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Frequently asked questions about eDNA

 

1. What is environmental DNA?

Environmental DNA (eDNA) is the genetic material left by organisms in the environment. We can extract this DNA from environmental samples – samples of water, soil, aquatic sediments, or ice – and identify the species from which the DNA originated. Generally, eDNA refers t DNA extracted from any type of environmental sample. In the materials hosted on this website, however, eDNA is defined as DNA left by macro-organisms (organisms that can be seen with the naked eye) in aquatic environments, without any visible sign of the source.

2. How long does eDNA persist in water?

Environmental DNA degrades relatively quickly in water, generally within a few weeks. In experiments that measured eDNA persistence in aquaria or artificial ponds, the length of time for which eDNA has been detected ranged from less than one day to a few weeks.

The rate of degradation varies depending on a number of environmental and biological factors. Ultraviolet radiation, acidity, and high temperatures help break down eDNA into small fragments that are difficult to detect and identify. Microbes, which release enzymes that degrade DNA, are often more abundant at higher levels of light and temperature as well. This means that eDNA can be expected to persist longer in some environments than others. For example, eDNA may remain detectable longer in cold, shaded streams with neutral pH than in acidic wetlands or in warmer streams with more solar radiation and higher microbial activity.

The short persistence time of DNA in water makes eDNA useful for tracking contemporary presence of a species in the water body. When a species’ DNA is detected in a water sample, we have a good idea that the species was probably there within a few days or weeks.

3. Does eDNA work in soil or sediment?

We can detect a species’ DNA in soil or in the sediment of lakes, ponds, rivers, or marine environments. However, eDNA often persists longer in soil or sediment (on the scale of years or decades) than in water, so the temporal inference is different. If we detect the eDNA of an aquatic species in water from a pond, we can be confident that the species was present there very recently. If we detect its eDNA in sediments from that pond, we don’t know if the species was there last week, last year, or 10 years ago, for example. For this reason, when we’re looking for at-risk or protected species and we need to know whether the species is present in an area now, eDNA from water samples is more likely to give us the information we need. When we’re trying to detect new invasions of nuisance species, the time scale is less important because we just want to know if the species has ever been present in a new area, and eDNA of the species in soil or sediment would give us that information.

4. Can we use eDNA to estimate the number of individuals or density?

Environmental DNA methods can tell you if a particular species was recently present; they can’t really indicate abundance and density.  Using quantitative PCR (qPCR), however, we can measure the amount of eDNA in a sample. An increasing number of studies have found that eDNA quantities correlate at some scale with estimates of abundance such as population density or biomass, and though right now we can’t use eDNA to estimate the total number of individuals in a population, methods for analyzing and interpreting eDNA samples are advancing rapidly.

5. Can eDNA detect hybrids?

The eDNA method does not allow for the detection of hybrids, though it can detect the presence of potentially hybridizing species. Most eDNA methods use mitochondrial DNA, which is maternally inherited, so eDNA can detect the presence of one of the parent species at a location. If we detect eDNA of the parent species in our water samples, it could come from either the parent species or a hybrid. This can be useful if we want to know if a potentially hybridizing species is in an area with our species of interest – for example, if brook trout have moved into an area with threatened bull trout – and it’s possible that hybridization could occur.

6. What are the advantages of using eDNA?

Environmental DNA technology can be highly cost efficient and effective for monitoring populations of rare species. In some systems, eDNA methods can actually be more sensitive to species presence than traditional field surveys. Using water samples instead of field surveys can shorten field search time, eliminate stress to sensitive species, and minimize disturbance of sensitive habitats.  One big advantage of eDNA methods is that multiple species can be identified from a single water sample, so eDNA sampling can be much more efficient than conducting field surveys for multiple species that require different survey methods.

If we don’t know where and when aquatic species are found, we might waste time and money on conservation and management programs in the wrong place or at the wrong time. Environmental DNA gives us accurate information about the location of aquatic species and the makeup of aquatic communities, and helps focus conservation and management actions where they’re most likely to protect rare species or prevent the spread of invasive species.

7. What are the potential drawbacks of using eDNA?

Environmental DNA methods can describe the presence of species, including target species, pathogens, potentially hybridizing individuals, or even whole communities.  These methods can’t, however, tell us about the species’ population size, reproductive status, age structure, disease status, or the presence of hybrids. Advances in eDNA technology may someday soon allow us to measure this type of information, but for now it needs to be learned using conventional field methods.

Although eDNA usually yields higher detection probabilities for target species, in some cases it’s more expensive than conventional survey methods. Moreover, conventional methods, where the specimen can be seen, can generate more interest from the public and government agencies. This may be an issue for citizen science programs, for example, in which some of the enthusiasm of volunteers is driven by the potential to observe or even capture the target organism.

8. Is eDNA more cost effective than standard sampling methods?

This depends on the target species.  For rare or elusive species, it’s often more cost efficient than traditional field methods because of its higher detection probability and because samples can be collected by people with minimal training. For species that are easy to observe or catch with traditional methods, eDNA is likely less cost effective because of lab analysis costs.  Comparisons between the methods also depend on whether field methods are time-intensive, need expensive equipment, or require extensive training or expertise for biologists conducting the surveys.

9. Is eDNA more accurate than standard sampling methods?

Environmental DNA methods are often more sensitive than conventional field methods, and many studies have demonstrated that the eDNA method is also as accurate as conventional methods. In other words, with eDNA we are more likely to detect a species when it’s present, and unlikely to falsely infer that the species is present when it’s not. The accuracy of the method relies on well-designed sampling strategies and strict adherence to field and lab protocols that minimize the risk of cross-contaminated samples.

10. How long is the process for analyzing eDNA samples?

The process generally can be completed in as little as one to two weeks for the single species eDNA approach using qPCR.  For the metabarcoding approach, in which high throughput sequencing is needed to detect many species simultaneously, raw data files containing all sequences must be analyzed to match the sequences to species in the database. This process may take several months.

In addition, it’s important to take into account the workload at the eDNA laboratory that’s processing the samples. Labs often have a backlog of samples needing analysis, and unless a rapid turnaround is imperative, incoming samples may be placed in queue, adding to sample processing time.

11. What laboratories are available in the US to process eDNA samples?

So far there are only a handful commercial and governmental labs in North America that process eDNA samples, with several others that are active in Europe. While there are a growing number of academic and governmental labs that also analyze eDNA samples, most are not set up to run as service labs, i.e., to run samples for other groups that are not part of specific research or monitoring programs. The number of commercial and governmental eDNA service labs is likely to increase as eDNA methods become more commonly used. A list of available labs is regularly updated on the “eDNA Labs” page on this site.