Understanding freshwater ecosystem health from a microbial perspective

Freshwater environments are exposed to stressors that contribute to the decline of freshwater species, ecosystems, and the services they provide. Understanding the causes of these declines is complex, as there are typically multiple, interacting pressures. Additionally, these pressures may be sporadic, for example in the form of pulses of chemical pollution or extreme weather events, which makes directly measuring stressor events a challenge. An established approach to understand both the condition of ecosystems and identify the causes of declines, is the use of bioindicators. These are typically based on the composition of fish, macroinvertebrate, diatom or macrophyte communities. However, bacterial, fungal, and eukaryotic microbial communities dominate freshwater biodiversity, both numerically and in terms of species and genetic diversity. These communities play fundamental roles in the functioning and maintenance of freshwater ecosystem health. They are primarily responsible for the decomposition of organic matter, are key drivers of biogeochemical cycles, photosynthetically fix carbon, and form the base of aquatic food webs. However, we lack an understanding of how microbial communities are structured within freshwaters and, critically, how they respond to ecosystem stressors such as nutrient and organic pollutants, and climatic and hydrological change. Due to the functional importance of these communities, it is a priority to understand more about their composition and distributions across freshwater catchments, as well as explore their ability reveal ecosystem condition.

Advances in High Throughput Sequencing (HTS) of DNA mean that we now can characterise whole microbial ecosystems in unprecedented detail, at low cost and in high throughput. This project will apply HTS of freshwater biofilms collected by the Environment Agency's structured freshwater monitoring programme (the River Surveillance Network). The project will utilise both existing data from the RSN and perform field sampling and molecular analysis to develop and refine approaches to enable the utilisation of molecular tools for routine regulatory biomonitoring.

In addition, this project will explore novel DNA-based approaches to characterise freshwater microbes, including long-read DNA sequencing (PacBio or Nanopore) to characterise whole communities. These data will be benchmarked against short-read DNA sequencing approaches (Illumina), generated by the Environment Agency's ongoing work into developing novel approaches for assessing freshwater ecosystem health. There will be opportunities to feed directly into regulatory policy.

The project will address the following key research questions:

1. How are freshwater microbial communities (bacterial, fungal, and eukaryotic) structured across river catchments in England?
2. How do different components of the freshwater microbial community respond to physicochemical and spatial drivers at a national scale?
3. How can novel statistical and machine learning approaches be used to identify bioindicator taxa that can be used determine freshwater ecosystem status and identify stressors?