A project commissioned by the Environment Agency’s (EA) that captures genetic information from microbial biofilm communities in English rivers has developed a new DNA-based dataset which will be used to help identify new microbial indicators of ecosystem health.

The research study commissioned by the EA’s Chief Scientist’s Group - Molecular data generation and preliminary analysis of river microbial biofilm communities – was carried out by the UK Centre for Ecology & Hydrology.

Biofilms are often found on the bed and banks of rivers and different microbes such as bacteria, fungi, algae and other tiny single celled organisms attach and grow on the moist surfaces. The dataset will serve as a foundational source of knowledge and help identify new microbial indicators of ecosystem health. Preliminary analysis describes the microbial communities associated with different types of land cover as well as other environmental factors that influence their distribution.

Microbial communities have an important role in rivers. They help break down organic material and cycle essential nutrients like nitrogen and carbon. This supports ecosystem health, promoting the growth of other organisms, and influencing exchange with the atmosphere and climate.

Microbes are known to respond to changing environmental conditions, making them valuable indicators of environmental change and ecosystem health. However, they are largely unexplored because they are too small to be seen with the naked eye and can be difficult to distinguish from one another using a microscope. Advances in molecular-based environmental monitoring are changing this.

The Environment Agency is using new techniques to identify different microbial species in biofilms through their genetic information. Metabarcoding allows multiple species to be identified from a single sample using their unique genetic codes. Metagenomics pieces together larger genetic fragments to offer insights into the entire microbial community and its ecological functions.

DNA was collected from 1,643 river biofilm samples from 700 sites between 2021 and 2023. High throughput DNA sequencing was used to generate metabarcoding data to characterise the microbial communities associated with all biofilm samples.

Metagenomic data from a subset of 450 samples from 146 sites were used to uncover the potential roles that microbes play within biofilms. Associated environmental data such as water chemistry, landcover, geology and habitat type were also collated. Preliminary analysis incorporated metabarcoding data from 1,248 samples and metagenomic data from 200 samples.

The large spatial scale of the study uncovered an immense diversity of bacteria, fungi, algae and other microbes living within river biofilms. The variety of microbial species (diversity) and the proportions of specific species (composition) within microbial communities were influenced by various environmental factors, including land cover and water quality parameters such as nutrient concentration.

The research has demonstrated the value and power of molecular-based technologies in generating new information and uncovering insights about the diversity and composition of an important group of organisms and their potential roles in keeping our rivers healthy.

Initial analysis has laid the foundation to support the development of effective indicators of ecosystem health.