Modelling environmental DNA transport in rivers reveals highly resolved spatio-temporal biodiversity patterns

Abstract

The ever-increasing threats to riverine ecosystems call for novel approaches for highly resolved biodiversity assessments across taxonomic groups and spatio-temporal scales. Recent advances in the joint use of environmental DNA (eDNA) data and eDNA transport models in rivers (e.g., eDITH) allow uncovering the full structure of riverine biodiversity, hence elucidating ecosystem processes and supporting conservation measures. We applied eDITH to a metabarcoding dataset covering three taxonomic groups (fish, invertebrates, bacteria) and three seasons for a catchment sampled for eDNA at 73 sites. We upscaled eDNA-based biodiversity predictions to approximately 1900 reaches, and assessed α- and β-diversity patterns across seasons and taxonomic groups over the whole network. Genus richness predicted by eDITH was generally higher than values from direct eDNA analysis. Both predicted α- and β-diversity varied depending on season and taxonomic group. Predicted fish α-diversity increased downstream in all seasons, while invertebrate and bacteria α-diversity either decreased downstream or were unrelated to network position. Spatial β-diversity mostly decreased downstream, especially for bacteria. The eDITH model yielded a more refined assessment of freshwater biodiversity as compared to raw eDNA data, both in terms of spatial coverage, diversity patterns and effect of covariates, thus providing a more complete picture of freshwater biodiversity.

Mudpot Geochemistry Reveals Subsurface Geologic Activity

“…Finally, the arthropod DNA found in “Consolation Prize” likely points to a “stick insect” meeting an unfortunate end after wandering into the mudpot. Although the mudpots contained DNA originating from outside the geothermal features, the lack of terrestrial taxonomic variety points to mudpots being poor candidates for use as terrestrial environmental DNA (eDNA) sources, unlike rivers and other aquatic habitats …”

eDITH: An R‐package to spatially project eDNA‐based biodiversity across river networks with minimal prior information

“…Such an attribution has been implemented for the first time by the development of the eDITH model (eDNA Integrating Transport and Hydrology; Carraro et al, 2017Carraro et al, , 2018Carraro et al, , 2021Carraro et al, , 2023Carraro, Mächler, et al, 2020), which couples a geomorphological and hydrological characterization of a watershed with a species distribution model and eDNA transport and decay dynamics. This model uniquely leverages spatially replicated eDNA measurements within a river network to infer the spatial distribution of any taxon of interest, expressed as relative density and/or detection probability.…”

Homogeneity in terrestrial land cover is reflected in fish diversity patterns in a Chinese river system

“…Communities identified by conventional techniques are local snapshots. By contrast, eDNA gets transported along the river system and therefore incorporates information across larger temporal scales (e.g., the time lag between DNA shedding and detection) and spatial scales (up to several km upstream) (Carraro et al, 2023; Deiner & Altermatt, 2014; Pont et al, 2018; Van Driessche et al, 2023). Landscape‐level integration of eDNA methods may allow the identification of riverine biodiversity on local‐ to catchment‐wide scales and better understand the spatial scale at which the aquatic matrix connects to the surrounding terrestrial matrix (Cantera et al, 2022; Zhang et al, 2023).…”

“…Communities identified by conventional techniques are local snapshots. By contrast, eDNA gets transported along the river system and therefore incorporates information across larger temporal scales (e.g., the time lag between DNA shedding and detection) and spatial scales (up to several km upstream) (Carraro et al, 2023;Deiner & Altermatt, 2014;Pont et al, 2018;Van Driessche et al, 2023).…”