Monitoring marine pollution effects through targeted environmental DNA (eDNA) testing in the Pacific northwest

Globally, coastal waters experience degradation from pollution associated with multiple discharges, including industrial and agricultural runoff, and municipal wastewater. Certain benthic infaunal taxa are tolerant of high nutrient input and anoxic conditions, while others are sensitive to these conditions. Using these indicator taxa as proxies for assessing organic enrichment is well established to characterize subsequent pollution impacts. Conventional assessment of macroinfauna involves the detailed analysis of each individual specimen within a sample by taxonomic experts, a resource intensive process. As an alternative, we developed sensitive quantitative polymerase chain reaction (qPCR) assays to detect these indicator taxa in a scalable and reliable way. Using whole genome shotgun sequencing, we generated full mitogenome sequences of selected indicator macroinfaunal polychaetes routinely used for monitoring programs in Pacific Northwest marine environments. These sequences were used to design five new, rigorously validated environmental DNA (eDNA) assays capable of detecting low levels of DNA that can be isolated from environmental samples. For nine sites at a wastewater treatment plant outfall in Vancouver, British Columbia, we tested three eDNA sample collection types: active filtration, a passive dip filter from water containing collected macroinfauna, and active filtration from water collected near the sea floor. Generalized linear models indicated that eDNA signal strength correlated with organism count particularly with passive dip sample collection type. eDNA occupancy modelling techniques estimated detection probabilities corresponding with organism count. The present study emphasizes the value of integrating eDNA into marine outfall monitoring efforts to enhance the assessment of environmental effects.