Mr Alex Coutts1, Dr Marie Thomas1, Emilie Perez-Wright1, Dr Laura Smith2, Dr Deepak Pazhayamadom2, Dr Madeline Green1
1Institute for Marine and Antarctic Studies (University of Tasmania), Taroona, Australia, 2NT Fisheries, Department of Agriculture and Fisheries, Berrimah, Australia
Biography:
Alex is a marine ecologist working on forensic monitoring of fisheries and aquaculture-environment interactions the University of Tasmania. Alex's research interests include advancing molecular laboratory and bioinformatic methods for fisheries monitoring, and understanding the influence of aquaculture on environmental microbiomes.
Abstract:
Environmental DNA has emerged as a promising tool for efficiently collecting high resolution fisheries catch data. However, existing metabarcoding assays do not reliably provide elasmobranch identification at the species level, limiting their applicability to the management of individual species within a fishery.
In this study, PCR primers were designed to amplify the entire ND2 gene from all elasmobranch families identified in catch data from two Australian fisheries (Eastern Tuna and Billfish Fishery and Northern Territory Demersal Fishery). To test the universality of the primers, they were tested on DNA from tissue samples of 44 species representing 10 of the 14 Australian elasmobranch orders. To evaluate the performance of the novel metabarcoding primers we conducted Oxford Nanopore sequencing of amplicons from 30 eDNA samples collected across six fishing events where sharks were visually observed, and 2 mock communities (MC) of previously barcoded specimens.
Amplification of all tissue samples was successful. At least 10 unique captured species were identified from eDNA metabarcoding using custom BLAST and a conservative lowest common ancestor heuristic. Denoised MC amplicon sequences were >99% similar to reference barcodes when the library contained no closely related species. However, accuracy dropped when there were multiple closely related species in the library. This work provides a new workflow which leverages the advantages of rapidly improving and accessible long-read sequencing technology for monitoring elasmobranchs in Australian fisheries. Given the wide taxonomic coverage of the new primers, they also represent a promising tool for eDNA biodiversity monitoring more broadly.