The River Ash in Hertfordshire is a chalk stream tributary of the River Lea and is one of the streams surveyed as part of the GeneFlow project.
Some of our most beautiful rivers in the UK are known as chalk streams. Their pure, constant water from underground springs, make them ideal for wildlife to thrive.
Principal Curator Ben Price shares how we monitor these waterways with the help of the crowd.
The critically endangered scarce brown sedge, Ironoquia dubia, is one of the rarest British caddisflies and relies on the unique habitat of chalk streams to survive.
Chalk stream health is crucial for a variety of specialised plants, insects, fish including salmon and trout, and mammals such as otters.
The streams are also a source of drinking water for humans. However, they are rare, with 85% of the world’s chalk streams found in England. They currently face challenges from climate change, population growth, water abstraction for drinking water and pollution.
The upper stretches of these rivers are temporary, meaning that they dry out completely during summer, and return in autumn.
Some unique invertebrate and plant species can only live in these dry-wet habitats, including:
These three species play a crucial role in chalk streams, being a source of food for fish, amphibians and birds. They also regulate the populations of other invertebrates by preying on them, they process leaf litter, detritus and organic particles, helping to maintain the rivers clean.
Some plants found in chalk streams have unique characteristics suited to the environment. The brook water-crowfoot, Ranunculus peltatus, which is adapted to long dry periods thanks to its resilient root system, and the watercress, Rorippa nasturtium-aquaticum, which has been historically cultivated in beds in these rivers. Some of these watercress beds, date back to the 1800s, adding an important cultural and historical value to chalk streams.
Aquatic vegetation at one of the sites of the project, River Mimram in Hertfordshire
To understand how healthy our chalk streams are, scientists monitor them for abundance of species and resilience over time. This can tell us about the habitat’s ability to withstand and recover from stress such as increased temperatures, decreased rainfall, increased pollution, and water being removed for humans to drink.
Traditionally, scientists survey rivers by physically searching for plants, animals or fungi that live there, or signs of them such as faeces or footprints. However, this can be very time-consuming, requires scientific expertise, and can miss small species or those that aren’t in the stream at the time of the survey.
A new project called GeneFlow aims to complement this traditional method using new, easy-to-use technology that motivates the public to get involved to help our collective understanding of these remarkable habitats. This is a collaborative project led by in-house freshwater entomologists Dr Ben Price and Dr Luis Moliner Cachazo, with The Riverfly Partnership, Herts and Middlesex Trust, CaSTCo, Chilterns Chalk Streams Project and River Chess Smarter Water Catchment.
GeneFlow is a pilot project to explore the aquatic wildlife of ten chalk streams in the Upper Lea, Thame and South Chilterns catchments through environmental DNA (eDNA).
Environmental DNA is the DNA present in organic matter such as dead skin cells, mucus and faeces, that is shed by living creatures when they move around. The use of eDNA also helps to identify species that are not visible to the naked eye.
While birds, mammals, invertebrates and plants are important inhabitants of waterways, tiny organisms such as microeukaryotes are also of interest to scientists studying this data, but harder to spot. These microscopic, single-celled organisms play a critical role in ecosystems, acting as predators, producers, and decomposers, and are essential for nutrient cycling. Understanding their role in chalk streams could help us understand more about nature recovery in these areas.
In order to take part in the project, community scientists were able to request free, sterile DNA sampling kits and instructions to enable them to collect eDNA from their chosen stream. Once this arrived, they were first asked to collect around one litre of water from their stream into a plastic sample bag. The next step for community scientists was to use a syringe to pull the water through a filter, which traps DNA.
Once completed, the filter is removed from the syringe and a preservation buffer is added to stabilise the DNA for transport. After labelling, both the sample and filtering kit can be posted back to the museum.
Scientists at the Museum then use laboratories on site to sequence and analyse the data. The DNA is extracted and multiple ‘barcode’ regions of the DNA are amplified for major groups like fish and invertebrates using an approach called metabarcoding. The DNA is sequenced and then compared to international reference libraries to match the sequences to scientific names.
Over 1,900 species were found. While the majority of these were insects (1,200-plus specimens), over 180 worms and 70 mammals were also discovered.
While we haven’t finished all the analysis for the project, we do have some exciting results which demonstrate the importance of these unique ecosystems.
Together with the crowd we surveyed 84 sites across ten rivers. Across all the samples, we have so far identified 50,000 unique sequences, relating to over 1,900 identified species. The most specious group recovered using our approach were insects, with flies being particularly dominant as they are a key part of freshwater food webs.
Many sequences are not yet identified to species due to gaps in the DNA reference libraries, but the team found eels, many freshwater fish species, hundreds of invertebrates and even water voles and kingfishers at some sites.
The team found several animals that are a priority for conservation including evidence of the European water vole, Arvicola amphibius. © Peter Trimming via Wikipeadia
Among the species identified, the team found several animals that are a priority for conservation including evidence of the European water vole, Arvicola amphibius. This semi-aquatic rodent is critically endangered in the UK.
Conservation efforts are ongoing for this species, including a recent reintroduction of water voles into the River Bulbourne, a Chalk stream in Hemel Hempstead. It is positive therefore that we recorded this data and will be able to share our findings to support others working on river restoration projects or to conserve other at-risk species.
As our DNA reference libraries continue to improve, we will learn more about the results that we have already collected from our UK chalk streams. There is also the potential to expand the pilot and use the same techniques to access the health of all UK rivers in the future.
The hope is that in addition to collecting data on valuable ecosystems, the project train new community scientists in new skills and connects people to nature and hopefully inspires them to protect it in the future.
To hear more about this project and our science work, follow @nhm_science on Instagram.
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