What is environmental DNA?

Abstract

DNA collected from the environment (eDNA) can provide valuable understanding of ecological patterns and processes. eDNA is highly physically heterogeneous, but this has not been well‐characterized, so most eDNA sampling strategies do not target any particular physical fraction. Consequently, we have limited evidence to understand and interpret the physical behavior of eDNA, to improve the efficiency of sampling, nor to target components of the eDNA spectrum for taxonomic and molecular attributes. We perform the first detailed characterization of the components of a marine eDNA sample using serial filtering from an 80 to <0.22 μm particle size gradient, a tree of life metabarcoding approach using taxon‐specific and universal assays, coupled with scanning electron microscopy and fluorescent confocal microscopy. We confirm that eDNA is manifest in a broad spectrum of physical states, ranging from extracellular DNA fragments to whole cells, tissue fragments, and whole organisms. The largest of these fractions of eDNA were embedded in microbial biofilms, rather than particulate. We show that the choice of filter size and types can target components of this spectrum, can affect the detectable species richness, and notably, also enrich samples for specific taxonomic groups. Our results imply that there is considerable scope to improve the efficiency of eDNA collection from aquatic environments, and its informativeness.