There is something romantic about environmental DNA. The ability to discover the presence of almost any species just by detecting the microscopic bread crumbs they leave behind? That is really just a deerstalker and pipette away from Sherlock-level science.
But if you are anything like me, aside from knowing that folks get excited about, you might not know what exactly is possible using eDNA and metagenomics. No matter what your familiarity with the field is, I’m betting you can learn something from this new review from Mikkel Pedersen and colleagues:
Here were my top three gee-whiz moments:
- The eDNA under examination may be hitching a ride.
Natural transformation is a process through which cells take up extracellular DNA from the surroundings and integrate it into their own genomes [46,47]. Many bacteria are known to be agents for natural transformation, as are some archaea and even a eukaryotic group of micro-invertebrates, the bdelloid rotifers [48–51]. The majority of DNA that microbes take up is quickly degraded and re-metabolized in the cell, but some DNA persists for long enough to recombine with the host genome .
- I knew contamination was one of the most difficult aspects of eDNA studies….but even the reagents?!
…..contaminants can be difficult to distinguish from endogenous DNA. For example, DNA contaminants from various sources are found in reagents [10,21,77–82]. Although most of these are from readily identified domesticated animals or cultivated plants, others such as Salix  are not and can be mistaken for genuine environmental diversity.
- Ice cores, soil samples, permafrost? Too easy. Let’s go find some whales!
Recently, two studies showed that seawater is also a source of macro-organismal eDNA for detection of whale species  and marine fish diversity  (figure 2). Importantly, eDNA from fresh and seawater appears to reflect contemporary rather than past diversity, as eDNA decays within a few days or weeks in the water column [16,17,61,196,197].
Pedersen M.W., L. Ermini, C. D. Sarkissian, J. Haile, M. Hellstrom, J. Spens, P. F. Thomsen, K. Bohmann, E. Cappellini & I. B. Schnell & (2014). Ancient and modern environmental DNA, Philosophical Transactions of the Royal Society B: Biological Sciences, 370 (1660) 20130383-20130383. DOI: http://dx.doi.org/10.1098/rstb.2013.0383