Mx Sarah Stephenson1, Dr Cecilia Villacorta-Rath2, Dr Sharon Hook3, Dr Geoff Collins4
1CSIRO & UQ, Australia, 2James Cook University, Australia, 3CSIRO, Hobart, Australia, 4OzFish Unlimited, Australia
Biography:
Sarah's current work focuses on examining aquatic communities using high-throughput sequencing. Sarah’s research interest lies in investigating biological community responses to water quality and environmental variables. Sarah has experience of metabarcoding environmental samples for DNA-based analysis of biological diversity. Often this biological data is analysed with environmental contextual data to observe correlations and interactions with environmental drivers of community structure. More recently Sarah’s research interest lies in eDNA assay primer development and single species detection qPCR assays for DNA monitoring coastal species including Irukandji jellyfish, (C. barnesi) and endangered river shark species (G.glyphis) in Far North Queensland.
Sarah recently started a HDR PhD program with Dr Ryan Turner at UQ and Dr Sharon Hook CSIRO as part of the Reef Catchments Partnership at UQ. The focus of the PhD thesis is investigating the potential for integrating eDNA monitoring into the Reef catchments monitoring reporting. The main question of the thesis is: Can eDNA provide ecologically relevant data for indicator metrics of water quality in the GBR catchment context?
Abstract:
Use of citizen scientists is increasingly popular, but frequently, modifications to sampling procedures must be made to allow for the inclusion of volunteer collected DNA samples in biodiversity surveys. In many studies, emphasis is placed on technical PCR conditions and assay design, but less validation has been performed with methods for how eDNA is collected from the environment. In this study, we hoped to optimise a sampling regime for a citizen scientist project; ensuring sampling was simple, safe and effective for collecting eDNA for downstream analysis targeting fish taxa. We compared the yield and richness of eDNA obtained from an encased eDNA passive sampler to longmires preserved water samples at three waterways in Far North Queensland. Samples were collected by volunteers in parallel (e.g. identical time and locations for the two sampling treatments, 5 replicate samples were collected at each site, including negative field blanks and lab control blanks.
Passive and longmires preserved samples were processed at James Cook University (JCU) Townsville laboratories following two distinct separate extraction protocols. Amplification of eDNA using two metabarcoding assays (COI and mt16S) were completed at JCU labs and then sent to AGRF for Illumina MiSeq sequencing. Raw fastq files for both assays were processed through the GHAP bioinformatics pipeline, with samples processed from mt16S processed together with controls and likewise for COI amplicons. Data was screened for ecological geographical distribution likelihood for fish taxa and reality checked by a fish ecologist. The results showed a significant difference in the diversity, composition and read abundance for the two different sampling and extraction treatments for both COI and mt16S. The longmires, water sample results demonstrated higher read abundances and greater richness for both assays. The composition of taxa were different with the different sampling treatments despite identical sampling locations and time. This small study has relevance for developing sampling approaches to citizen science, ecological surveys in aquatic systems.