eDNA in the Cornish blue

Project Overview

Environmental DNA (eDNA) is genetic material that is shed from macro-organisms. Recent years have seen the piloting of eDNA barcoding in British marine waters. This project looks to collect pilot data from Cornish coastal marine environments to describe the spatial behaviour of blue & porbeagle sharks and their main teleost prey.

Additionally, to make the most impactful use of the efforts of researchers and citizen scientists alike, we will be investigating the wider marine biodiveristy, expanding our target species beyond the elasmobranchs of regional interest, using metabarcoding and qPCR to look for eDNA from cetaceans, pinnipeds, and jellyfish.

Fisheries and tour independent data is rare in this region, resulting in an unknown true abundance and diversity for marine vertebrates, and invertebrates. This study looks to be one of the first to fill this gap, using novel non-invasive approaches.

This project is based at the Centre of Ecology and Conservation, at University of Exeter Penryn campus.

Study Area

The area of interest is the pelagic sub-tidal waters off of Cornwall and the Isles of Scilly (UK), shown in this image as the blue shaded area.

Methods

Samples of sea water will be collected either in sterilised litre water bottles, before being filtered and processed using qPCR techniques; or in protoypic sampling technology called 'Metaprobes' (see more below).

qPCR, specific to eDNA, is the approach where specific species genomes are amplified and detected via bioinformatics from filtered samples of ocean water. Martin Genner at the University of Bristol has been instrucmental in helpign define the project protocol and facilitating the processing of samples.

To collect water samples form this vast study area (blue shaded region in image), I am working with local tour operatrs, and government entities, creating partnerships which facilitate the colleciton of samples at regular intervals throughout the year at consistent locations. Furthermore, harnessing the potential of social media, I am recruiting citizen scientist sailors to help collect samples from this vast area of interest, particularly on the route from Land's End to the Isles of Scilly.

Research Questions

Proof of concept - can we confirm work done in Plymouth that these elasmobranch and teleost species can be detected via water bottle sampling and qPCR in the southwest UK marine environment?
What are the temporal trends in the relative abundance and spatial behaviour of blue sharks and porbeagles? and their associated teleost prey?
What oceanographic and bathymetric variables relate to these trends in abundance and spatial behaviour of these shark and teleost species?
What is the picture of wider biodiversity in the southwest pelagic seascape of England? What species are detected and when?

Further work will look to explore punctuated increases in detected abundances of these sharks and fish.

And concurrent work in this project is deploying and testing a novel method of eDNA sampling - the Metaprobe 2.0, not our creation but a collaborators (check it out here). We will be looking to cross-validate the Metaprobe 2.0 with BRUVs in the Isles of Scilly; and with water bottle sampling off of Cornwall.

Novel tech with vast implications: Metaprobe 2.0

The Metaprobe 2.0 is a piece of equipment developed at Liverpool John Moore University by Stefano Mariani and Guilia Maiello (GitHub Repo). The Metaprobes are 3D-printed spheres which are deployed with gauze-wrapped cotton, to collect eDNA from water which can passively flow through the holes in the sphere.

This method of sampling is an order of magnitude cheaper than the traditonal water bottle sampling. Based on collaborators work testing the Metaprobes against a trawl survey, there is good evidence that the Metaprobes will perform as well, if not better, than traditional waterbottle methods.

In this project, we will test the Metaprobes against traditional water bottle sampling and baited remote underwater surveys in Cornwall and the Isles of Scilly. If we can establish the veracity of eDNA detection via Metaprobe sampling, this work will be very impactful as this method of eDNA sampling and extraction is comparatively more accessible, and could therefore be adopted globally as the new industry standard for eDNA research in the marine environment.

Outreach and Citizen Science

This project is allowing me to engage with the local and visiting Cornish community. For 2023, the project is working with over 6 different local operators, and a growing number of citizen science sailors.

If you are planning a journey to/from the Isles of Scilly, or around the offshore waters of Cornwall between April and November, please do get in contact using the Form below.

Citizen Scientists & Metaprobes

Most of our citizen scientists have and will be sent out with Metaprobes, as they are a far more accessible method of collecting eDNA samples from the marine environment than traditonal water bottle sampling, do not require filtration in the field, and require only a small bags amount of kit.

Here are some materials we have made for those interested and partaking in our research using Metaprobes.

Protocols & Videos

Many of our protocols and materials are availabe on the project's GitHub.

I share videos which I host on Youtube via my Twitter and Blog & Media.

For example, I filmed a video demonstratng how to assemble a Metaprobe for marine sampling. And this has been shared to my Blog and YouTube page.