Environmental DNA (eDNA) review article
Updated: Jan 29
This is a synopsis of the article: "Past, present and future perspectives of environmental DNA (eDNA metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA" Ruppert et al., 2019
Ruppert and others (2019) offer a comprehensive review of all the ways scientists have utilized eDNA in the last 10 years. Examples include marine sediments (Sinniger et al., 2016; Guardiola et al., 2016, 2015; Pawlowski et al., 2011), biofilms (Leray and Knowlton, 2015), estuarine monitoring (Avó et al., 2017; Chariton et al., 2010, 2015), freshwater monitoring, fecal matter or stomach contents (Buglione et al., 2018) .
They include two sections that describe what constitutes eDNA as well as a discussion on the different methods for different sample types.
eDNA is DNA captured from an environmental sample without first isolating any target organisms (Taberlet, Coissac, Hajibabaei, & Rieseberg,2012). Traces of DNA can be from feces, mucus, skin cells, organelles, gametes or even extracellular DNA. Environmental DNA can be sampled from modern environments (e.g., seawater, freshwater, soil or air) or ancient environments (e.g., cores from sediment, ice or permafrost, see Thomsen & Willerslev, 2015).
As a new fish biologist, currently using eDNA and qPCR to detect Hoolies in the Nooksack, I kept wondering about whether or not certain signals last longer than others from different species (if oils or organics in certain fish preserve their DNA). eDNA can remain viable from weeks to hundreds of years.
The article further reminds us though of the complications and the limitations of the current technology. In fact, there is a section that emphasizes the importance of primer design.
Image 1. Picture of Birch Bay State Park. While reading this article, I kept thinking of ways that this method could be used to examine ocean microbiome circulation.
The implementation of eDNA metabarcoding would benefit from optimized bioinformatics, improved database quality, and taxonomic resolution.
For soil and sediment samples, large volumes of sample over larger spatial scales are required from larger size classes of organisms.
“eDNA has the application of citizen science by engagement of citizen collection of eDNA using commercially available sampling kits, involving the public in biodiversity sampling in a way that could be complementary to already established methods.”
The articles has a great tie-in to community outreach and citizen science. It was unexpected and an will be interesting concept to try to tie into future research endeavors and grant proposals.
Example of deep-sea sediment eDNA metabarcoding results
Figure 1 from Pawlowski et al. (2011). They used metabarcoding on marine sediments in abyssal Arctic and Southern Ocean environmental to examine deep-sea eukaryotic richness. They detected 942-1756 taxa per sample, dominated by dinoflagellates, cercozoans, ciliates, and euglenozoans; even photosynthetic taxa were present.
Avó, Ana & Daniell, Tim & Neilson, Roy & Oliveira, Solange & Branco, Jordana & Adão, Helena. (2017). DNA Barcoding and Morphological Identification of Benthic Nematodes Assemblages of Estuarine Intertidal Sediments: Advances in Molecular Tools for Biodiversity Assessment. Frontiers in Marine Science. 4. 10.3389/fmars.2017.00066.
Buglione, Maria & Maselli, Valeria & Rippa, Daniela & de Filippo, Gabriele & Trapanese, Martina & Fulgione, Domenico. (2017). A pilot study on the application of DNA metabarcoding for non-invasive diet analysis in the Italian hare. Mammalian Biology. 88. 10.1016/j.mambio.2017.10.010.
Guardiola M, Uriz MJ, Taberlet P, Coissac E, Wangensteen OS, et al. (2016) Correction: Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons. PLOS ONE 11(4): e0153836.
Leray M, Knowlton N. DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. Proc Natl Acad Sci U S A. 2015;112(7):2076-2081. doi:10.1073/pnas.1424997112.
Pawlowski J, Christen R, Lecroq B, Bachar D, Shahbazkia HR, Amaral-Zettler L, et al. (2011) Eukaryotic Richness in the Abyss: Insights from Pyrotag Sequencing. PLoS ONE 6(4): e18169. https://doi.org/10.1371/journal.pone.0018169.
Ruppert, K. M., Kline, R. J., & Rahman, M. S. (2019, January 1). 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. Elsevier B.V. https://doi.org/10.1016/j.gecco.2019.e00547.
Sinniger, F., Pawlowski, J., Harii, S., Gooday, A.J., Yamamoto, H., Chevaldonné, P., Cedhagen, T., Carvalho, G., & Creer, S. (2016). Worldwide Analysis of Sedimentary DNA Reveals Major Gaps in Taxonomic Knowledge of Deep-Sea Benthos. Frontiers in Marine Science, 3, 1-14.