A Guide to eDNA Applications: Lessons from a 12-Year Marine Biodiversity Study
The arrival of DNA methods has revolutionized the way biodiversity is studied. Genetic methods offer higher precision when identifying animals and plants, especially in the case of elusive, endangered and extinct species.
However, being precise can also have its challenges. Highly-sensitive DNA methods can be prone to contamination, for instance, so there are several ways to mitigate uncertainty when collecting genetic information. Long-term DNA studies can help account for these challenges, providing robust data and highlighting methodological best practices.
In a latest NTC Now session, the Nature Tech Collective was joined by Sebastian Mynott, Founder and General Manager of Applied Genomics, a UK-based consultancy. Sebastian offers critical insights on eDNA best practices based on their 12-year marine eDNA study. You can watch the full NTC Now session here to explore Sebastian’s step-by-step guidance on designing, executing, and interpreting eDNA studies.
Environmental DNA (eDNA) refers to the fragments of genetic material left behind by organisms in their natural environments (such as soil, water, or air) due to shedding of skin, scales or feces. Analyzing eDNA is therefore a non-invasive alternative for biodiversity monitoring, allowing researchers to identify species without needing to capture or observe them directly.
Who is Applied Genomics?
Applied Genomics works across sectors, utilising precise, data-driven biodiversity insights to help organizations make environmental decisions. They use a range of eDNA techniques to collect and analyze eDNA from different environments, including:
Detecting contaminants in rivers,
Analysing animal diets through fecal samples,
Identifying endangered species in soil, and,
Tracing plant sources in honey
One of Applied Genomics’ most impressive case studies is a 12-year time-series of fish population trends, conducted in collaboration with the Plymouth Marine Laboratory and the Western Channel Observatory in Southern England.
Stock Image: Unsplash
Learnings from Applied Genomics’ 12-Year Marine Study: The Do’s and Don'ts of Working with eDNA
Capturing Precise Species Information with eDNA
For their long-term study, Applied Genomics collected marine DNA using the inDepth eDNA sampler. This programmable device collects water samples using advanced filters to minimize contamination. Automated samplers like this one are particularly useful for remote or inaccessible sites. Using DNA barcodes, 460 water samples were analyzed to identify marine species.
The results are striking: a 100% sample success rate, detecting 213 unique fish varieties, including sharks and rays. Compared to bottom trawling – a more traditional method of sampling – eDNA sampling captures over 150% more species. This high sample success rate makes eDNA a reliable and scalable tool for long-term fisheries monitoring, enabling better marine monitoring and conservation planning. Meanwhile, eDNA's comprehensive species detection provides richer data for improved impact assessments and environmental regulations.
Toolkit: What Makes a Robust Marine eDNA Study? Red Flags to Avoid
This 12-year marine analysis also revealed ways in which eDNA collection and analysis can be strengthened to improve biodiversity monitoring techniques. Applied Genomics apply the following principles to make sure their process is transparent, replicable, and accurate.
1/ Mitigating Contamination Risks:
Presenting all results with the same confidence weighting. The sensitivity of eDNA is what makes for precise species detection, but can also make analyses prone to false positives. For instance, samples can become contaminated with external DNA, such as bycatch material in marine environments.
What does Applied Genomics do about this?
A good way of making sure DNA data is reliable is by cross-checking eDNA results with multiple sources of species data. This is what Applied Genomics refer to as credibility detection analyses, which also involves comparing eDNA data to historical data. Besides, they account for proportions of genetic material, which indicates persistence – that is the probability of a fish having lived in that environment versus just having visited recently, for example.
When presenting their results, Applied Genomics also use indices to represent how confident the species identification is. Altogether, these analyses help discard uncertainty and ensure a sound eDNA process.
2/ Accounting for duplicates
Collecting marine samples too close together (less than 5 km apart)
In marine environments, tides and currents have a greater influence on species distribution than in air or soil environments, for example, as species can relocate over larger distances. This means that the chance of detecting the same individual organisms (like fishes) increases the closer water samples are collected – leading to duplicates and spatial autocorrelation.
So, what to do about this?
To avoid erroneous data correlation, Applied Genomics samples eDNA with a minimum of 100 km distance, which ensures that each sample is from a different organism. This process is validated by studies from Natural England, the UK’s national environmental public body, which strengthens the accuracy of data collection.
3/ Water Collection is regulated automatically
Overlooking seawater changes at sampling sites
Time series studies – such as this 12-year one – will often encounter changes in water levels, not just biodiversity. A crucial aspect of water samples are the pump filters, which draw water from the sea at fixed pressure. This ensures an even distribution of water over the tidal cycle.
Applied Genomics takes this a step further. To mitigate any issue with these water pumps, they have computer models that regulate the volume of water collected. For instance, if the pump filter gets clogged, the models compensate and even out the water volume captured at a given time. It is crucial in time series studies to always compare the same volume size in each sample collection, like “comparing apples to apples”.
In short – in choosing a reliable company for eDNA studies, one must watch out for the following:
Are they transparent about their species credibility analyses and rating?
What is their minimum sampling distance?
How do they maintain the sampling site technology?
Ensuring an open and transparent methodological process is crucial in any eDNA study.
Revealing Key Insights for Marine Conservation
As a result of their long-term eDNA study, Applied Genomics uncovered some critical fish population trends.
Their analysis found that 69% of sampled fish species are in decline, including commercially important fish like haddock, herring and mackerel. These results have major implications for the fishing industry, marine conservation, and environmental policy, which highlights the potential of eDNA sampling tools.
This 12-year marine study exemplifies how powerful eDNA techniques can be – if the methods employed are analytically robust, and the data is presented in a transparent way. By integrating novel eDNA methods in biodiversity monitoring, Applied Genomics provides reliable and precise tools to support data-driven environmental policy.
Next Steps: Scaling eDNA for Environmental Monitoring
eDNA methods have the potential to be scaled and unified for comprehensive, long-term biodiversity monitoring. By integrating biodiversity data with other environmental indicators, Applied Genomics also provides guidance for ESG reporting, natural capital valuation, and Biodiversity Net Gain assessments.
Furthermore, Applied Genomics envisions a collaborative, publicly accessible database to support decision making across the environmental industry and academic institutes. Interested in contributing to a large-scale marine biodiversity monitoring project around the British Isles? Find out more and register your interest here.
Biodiversity loss is an urgent global issue, which underscores the need for scalable tools such as eDNA to quickly assess environmental health for accurate policy decisions. With companies such as Applied Genomics, environmental monitoring can become more precise, accurate, and replicable; leading to more effective biodiversity conservation policies.
Follow Sarita Mahtani-Williams on LinkedIn to stay updated on her latest projects, and explore the important work of Applied Genomics by following them on LinkedIn or visiting their website for the latest on their innovative eDNA monitoring work.