Miss Chjara Ito Pellegri1, Mark Hamman1, Cecilia Villacorta-Rath1
1Tropwater, James Cook University, Australia
Biography:
Chjara is a master student at James Cook University studying Maine Biology. After volunteering in the eDNA lab of TropWATER during her first year at JCU, she decided to conduct her thesis research in the same lab the next year, focusing on eDNA sample collection methods, which she will present here.
Abstract:
Mainstream environmental DNA sampling method consists of filtrating water; a method efficient at collecting small eDNA particles in high concentration but challenging in turbid waters. Alternatively, whole water samples can be collected and preserved in situ for later DNA extraction via precipitation. Recently, a novel sampling method using suspended glass fibres (SGF) was developed: once introduced into the sampled water, the fibres bound with eDNA, are then filtered and collected. This study compared user friendly field methods for eDNA sample collection in turbid environments using both eDNA metabarcoding and targeted qPCR. The methods used were: (1) a glycogen-aided precipitation from (a) 100mL and (b) 300mL water samples, (2) onsite filtration of 300mL water using SGF, (3) laboratory-based filtration of 1L water, and (6) laboratory-based filtration of 1L water with an added buffer to reduce inhibitors. qPCRs targeted the Rhinella marina, Oreochromis mossambicus, and Cabomba caroliniana. Additionally, eDNA metabarcoding targeted fish and vertebrate assemblages using the 16s Berry fish and 12sV universal primers. Both ease of use in the field (collection time), and eDNA recovery (replicate amplification rates for targeted eDNA and species richness for metabarcoding) of each method were assessed. Laboratory filtration yielded higher total DNA concentrations than on-site filtration and precipitation. However, targeted eDNA analysis showed better performance from the 100mL precipitation method for detecting tilapia and cane toad eDNA. We expect the methods processing larger volumes of water to perform better in eDNA metabarcoding. These findings will advance eDNA methods in turbid environments and validate new user-friendly approaches.