Environmental DNA

Environmental DNA or eDNA is DNA that is collected from a variety of environmental samples such as soil, sediment, freshwater, seawater, snow or air, rather than directly sampled from an individual organism. As various organisms interact with the environment, DNA is expelled and accumulates in their surroundings from various sources. Such eDNA can be sequenced by environmental omics to reveal facts about the species that are present in an ecosystem — even microscopic ones not otherwise apparent or detectable. This approach enables low-cost, large-scale, and standardized biodiversity inventories, all without negatively impacting ecosystems.

In recent years, eDNA has been used as a tool to detect endangered wildlife that were otherwise unseen. In 2020, human health researchers began repurposing eDNA techniques to track the COVID-19 pandemic.

Example sources of eDNA include, but are not limited to, feces, mucus, gametes, shed skin, carcasses and hair. Samples can be analyzed by high-throughputDNA sequencing methods, known as metagenomics, metabarcoding, and single-species detection, for rapid monitoring and measurement of biodiversity. In order to better differentiate between organisms within a sample, DNA metabarcoding is used in which the sample is analyzed and uses previously studied DNA libraries, such as BLAST, to determine what organisms are present.

eDNA metabarcoding is a novel method of assessing biodiversity wherein samples are taken from the environment via water, sediment or air from which DNA is extracted, and then amplified using general or universal primers in polymerase chain reaction and sequenced using next-generation sequencing to generate thousands to millions of reads. From this data, species presence can be determined, and overall biodiversity assessed. It is an interdisciplinary method that brings together traditional field-based ecology with in-depth molecular methods and advanced computational tools.

The analysis of eDNA has great potential, not only for monitoring common species, but to genetically detect and identify other extant species that could influence conservation efforts. This method allows for biomonitoring without requiring collection of the living organism, creating the ability to study organisms that are invasive, elusive, or endangered without introducing anthropogenic stress on the organism (depends on the robustness of the methods used, see below). Access to this genetic information makes a critical contribution to the understanding of population size, species distribution, and population dynamics for species not well documented. Importantly, eDNA is often more cost-effective compared to traditional sampling methods. The integrity of eDNA samples is dependent upon its preservation within the environment.

Soil, permafrost, freshwater and seawater are well-studied macro environments from which eDNA samples have been extracted, each of which include many more conditioned subenvironments. Because of its versatility, eDNA is applied in many subenvironments such as freshwater sampling, seawater sampling, terrestrial soil sampling (tundra permafrost), aquatic soil sampling (river, lake, pond, and ocean sediment), or other environments where normal sampling procedures can become problematic.

On 7 December 2022 a study in Nature reported the recovery of two-million year old eDNA in sediments from Greenland, which is currently considered the oldest DNA sequenced so far.

Environmental DNA (eDNA) is applied using a wide range of sampling and analytical protocols, and the reliability of results strongly depends on the robustness of the methods used. In aquatic environments (freshwater and marine), sampling strategy is a key determinant of detection success. Larger filtered water volumes generally yield greater amounts of DNA, increasing the likelihood of detecting organisms present at a site. Because eDNA is often spatially heterogeneous and locally distributed, filtering larger volumes of water along integrated transects provides a more representative and accurate snapshot of biodiversity.

Laboratory procedures also play a critical role, particularly the number of polymerase chain reaction (PCR) replicates performed. PCR replication refers to the repeated amplification of the same DNA extract in independent reactions. Increasing the number of replicates improves detection probability, as PCR is subject to stochastic variation and a given species' DNA may fail to amplify in some reactions but succeed in others. For example, using 12 PCR replicates involves amplifying the sampled DNA in 12 independent subsamples, reducing the risk of false negatives.

Sequencing depth is another major factor influencing detection power. It refers to the total number of DNA sequences (reads) generated and analyzed from a sample. Higher sequencing depth increases the probability of detecting rare or low-abundance DNA fragments. Sequencing hundreds of thousands of reads in freshwater systems (up to 500 thousand) or up to around one million reads in marine systems can substantially enhance detection compared to lower-depth protocols, particularly for species present at low concentrations.

When robust sampling, replication, and sequencing strategies are applied, eDNA approaches are especially effective for detecting rare, elusive, or cryptic species, including protected, threatened, and invasive taxa.