Environmental DNA

Environmental DNA (eDNA) is DNA that an organism leaves behind as it moves through an environment. Generally, eDNA follows a pattern of exponential decay over time. The fish above leaves its eDNA behind as it moves through the aquatic environment. The eDNA stays behind in the environment, and slowly dissipates over time.

Environmental DNA or eDNA is DNA that is collected from a variety of environmental samples such as soil, seawater, 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, 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).[3] 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.[4] 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.[5] 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),[6] or other environments where normal sampling procedures can become problematic.[5]

Collection

Terrestrial sediments

The importance of eDNA analysis stemmed from the recognition of the limitations presented by culture-based studies.[4] 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.[5] The earliest version of this analysis began with ribosomal RNA (rRNA) in microbes to better understand microbes that live in hostile environments.[7] 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.[8] Samples extracted from these terrestrial sediments are commonly referenced as 'sedimentary ancient DNA' (sedaDNA or dirtDNA).[9] The eDNA analysis can also be used to study current forest communities including everything from birds and mammals to fungi and worms.[5]

Aquatic sediments

The sedaDNA was subsequently used to study ancient animal diversity and verified using known fossil records in aquatic sediments.[5] The aquatic sediments are deprived of oxygen and are thus protect the DNA from degrading.[5] 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.[10] 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.[6] 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.[6] 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.[6][11] 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.[11] eDNA degrades relatively fast in the water column, which is very beneficial in short term conservation studies such as identifying what species are present.[5]

Application

eDNA can be used to monitor species throughout the year and can be very useful in conservation monitoring.[12][13] eDNA analysis has been successful at identifying many different taxa from aquatic plants,[14] fishes,[13] mussels,[12] fungi [15][16] and even parasites.[7] 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.[17][18] The most prevalent use in current research is using eDNA to study the locations of threatened or endangered species across all environments.[17] 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.[4][17] However, eDNA is unable to give an indication of abundance in a particular species which limits its uses in conservation efforts, but is still used as an indicator of where more involved methods should begin.[5] eDNA also relies on the efficiency of genomic sequencing and analysis which continues to become more efficient and cheaper (e.g. PacBio and Illumina).[19]

See also

References

  1. ↑ Ficetola, Gentile Francesco; Miaud, Claude; Pompanon, François; Taberlet, Pierre (2008). "Species detection using environmental DNA from water samples". Biology Letters. 4 (4): 423–425. doi:10.1098/rsbl.2008.0118. ISSN 1744-9561. PMC 2610135. PMID 18400683.
  2. ↑ "What is eDNA?". Freshwater Habitats Trust.
  3. ↑ 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: 1–16. doi:10.1371/journal.pone.0157505. ISSN 1932-6203 – via Directory of Open Access Journals.
  4. 1 2 3 Bohmann, Kristine; Evans, Alice; Gilbert, M. Thomas P.; Carvalho, Gary R.; Creer, Simon; Knapp, Michael; Yu, Douglas W.; de Bruyn, Mark (2014-06-01). "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.
  5. 1 2 3 4 5 6 7 8 Thomsen, Philip Francis; Willerslev, Eske (2015-03-01). "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. doi:10.1016/j.biocon.2014.11.019.
  6. 1 2 3 4 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.
  7. 1 2 Bass, David (2015). "Diverse Applications of Environmental DNA Methods in Parasitology". Trends in Parasitology. 31 (10): 499–513. doi:10.1016/j.pt.2015.06.013. PMID 26433253.
  8. ↑ Willerslev, Eske; Hansen, Anders J.; Binladen, Jonas; Brand, Tina B.; Gilbert, M. Thomas P.; Shapiro, Beth; Bunce, Michael; Wiuf, Carsten; Gilichinsky, David A. (2003-05-02). "Diverse Plant and Animal Genetic Records from Holocene and Pleistocene Sediments". Science. 300 (5620): 791–795. doi:10.1126/science.1084114. ISSN 0036-8075. PMID 12702808.
  9. ↑ Andersen, Kenneth; Bird, Karen Lise; Rasmussen, Morten; Haile, James; Breuning-Madsen, Henrik; Kjaer, Kurt H.; Orlando, Ludovic; Gilbert, M. Thomas P.; Willerslev, Eske (2012-04-01). "Meta-barcoding of 'dirt' DNA from soil reflects vertebrate biodiversity". Molecular Ecology. 21 (8): 1966–1979. doi:10.1111/j.1365-294X.2011.05261.x. ISSN 1365-294X. PMID 21917035.
  10. ↑ Turner, Cameron R. (2014). "Fish environmental DNA is more concentrated in aquatic sediments than surface water". Biological Conservation. 183: 93–102. doi:10.1016/j.biocon.2014.11.017. ISSN 0006-3207.
  11. 1 2 Schultz, Martin (2015). "Modeling the Sensitivity of Field Surveys for Detection of Environmental DNA (eDNA)". PLOS ONE. 10: 1–16. doi:10.1371/journal.pone.0141503. ISSN 1932-6203.
  12. 1 2 Stoeckle, Bernhard (2016). "Environmental DNA as a monitoring tool for the endangered freshwater pearl mussel (Margaritifera margaritifera L.): a substitute for classical monitoring approaches?". AQUATIC CONSERVATION: MARINE AND FRESHWATER ECOSYSTEMS. 26 (6): 1120–1129. doi:10.1371/journal.pone.0156217. ISSN 1932-6203.
  13. 1 2 Souza, Lesley (2016). "Environmental DNA (eDNA) Detection Probability Is Influenced by Seasonal Activity of Organisms". PLOS ONE. 11: 1–15. doi:10.1371/journal.pone.0165273. ISSN 1932-6203.
  14. ↑ Saeko, Matsuhashi (2016). "Evaluation of the Environmental DNA Method for Estimating Distribution and Biomass of Submerged Aquatic Plants". PLOS ONE. 11 (6): 1–14. doi:10.1371/journal.pone.0156217. ISSN 1932-6203.
  15. ↑ Tedersoo, Leho; Bahram, Mohammad; Põlme, Sergei; Kõljalg, Urmas; Yorou, Nourou S.; Wijesundera, Ravi; Ruiz, Luis Villarreal; Vasco-Palacios, Aída M.; Thu, Pham Quang (2014-11-28). "Global diversity and geography of soil fungi". Science. 346 (6213): 1256688. doi:10.1126/science.1256688. ISSN 0036-8075. PMID 25430773.
  16. ↑ Detheridge, Andrew Paul; Comont, David; Callaghan, Tony Martin; Bussell, Jennifer; Brand, Graham; Gwynn-Jones, Dylan; Scullion, John; Griffith, Gareth Wyn (2018-06). "Vegetation and edaphic factors influence rapid establishment of distinct fungal communities on former coal-spoil sites". Fungal Ecology. 33: 92–103. doi:10.1016/j.funeco.2018.02.002. ISSN 1754-5048. Check date values in: |date= (help)
  17. 1 2 3 Bergman, Paul (2016). "Detection of Adult Green Sturgeon Using Environmental DNA Analysis". PLoS ONE. 11: 1–8. doi:10.1371/journal.pone.015350. ISSN 1932-6203.
  18. ↑ "A Guide to Environmental DNA (eDNA) by Biomeme". Biomeme.
  19. ↑ Wang, Xinkun (2016). Next-generation Sequencing Data Analysis. Boca Raton: CRC Press. ISBN 9781482217889. OCLC 940961529.
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