DNA metabarcoding of freshwater metazoan communities through analysis of environmental DNA (eDNA) captured on filters offers new opportunities for biodiversity assessment. Filtering of water in the field usually is an advantage compared to transport of water to the nearest lab, for both logistical reasons and to avoid DNA degradation. Thus, appropriate filter preservation becomes crucial for maximum DNA recovery and sample replicability. Here, the effect of two filter types, pre-filtration and four different filter preservation strategies were evaluated by measuring DNA yield, metazoan diversity and community composition, using eDNA collected from a river and a lake ecosystem. At the river site, sterile, individually packed 0.2-µm polyethersulfone (PES) and 0.45-µm mixed cellulose ester (CN) filters were used. At the lake site, 0.45-µm CN filters and pre-filtration using 12-µm CN filters were tested. To test different preservation strategies, the filters were preserved in ethanol, in lysis buffer, dry in silica gel and cold on ice. Our results show that 0.45-µm CN filters yield higher DNA concentration, higher number of taxa and more consistent community composition than 0.20-µm PES filters; pre-filtration yields lower DNA concentration, lower number of taxa, but more consistent community composition than direct filtration; and filters preserved either dry or in lysis buffer give the most consistent community composition. Ethanol may be a poor filter preservative as the number of taxa is lower and community composition is more variable than using other preservation strategies. Our study sets the stage for developing guidelines for aquatic community-level eDNA biomonitoring applications.
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