What’s in a river? We’re using eDNA to find out

What’s in a river? We’re using eDNA to find out

Dr Lewis Campbell, one of our Catchment Managers, reports how we have introduced a modern method of assessing what’s in rivers to our armoury.

Traditionally, a variety of methods have been used to evaluate biodiversity and to understand whether or not a specific species is in a particular place in the countryside. When it comes to fish, for example, these survey methods might involve the use of nets or electrofishing equipment. For mammals, methods can involve field surveys looking for footprints, droppings, burrows and dens, or installing hidden cameras that are automatically triggered with movement. When studying birds, ecologists might spend time in the field searching for visual signs or identifying different species by their calls.

Our work seeks to help trout recolonise the Hogsmill. Picture via Canva

For smaller creatures, such as amphibians, reptiles and even invertebrates, various types of traps can be deployed so that the animals can be collected and counted before being released again.

One thing that this diverse set of methods all have in common is that they require a large amount of time to be spent on site. More recently, conservationists have begun to use environmental DNA, or eDNA for short, as a tool to understand species distribution. As animals go about their daily lives, they are continually shedding cells into their environment. These cells might come from their hair, skin, saliva, or even their waste, but they all contain the genetic material (DNA) belonging to that animal within their nucleus. This is environmental DNA.

Rivers could be compared to a soup containing cells and DNA from all of the organisms that live in or near by the water.

Simply by collecting a water sample, we can gain a snapshot of all the animals that were in the local vicinity at the time. We pass river water through an extremely fine grade filter, then generate and analyse the genetic sequences that the sample contains. A single water filter sample can reveal the presence of hundreds of different species from right across the animal kingdom.

eDNA is quite a modern technique. The first example to detect species in a freshwater environment was in 2008, when French researchers used the technology to detect invasive American bullfrog. Since then, technology and its potential applications have improved and expanded rapidly.

Preparing to take a sample
Preparing to take a sample to find out the DNA of the Hogsmill

The analysis portion of this work requires numerous pieces of cutting edge technology and very powerful computers, but collecting a water filter sample is very straightforward and quick. This means that it is possible to comprehensively survey the biodiversity at a location much more efficiently than is possible using many traditional methods.

The only major drawback of eDNA surveys is that they can currently only provide information on whether a species was or was not in a given location  but not how many were there. For example, using eDNA you could say “I did detect salmon in my river” but not “there were 50 salmon in my river”.

This means that it is a particularly powerful first pass tool for determining presence or absence of a species, which would then by followed up with more targeted traditional surveys. Therefore, eDNA will never replace the valuable work of professional ecologists, but is certainly a very important emerging tool in the conservationist’s arsenal.

At the South East Rivers Trust we are beginning to use eDNA to understand the biodiversity in our rivers before, during, and after our restoration work. This is critical to developing an understanding of whether or not the projects that we undertake are having the desired positive outcomes for the wildlife that call our rivers home.

An important example of this type of baselining is our WET Hogsmill. This is funded by Natural England and aims to kick start the recovery of several species of concern in the River Hogsmill in South West London.

These species – water vole, European eel, and brown and sea trout – are imperiled across our river network, but all of them historically called the Hogsmill home.

Water Vole
The presence of water voles was detected in the Hogsmill by eDNA. Picture via Canva

Our WET Hogsmill project will enhance the river to make it more accessible and more useable for these species, aiding their recolonisation of the river. Environmental DNA is a great tool for us to demonstrate where these species are living along the river. The aim is that over time this will document increases in the numbers of places where specific species are found along the river.

So far we have undertaken a baseline eDNA survey at several points along the Hogsmill, from near its source, to its confluence with the Thames at Kingston. We collected water samples that were used to detect a wide variety of vertebrate species. We found mammals including red fox, grey squirrels, and wood mice. We detected fish including barbel, chubb, stickleback, and many others. We also found birds including the majestic kingfisher, grey heron, magpie, moorhen, coots, and parakeets.

Importantly, we also detected the presence of eel, water vole and brown trout at locations on the Hogsmill, so we know those species are present and we hope that our work will help them to become better established on the river.

The initial survey’s results can be found on our Storymap and we will continue to monitor the river with annual eDNA surveys – so watch this space!





Busting myths about weirs

The South East Rivers Trust regularly works towards removing weirs or installing fish passes. In the second of a series of blogs about the problems weirs cause to rivers, Dr Chris Gardner, Head of Science and Partnerships, writes about two big issues. These are the movements of fish (which he tracked for his PhD) and drought resilience. Here, he addresses some myths about both aspects.

‘Migratory’ fish? All fish migrate

It is often thought that weirs and other barriers that restrict the movement of fish only affects ‘migratory’ species such as salmon, sea/brown trout and eels, as their migrations are relatively easy to observe and are well known.

A proportion of brown trout will migrate to sea and return as sea trout
A proportion of brown trout will migrate to sea and return as sea trout if their migratory pathway is unimpeded. Returning sea trout are very important in maintaining brown trout populations.

However, all fish migrate to some extent, and all fish have life stage specific habitat requirements affected by habitat degradation. Coarse (or freshwater) species such as barbel, chub and dace are affected by habitat fragmentation and degradation caused by weirs.

Higher water velocities on riffles encourages plants such as water crowfoot to grow. Plant growth on riffles makes it difficult for predatory fish to hunt. This also provides an abundant food supply of invertebrates and overhead cover that hides fish from predatory birds and animals.

Riffles are great places for baby trout and young salmon to live, they are also the preferred habitat for juvenile barbel. However, riffles hidden under lake-like habitats upstream of a weir lack the characteristics that make them great juvenile barbel habitats. And if there are low numbers of small barbel then there will be fewer numbers of big barbel and eventually no barbel at all.

Here, the trout and salmon fraternity are ahead of the game. The economic value of salmon (commercial and recreational) and the large declines in salmon populations since the 1980s have caused scientists and anglers alike to research and understand what the habitat requirements are for all life stages of these fish.

They have used this information to minimise potential population bottlenecks or limiting factors because of available habitat. There are many things impacting our fish populations, but in-river habitat is the one thing that is relatively easy to address and benefits all wildlife. Organisations such as the Wild Trout Trust have been encouraging progressive thinking and educating game anglers in fisheries management and river restoration.

Research shows why fish need to access the whole river

Coarse fish migrate and need to move around a river system to locate specialised habitats required at certain times and during certain conditions. Fish are streamlined, live in a near weightless and frictionless environment and need to constantly swim just to maintain a static position in the river. Hence, fish have great potential to be highly mobile.

Modern tracking studies using implanted radio or acoustic tags have revealed these migrations. For example, in 2010 Dr Karen Twine, of the Environment Agency, radio tracked 20 adult barbel (6-15lb) in an 8.2km reach (between two impassable weirs) of the Great Ouse for 18 months. She demonstrated that the barbel utilised most of the river length available to them and made seasonal movements to spawning and over wintering habitats.

Barbel migrate and use different habitats at different times of year
Barbel migrate and use different habitats at different times of year and at different stages in their lives

Similarly, in 1993 Dr Martyn Lucas, of Durham University, radio tracked 31 adult barbel (2-6lb) over 15 months in a 7.2km reach of the River Nidd, a tributary of the Yorkshire Ouse, with open access to the Ouse.

Again, these fish were highly mobile, ranging over sections of river from 2-20km in length. Their movements were associated with seasonal shifts in habitat, upstream spawning migrations and their downstream migrations to ‘over wintering’ habitats in the lower reaches and main River Ouse.

Basically, fish will move as far as they are able to fully exploit the best available habitat/resources: the more limited the resources, the further they will travel.

Other studies on less fragmented rivers with more limited essential habitats have shown that fish have the potential to move over very long distances.

Study shows the benefits of free passage

During my PhD in 2006, I tracked the movements of 80+ adult common bream (4-7lb) over four years in a long 40km reach of the Lower River Witham, a very uniform fenland river in Lincolnshire.

Returning a tagged bream to the main river during my PhD
Returning a tagged common bream to the River Witham during my PhD, to demonstrate how mobile fish can be in open, barrier free habitats

My bream were tightly shoaled and relatively immobile in a deep tributary off the main river at the upstream extent of the reach during the winter, moving short distances of, on average, less than 5km a month up and downstream.

In the spring, they became highly mobile moving on average 30-40km a month, utilising the entire length of the river available, with one individual moving more than 120km in a single month!

At this time, they were visiting shallow tributaries off the main river, before using these for spawning in late May/early June. Once they had spawned, they spread out and spent the rest of the summer in the main river foraging, again moving on average 20-30km a month up and downstream. In the autumn, they moved back upstream to the deep tributary for the winter. This same yearly pattern was observed throughout the study.

These studies demonstrate that adult fish use different habitats at different times of the year and require free passage between them.

Habitat requirements are different for adult and juvenile fish. So, during a fish’s life it will have many different habitat requirements. These requirements will be more crucial for juvenile fishes because of their vulnerability to predators and therefore their need to find safe cover.

If any single habitat type is lacking, limiting or inaccessible, there will be consequences for individual survival and therefore the population as a whole. Weirs often restrict populations to those reaches that have sufficient habitats to enable life-cycle completion.

The “weirs” thing about drought resilience …

A common misconception is that weirs delay river discharge and therefore make the river more resilient to drought. Weirs do hold back a quantity of water in the upstream section, which is “impounded” – leaving the river more like a still canal or pond. However, a weir just stores water in the upstream area – and once the river is full, river flows over the weir at the same rate it enters the impoundment.

Imagine an impounded section of river as being like a kettle being filled from a tap. Once full, the kettle overflows at exactly the same rate as the tap runs and the water bill ticks up exactly the same.

A river in Kent that dried up in the summer of 2022
A river in Kent that dried up in the summer of 2022

In the event of drought, rivers tend to dry from their upstream end first. Impoundments upstream of weirs can and do provide refuge areas for fish in such an event. However, these areas are likely to be heavily silted because of the lack of flow, and will quickly deoxygenate because of biological processes in the silt, leading to fish deaths.

Fish will move downstream naturally in response to a drying river using the river’s flow to navigate.

However, if the fish encounter an impoundment upstream of a weir, and there is no flow going over the weir (because of the drought), there will be no flow cues to navigate by and the fish will simply be unable to move any further and become trapped where they will die as the water in the impoundment deoxygenates.

If no weirs exist fish will move downstream, seeking out deeper, fresher water in the river’s lower reaches. Once the drought has broken, they will then move back upstream.

So, perhaps counterintuitively, weirs actually reduce a river’s resilience to drought.

In conclusion, the impacts caused by weirs are problems for freshwater fish as well as salmon and trout: the principles might not be as well understood or as popular, but they are real. If our rivers are to fulfil their ecological potential, we need to address this and other factors that are limiting fish populations.