5 Considerations for eDNA in Spatial Ecology

We’ve introduced eDNA in a previous Geoversity article, "What is eDNA?".

As a technique used in spatial ecology, eDNA offers several benefits.

By extracting genetic material from samples of water, soil, and even air, eDNA analysis can gather a broad range of information required by spatial ecological studies, from the distribution of individual species and overall biodiversity to the functioning of ecosystems.

Genetic material can be extracted from samples of water, soil and even air. 

A substantial decrease in laboratory costs over the last decade also means that collecting samples for eDNA research requires less time and effort compared to traditional field monitoring studies.

Moreover, by identifying animals and plants based on their DNA, we can detect organisms at any life stage, distinguish look-alike species, and survey very diverse communities without the need for taxonomic expertise.

As a result of these benefits, eDNA-based observations are rapidly supplementing and replacing traditional in situ observations used in spatial ecology.

Five considerations

While eDNA brings many benefits, there are certain aspects that researchers should keep in mind. In this article, we’ll explain five important considerations when using eDNA in spatial ecology.

1. No Life Stage/Alive-Dead Distinction

eDNA can show us which animals or plants are present, but it currently can't tell if they were alive or dead when the sample was taken.

It also doesn't provide certain details, like the life stage, size, behaviour or condition of the organisms. This is because the genetic material used doesn’t change based on these factors.

2. No abundance or density information

The amount of DNA released by different species varies significantly, depending on the species and environment. This makes it hard to link DNA levels to the number of individuals. eDNA can therefore tell us which species are present, but it can't tell us how many there are or provide us with information on their density.

While eDNA can show relative trends in species changes over time and space, this data varies between species and should be interpreted carefully.

eDNA can tell us which species are present, but not the population density.

3. Taxonomic Resolution

eDNA might not always identify the exact species of an organism. Sometimes, it can only identify the broader group, like the family or even the phylum.

To be identified, the organism's DNA must be listed in a public database. The accuracy of these identifications depends on how complete and reliable these databases are.

Some databases are much more complete than others. Those for mammals and fish, for example, are more complete than invertebrates or bacteria.

4. Data compatibility

eDNA data can be collected and processed using various methods, but these methods are not yet standardized. This means that different studies can produce different results in detecting species and estimating their abundance.

So, when combining data from different sources, it's important to make sure the methods used to collect and process the data are consistent.

5. Spatial and temporal variation

eDNA interacts with its surroundings independently of the organism it comes from, meaning traces of species can be found in areas where they no longer exist or were never present.

For example, spores can travel long distances by wind, and fish DNA can flow downstream in rivers.

Furthermore, some DNA breaks down quickly, while other fragments can last much longer.

In seawater, eDNA can degrade in days or weeks, depending on factors like temperature and sunlight; whereas in permafrost, it can remain intact for thousands of years.

In certain environments - like permafrost - traces of DNA can remain intact for thousands of years after the species has been present.

So, because eDNA can travel and last in the environment, it can lead to differences in when and where we detect species through their DNA compared to where they are actually present.

To use eDNA data for spatial studies, we need to understand the ecosystem and the factors that affect how eDNA is spread and conserved.