Environmental DNA

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A fish leaves DNA behind when it swims, which is broken down over time

Environmental DNA ( English environmental DNA , eDNA for short ) refers to free DNA in the environment . It is released into the environment in small quantities by organisms .

properties

Environmental DNA is used to prove the current or previous presence of certain species in certain places (initial detection and biomonitoring ) and thus to draw conclusions about biodiversity and its changes. The monitoring of entire habitats using environmental DNA to determine the species population is also known as metabarcoding . Such examinations are of particular importance when examining prokaryotes , since a large number of species occurring in the natural environment cannot be cultivated on artificial nutrient media and thus remain undetected by classic microbiological working methods.

Sources of eDNA can be all excretions from living beings, such as urine , feces or body cells . Environmental DNA is mainly obtained from water, but it can come from the soil or sediment.

The type is determined by sequencing the DNA obtained, for example by second generation DNA sequencing and / or DNA barcoding . Often the mitochondrial DNA (mtDNA) is used for this because of its quantitatively much larger occurrence in the samples. To do this, of course, the mtDNA sequence of the species to be determined must be known, which is now the case for many species.

Depending on the underlying question, different investigation methods are used, such as species-specific presence, frequency of presence and cross-species presence.

advantages and disadvantages

Species monitoring has traditionally been used to identify different species based on their physical characteristics. An example of this is bird watching and counting. However, among other things, these methods have disadvantages when it comes to identifying closely related species and in some cases also intervene in the ecosystem of the species to be identified. One advantage of eDNA analysis compared to traditional methods such as the visual or acoustic search for species, for example when analyzing water samples, is that even small amounts of non-invasively obtained water (15 ml ) can be sufficient to detect several species in still waters . This is sometimes juxtaposed with invasive, visual searches for days or weeks. Furthermore, a precise determination of the species is possible, which, for example, with some water frogs would not be possible morphologically or acoustically alone.

A problem with the determination of species using environmental DNA is the presence of DNA from many different species and the potential contamination of the samples and the resulting possibility of false-positive results. Contamination can occur both when collecting the sample and in the laboratory. Due to the multiple amplification of genetic material, there are billions of copies of DNA or DNA fragments in laboratories that can easily get into another sample. The collection of the eDNA samples also has poor reproducibility . Errors can also occur in the sequencing of the DNA.

Detection limit

In experiments with amphibians , researchers found that the eDNA concentration rose continuously when the animals were used in mesocosms and was within the measurable range after a few days. EDNA degrades relatively quickly in water; it is still detectable about one to two weeks after the species has been removed. EDNA can be detected much longer in sediment. Environmental DNA is therefore rather unsuitable for detecting species that have only been to a specific location for a short time.

literature

Individual evidence

  1. ^ MA Barnes, CR Turner, CL Jerde, MA Renshaw, WL Chadderton, DM Lodge: Environmental conditions influence eDNA persistence in aquatic systems. In: Environmental Science & Technology . Volume 48, number 3, 2014, pp. 1819-1827, doi : 10.1021 / es404734p , PMID 24422450 .
  2. ↑ a b c d Schmidt, BR; Ursenbacher, S: Environmental DNA as a new method for species detection in water. (PDF) Zurich Open Repository and Archive, University of Zurich, 2015, p. 3 , accessed on August 6, 2018 .
  3. ↑ K. Bohmann, A. Evans, MT Gilbert, GR Carvalho, S. Creer, M. Knapp, DW Yu, M. de Bruyn: Environmental DNA for wildlife biology and biodiversity monitoring. In: Trends in ecology & evolution. Volume 29, Number 6, June 2014, pp. 358-367, doi : 10.1016 / j.tree.2014.04.003 , PMID 24821515 .
  4. ↑ MW Pedersen, S. Overballe-Petersen, L. Ermini, CD Sarkissian, J. Haile, M. Hellstrom, J. Spens, PF Thomsen, K. Bohmann, E. Cappellini, IB Schnell, NA Wales, C. Carøe, PF Campos, AM Schmidt, MT Gilbert, AJ Hansen, L. Orlando, E. Willerslev: Ancient and modern environmental DNA. In: Philosophical transactions of the Royal Society of London. Series B, Biological sciences. Volume 370, number 1660, January 2015, p. 20130383, doi : 10.1098 / rstb.2013.0383 , PMID 25487334 , PMC 4275890 (free full text).
  5. ↑ Yinqiu Ji Louise Ashton, Scott M. Pedley, David P. Edwards, Yong Tang, Akihiro Nakamura, Roger Kitching, Paul M. Dolman, Paul Woodcock, Felicity A. Edwards, Trond H. Larsen, Wayne W. Hsu, Suzan Benedick , Keith C. Hamer, David S. Wilcove, Catharine Bruce, Xiaoyang Wang, Taal Levi, Martin Lott, Brent C. Emerson, Douglas W. Yu (2013): Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecology Letters 16: 1245-1257. doi: 10.1111 / ele.12162
  6. ↑ Lindsey Solden, Karen Lloyd Kelly Wrighton (2016): The bright side of microbial dark matter: lessons learned from the uncultivated majority. Current Opinion in Microbiology 31: 217-226. doi: 10.1016 / j.mib.2016.04.020
  7. ↑ Melania E. Cristescu, Paul DN Hebert: Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation. In: Annual Review of Ecology, Evolution, and Systematics. 49, 2018, doi : 10.1146 / annurev-ecolsys-110617-062306 .
  8. ↑ S. Shokralla, JL Spall, JF Gibson, M. Hajibabaei: Next-generation sequencing technologies for environmental DNA research. In: Molecular ecology. Volume 21, Number 8, April 2012, pp. 1794-1805, doi : 10.1111 / j.1365-294X.2012.05538.x , PMID 22486820 .
  9. ^ JE Littlefair, EL Clare: Barcoding the food chain: from Sanger to high-throughput sequencing. In: Genome. Volume 59, Number 11, November 2016, pp. 946-958, doi : 10.1139 / gen-2016-0028 , PMID 27767337 .
  10. ^ A b Philip Francis Thomsen, Eske Willerslev: Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity. In: Biological Conservation. 183, 2015, p. 4, doi : 10.1016 / j.biocon.2014.11.019 .
  11. ^ Benedikt Schmidt: Amphibian monitoring with environmental DNA. (PDF) p. 8 , accessed on August 6, 2018 .
  12. ↑ IA Dickie, S. Boyer, HL Buckley, RP Duncan, PP Gardner, ID Hogg, RJ Holdaway, G. Lear, A. Makiola, SE Morales, JR Powell, L. Weaver: Towards robust and repeatable sampling methods in eDNA based studies. In: Molecular ecology resources. [Electronic publication before going to press] May 2018, doi : 10.1111 / 1755-0998.12907 , PMID 29802793 .