Alongside our nature restoration projects, we want to understand the biodiversity status of Chiddingly Parish – in other words, what animals, birds and insects are living here. Since 2024, we have been using cutting-edge science to sample the environmental DNA (or eDNA for short) of river water at sites across the Bull River catchment. The results allow us to identify the species living along our rivers, track biodiversity changes, and understand the impact of our nature restoration projects upon wildlife. They also help us plan future projects. Sampling and analysis has been funded by the Chalk Cliff Trust with support from the University of Brighton. Environmental DNA analyses were carried out by NatureMetrics.

What is eDNA and how do you sample it?

Environmental DNA is a term for the DNA shed by animals and insects as cellular material as they go about their daily lives. eDNA doesn’t survive long in water but when analysed can provide remarkable insights into the diversity of species living in or near a river or stream. Analysing eDNA allows scientists to detect the species present in an area without actually collecting or observing the creatures themselves. This can be a very efficient way to obtain a snapshot of the biodiversity of a water body, especially since many species are rare or difficult to detect using traditional survey methods. For example, many fish can sense the presence of nets as they move through the water and actively avoid being caught. eDNA analysis offers a tool to detect those species, providing a more nuanced understanding of ecosystems.

With advice from external experts, we have identified five locations along the main stream and tributaries of the Bull River to conduct eDNA sampling. Each is immediately downstream of one of our project sites. You can view the site locations and their unique site codes on the map. Use the +/- buttons to zoom in/out.

The eDNA sampling method is illustrated in the photos below. At each site, a sample of stream water is collected from various points across the channel. Using a syringe, around 2-3 litres of the water sample is passed through a filter that traps cellular material. Once no more water can be passed through the filter, any air and water is pushed out. The filter is then sealed with a resin primer and sent off for analysis.

To sample eDNA, 2-3 litres of river water is passed through a filter using a syringe (image © Gail Giles)

Once sampling is done, air and water are pushed out of the filter and it is sealed with resin (image © Sally Ashby)

The site location, weather conditions and water quality are recorded for each site (image © Gail Giles)

What do the results show?

So far, we have one set of eDNA analyses from samples collected in July 2024. This provides us with baseline data against which we can compare future results. Samples have been analysed for the invertebrate, fish, bird and mammal DNA that is present. While they are site- and time-specific, the results provide a detailed record of the diversity of our river network. eDNA data are reported in terms of the Operational Taxonomic Units detected in the sample. An OTU is broadly equivalent to a species in most cases, but where the individual species cannot be identified it may refer to a genus or family. 

Over 250 distinct OTUs have been detected across our five sampling sites, with an average species richness of over 100 species per site. Species detected include six types of fish, one species of lamprey (likely Lampetra planeri, the brook lamprey), 13 species of worm, 25 species of beetle, and a remarkable 174 species of fly. The fish species include brown trout (Salmo trutta), European bullhead (Cottus gobio), stone loach (Barbatula barbatula), common minnow (Phoxinus phoxinus), three-spined stickleback (Gasterosteus aculeatus) and an unidentified species of carp (Cyprinidae). DNA from various unidentified duck, goose, dove and pigeon species were also detected.

We did not ask for our sample analyses to include the detection of any crustacean species that might be present in our rivers. Worryingly, however, the DNA of one crustacean – the signal crayfish (Pacifastacus leniusculus) – was present in such abundance that it was detected regardless. The signal crayfish is a highly invasive species that was introduced into Europe in the 1960s to supplement fisheries stocks of the European crayfish (Astacus astacus), and has subsequently outcompeted its European cousin in many UK rivers and streams. 

Brown trout (Salmo trutta). Image credit: Creative commons.

Stone loach (Barbatula barbatula). Image credit: Creative commons.

European bullhead (Cottus gobio). Image credit: Creative commons.

Common minnow (Phoxinus phoxinus). Image credit: Creative commons.

Brook lamprey (Lampetra planeri). Image: Creative commons.

Signal crayfish (Pacifastacus leniusculus). Image: South West Water.

What species were present?

The Tree of Life to the right provides a detailed view of the species detected and their taxonomic relationships. On the diagram, names on the same branch of the 'tree' are more similar than those on different branches. The chart is structured with the highest taxonomic rank at the centre (e.g. kingdom, phylum, class), moving through the ranks of order, family, genus, species as you move to the outer edge.

The legend in the bottom right of the chart indicates how to relate the colour in the branches to the number of species. The colour scale goes from grey - indicating very few species, to blue - indicating a lot of species.

The diagram shows the dominance of fly species (Diptera) in our data. The eDNA analyses detected a wide variety of may-flies hover-flies, fruit-flies, dung-flies, mosquitoes, midges, house-flies, bluebottles, horse-flies and crane-flies, all important food sources for birds and fish.

The Tree of Life resulting from the eDNA analyses across our five sites, showing the dominance of flies (Diptera) in our water samples.

Were there differences between sites?

Water samples from the Bull River at Peke's Farm (PEKE24) and Hale Farm (HALE24) showed the greatest species diversity. This is unsurprising as the sites are on the main river channel and therefore contain a wider range of riverine habitats. Hale Farm was also the only site where European bullhead DNA was detected. The sample from Stream Mill Smallholding showed the lowest overall species diversity. However, the site was the only location where brown trout and lamprey were recorded. 

It will be interesting to see if data from eDNA sampling in summer 2025 show the same pattern of results.

Variations in species richness across our sampling sites. The blue portion of each bar indicates the number of OTUs that could be identified to species level. High Species Richness generally indicates a healthier and better functioning ecosystem and is the simplest biodiversity metric that is consistently reported in biodiversity monitoring.