Environmental DNA

Environmental DNA (eDNA) refers to DNA obtained from an environmental sample, most usually water, soil or air. For larger species (including humans), eDNA is recovered from fragments of cellular material shed into the environment e.g. saliva, faeces, hair or skin cells, whereas for insects or microbial communities, whole organisms and their genomes may be captured. This is different from more traditional DNA analysis where samples are taken directly from the organisms themselves.

eDNA samples can be collected from a wide range of environmental sources, such as soil, water or air, or from surfaces or dust. Once in the laboratory, fragments of DNA can be extracted from these samples. Either specific DNA markers can be detected using DNA assays, or the DNA can be sequenced and then compared to sequences in a reference database. Using computational biology or bioinformatics, so called ‘barcode regions’ of DNA, or fragments of DNA, can then be used to identify which types of organisms were, or had been, present in the environment from which the samples were taken.

These technologies rely either on a combination of DNA detection and amplification methods such as Polymerase Chain Reaction (PCR) or quantitative PCR (qPCR), or DNA sequencing approaches such as High Throughput Sequencing (HTS). They also rely on a reference genome, or sets of genes (termed barcodes), being available for the organism in question.

The use of environmental DNA is most established for biodiversity monitoring, however new advancements in methodologies are making these techniques applicable to a far wider range of applications and sectors. These include understanding environmental quality and pollution, biosecurity and defence, crime and forensic science, health and disease monitoring and for understanding the effects of environmental change.

Examples include using eDNA to monitor the Covid-19 pandemic through wastewater surveillance, using air capture eDNA technologies to detect crop pests and diseases, using eDNA to monitor bioterror threats, and using eDNA to trace illegal trade routes. This breadth of applications is outlined in detail within our report and presented in the set of case study cards that accompanies this.

The progress made in the eDNA field during these last ten years has been exceptional. The technological advances in high‐throughput sequencing, data analysis and interpretation tools have greatly facilitated the access to and availability of eDNA data. The amount of data that can be obtained using these methods has, and is still, increasing rapidly in terms of its accuracy, level of detail and the speed at which it can be analysed. This has led to a boom in eDNA research across a the range of different disciplines that we have outlined.

Due to this, eDNA will increasingly have relevance and potentially beneficial applications to a number of current government priority areas, including tackling the climate and biodiversity crises, ensuring food and water security and supporting economic resilience. In terms of the private sector, the efficiency and amount of data that can be obtained using eDNA technologies make them a very attractive addition to a number of growing markets including environmental consulting, forensic technologies, agricultural pest control and bioterror defence. 

As well as describing the current range of eDNA applications, this report also outlines the latest developments in eDNA research and the future opportunities this may facilitate.

Some of the most exciting new areas of development include:

• Air sampling technologies
  Air capture eDNA sampling technologies have the potential to revolutionise the application of eDNA to a number of sectors. They are already being used for newer applications relating to defence, pathogen and pollution monitoring. Air capture eDNA techniques will also likely eventually be accurate enough to allow researchers or investigators to understand exactly which and how many people, pathogens or species have recently been in a room or enclosed space. This may be useful not only for crime or justice applications, but also for routinely monitoring the number of people using public transport such as trains or railway stations, or other public spaces such as libraries, and so help to inform infrastructure and planning.
• Portable and/or autonomous eDNA samplers
  In recent years portable and/or autonomous eDNA collection and analysis has opened up the field of eDNA research to a far broader audience, due to less reliance on specialist labs. These advances will likely have important policy applications in a number of sectors in terms of their potential to improve the safety of personnel as well as reduce the time and cost of monitoring the environment. Alongside the use of these technologies for biodiversity monitoring, autonomous sampling could also be used to more safely detect bioterror threats, for routine water quality assessment, or for the routine monitoring of disease, invasive species or pathogens. It may be possible to mostly automate eDNA sampling in the future.
• eRNA based approaches
  eRNA based approaches are already routinely used for monitoring RNA viruses, such as SARS-CoV-2 and poliovirus. However, for other applications eRNA represents a relatively new but potentially useful complement to eDNA. Whereas eDNA represents fragmented genomes of cellular organisms present in the environment, eRNA represents only the expressed parts of those genomes. Gene expression is influenced by external factors, therefore it can allow more direct inferences on the response of different organisms to environmental stressors. eRNA also generally degrades faster in the environment than eDNA. By comparing the ratio of eRNA to eDNA, this rapid degradation can be exploited to allow researchers to understand how recently an organism is likely to have been present.

Some of the current limitations and challenges with eDNA include:

• eDNA analysis is only as good as the reference library on which it is based. 
  Currently, only 52% of UK species have reference database sequences, which is the biggest limiter of eDNA based research. With continued funding and the right initiatives, the UK has the potential to be one of the first countries in the world to have publicly available genome sequence data for all of its eukaryotic species. The Wellcome-Sanger Darwin Tree of Life programme, and the UK Barcode of Life consortium, are currently working on providing a comprehensive lists of reference genomes and barcodes for UK species.
• The risk of contamination.
  An important limitation of eDNA sampling methods is the risk of false positive results due to contamination. Contamination of samples can occur in a variety of ways, from a researcher sneezing on a sample, to a boat discarding biological debris into water. DNA itself is also highly mobile, being easily transferred via water, air or on moving vehicles or organisms. It can be hard to determine if, how or when a sample may have been contaminated versus when it is a genuinely surprising result – therefore contamination remains a significant challenge. For use in defence, forensic science or to trace the illegal wildlife trade, understanding the accuracy of an eDNA result is crucial, as there is a chance that false positives could result in false bioterror alarms or miscarriages of justice.
• The need for benchmarking. 
  The development of different eDNA methodologies and analytical techniques is happening in silos, both within and between the different disciplines that utilise these techniques. There is therefore an urgent need for benchmarking initiatives to understand the relationship between the different methodologies. This is so that the relative strengths or weaknesses of different approaches is well understood and so that results can be compared across time and space. Standardisation and benchmarking tools will also increase the confidence that decision makers can attach to eDNA findings.
• Ethical concerns around the capture of human eDNA. 
  As eDNA technologies advance, they will have the potential to either intentionally or unintentionally capture human DNA, possibly sufficient enough to identify and phenotype an individual – but without legal and ethical frameworks or informed consent. Mitigating concerns and developing appropriate regulation will require input from all stakeholders, including scientists from across eDNA disciplines, end users such as policymakers or public health authorities, legal and ethical experts and the general public.