals. Terrestrial pollutants from agriculture, defor- estation, and construction flow into coastal areas through the hydrologic system, mainly through rivers [3–5]. Therefore, humans affect first the estuaries and coastal areas, whose envi- ronmental conservation is indicated by the extent of biodiversity. Consequently, comprehen- sive monitoring of biodiversity is essential for conservation of ecosystems. Although 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 PLOS ONE PLOS ONE | https://doi.org/10.1371/journal.pone.0231127 October 6, 2020 1 / 15 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 OPEN ACCESS Citation: Ahn H, Kume M, Terashima Y, Ye F, Kameyama S, Miya M, et al. (2020) Evaluation of fish biodiversity in estuaries using environmental

DNA metabarcoding. PLoS ONE 15(10): e0231127. https://doi.org/10.1371/journal.pone.0231127 Editor: Hideyuki Doi, University of Hyogo, JAPAN Received: March 16, 2020 Accepted: September 8, 2020 Published: October 6, 2020 Copyright: © 2020 Ahn et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. The FASTQ files of all sampling stations have been submitted to DDBJ (Accession No.: DRA010703) and available from https://ddbj.nig.ac. jp/DRASearch/. Funding: This study was conducted under the Link Again Program, part of Connectivity of Hills, Humans and Oceans, funded by the Nippon Foundation (www.nippon-foundation.or.jp), attained by YY. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.