eDNA - Past and Present ecology on a molecular scale

“Who lives here now? and “Who lived here previously” are fundamental questions of biology, but observing living things in their natural habitats is not always so straightforward. Tracking down rare, elusive, and microscopic species through harsh or inaccessible environments has challenged biologists for centuries.

 

In 1987, a research group studying terrestrial microbiology at the University of Tennessee addressed challenges related to microbial sediment communities in a paper published by the Journal of Microbiological Methods. The group thought the traditional method of extracting DNA by filtering out the sediment particles excluded small cells that adhere to particles in sticky biofilms (1). The group proposed a new method of extracting DNA directly from the sediment. 

 

 

 

What is eDNA?

 

The soup of genetic material extracted by Ogram and colleagues in 1987 was called environmental DNA (eDNA). Today, eDNA refers to all the extractable DNA that is released by organisms as they move around their environments, notably soil, air, water, and even snow. (2). For example, a sea ice core from Antarctica can contain eDNA from living cells, dissolved extracellular DNA, and preserved DNA from organisms of the ancient past (3). Because DNA is the universal genetic blueprint for all cells, eDNA can include information from all kingdoms of life and some viruses. 



Why is eDNA important?

 

Sampling eDNA is non-invasive, and it has been rapidly adapted for studies on ecosystem monitoring and conservation. For studying microbe communities, microbiologists can extract bacterial DNA directly from the environment without needing to culture cells in the lab.  At the species level, ecologists can forgo disturbing animals in the wild by searching for species-specific DNA barcodes. Finally, for studying whole ecosystems and even biomes, environmental scientists can monitor the population of multiple organisms at once through one environmental sample (3). eDNA has revolutionized biology by opening up a previously untapped data source.  The many applications of eDNA include rapid detection of invasive species, monitoring the effects of climate change on communities, tracking rare animals, and distinguishing between populations with similar morphologies. 

How does it work?

 

The two main methods for extracting eDNA from an environmental sample are precipitation and filtration. Studies have shown that filtration through PES Membrane or MCE Membrane with a pore size of  0.45 μm improves eDNA recovery from water samples (4,8). Filtration can be performed simultaneously on multiple samples with one-handed test kit or using an Analytical Funnel (some remove the MCE membrane and replace with a PES).   After extraction, purification, and amplification by PCR (if necessary), the DNA is sequenced. Traditionally, species-specific studies use PCR to amplify a region of interest before DNA sequencing. However, recent developments in next generation sequencing (NGS) enable detection of multiple unique sequences from one sample, even at low concentrations of eDNA (5, 6). The field of metagenomics, which studies genetic material in the environment, emerged from coupling eDNA with NGS methods (2).

 

What is the future of eDNA?

 

It wasn’t until the advancement of rapid sequencing methods that eDNA was fully recognized for its potential in answering “Who lives here?”. These days the potential for eDNA grows hand-in-hand with technology. Advances in sampling and filtration equipment reduce DNA degradation and improve extraction yields. Advancements in bioinformatics and data sharing increase the speed and accuracy of identifying new DNA barcodes. Finally, advancements in NGS can make sequencing more accessible and increase the power for identifying multiple sequences from one sample.

 

The rapid growth of eDNA spurred innovations for monitoring other trace materials that organisms imprint on their environments. Because RNA is less stable than DNA, eRNA can give a more recent snapshot of the organisms in an environment, and studies monitoring eproteins can track how gene expression shifts over time in response to environmental change (3,7). 

 

The capability to observe biomolecules directly in the environment applies a molecular level of magnification over a huge spatial scale. eDNA has uncovered hidden ecosystem interactions, allowed us to sample for life in impossible environments, and opened up a source of biological data, the depth of which we are only beginning to discover.

 

References

 

  1. Ogram A, Sayler GS, Barkay T. The extraction and purification of microbial DNA from sediments. J Microbiol Methods. 1987;7: 57-66. 
  2. Seymour M. Rapid progression and future of environmental DNA research. Commun Biol. 2019;2(80). https://doi.org/10.1038/s42003-019-0330-9
  3. Barnes MA, Turner CR. The ecology of environmental DNA and implications for conservation genetics. Conserv Genet. 2016;17: 1-17. https://doi.org/10.1007/s10592-015-0775-4
  4. Rey A, Carney KJ, Quinones LE, Pagenkopp Lohan KM, Ruiz GM, Basurko OC et al. Environmental DNA Metabarcoding: A Promising Tool for Ballast Water Monitoring. Environ. Sci. Technol. 2019;53(20): 11849-11859. https://doi-org.ezproxy.ub.gu.se/10.1021/acs.est.9b01855
  5. A Powerful tool for studying ecosystem biodiversity (2020). Retrieved from https://emea.illumina.com/techniques/sequencing/dna-sequencing/targeted-resequencing/environmental-dna.html
  6. Taberlet P, Coissac E, Hajibabaei M, Rieseberg L. Environmental DNA. Mol Ecol. 2012; 21(8): 1789-1793. https://doi-org.ezproxy.ub.gu.se/10.1111/j.1365-294X.2012.05542.x
  7. Wang P, Yan Z, Yang S, Wang S, Zheng X, Fan J, et al. Environmental DNA: An Emerging Tool in Ecological Assessment. Bull Environ Contam Toxicol. 2019; 103: 651-656. https://doi.org/10.1007/s00128-019-02720-z
  8. Hinlo R, Gleeson D, Lintermans M, Furlan E. Methods to maximise recovery of environmental DNA from water samples. PLoS One. 2017; 12(6): e0179251. https://doi.org/10.1371/journal.pone.0179251