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

• Grant number: 21/13994-0
• Support Opportunities: Research Grants - Innovative Research in Small Business - PIPE
• Start date: July 01, 2022
• End date: March 31, 2023
• 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 ; Atividades profissionais, científicas e técnicas não especificadas anteriormente
• City: Botucatu
• Pesquisadores principais: Felipe Pontieri de Lima
• Associated researchers: Claudio de Oliveira
• Associated research grant(s): 23/11450-9 - Development and application of environmental DNA (e-DNA) protocol as a fast, precise, and non-invasive method for monitoring freshwater ichthyofauna, AP.PIPE
• Associated scholarship(s): 22/14144-3 - Water filtration and DNA extraction protocol enhancement for environmental DNA studies, BP.TT

Abstract

Environmental licensing studies in aquatic environments are inseparable from the studies of ichthyofauna, mainly in enterprises directly related to these environments, such as hydroelectric plants and reservoirs. However, traditional ichthyofauna sampling techniques, such as the gill net, trawl and sieve, are invasive, often leading to the death of captured individuals. In addition to this impact on the ichthyofauna, these techniques, however varied they may be, do not guarantee total sampling efficiency, and, generally, rare species in the environment or recently introduced, are often not captured. The non-detection of species, especially those of low occurrence, in licensing processes, can lead to mistaken decision-making and management actions, with damage to the ichthyofauna and consequently to the environmental balance. Several molecular techniques have been applied to ecological studies, with DNA barcode / metabarcode and environmental DNA (environmental DNA: e-DNA), considered tools with the potential to solve several difficulties in environmental studies. Environmental DNA consists of obtaining, either from water or sediment, DNA samples from the organisms of interest, without the need for contact with them, avoiding deaths and increasing accuracy in identification. Based on this assumption, the objective of Ictiológica Consultora Ambiental is to develop and apply an environmental DNA protocol to be used in ichthyofauna studies related to licensing processes in Brazil. The project was divided into three stages, distributed between Phases I (step 1) and II (steps 2 and 3) of PIPE. In PIPE phase I, the technique of DNA extraction, amplification and sequencing from water and sediment samples from experimental tanks will be established, with different species and numerical density (step 1). The tank experiment aims to demonstrate viability, as well as the standardization of the methodology to be used in the other stages. In phase II of PIPE, step 2 of the project will begin, which will consist of the application of the protocol outlined in streams in the Cuesta de Botucatu, an environment considered as a transition between the laboratory and natural environment phases, and in step 3, the methodology will be applied in rivers and dams. As a result, it is expected to develop an effective and replicable protocol, on a large scale of use, of environmental DNA for studies of freshwater ichthyofauna, where through samples of water or sediment, it is possible to infer qualitatively and quantitatively the local ichthyocenosis, replacing the existing traditional techniques, improving the effectiveness of studies and decreasing mortality and impacts from traditional techniques. (AU)