Comparing eDNA and eRNA Sampling Methodologies From Pond Environments

Abstract

Molecular traces are increasingly being applied to assess the presence of species and communities. Studies on environmental DNA (eDNA) have, to a large extent, become common practice in species detection, but less studies have compared biodiversity estimations with the more temporary environmental RNA (eRNA). This study compares metabarcoding results from pond water obtained from both molecule types by sequencing the V4 region in the 18S rRNA marker. Water was collected from two depths, 20 and 80 cm, and filtered sequentially through two filter porosities, 0.45 and 0.22 μm. Each filter was cut in half before fixation in either 96% ETOH or RNAlater. The results showed no differences between the fixatives for either molecule. Overall, biodiversity estimates from eDNA significantly overperformed eRNA, likely due to higher concentrations of eDNA from terrestrial sources. Comparisons of the two depths showed variation for eDNA only, with increasing levels of biodiversity found at the upper water layer. Both filter pore sizes captured distinctive compositions of taxa, where about 30% of the diversity was uniquely identified from the second, finer filter. Taken together, these findings imply that the choice of molecular marker, depth and filter pore size affects the obtained biodiversity estimations in a pond.