Development and application of environmental DNA (e-DNA) protocol as a fast, precise, and non-invasive method for monitoring freshwater ichthyofauna

• Grant number: 23/11450-9
• Support Opportunities: Research Grants - Innovative Research in Small Business - PIPE
• Start date: March 01, 2024
• End date: February 28, 2026
• Field of knowledge: Agronomical Sciences - Fishery Resources and Fishery Engineering - Inland Water Fishery Resources
• Principal Investigator: André Batista Nobile
• Grantee: André Batista Nobile
• Company: Ictiológica Consultoria Ambiental Ltda. - ME
• CNAE: Pesquisa e desenvolvimento experimental em ciências físicas e naturais
• City: Botucatu
• Pesquisadores principais: Felipe Pontieri de Lima
• Associated researchers: Claudio de Oliveira
• Associated research grant: 21/13994-0 - Development and application of an environmental DNA protocol (e-DNA) as a fast, accurate and non-invasive method for monitoring freshwater ichthyofauna, AP.PIPE
• Associated scholarship(s): 25/05742-2 - Improvement of water filtration and DNA extraction protocol for environmental DNA studies, BP.TT; 24/19319-1 - Improvement of water filtration and DNA extraction protocol for environmental DNA studies, BP.TT; 24/01719-3 - Development and application of environmental DNA protocol (e-DNA) as a rapid, accurate, and non-invasive method for monitoring freshwater ichthyofauna, BP.PIPE

Abstract

Environmental licensing studies in aquatic environments are inseparable from ichthyofauna studies, especially in projects directly related to these environments, such as hydroelectric power plants and reservoirs. However, traditional techniques for ichthyofauna sampling, such as gillnets, trawling, and sieving, are invasive and often result in the mortality of captured individuals. Besides impacting the ichthyofauna, these techniques, no matter how diverse they may be, do not guarantee complete sampling efficacy, often failing to capture rare or newly introduced species. The failure to detect species, especially those with low occurrence, during licensing processes can lead to erroneous decision-making and management actions, harming the ichthyofauna and consequently the environmental balance. Various molecular techniques have been applied to ecological studies, among which DNA barcoding/metabarcoding and environmental DNA (e-DNA) are considered tools with the potential to address several challenges in environmental studies. Environmental DNA involves obtaining DNA samples from the organisms of interest, either from water or sediment, without the need for direct contact, thereby avoiding mortality and increasing accuracy in identification. Based on this premise, the goal of Ictiológica Environmental Consulting is to develop and implement an environmental DNA protocol to be used in ichthyofauna studies related to licensing processes in Brazil. The project has been divided into three stages, distributed between Phases I (Stage 1) and II (Stages 2 and 3) of the PIPE program. During PIPE Phase I, the extraction, amplification, and sequencing technique of DNA from water and sediment samples from experimental tanks, containing different species and numerical density, was established (Stage 1). The tank experiment aimed to demonstrate viability as well as standardize the methodology to be employed in the subsequent stages. In PIPE Phase II, Stage 2 of the project will begin, which involves applying the outlined protocol in streams of the Cuesta de Botucatu, an environment considered a transition between laboratory and natural environment, and in Stage 3, the methodology will be applied in rivers and reservoirs. As a result of Phase II, the aim is to develop an effective and replicable environmental DNA protocol, suitable for large-scale use, for freshwater ichthyofauna studies. Through water or sediment samples, this protocol should allow the qualitative and quantitative inference of the local ichthyocenosis, replacing existing traditional techniques, improving study efficacy, and reducing mortality and impacts arising from these traditional techniques. (AU)