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eDNA literature

  • Pawlowski, J., Kelly-Quinn, M., Altermatt/ F., Apotheloz-Perret-Gentil, L., Beja P. et al. (2018) The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems. Science of the Total Environment, 637-638, 1295-1310. Science Direct

    A review looking at how and if eDNA monitoring can be used as part of biomonitoring. Both problems and promises with eDNA has to be taken into consideration. The major issue with the approach as it stands is the lack of standardized procedures as well as the lack of knowledge regarding primer biases. This coupled with incomplete reference databases makes it very challenging to convert read counts to species and compare with traditional phenotypically based estimation of species abundance/diversity. For some organisms groups we are closer to having a working standard. For fish species they do for example argue for national efforts to fill in gaps in reference databases and take of efforts to include eDNA data in estimates of biological indexes.

    An interesting part of the paper discuss the use of machine-learning for estimating indexes from eDNA data. This could be useful as it would in theory make it possible to use all sequence data without converting reads to species. Hence instead of relying on incomplete databases and massive loss of data from the read data we would make use of knowledge obtained in certain system and learn about the expected eDNA signals stemming from such a water and algorithmically estimate indexes based on these.

  • Thomsen, P.F., Møller, P.R., Sigsgaard, E.E., Knudsen, S.W., Jørgensen, O.A. and Willerslev, E. (2016). Environmental DNA from seawater samples correlate with trawl catches of subarctic, deepwater fishes. PloS one, 11(11), p.e0165252 PloS one

    This paper shows a strong agreement between species composition found by trawling and eDNA sequencing. They use 12sRNA and despite using a blocking primer to prevent human DNA the most common contaminants seen were still human.

  • Rees, H. C., Maddison, B. C., Middleditch, D. J., Patmore, J. R., & Gough, K. C. (2014). The detection of aquatic animal species using environmental DNA–a review of eDNA as a survey tool in ecology. Journal of Applied Ecology, 51(5), 1450-1459 Journal of Applied Ecology

    Among things they discuss the sampling strategy and emphasis that taking at least three samples from a water body increases the chance of detecting species in the water. Most studies uses between 3-10 PCR replicates when using q-PCR. Using both positive and negative controls is essential for correct conclusions.

    They highlight some differences in cost for detecting invasive species

    “In terms of sampling effort, eDNA analysis can have considerable time and cost benefits over traditional survey methods, especially when looking at the distribution of rare or threatened species. In a study of invasive Asian carp in Chicago, Illinois, it took 93 days of person effort to detect one silver carp by electrofishing at a site, whereas eDNA analysis required only 0.174 days person effort to achieve a positive detection (Jerde et al. 2011)”

    In spite of high cost for sequences there are hence money to save by using clever sampling strategies and DNA sequencing, compared to more traditional monitoring approaches.

  • Shaw, J. L., Clarke, L. J., Wedderburn, S. D., Barnes, T. C., Weyrich, L. S., & Cooper, A. (2016). Comparison of environmental DNA metabarcoding and conventional fish survey methods in a river system. Biological Conservation, 197, 131-138 Biological Conservation

    The effect of taking multiple samples from both water and sediment is discussed. One of the main conclusion is that the water samples correlates better with netting compared to sediments. In addition the detection of DNA from the less common species is more effecient at sample size 5 compared to only 2 samples.

  • Hinlo, R., Gleeson, D., Lintermans, M., & Furlan, E. (2017). Methods to maximise recovery of environmental DNA from water samples. PloS one, 12(6), e0179251 PLoS ONE

    This paper compares both the effects of different approaches of extracting DNA from water. They testing the effect of type of filter paper as well as extraction and storage of water after sampling. In short one see differences between types of filters. They also note that filtering samples as soon as possible (the same day) or DNA is lost. Especially freezing seems to negatively effect the concentration of DNA.