Insights into the representativeness of biodiversity assessment in large reservoir through eDNA metabarcoding

RESEARCH ARTICLE Insights into the representativeness of biodiversity assessment in large reservoir through eDNA metabarcoding Thaina´ CortezID1☯*, Andre´ TorresID2☯, Murilo Guimarães3, Henrique Pinheiro1, Marcelo Cabral4, Gabriel Zielinsky4, Camila Pereira5, Giovanni de Castro5, Luana Guerreiro5, Juliana Americo1, Danielle do Amaral1‡, Mauro Rebelo1‡ 1 Bio Bureau Biotechnology, Rio de Janeiro, Rio de Janeiro, Brazil, 2 Laborato´ rio de Biologia, Controle e Vigilaˆ ncia de Insetos Vetores, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil, 3 Biology Institute, Federal University of Piauı´, Teresina, Piauı´, Brazil, 4 Prooceano, Rio de Janeiro, Rio de Janeiro, Brazil, 5 Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil ☯ These authors contributed equally to this work. ‡ DA and MR also contributed equally to this work. * thainacortezs@gmail.com Abstract Monitoring biodiversity on a large scale, such as in hydropower reservoirs, poses scientific challenges. Conventional methods such as passive fishing gear are prone to various biases, while the utilization of environmental DNA (eDNA) metabarcoding has been restricted. Most eDNA studies have primarily focused on replicating results from traditional methods, which themselves have limitations regarding representativeness and bias. In our study, we employed eDNA metabarcoding with three markers (12SrRNA, COI, and 16SrRNA) to eval- uate the biodiversity of an 800 km2 reservoir. We utilized hydrodynamic modeling to deter-

mine water flow velocity and the water renewal ratio throughout the study area. Additionally, we conducted statistical comparisons—rarefaction curves and multivariate methods— among samples as an alternative approach to assess biodiversity representation. The eDNA identified taxa previously documented in the reservoir by traditional monitoring meth- ods, as well as revealed 29 –nine fishes and 20 non-fish—previously unreported species. These results highlight the robustness of eDNA as a biodiversity monitoring technique. Our findings also indicated that by randomly sampling 30% of the original number of samples, we could effectively capture the same biodiversity. This approach enabled us to compre- hend the reservoir’s biodiversity profile and propose a straightforward, cost-effective moni- toring protocol for the future based on eDNA. Introduction Increasing the accuracy of biodiversity estimation has been a challenge in the face of lacking detailed information about population dynamics, habitat-based models, and either the occur- rence or abundance of a species, especially for rare or elusive species [1–3]. Advancements in PLOS ONE PLOS ONE | https://doi.org/10.1371/journal.pone.0314210 January 24, 2025 1 / 22 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 OPEN ACCESS Citation: Cortez T, Torres A, Guimarães M, Pinheiro H, Cabral M, Zielinsky G, et al. (2025) Insights into the representativeness of biodiversity assessment in large reservoir through eDNA metabarcoding. PLoS ONE 20(1): e0314210. https://doi.org/10.1371/journal.pone.0314210

Editor: Petr Heneberg, Charles University, CZECHIA Received: May 17, 2024 Accepted: November 7, 2024 Published: January 24, 2025 Copyright: © 2025 Cortez 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: The sequences data underlying the results presented in the study are available from NCBI SRA (BioProject PRJNA1105563). Funding: This work was financed by Tijoa´ Energia through the Agência Nacional de Energia Ele´trica (ANEEL) Research and Development Program (Grant PD-09151-2001/2020). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.