Environmental DNA (eDNA) removal rates in streams differ by particle size under varying substrate and light conditions

Sampling eDNA at outflows from artificial drainage systems: what is the potential to monitor landscape degradation?

Wetlands have been drained extensively for productive land use, transforming the biodiversity of whole landscapes. Such transformation primarily affects the huge biodiversity across the terrestrial and aquatic environments that is difficult to observe directly, especially in the case of microorganisms. We explored whether environmental DNA (eDNA) from the flowing water could serve as a data source for characterizing the level of biological degradation of drained and managed forest-wetland landscapes. We took spatially and seasonally replicated samples from nine hydrologically monitored outflows at small drained catchments in Estonia in order to understand the variation in their eDNA-based diversity. Using PacBio long-read sequencing, we detected a large taxonomic diversity of eukaryotes (approx. 6000 operational taxonomic units (OTUs)), which was spatially and seasonally structured, but also highly variable within individual ditches. Even in fungi (the best-represented taxon group), the OTU accumulation curves did not level off despite high volumes of filtered water; however, many interesting species records were obtained (particularly on pathogenic microorganisms). We conclude that eDNA can provide valuable insights into the biodiversity of hydrologically drained areas, but our results indicate high heterogeneity among samples (apparently due to both actual assemblage differences and sampling errors) as a major problem for standard environmental assessment. Combining eDNA methods with other ecological assessment techniques is a priority for further research in these systems.

Parameterizing the particle size distribution of environmental DNA provides insights into its improved availability from the water

Previous studies estimated the particle size distribution (PSD) of environmental DNA (eDNA) to infer its persistence state in the water and to determine the size fraction in which eDNA particles are concentrated. These results, however, depend on the combination of filter pore sizes and may not necessarily provide the proper implications for the eDNA state and availability in the water. To address this issue, the present study proposes parameterizing the PSD using the Weibull distribution model, which has been widely used for various materials. Re-analyses of previous datasets show the Weibull parameters (representing the PSD profiles) significantly depend on species traits, marker types, temperature, and time passages after the removal of the individuals. The results allowed for calculating the proportion of eDNA captured using a given filter pore size and the filter pore size required to collect a given percentage of eDNA particles under various study designs and environmental conditions. The results also posed caveats indicating that the strategy for a sufficient eDNA collection method is not always uniform across experimental and environmental conditions. The findings contribute to a better understanding of the eDNA state and improved eDNA availability, refining eDNA-based biodiversity and ecosystem monitoring.

An overlooked source of false positives in eDNA-based biodiversity assessment and management

Biodiversity conservation and management in urban aquatic ecosystems is crucial to human welfare, and environmental DNA (eDNA)-based methods have become popular in biodiversity assessment. Here we report a highly overlooked source of significant false positives for eDNA-based biodiversity assessment in urban aquatic ecosystems supplied with treated wastewater - eDNA pollution originating from treated wastewater represents a noteworthy source of false positives. To investigate whether eDNA pollution is specific to a certain treatment or prevalent across methods employed by wastewater treatment plants, we conducted tests on effluent treated using three different secondary processes, both before and after upgrades to tertiary treatment. We metabarcoded eDNA collected from effluent immediately after full treatment and detected diverse native and non-native, commercial and ornamental fishes (48 taxa) across all treatment processes before and after upgrades. Thus, eDNA pollution occurred irrespective of the treatment processes applied. Release of eDNA pollution into natural aquatic ecosystems could translate into false positives for eDNA-based analysis. We discuss and propose technical solutions to minimize these false positives in environmental nucleic acid-based biodiversity assessments and conservation programs.

Changes in the level of biofilm development significantly affect the persistence of environmental DNA in flowing water

As one of the powerful tools of species biomonitoring, the utilization of environmental DNA (eDNA) technology is progressively expanding in both scope and frequency within the field of ecology. Nonetheless, the growing dissemination of this technology has brought to light a multitude of intricate issues. The complex effects of environmental factors on the persistence of eDNA in water have brought many challenges to the interpretation of eDNA information. In this study, the primary objective was to examine how variations in the presence and development of biofilms impact the persistence of grass carp eDNA under different sediment types and flow conditions. This investigation encompassed the processes of eDNA removal and resuspension in water, shedding light on the complex interactions involved. The findings reveal that with an elevated biofilm development level, the total removal rate of eDNA gradually rose, resulting in a corresponding decrease in its residence time within the mesocosms. The influence of biofilms on the persistence of grass carp eDNA is more pronounced under flowing water conditions. However, changes in bottom sediment types did not significantly interact with biofilms. Lastly, in treatments involving alternating flow conditions between flowing and still water, significant resuspension of grass carp eDNA was not observed due to interference from multiple factors, including the effect of biofilms. Our study offers preliminary insights into the biofilm-mediated mechanisms of aquatic eDNA removal, emphasizing the need for careful consideration of environmental factors in the practical application of eDNA technology for biomonitoring in natural aquatic environments.