A molecular snapshot in time: eRNA recovers similar diversity but
captures species turnover more rapidly than eDNA across an acid-base
gradient
Abstract
Major ongoing declines in global biodiversity necessitate biomonitoring
strategies that enable precise estimates of community diversity on a
fine spatial and temporal scale. While environmental DNA (eDNA) has been
established as a powerful tool for biodiversity assessment, studies
investigating the comparative performance of environmental RNA (eRNA)
are limited. Here, we performed eDNA/eRNA metabarcoding of zooplankton
communities in outdoor freshwater mesocosms subject to a dynamic range
of pH conditions. We comparatively assessed i) the sensitivity of
eRNA metabarcoding relative to eDNA and traditional survey methods in
capturing zooplankton diversity, ii) the influence of pH on
eDNA/eRNA detectability, and iii) the propensity of eRNA to
capture contemporary biological assemblages (i.e., rapid species
turnover) with high spatial and temporal acuity. Zooplankton richness
was similar amongst eDNA/eRNA metabarcoding and traditional survey
methods; however, the composition of zooplankton communities detected
was more analogous between eDNA and eRNA metabarcoding than with
traditional methods. Both eDNA and eRNA captured similar ZOTU richness
and frequency of false negative detections (irrespective of
site-specific pH); however, eRNA captured species turnover more rapidly
than eDNA. Collectively, our findings suggest that i) relative to
traditional methods, eDNA and eRNA metabarcoding may provide users with
complementary rather than congruent estimates of biodiversity,
ii) eDNA and eRNA provide comparable estimates of species
richness irrespective of site-specific pH conditions, and iii)
eRNA is able to capture short-term community responses with higher
spatial and temporal acuity than eDNA. Overall, our findings support the
use of eRNA for characterizing contemporary biodiversity in complex and
dynamic aquatic environments.