Frontier forensics: the rise of environmental DNA analysis

By Alexander Evans, University of Leeds 

The natural world is under threat from many anthropogenic sources, such as the spread of harmful invasive species and the decline of native populations due to habitat loss and climate change. Finding new technologies and methods to assess and tackle these increasingly global problems is crucial. However, in order to tackle big problems, sometimes you need small solutions. One such emerging tiny tool is the sequencing of environmental DNA (eDNA)!

What is eDNA?

eDNA is simply DNA that has been sampled from a source other than the organism itself, such as the soil or water the animal lives in. Animals and other lifeforms often leave behind a DNA ‘footprint’ from their skin, hair, mucous, faeces, eggs, sperm and other cellular sources that can be traced. The concept of using this DNA footprint to investigate the presence of certain lifeforms first began in the 1980s with researchers interested in hunting for microbes. It wasn’t until a few decades later in the early 2000s that these techniques were further developed and eDNA became more extensively used to assess complex life from a range of environmental substrates including soil, permafrost, freshwater and seawater.

Coupled with next-generation sequencing (NGS) and DNA metabarcoding, eDNA is proving to be an increasingly attractive choice for ecological researchers with limited time and money. After collecting environmental samples, the polymerase chain reaction (PCR) can be used to amplify the DNA found within the samples, but typically only short DNA sequences are used for eDNA analysis as these are more reliably found in environmental samples due to the degradation of discarded genetic material over time.

Currently, researchers have two options on how to analyse eDNA samples for the presence and absence of species in certain locations. If the researchers are interested in a single species, specific genetic primers can be used to quickly identify their presence in the sample. On the other hand, if the researchers are interested in a whole community of species, they can use generic primers and run the amplified eDNA sequences through a DNA database in order to find matches and generate a list of present species. With this DNA metabarcoding technique, genetic information about entire populations and communities can be extracted from a single sample to create a depiction of the living landscape.

AE-pic1

Depiction of eDNA extraction and analysis from a range of species and environments. Drawing by Lars Holm.

What is it used for?

One of the earliest applications of eDNA analysis was actually the tracking of sources of faecally contaminated surface water by testing for the presence of human and animal DNA, but eDNA is now beginning to find a firm footing as a popular and reliable tool for biodiversity monitoring. Species range shifts and population declines due to invasive aliens and climate change are a big area of research for ecologists, and eDNA sequencing brings many benefits beyond those offered by traditional monitoring techniques.

For example, in the case of highly endangered or potentially dangerous species, it may be unwise or even illegal to interfere directly with the animals, but by monitoring through eDNA sampling, the researchers can gain important insights into the animal’s lifestyle while completely removing human interaction. A recent example of eDNA use in this non-invasive fashion includes the monitoring of endangered great crested newt populations in the UK, and the Food and Environment Research Agency (FERA) now produce their own eDNA testing kits!

Interestingly, eDNA isn’t just limited to the study of living organisms, as it has also been used to analyse the ‘sedimentary ancient DNA’, or sedaDNA, of long extinct species. In fact, eDNA has recently been used to show that Alaskan woolly mammoths held off extinction for thousands of years longer than was previously thought! As exciting as the prospects of these prehistoric discoveries seem, finding usable ancient eDNA represents a significant challenge due to the degradation of DNA, and the most well preserved eDNA samples appear to be those kept in stable anoxic conditions, such as deep in aquatic sediment or permafrost.

What does the future hold for eDNA?

eDNA is an impressive resource, but of course, it is not without issue. One of the biggest limitations of eDNA is that it can only provide an indication of species presence and not abundance, meaning that traditional methods are often also required in order to obtain the full story. Also, since it is no longer a part of the host animal, eDNA can have a tendency to wander in certain environments. For example, eDNA that originates high in the water column can drift around before landing, and eDNA that eventually settles into aquatic sediments can be easily shifted, making it hard to be certain of its true origin.

eDNA analysis is still very much in its infancy, but with increases in modern genetic sequencing technology, eDNA analysis is proving to be an efficient, non-invasive and relatively cheap method of analysing wild species, and high throughput sequencing allows DNA metabarcoding to search through existing genetic libraries for everything from tiny parasites to entire ecosystems. As genomic technology becomes faster and cheaper to run, you can expect that field-ready eDNA analysis kits will become increasingly prevalent and hopefully become essential tools in the eco-biochemist’s arsenal.

Further Reading

Barnes, Matthew A., and Cameron R. Turner. “The ecology of environmental DNA and implications for conservation genetics.” Conservation Genetics 17.1 (2016): 1-17.

Thomsen, Philip Francis, and Eske Willerslev. “Environmental DNA–An emerging tool in conservation for monitoring past and present biodiversity.” Biological Conservation 183 (2015): 4-18.

Pedersen, Mikkel Winther, et al. “Ancient and modern environmental DNA.” Phil. Trans. R. Soc. B 370.1660 (2015): 20130383.

alex1About Me

I’m a PhD student at the University of Leeds working on the energetics and biomechanics of bird flight. I like birds, bees, board games and writing about the natural world. I can be found blogging about bioscience at Bird Brained Science and jabbering about birds on Twitter.

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