Environmental DNA

"Environmental omics" redirects here. It is not to be confused with enviromics.

The longhorn beetle, Leptura quadrifasciata, is an example of a flower‐visiting insect found in a study which showed that environmental DNA (eDNA) from arthropods is deposited on wild flowers after interactions [1]
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Environmental DNA or eDNA is DNA that is collected from a variety of environmental samples such as soil, 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.[2] 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.

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.[3]

Example sources of eDNA include, but are not limited to, feces, mucus, gametes, shed skin, carcasses and hair.[2][4] Samples can be analyzed by high-throughput DNA 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.[5]

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.[6]

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.[7] 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. Importantly, eDNA is often more cost-effective compared to traditional sampling methods.[8] 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.[9] 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),[10] or other environments where normal sampling procedures can become problematic.[9]

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.[11][12]

  1. ^ Cite error: The named reference Thomsen2019 was invoked but never defined (see the help page).
  2. ^ a b Stewart, Kathryn A. (1 April 2019). "Understanding the effects of biotic and abiotic factors on sources of aquatic environmental DNA". Biodiversity and Conservation. 28 (5): 983–1001. Bibcode:2019BiCon..28..983S. doi:10.1007/s10531-019-01709-8. hdl:11245.1/1caeb8dd-3d0b-493c-90dd-c180c9c8f21c. ISSN 1572-9710. S2CID 61811470.
  3. ^ "Environmental DNA – how a tool used to detect endangered wildlife ended up helping fight the COVID-19 pandemic". 21 April 2021.
  4. ^ "What is eDNA?". Freshwater Habitats Trust.
  5. ^ Fahner, Nicole (2016). "Large-Scale Monitoring of Plants through Environmental DNA Metabarcoding of Soil: Recovery, Resolution, and Annotation of Four DNA Markers". PLOS ONE. 11 (6): 1–16. Bibcode:2016PLoSO..1157505F. doi:10.1371/journal.pone.0157505. ISSN 1932-6203. PMC 4911152. PMID 27310720 – via Directory of Open Access Journals.
  6. ^ Ruppert, Krista M.; Kline, Richard J.; Rahman, Md Saydur (2019). "Past, present, and future perspectives of environmental DNA (EDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA". Global Ecology and Conservation. 17: e00547. doi:10.1016/j.gecco.2019.e00547. S2CID 133855497. Modified text was copied from this source, which is available under a Creative Commons Attribution 4.0 International License.
  7. ^ Bohmann, Kristine; Evans, Alice; Gilbert, M. Thomas P.; Carvalho, Gary R.; Creer, Simon; Knapp, Michael; Yu, Douglas W.; de Bruyn, Mark (1 June 2014). "Environmental DNA for wildlife biology and biodiversity monitoring". Trends in Ecology & Evolution. 29 (6): 358–367. doi:10.1016/j.tree.2014.04.003. ISSN 1872-8383. PMID 24821515.
  8. ^ Qu, Chanjuan; Stewart, Kathryn A. (18 February 2019). "Evaluating monitoring options for conservation: comparing traditional and environmental DNA tools for a critically endangered mammal". The Science of Nature. 106 (3): 9. Bibcode:2019SciNa.106....9Q. doi:10.1007/s00114-019-1605-1. hdl:11245.1/d02ea724-b763-42b2-8f97-696ef88db996. ISSN 1432-1904. PMID 30778682. S2CID 66881381.
  9. ^ a b Thomsen, Philip Francis; Willerslev, Eske (1 March 2015). "Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity". Biological Conservation. Special Issue: Environmental DNA: A powerful new tool for biological conservation. 183: 4–18. Bibcode:2015BCons.183....4T. doi:10.1016/j.biocon.2014.11.019.
  10. ^ Tsuji, Satsuki (2016). "Effects of water pH and proteinase K treatment on the yield of environmental DNA from water samples". Limnology. 18: 1–7. doi:10.1007/s10201-016-0483-x. ISSN 1439-8621. S2CID 44793881.
  11. ^ Cite error: The named reference NYT-20221207 was invoked but never defined (see the help page).
  12. ^ Cite error: The named reference NAT-20221207 was invoked but never defined (see the help page).