Fishing for DNA: using aquatic environmental DNA to map biodiversity across Coventry
See below for the story behind Mansha Kapur — a master's student who graduated from the Global Decarbonisation and Climate Change programme.
Greenspaces are vital habitats for local species in urban areas. But their proximity to human activity and society can disrupt natural food webs, and urban areas are often conducive to the spread of invasive species. Monitoring biodiversity is important for understanding the health of these ecosystems and evaluating the success of conservation projects.
In partnership with the Warwickshire Wildlife Trust, Canal and Rivers Trust, Natural England, and Coventry City Council, my master’s thesis aimed to assess the biodiversity of water bodies in Coventry’s urban greenspaces and map the spread of the invasive Signal Crayfish.
What is eDNA?
Traditional monitoring can be costly, time consuming, and ineffective at picking up rare or elusive species. It also demands great ecological expertise into the target species. Through this project, therefore, we wanted to demonstrate the power of a new, cost- and time-effective method to identify even thousands of elusive species at once: eDNA sampling.
eDNA (environmental DNA) is genetic information that organisms shed in their habitats. We can extract this DNA from soil, water, or air samples and sequence it in the lab. Modern bioinformatic tools can be used to identify the species in our samples through species-specific assays to quantify populations, or high throughput metabarcoding to analyse multiple sequences at a time.
Our Campaign
We sampled 41 sites across eight greenspaces in Coventry, including sites along the River Sowe, the River Sherbourne, and in a few lakes and ponds. On the Warwick Campus, we took two samples from Canley Brook and one each from Tocil and Teardrop Lakes.
We used quantitative PCR (qPCR) to target Signal Crayfish sequences in our samples and measure their population sizes. To identify more species, we used the synthetic COI primer that universally binds to many vertebrate and invertebrate sequences. Known as amplicon sequencing and metabarcoding, this also allowed us to calculate biodiversity metrics for each site based on the number (richness) and proportions (evenness) of the species we found.
What We Discovered
We successfully mapped Signal Crayfish populations across Coventry. By identifying sites where they have not yet spread and detecting early invasions into new habitats, our data can help prevent their further dispersal.
Through metabarcoding, we detected indicator and keystone species that are important cues for environmental management decisions. In Coventry Canal, for example, a high proportion of Rotifera could indicate eutrophication. We also found species, such as the invasive American Ball Waterflea, that we might not have known to look for — a powerful feature of eDNA studies.
Using statistical tools to quantify and analyse biodiversity, I found that biodiversity differed significantly across the 8 regions. Signal Crayfish presence also undermined aquatic community composition. Further study and engagement with local stakeholders can help us understand why some greenspaces thrive more than others and how we might improve the health of less biodiverse areas. Charterhouse, a region zoned for largescale ecological expansionLink opens in a new window, was found to be one of the more biodiverse sites. While good news, this is also a strong sign to monitor and conserve the rich ecosystem as the development unfolds.
A map of the 41 sites sampled across 8 urban greenspaces in Coventry and positive or negative Signal Crayfish detections.
Collecting an aquatic eDNA sample by pumping water from the River Sowe through a filter at Lakeview Park, Coventry.
Overall, our eDNA campaign was vastly insightful. Learnings from this study also highlight ways to improve our methodology, which will be crucial as conservation organisations add eDNA to their repertoire of ecological assessment tools. eDNA can also benefit from citizen science; sampling is an easy way to explore wonderful greenspaces around you while enhancing the reach of an eDNA campaign.
This project has been a fulfilling opportunity for me to conduct research with tangible value for local conservation while enjoying expansive greenspaces around the city that I didn’t know existed. Thus, I completed my thesis with a rich set of data for our partners, as well as a surprisingly greener impression of Coventry. I hope this case study inspires similar academic and non-profit partnerships to enhance biodiversity monitoring and leverage the power of both eDNA and collaborative science.
I would like to thank my supervisors Dr Molly A. Williams, Dr Gary Bending, and Dr Sarah Cook, as well as and the Bending Lab members, for making this project possible.