What is eDNA?

815 views November 25, 2015 cameron 21

Environmental DNA (eDNA) is genetic material found in bulk environmental samples (e.g., soil, water, air) without isolating the individual organisms or their parts. It is defined by the process used to collect it. So extracting DNA directly from a shovelful of mud gives you environmental DNA, while picking out the earthworms and extracting DNA from each one gives you earthworm DNA. Admittedly, it’s a somewhat fuzzy definition that grows fuzzier as it is applied to a broader range of samples and organisms. But the general concept from its original use remains consistent: you don’t know whose DNA is in the sample until you conduct genetic analysis.

The term “environmental DNA” originated in the field of microbiology [1] – the science that studies microbes such as bacteria or algae. Microbiologists first detected and quantified eDNA in seawater, attempting to learn if the amount of DNA could be an indicator for the amount of plankton [2]. Since then, scientists have found eDNA in many different environments and from many different organisms, including permafrost soil eDNA from mammoths that died 10,000 years ago [3].



As shown in the diagram above, eDNA can be intraorganismal or extraorganismal. Intraorganismal eDNA (ieDNA) is often from microbes and small organisms that live in the soil, water, or air. Extraorganismal eDNA (eeDNA) may be dead organisms, waste products, or pieces shed into the environment by large organisms. The distinction between these two types of eDNA is important because extraorganismal eDNA can stick around in the environment after an organism leaves. This makes eeDNA a very useful source of information about rare or elusive organisms. However, it also creates some uncertainty about when the organism was at the spot where its eeDNA was found and where it is now. Natural movement of soil, water, and air can also transport eeDNA away from an organism. For these reasons, important research is being conducted to understand the spatiotemporal context of eeDNA.



1. Ogram, A., Sayler, G. S. and Barkay, T. 1987. The extraction and purification of microbial DNA from sediments. Journal of Microbiological Methods 7, 57-66.
2. Holm-Hansen, O., Sutcliffe, W. H., Jr. and Sharp, J. 1968. Measurement of Deoxyribonucleic Acid in the Ocean and its Ecological Significance. Limnology and Oceanography 13, 507-514.
3. Haile, J., Froese, D. G., MacPhee, R. D. E. et al. 2009. Ancient DNA reveals late survival of mammoth and horse in interior Alaska. Proceedings of the National Academy of Sciences 106, 22352-22357.