Data from: Wastewater treatment effectively eliminates exogenous eDNA, preventing downstream false-positive detections

This dataset accompanies the study “Wastewater treatment effectively eliminates exogenous eDNA, preventing downstream false-positive detections” and contains environmental DNA (eDNA) quantification data from a controlled spiking experiment conducted at four wastewater treatment plants in Flanders, Belgium. Data were collected on 9 and 10 September 2024 and comprise droplet digital PCR (ddPCR)–based, species-specific eDNA concentrations measured at three locations within each facility (influent, effluent, and downstream river) before and after a controlled spiking event with target taxa. The dataset includes fully processed and thresholded eDNA concentrations derived from standardized laboratory workflows and is designed to assess the fate of exogenous, consumption-derived eDNA during wastewater treatment. Additionally, the samples were subjected to metabarcoding analyses to allow detection of non-target species. Together with the accompanying analysis script, these data enable evaluation of eDNA removal efficiency in wastewater treatment systems and support interpretation of downstream eDNA signals in anthropogenically impacted aquatic environments.

Dataset

Data_eDNAWastewaterTreatment_Clean.csv, created on the 16th of December 2025. This is the cleaned, ready-to-use dataset containing the final eDNA concentrations per ddPCR target replicate per wastewater treatment site. This dataset can be used with the provided script Script_eDNAWastewaterTreatment_Clean.R. It has the following columns:

• Target: Refers to species specific primer/probe assay used for targeted eDNA detection and quantification. Included are Solea E-569 (targeting Solea solea), Pleuronectes E-568 (targeting Pleuronectes platessa), SK_oud+SK_Lin(58)(targeting Lithobates catesbeianus), MisB-COI (targeting Misgurnus bipartitus), GMK_Q(56) (targeting Misgurnus fossilis) and AKK (targeting Xenopus laevis).
• QuantaSoftFileName: Refers to the raw datafiles per PCR replicate and analyzed in the QuantaSoft software to calculate eDNA concentrations per assay.
• Samplecode: Unique code of the used eDNA filter.
• City: Name of the city where the studied wastewater treatment plant was located.
• Pre_Post: Experimental timing, either pre or post spiking event.
• SiteLocation: One of three locations studied within each wastewater treatment plant, namely at the influent or effluent of the installation, or in the river downstream of the effluent. 
• Concentration: Final eDNA concentration in number of copies/µL/L filtered water.

Data_eDNAWastewaterTreatment_MBAnnex.csv, created on the 3rd of March, 2026. This is the cleaned, ready-to-use community dataset containing the final absolute reads per taxon per sample resulting from the metabarcoding analyses targeting a ~142bp fragment of the mitochondrial 12S rRNA gene using vertebrate-specific Riaz primers. This dataset can be used with the provided script Script_eDNAWastewaterTreatment_Clean.R. It has the following columns:

• ID: numerical identification of the datarow. 
• Samplecode: Unique code of the used eDNA filter.
• City: Name of the city where the studied wastewater treatment plant was located.
• SiteLocation: One of three locations studied within each wastewater treatment plant, namely at the influent or effluent of the installation, or in the river downstream of the effluent. 
• Pre_Post: Experimental timing, either pre or post spiking event.
• Species: Refers to the species detected with the metabarcoding analyses.  
• Reads: Number of reads assigned to the concerned target species during metabarcoding analyses.
• n_replicates: Number of technical replicates considered for the number of reads per sample.
• TotalReads: Total number of reads detected in the sample. 

Script

Script_eDNAWastewaterTreatment_Clean.R, created on the 16th of December 2025, updated on the 3rd of March 2026. This R script contains the statistical analyses applied to the dataset in support of Van Driessche et al. (2026).