Environmental DNA time series analysis of a temperate stream reveals
distinct seasonal community and functional shifts but no influence of
within-stream sampling position
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, location, 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 102
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.
We analyzed macroinvertebrate species and molecular Operational
Taxonomic Unit (OTU) richness and temporal community turnover across
seasons and sampling positions based on COI metabarcoding data. Using
Generalized Additive Models, we found a significant influence of
sampling season but not sampling position on community composition.
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
community composition, higher discharge reduced the number of Annelida
and Ephemeroptera species detectable with eDNA. Most macroinvertebrate
taxa showed the highest detection rates 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.