Tuesday, May 27, 2014

eDNA particle size

Aquatic eDNA monitoring is emerging as a powerful way to detect harmful species like invasive Asian carp (a variety of carps including Silver Carp and Bighead Carp) and Burmese pythons or beneficial species like Chinook salmon and Idaho giant salamander. Because this approach is rather new, little is known about these small DNA fragments and how to best capture them from water.Origin, state, and fate of those DNA containing particles collectively determine how well eDNA can serve as a proxy for directly observing organisms and how it should be captured, purified, and assayed.

Actually the size of aquatic particles provides clues about all of the three parameters mentioned above (origin, state, fate). 

A new study from the University of Notre Dame compared performance across different types of eDNA capture methods such as centrifugation and filtration by measuring the particle size distribution. One outcome is a simple equation for calculating combinations of filter pore size and water volume to capture equivalent amounts of eDNA. Using common carp, one of the 30 worst invasive species worldwide in terms of impact, the researchers found eDNA in particles ranging from smaller than a mitochondrion to larger than a grain of table salt. They used a highly specific quantitative PCR test to measure carp eDNA, but they also quantified total eDNA—the DNA from any species—and found it was most concentrated in particles smaller than 1 micrometer. Because abundant total eDNA can interfere with the detection of eDNA from a rare species, this result further recommends the use of filter pore sizes greater than 1 micrometer.

Our results suggest that aqueous macrobial eDNA predominantly exists inside mitochondria or cells, and that settling may therefore play an important role in its fate. For optimal eDNA capture, we recommend 0.2 µm filtration or a combination of larger pore size and water volume that exceeds the 0.2 µm isocline. In situ filtration of large volumes could maximize detection probability when surveying large habitats for rare organisms.

Our description of  particle size for aqueous macrobial eDNA provides immediate guidance for practitioners and a tested method for researchers. For example, because large particles sink faster than small particles eDNA-based surveys aimed at determining very recent and local organism presence may need to target larger eDNA-containing particles. 

To my knowledge this is the first detailed investigation of just how small (or big) eDNA particles really are, results that provide important guidance for all eDNA-based monitoring programs.

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