Comparative assessment of phytoplankton community using different filtration methods based on environmental DNA metabarcoding—a case study of Caohai Wetland

In environmental DNA (eDNA) metabarcoding, the choice of filter membrane material and pore size governs DNA enrichment, detection sensitivity, and taxonomic representativeness of aquatic communities. This study employed eDNA metabarcoding to evaluate the influence of various filter membranes on the phytoplankton community within Caohai Wetland. Four membrane materials with a pore size of 0.22 μm were tested: mixed cellulose esters (MCE), polyethersulfone (PES), nylon (NY), and polytetrafluoroethylene (PTFE), and three pore sizes were tested with the MCE membranes: 0.22 μm, 0.45 μm, and 0.8 μm. The results demonstrated that among the tested materials, MCE filters achieved the best detection performance, yielding higher eDNA recovery, taxonomic counts, class coverage, and Chao1 richness than PES, NY, and PTFE membranes, owing to their superior retention of eDNA and algal particles. Alpha diversity was broadly consistent across filters, and β-diversity analyses revealed no significant differences in overall community structure. The dominant phytoplankton classes detected via these membranes were Cyanophyceae, Euglenida, and Raphidophyceae. For pore sizes, 0.22 μm and 0.45 μm produced highly congruent communities (> 95% taxon sharing). Considering detection efficiency, practicability, and robustness, 0.45 μm MCE filters we recommend as the optimal filtration medium for phytoplankton eDNA monitoring. This study provided empirical evidence for the selection of filtration methods in eDNA monitoring of shallow plateau lakes, and offered critical reference insights for the assessment and management of regional aquatic ecosystem health.