Pilot study to validate an environmental DNA sampler for monitoring inshore fish communities.
Abstract
The utility of environmental DNA (eDNA) techniques for monitoring species diversity are gaining acceptance amongst industry and government decision-makers. This interest is driven by the pressing need to better understand the effects of anthropogenic pressures on ecological communities and the capability of eDNA methods to deliver more biodiversity data at reduced effort and cost. Sample collection presents the greatest risk for any environmental survey and particularly so for eDNA surveys. The importance of good survey design should not be underestimated. Despite its known importance in conventional ecology, few eDNA studies have examined sampling effort, the effect of sample volume and sampling duration on the probability of eDNA capture (Grey et al. 2018). Simply put, the greater the sampling effort, the greater is the probability of detection. Applied Genomics have addressed this by developing a marine eDNA sampler capable of sampling up to 50 litres of demersal seawater over a programmable time period of several hours to several days. This document presents a report on a pilot study project to investigate the feasibility of monitoring inshore fish communities using a large-volume marine eDNA sampler. Three replicate sample collections were conducted at each of three sampling sites. Recovered samples were processed, DNA purified, fish-specific metabarcode amplicons for 12S and CytB genes were produced. Sequencing was undertaken on an Illumina MiSeq DNA sequencer. The resulting sequence data were subjected to bioinformatic processing, taxonomic assignment and biostatistical analyses. Our methods characterised a total of 74 unique fish and marine mammal species to species level, of which 14 were identified as listed protected species. We provided data and visualisation of species haplotype diversity, which is an indication of the diversity of breeding individuals within each sampled population. In addition to assessing the performance of our sampling strategy, we undertook fish community analyses for alpha, beta and gamma diversity, and compared our results to historical data for recorded fisheries landings. Whilst the study suffered from low statistical power, we were able to demonstrate the considerable potential of this sampling system for the cost-effective, independent and unbiased monitoring of fish communities and of marine biodiversity. The data resulting from the ongoing monitoring of inshore marine habitats using large-volume eDNA samples, such as these, could serve the remit of multiple government agencies, thereby providing an unprecedented level of information about the health of our fisheries and the wider coastal ecosystem at relatively low cost.