Environmental DNA

Environmental DNA or eDNA is DNA that is collected from a variety of environmental samples such as soil, seawater, snow or even air [1] rather than directly sampled from an individual organism. As various organisms interact with the environment, DNA is expelled and accumulates in their surroundings. Example sources of eDNA include, but are not limited to, feces, mucus, gametes, shed skin, carcasses and hair.[2] Such samples can be analyzed by high-throughput DNA sequencing methods, known as metagenomics, metabarcoding, and single-species detection[3], for rapid measurement and monitoring 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 to determine what organisms are present (e.g. BLAST).[4] 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.[5] 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. 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. 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.[6] 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),[7] or other environments where normal sampling procedures can become problematic.[6]

In this example, the fish leaves its eDNA behind as it moves through the water, but its eDNA slowly dissipates over time.

Collection

Terrestrial sediments

The importance of eDNA analysis stemmed from the recognition of the limitations presented by culture-based studies.[5] Organisms have adapted to thrive in the specific conditions of their natural environments. Although scientists work to mimic these environments, many microbial organisms can not be removed and cultured in a laboratory setting.[6] The earliest version of this analysis began with ribosomal RNA (rRNA) in microbes to better understand microbes that live in hostile environments.[8] The genetic makeup of some microbes is then only accessible through eDNA analysis. Analytical techniques of eDNA were first applied to terrestrial sediments yielding DNA from both extinct and extant mammals, birds, insects and plants.[9] Samples extracted from these terrestrial sediments are commonly referenced as 'sedimentary ancient DNA' (sedaDNA or dirtDNA).[10] The eDNA analysis can also be used to study current forest communities including everything from birds and mammals to fungi and worms.[6]

Aquatic sediments

The sedaDNA was subsequently used to study ancient animal diversity and verified using known fossil records in aquatic sediments.[6] The aquatic sediments are deprived of oxygen and are thus protect the DNA from degrading.[6] Other than ancient studies, this approach can be used to understand current animal diversity with relatively high sensitivity. While typical water samples can have the DNA degrade relatively quickly, the aquatic sediment samples can have useful DNA two months after the species was present.[11] One problem with aquatic sediments is that it is unknown where the organism deposited the eDNA as it could have moved in the water column.

Aquatic (water column)

The use of eDNA in aquatic sediment has been useful, but can even be applied to open water for present day study.[7] Before eDNA, the main ways to study open water diversity was to use fishing and trapping, which requires funding and skilled labour, and other various resources, but eDNA only needs samples of water.[7] This method is effective as pH of the water does not affect the DNA as much as previously thought, and can be made more sensitive with relative ease.[7][12] Sensitivity is how likely the DNA marker will be present in the sampled water, and can be increased simply by taking more samples, having bigger samples, and increasing PCR.[12] eDNA degrades relatively fast in the water column, which is very beneficial in short term conservation studies such as identifying what species are present.[6]

Snow tracks

Wildlife researchers in snowy areas also use snow samples to gather and extract genetic information about species of interest. DNA from snow track samples has been used to confirm the presence of such elusive and rare species as polar bears, arctic fox, lynx, wolverines, and fishers.[13][14][15]

Application

eDNA can be used to monitor species throughout the year and can be very useful in conservation monitoring.[16][17] eDNA analysis has been successful at identifying many different taxa from aquatic plants,[18] fishes,[17] mussels,[16] fungi [19][20] and even parasites.[21][8] eDNA has been used to study species while minimizing any stress inducing human interaction, allowing researchers to monitor species presence at larger spatial scales more efficiently.[22][23] The most prevalent use in current research is using eDNA to study the locations of species at risk, invasive species, and keystone species across all environments.[22] eDNA is especially useful for studying species with small populations because eDNA is sensitive enough to confirm the presence of a species with relatively little effort to collect data which can often be done with a soil sample or water sample.[5][22] eDNA relies on the efficiency of genomic sequencing and analysis as well as the survey methods used which continue to become more efficient and cheaper.[24] Some studies have shown that eDNA sampled from stream and inshore environment decayed to undetectable level at within about 48 hours.[25][26]

Environmental DNA can be applied as a tool to detect low abundance organisms in both active and passive forms. Active eDNA surveys target individual species or groups of taxa for detection by using highly sensitive species-specific quantitative real-time PCR [27] or digital droplet PCR markers[28]. CRISPR-Cas methodology has also been applied to the detection of single species from eDNA [29]; utilising the Cas12a enzyme and allowing greater specificity when detecting sympatric taxa. Passive eDNA surveys employ massively-parallel DNA sequencing to amplify all eDNA molecules in a sample with no a priori target in mind providing blanket DNA evidence of biotic community composition.[30]

See also

References
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  15. Roth, Annie (2018-11-19). "How DNA from snow helps scientists track elusive animals". National Geographic. Retrieved 2018-11-26.
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