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Environmental DNA or eDNA is DNA that is collected from a variety of environmental samples such as soil, seawater, or even air 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. Such samples can be analyzed by high-throughput DNA sequencing methods, known as metagenomics, 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. 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. 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. 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.
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Terrestrial sediments
The importance of eDNA analysis stemmed from the recognition of the limitations presented by culture-based studies. 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. The earliest version of this analysis began with ribosomal RNA (rRNA) in microbes to better understand microbes that live in hostile environments. 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. Samples extracted from these terrestrial sediments are commonly referenced as 'sedimentary ancient DNA' (sedaDNA or dirtDNA). The eDNA analysis can also be used to study current forest communities including everything from birds and mammals to fungi and worms.
Aquatic sediments
The sedaDNA was subsequently used to study ancient animal diversity and verified using known fossil records in aquatic sediments. The aquatic sediments are deprived of oxygen and are thus protect the DNA from degrading.
Aquatic
The use of eDNA in aquatic sediment has been useful, but can even be applied to open water for present day study. Before eDNA, the main ways to study open water diversity was to use fishing and trapping, which requires funding and skilled labor, but eDNA only needs samples of water. 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. 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. eDNA degrades relatively fast in the water column, which is very beneficial in short term conservation studies such as identifying what species are present.
Application
eDNA can be used to monitor species throughout the year and can be very useful in conservation monitoring. eDNA analysis has been successful at identifying many different taxa from aquatic plants, fishes, mussels, and even parasites.