eDNA - the next big thing in conservation monitoring?

Gathering data on the distribution and abundance of species is essential for biodiversity conservation, but it can be a long and laborious task. Could the use of environmental DNA (eDNA) be about to revolutionise biological monitoring?

Just imagine trying to find a jaguar in the depths of a vast, tangled Amazonian rainforest or a single salamander in a river system. Even if you have a good idea where to look for a particular species, it can take a lot of time, effort and money, employing surveyors with taxonomic expertise and carrying out numerous field surveys with no guarantee that you'll find what you're looking for, especially if the species is rare, cryptic or leads an elusive lifestyle.

Even if you don't have any luck finding the animal, however, there may still be traces of its presence left in the environment. This could be anything from hair or skin, to urine, faeces, gametes or bits of carcasses. The DNA from excreted cells or tissues such as these can persist in the environment, in the soil or water for example, allowing us to sample, extract and analyse it anything from a few weeks in temperate water, to hundreds of thousands of years later in cold, dry permafrost. The use of this environmental DNA, known as eDNA for short, is a rapidly growing area of biodiversity conservation. So what's all the hype about?

As Thomsen and Willerslev (2015) discuss in this month's special eDNA issue of Biological Conservation, there are some big advantages of using eDNA to assess the presence and abundance of species. It's non-invasive, so it inflicts little, if any, damage on the target species or its habitats, and it's a simpler sampling approach, in that those carrying out surveys do not need specialist taxonomic knowledge or expertise on the species. Using eDNA also makes it easier to detect cryptic species or those which have juvenile states that closely resemble other species (meaning it would be harder to a surveyor to identify them physically in the field). Plus, sampling can be carried out under most weather conditions and in some cases can be more cost effective, especially with the steadily decreasing costs of DNA sequencing.

It's no miracle technique, however. As with any DNA sequencing there's the possibility of contamination - if target DNA were accidentally transferred from one site to the next when sampling several locations in a row for example - which could produce a false positive result and the potential overestimation of a species' occurrence. There is also the danger of interference from humus or humic acids (the organic component of soil) which can inhibit some of the enzymes involved in PCR (Polymerase Chain Reaction, the process used to amplify DNA segments). This could lead to false negatives, preventing a species' DNA from being detected at a site where it was present, resulting in an underestimation of species' occurrence.

Two other drawbacks are that the presence of eDNA does not tell us what life stage the animal is at, or indeed whether it was dead or alive at the time it was shed. It also does not tell us how long ago the animal was there. In water eDNA degrades quite quickly so is likely to indicate the animal was there fairly recently (within the last couple of weeks or so). In soil it seems able to persist for decades or even centuries. This is also the case for sediment, meaning there is always a risk that older, even ‘ancient' DNA could be stirred from bottom sediments into the water column.

Finally, eDNA could be transported from another locality by flowing freshwater or marine currents, predators, or human activity, meaning the proximity of a target animal to the site the eDNA was sampled may not always be so close.

Hunting for hellbenders

Using quantitative PCR, they detected hellbender eDNA at 33 sites, including 71% of those with recent or historic hellbender presence (through field surveys), and nine sites where hellbenders had never before been recorded. This suggests that eDNA was much more successful at assessing presence than the usual snorkelling surveys the team would carry out, and they are now monitoring these sites to try to confirm the eDNA evidence. Levels of eDNA were also found to be much higher in September, during the peak breeding period, suggesting that this may be a good time to carry eDNA surveys in other amphibious or aquatic organisms. They also hope that eDNA may hold potential for determining the reproductive status of populations.

However, they found no relationship between the eDNA estimates and the field survey numbers in terms of abundance or biomass (although it is worth noting that many other studies have found a correlation between the two). So whilst eDNA samples were great for detecting hellbender presence, inferring abundance and demographic information from eDNA is still a key area for improvement. Spear et al. also recommend further research into how eDNA shedding rates vary within and among species, influences on how far eDNA travels from its source, and factors affecting degradation rates.

eDNA use is clearly still in its infancy, but with newly emerging sequencing technologies, such as next generation sequencing, there is a great deal of optimism around the potential of eDNA in biological monitoring. Thomsen and Willerslev envisage that it will move from single-marker analyses of species to meta-genomic surveys of entire ecosystems in order to predict spatial and temporal patterns in biodiversity.

Furthermore, because eDNA survey methods don't require any taxonomic training, it's relatively easy for anyone to go out and do - as evidenced by the success of a citizen science project that had members of the public survey local ponds for eDNA of great crested newts, an endangered species in the UK.

However, it is likely eDNA will complement rather than replace traditional surveying methods, offering fast and efficient insights into the distribution of species and hopefully, in the future, population sizes. For now, it provides a valuable non-invasive tool in detecting rare and elusive species for conservation monitoring programs.

Further reading:
For more information see the March 2015 special issue of Biological Conservation all about eDNA.

eDNA sampling is also being used to monitor sharks in a study to be published at the end of this year: BBC News ‘Shark eDNA study could be conservation 'game-changer'

References:

Spear, S. F., et al. (2015) Using environmental DNA methods to improve detectability in a hellbender (Cryptobranchus alleganiensis) monitoring programs. Biological Conservation 183 pp. 38-45.

Thomsen, P. F. and Willerslev, E. (2015). Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity. Biological Conservation 183 pp.4-18.

Image credits:

DNA - Public domain images on pixabay.com
Hellbender in hand - U.S. Fish and Wildlife Service on Flickr