DNA, genetic material, helix. Image by Gerd Altmann from Pixabay
Environmental DNA (eDNA)

Science challenge

Understanding how biodiversity is changing over time is critical to determine how human activity is changing ecosystems and the services they provide. However, conventional approaches to identifying species using observable features, whilst often providing a gold standard, are often time-consuming and rely on a dwindling pool of expertise, especially for cryptic, rare or small species. DNA based approaches for assessing community composition have great potential to reduce costs, both through reductions in sampling and identification time, as well as the ability to identify cryptic genetic diversity and to gain insights into less well-studied organisms.

Project summary

The environmental DNA (eDNA) task in UK-SCAPE aims to develop, apply and evaluate DNA sampling techniques based on high throughput sequencing to characterise terrestrial and freshwater ecosystems, demonstrating the applicability of these approaches for national-scale monitoring of biodiversity.

The use of environmental DNA (eDNA) to detect individual species or to characterise whole communities is a rapidly growing field, and has matured to the point where national monitoring agencies such as the EA, SEPA, NRW and Natural England are exploring the use of these approaches to supplement or replace existing biological monitoring programmes. This creates a significant opportunity to repurpose existing samples and environmental eDNA samples, collected under a range of monitoring activities, to characterise biodiversity for a wider range of species in more taxonomic detail. By leveraging existing sampling programmes this approach has the potential to be an extremely cost-effective and rapid workflow for generating freshwater biodiversity data at a nationwide scale.

Objectives

  • Obtain and archive the existing environmental eDNA samples along with relevant site data.
  • Apply high throughput DNA sequencing to characterise biodiversity across a wide range of taxonomic levels, from microbes to invertebrates, vertebrates and plants.
  • Explore informatics approaches for analysing, displaying and sharing eDNA biodiversity data with the research community and the statutory monitoring agencies.

Resources

Papers and outputs

Data

  • National-scale data on plant eDNA composition from soils.
  • Dataset from England and Wales describing biofilm microbial community composition.

Research facilities

  • Wallingford Molecular Biology laboratories, including liquid handling robots for sample processing and preparation, in house DNA sequencing on Illumina MiSeqs and high throughout computing for data processing and analysis.

Interactions

UKCEH national capability

  • This activity will work closely with other UK-SCAPE teams to explore how DNA-based biodiversity data can be integrated into existing biological recording data platforms.
  • We work with long-term research activities under UK-SCAPE such as the Cumbrian Lakes monitoring platform to apply DNA based techniques for biological monitoring.

Partnerships

  • We work closely with eDNA researchers at the University of Hull to develop and deploy eDNA techniques for describing freshwater biodiversity.
  • We work with the UKEOF DNA Working Group to link researchers and users of eDNA techniques, as well as support and encourage best practice to increase awareness of how DNA-based methods can help improve the effectiveness of environmental monitoring.
  • We welcome the opportunity to collaborate and develop new partnerships. Please get in touch if you would like to work with UKCEH researchers on eDNA projects or access our molecular biology and eDNA facility.

Project lead - Dan Read