Environmental DNA provides higher resolution assessment of riverine biodiversity and ecosystem function via spatio-temporal nestedness and turnover partitioning

Abstract

Rapidly assessing biodiversity is essential for environmental monitoring; however, traditional approaches are limited in the scope needed for most ecological systems. Environmental DNA (eDNA) based assessment offers enhanced scope for assessing biodiversity, while also increasing sampling efficiency and reducing processing time, compared to traditional methods. Here we investigated the effects of landuse and seasonality on headwater community richness and functional diversity, via spatio-temporal dynamics, using both eDNA and traditional sampling. We found that eDNA provided greater resolution in assessing biodiversity dynamics in time and space, compared to traditional sampling. Community richness was seasonally linked, peaking in spring and summer, with temporal turnover having a greater effect on community composition compared to localized nestedness. Overall, our assessment of ecosystem function shows that community formation is driven by regional resource availability, implying regional management requirements should be considered. Our findings show that eDNA based ecological assessment is a powerful, rapid and effective assessment strategy that enables complex spatio-temporal studies of community diversity and ecosystem function, previously infeasible using traditional methods.

A triad of kicknet sampling, eDNA metabarcoding, and predictive modeling to assess aquatic macroinvertebrate biodiversity

“…The study of diversity on a regional scale (gamma diversity) shows the ability of environmental DNA to detect many taxa also identified by the traditional kicknet method. This result is in line with previous studies which reported several EPT taxa detected by both methods (Mächler et al 2019, Seymour et al 2021). However, a significant number of taxa known to be present in these rivers (according to the kicknet sampling) could not be detected by either the mlCOIintF/HCO2198 or fwhF2/EPTDr2n primers.…”

A practical guide to DNA-based methods for biodiversity assessment

“…Inferrering community ecological indices from metabarcoding data can be relatively straightforward to adapt, at least from an analysis standpoint. Taxon richness can be easily calculated from metabarcoding data (Seymour et al 2021), while abundance based indices, including Shannon and Simpson indices, can be derived by calculating Hill numbers from relative read abundances using an index based approach to existing statistical methods (Chao et al 2014, Alberdi and.…”

Novel insights into marine fish biodiversity across a pronounced environmental gradient using replicated environmental DNA analyses

“…A two-step PCR-based library preparation protocol was performed after initially optimizing the PCR methods, based on the two-step adapter system outlined by Miya et al, 2015 andothers (e.g., Brennan et al, 2019;Holman et al, 2021;Seymour et al, 2021). In summary, each biological replicate was prepared as a single library; thus, three libraries resulted from each site for each sampling event.…”

“…Distribution data for fishes, which are among the most well-studied marine species, are often based on catch data from commercial fishing practices or ecological studies, which can be biased toward certain species and highly dependent on sampling strategy and timing (Boenish et al, 2020;Pope et al, 2010). As such, traditional methods can limit biodiversity surveys both temporally and spatially, where data cannot be systematically collected and compared (McElroy et al, 2020;Seymour et al, 2021).…”

“…Fishes have been assessed in a large body of eDNA-based research for validating eDNA methodology (Miya et al, 2015;Valentini et al, 2016), developing quantitative methods (Hänfling et al, 2016), and for fisheries management (Hansen et al, 2018;Jerde, 2019;Miya et al, 2020). The potential applications of eDNA metabarcoding are well documented and have been applied successfully in freshwater, estuarine, and marine environments, ranging from single species detection to the characterization of whole communities (Creer et al, 2016;Deiner et al, 2017;Garlapati et al, 2019;Hansen et al, 2018;Miya et al, 2015;Ruppert et al, 2019;Valentini et al, 2016), and across various spatiotemporal scales (Miya et al, 2020;Seymour et al, 2021;Sigsgaard et al, 2017). Fish eDNA studies have described species distributions (Lacoursière-Roussel et al, 2018), the distribution of fishes vertically in the water column (Littlefair et al 2020), and for detecting invasive species (Adrian-Kalchhauser & Burkhardt-Holm, 2016).…”