DNA analysis of our rivers and lakes could reveal new secrets about their biodiversity

DNA analysis of our rivers and lakes could reveal new secrets about their biodiversity



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Freshwater ecosystems are the lifeblood of the natural world, yet they face a silent crisis. A 2022 report from the World Wildlife Fund reveals a staggering 83% decline in global freshwater vertebrate populations since 1970, more than any other habitat.
The level of degradation of nature is alarming, but ecosystems are complex, and the impacts of human activities are also complex.Therefore, the story is often more subtle.
Our research explains how to conduct the analysis Environmental DNA (eDNA) – the DNA left behind by organisms in life and death – could reveal the secrets hidden in freshwater streams, rivers and lakes. This has raised hopes for more efficient monitoring of these vital ecosystems.
While fish and birds usually hog the limelight, Freshwater biodiversity It's a hidden metropolis, with lesser-known inhabitants. Macroinvertebrates such as mayflies and midges, which are visible to the naked eye, play a vital role in a healthy ecosystem. They have been monitored for decades and can give us a more representative view of how freshwater habitats are responding to human pressures.
Human activities pose varying degrees of threat in different parts of the world. For example, river water quality has improved greatly over the past century across Europe – mainly due to improved sanitation, de-industrialisation and better regulation, resulting in the restoration of macroinvertebrate biodiversity.
But the good news only goes so far. Since 2010, improvements in freshwater biodiversity have stagnated. Meanwhile, old environmental pressures are being replaced by new ones, from climate change to emerging pollutants released from old sewage systems.
Arguably, understanding the health of freshwater ecosystems has never been more important. To do this effectively, there is a need for comprehensive monitoring of which species are present. This is only possible by integrating new technologies – including the analysis of eDNA, which can come from many sources including feces, mucus and tissue fragments – with traditional monitoring programmes.
Current methods of monitoring biodiversity
The majority of freshwater present Biodiversity monitoring This study focused on a relatively narrow animal group – fish and macroinvertebrates.
Fish are usually tracked by “electrofishing,” where an electric current is passed through the water that temporarily stuns the fish. Any fish that float to the surface are identified and counted.
Macroinvertebrates are largely collected using “kick-net sampling”, where a person stands in the river, stirs up sediment, then catches whatever flows downstream in a net.
Both of these methods have their limitations. With electrofishing, it can be difficult to keep the current constant between sample runs, due to differences in conductivity between rivers. Larger fish are also more sensitive to shocks, so smaller fish are likely to be missed, which can lead to bias.
With kick-net sampling, some river substrates may give better results, while some species are better at avoiding or evading the nets.
In either approach, some sites may not be favorable at all. Standardization between sites can be difficult, so results may depend on the experience of the sampler. These approaches are also time-consuming, labor-heavy, and above all, destructive.
Environmental DNA
eDNA, on the other hand, can be filtered out of a water sample, eluted from the filter, analyzed for the taxonomic group of interest, then sequenced in a process called “metabarcoding.” This allows us to cross-reference the results with databases, identifying the organism the DNA came from.
There are many advantages to using eDNA. The work is easily standardised and automated. Sample collection is easy and does not require expertise, allowing the participation of citizen scientists. A very large range of organisms can be identified, including many small organisms. And most importantly, it does not disturb the environment.
But eDNA analysis It has its limitations. Unlike traditional methods, which can count individual fish, eDNA cannot distinguish a juvenile salmon from a spawning adult. It also lacks the rich, multi-decade datasets that have been created using traditional methods of analysis. This can make it difficult to use eDNA findings to inform current conservation policies.
Concerns have also been raised that in rivers you are detecting eDNA from organisms carried several kilometres upstream – leaving you unable to understand where in the whole river range a species signal has come from. This would make eDNA a poor tool for understanding biodiversity change.
However, our recent study shows that this is not the case. We took 798 water samples from the River Conwy in North Wales at 14 locations and 19 time points over the course of a year. We also took samples from rivers in England, Switzerland and the US. Our research shows that DNA shed by different organisms in a river does not travel far. Most of it becomes so faint that it is difficult to detect it just a kilometre downstream.
This is great news – since each sample of eDNA taken in a river represents a relatively small portion, it allows us to detect changes in the distribution of organisms across a river catchment. With this information, researchers can begin to figure out what is causing biodiversity decline, even in local areas of a freshwater ecosystem, and then identify how to stop it.
As eDNA analysis becomes more popular, scientists like us are working to bridge the gap between research and real-world conservation. Initiatives like the UKDNA Working Group foster collaboration, giving us the chance to share knowledge with government agencies and environmental stakeholders. By building comprehensive datasets that capture biodiversity changes in space and time, we can uncover the secrets hidden within eDNA.
This new knowledge is the key to creating effective management solutions, and will ensure a brighter future for our precious freshwater ecosystems.





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