The study of environmental DNA (eDNA) of microbes has the potential to transform the way we assess and manage freshwater ecosystems. Dr Amy Thorpe, a molecular ecologist at the UK Centre for Ecology & Hydrology, discusses the findings of the first national survey of microbial eDNA in English rivers, involving the analysis of hundreds of biofilm samples…
Rivers are vital ecosystems that support high biodiversity and provide essential ecosystem services such as drinking water, irrigation and recreation. Often overlooked within these habitats are the microscopic organisms that form the foundation of aquatic food webs and drive the cycling of nutrients and organic matter.
River biofilms, the green or brown slimy material that grows on the surface of rocks, are home to diverse communities of microbes and are hotspots of microbial activity. These microbes are essential for maintaining the health and function of river ecosystems but their diversity remains hidden beneath the surface.
More than 1,600 biofilm samples were collected from rivers and streams across England and analysed by scientists at the UK Centre for Ecology & Hydrology (UKCEH) and the Environment Agency to study the microbial DNA found within them.
This environmental DNA (eDNA) – which refers to the genetic material organisms leave behind in their environment through cells, scales, fur or skin, for example – can be analysed using two key approaches:
- Metabarcoding, which involves sequencing specific genes or regions of DNA to identify the species present.
- Metagenomics, where all the DNA fragments from the genomes of all organisms is sequenced.
Both techniques enable the identification of the species present. Metagenomics goes further by enabling the identification of a variety of genes in an organism, giving an indication of the functions it performs such as metabolising and breaking down nutrients, organic matter and toxins, allowing a deeper assessment of the functional roles of various species within the biofilm.
Key findings
The results of this national survey revealed the remarkable complexity and ecological importance of microbial life within river biofilms, representing a significant advancement in our understanding of river microbial ecology and the vital roles microbes play in ecosystem function and health.
The main findings are:
- River biofilms are biodiverse habitats. Over 6,000 unique microbe types were identified, representing one of the most comprehensive surveys of river microbial communities.
- Biofilm microbes play diverse ecological functions. Our analysis revealed these microbes are essential for a range of ecological processes, such as nutrient cycling, pollutant breakdown and carbon sequestration, which are vital for sustaining the overall health and stability of river ecosystems.
- Biofilm microbial communities are sensitive to environmental change. Understanding how microbes respond to land use, temperature and nutrients, for example, provides valuable insights into how rivers can be managed and protected in the face of ongoing environmental challenges such as pollution and climate change.
- Microbes are important indicators of river health. Specific microbial groups were identified as potential indicators for monitoring pollution, which could help track the health of rivers and enable more accurate water quality assessments.
In the face of increasing environmental pressures from climate change and pollution, the ability to understand and monitor microbial communities is critical for ensuring the long-term health and sustainability of our rivers.
The survey highlights the value of eDNA metabarcoding and metagenomics in environmental monitoring. This advanced analysis offers a non-invasive and time-efficient method that is transforming our ability to monitor microbial diversity at a large scale, and has the potential to help us better manage freshwater ecosystems.
Further information
The research included Amy Thorpe, Susheel Bhanu Busi, Joe Taylor and Daniel Read from UKCEH. A report has been published on gov.uk
It forms part of the Environment Agency's Chief Scientist’s Group research programme to explore new ways to use eDNA to monitor ecosystem health, and supports the River Surveillance Network, a national initiative within the government’s Natural Capital Ecosystem Assessment (NCEA) programme designed to monitor and assess the state and condition of English rivers.