Which filter should I use? A comparative study of environmental DNA concentration methods for detection of freshwater species

Environmental DNA (eDNA) is a valuable tool for detecting aquatic species, but the efficiency of eDNA recovery is influenced by concentration methods. This study investigated the effectiveness of different eDNA concentration methods to optimise detection protocols for aquatic species in freshwater samples. Using water samples collected from controlled experimental systems, we tested ten types of filters, three pore sizes and an ethanol precipitation protocol to recover eDNA particles. Two invasive aquatic species, the benthic golden mussel (Limnoperna fortunei) and the limnetic Nile tilapia (Oreochromis niloticus), were used as biological models. Differences in DNA concentration were observed among samples from the two tested species. For Nile tilapia, filter materials showed uniform performance without significant differences, whereas cellulose nitrate filters yielded the highest eDNA concentrations for golden mussels. Ethanol precipitation was the least effective method for both species. Filtration time analysis revealed that polytetrafluoroethylene (PTFE) filters had the slowest filtration rates, whereas glass fibre filters had the fastest. A significant negative correlation was observed between filter pore size and eDNA retention for both species, with 0.4-μm and 0.2-μm pore sizes being more effective. These findings highlight the importance of selecting adequate filters and pore sizes to optimise eDNA capture efficiency. This study contributes to standardised protocols, enhancing precision and reproducibility in ecological assessments.