Application of eDNA metabarcoding as a tool for accessing estuarine ictiofaunal biodiversity in São Paulo State coastline

• Grant number: 23/07311-3
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• Start date: August 01, 2023
• End date: July 31, 2024
• Field of knowledge: Biological Sciences - Genetics - Animal Genetics
• Principal Investigator: Danillo Pinhal
• Grantee: Arthur Padial da Mota
• Host Institution: Instituto de Biociências (IBB). Universidade Estadual Paulista (UNESP). Campus de Botucatu. Botucatu , SP, Brazil

Abstract

In recent decades, coastal ecosystems have been affected by considerable environmental changes caused by human activities, leading to loss of biodiversity. To address this issue, species surveys of these transition areas between rivers and seas are a crucial tool for ecosystem preservation. However, conducting traditional surveys in marine and coastal environments can be expensive and challenging due to the sampling difficulties and the required invasive techniques. Environmental DNA (eDNA) offers an alternative that is more efficient, particularly when combined with high throughput sequencing (eDNA metabarcoding), which enables the identification of a broad range of aquatic fauna. eDNA consists of DNA molecules found in the species composition of the environment, originating from organisms that can provide information about the entire local community. The aim of this project is to evaluate the biodiversity of the São Paulo State coastal region using the eDNA metabarcoding method. Water samples will be collected from the estuarine regions of Juqueriquerê River (Caraguatatuba, SP) and Escuro River (Ubatuba, SP). Subsequently, DNA will be extracted and amplified from the mitochondrial gene 12S using PCR, followed by high throughput sequencing (MiSeq). The obtained reads will be processed and compared to a database for species identification. In addition, in situ environmental information (multi-parameter probe, depth, transparency) and samples for laboratory determinations (chlorophyll, total solids and phosphorus) will be obtained to assess the impact of water quality on species diversity. In the end, the data will be made available in public databases, to assist governmental initiatives for environmental conservation.