Dr Mieke Van Der Heyde1, Michael Curran2,5, Dr Paul Nevill1, Dr Nicole White1, Stephanie Floeckner2, Andy Austin3, Michelle Guzik3,4
1Trace and Environmental DNA (TrEnD) laboratory, Curtin University, Bentley, Australia, 2Biologic Environmental, East Perth, Australia, 3Department of Ecology & Evolutionary Biology, The University of Adelaide, Adelaide, Australia, 4South Australia Museum, North Terrace, Adelaide, Australia, 5RioTinto, Perth, Australia
Biography:
Mieke is currently a Researcher with the Trace and Environmental DNA (TrEnD) Laboratory. Her research focus is developing and applying eDNA methods to monitor terrestrial and subterrestrial ecosystems.
Abstract:
substantial sampling difficulties. Environmental DNA (eDNA) metabarcoding is a promising tool to help monitor these ecosystems, but it faces challenges such as primer bias and non-target amplification. Therefore, rigorous validation of metabarcoding primers is essential to ensure accurate and comprehensive assessment of subterranean fauna diversity. This study addressed a need for robust primer validation through silico and in vitro analyses, providing insights into primer performance across a range of subterranean taxa. Our objectives were to evaluate the efficacy of COI metabarcoding primers for assessing subterranean fauna diversity, addressing the challenges posed by traditional sampling methods. In silico analyses involved curating COI sequences from the Barcode of Life Database (BOLD) and selecting 14 primer combinations for subsequent in vitro testing using mock communities. Results demonstrate varied primer performance in PCR efficiency and detection limits across subterranean taxa. One assay (BF1/jgHCO2198) was able to detect 82% of taxa in the mock community, but only in at high DNA concentrations of target taxa. The greatest proportion of subterranean fauna taxa detected in a diluted mock community was 68% with the fwhF2/fwhR2n primer combination. Our findings underscore the potential of COI metabarcoding for assessing subterranean fauna diversity while highlighting the importance of primer selection and optimization. Overall, this study contributes valuable methodological development for future studies targeting the conservation and management of subterranean fauna biodiversity.