Environmental DNA time series analysis of a temperate stream reveals
distinct seasonal community and functional shifts
Abstract
Environmental DNA (eDNA) extracted from water is routinely used in river
biodiversity research, and via metabarcoding eDNA can provide
comprehensive taxa lists with little effort and cost. However,
eDNA-based species detection in streams and rivers may be influenced by
sampling season and other key factors such as water temperature and
discharge. Research linking these factors and also informing on the
potential of eDNA metabarcoding to detect shifts in ecological
signatures, such as species phenology and functional feeding groups
across seasons, is missing. To address this gap, we collected water
samples every two weeks for 15 months at a long-term ecological research
(LTER) site and at three different positions in the river’s cross
section, specifically the water surface, riverbed, and riverbank. For
these 102 samples, we analyzed macroinvertebrate species and molecular
Operational Taxonomic Unit (OTU) richness and temporal community
turnover across seasons based on COI metabarcoding data. Using
Generalized Additive Models, we found a significant influence of
sampling season on species richness. Community turnover followed a
cyclic pattern, reflecting the continuous change of the
macroinvertebrate community throughout the year (‘seasonal clock’).
Although water temperature had no influence on the inferred species
richness, higher discharge reduced the number of Annelida and
Ephemeroptera species detectable with eDNA. Most macroinvertebrate taxa
showed the highest species richness in spring, in particular merolimnic
species with univoltine life cycles. Further, we detected an increase in
proportion of shredders in winter and of parasites in summer. Our
results show the usefulness of highly resolved eDNA metabarcoding time
series data for ecological research and biodiversity monitoring in
streams and rivers.