A large scale temporal and spatial environmental DNA biodiversity survey of marine vertebrates in Brazil following the Fundão tailings dam failure

Seawater contains a wealth of genetic information, representing the biodiversity of numerous species residing within a particular marine habitat. Environmental DNA (eDNA) metabarcoding offers a cost effective, non-destructive method for large scale monitoring of environments, as diverse taxonomic groups are detected using metabarcoding assays. A large-scale eDNA monitoring program of marine vertebrates was conducted across three sampling seasons (Spring 2018, Autumn 2019 and Spring 2019) in coastal waters of Brazil. The program was designed to investigate eDNA as a testing method for long term monitoring of marine vertebrates following the Fundão tailings dam failure in November 2015. While no baseline samples were available prior to the dam failure there is still value in profiling the taxa that use the impacted area and the trajectory of recovery. A total of 40 sites were sampled around the mouths of eight river systems, covering approximately 500km of coastline. Metabarcoding assays targeting the mitochondrial genes 16S rRNA and COI were used to detect fish, marine mammals and elasmobranchs. We detected temporal differences between seasons and spatial differences between rivers/estuaries sampled. Overall, the largest eDNA survey in Brazil to date, revealed 69 families from Class Actinopterygii (fish), 15 species from Class Chondrichthyes (sharks and rays), 4 species of marine and estuarine mammals and 23 species of conservation significance including 2 species of endangered dolphin. Our large-scale study reinforces the value eDNA metabarcoding can bring when monitoring the biodiversity of coastal environments and demonstrates the importance of collection of time-stamped environmental samples to better understand the impacts of anthropogenic activities. 

Methods
Seawater samples were collected at 40 sites along the coastline of Brazil. DNA was extracted using the DNeasy blood and tissue kit (Qiagen). Two PCR assays used in this study were the 16S rRNA primer set Fish_Sygnathid_Short (Nester et al., 2020) and the COI Elasmobranch multiplex (West et al., 2020).  Multiplex identifier-tagged amplicons were blended into libraries and sequenced on an Illumina MiSeq instrument. 

Environmental factors including turbidity (Tu; NTU), temperature (Tm; °C), dissolved oxygen (DO; mg/L), chlorophyll-a fluorescence (Ch; μg/L, salinity (S; PSU), conductivity (Co; mS/cm) and photosynthetically active radiation (PAR; μMol/m²/s) were measured near the surface using an oceanographic grade XR Data Logger (RBR XRX-620).