Fish eDNA metabarcoding from aquatic biofilm samples: Methodological aspects.

Area of Science:

• Environmental DNA (eDNA) research
• Aquatic ecology
• Biodiversity monitoring

Background:

• Traditional fish eDNA metabarcoding relies on filtering large water volumes, which is time-consuming.
• Passive samplers are used in marine environments, but their freshwater application for fish eDNA is less explored.
• Aquatic biofilms have shown potential for eDNA capture in freshwater macroinvertebrate studies.

Purpose of the Study:

• To evaluate the efficacy of aquatic biofilms as passive samplers for fish eDNA in a large lake.
• To compare fish eDNA metabarcoding results from biofilms versus traditional water filtration.
• To validate methodological aspects of using biofilms for fish eDNA analysis.

Main Methods:

• Collected aquatic biofilms and water samples from a large lake.
• Performed fish eDNA metabarcoding on both sample types.
• Validated methodological parameters (PCR replicates, bioinformatics) using a mock community.
• Compared species inventories, richness, and diversity between biofilm and water approaches.

Main Results:

• Aquatic biofilms effectively entrapped fish eDNA, yielding comparable inventories to water filtration in sheltered habitats.
• Species richness and diversity were similar between biofilm and water-based eDNA metabarcoding.
• Differences between the two approaches were primarily observed for rare taxa.

Conclusions:

• Aquatic biofilms serve as effective passive eDNA samplers for fish in freshwater lakes.
• Biofilm-based eDNA metabarcoding offers an efficient alternative for monitoring fish communities.
• This approach can be extended to monitor diverse biological groups (diatoms, macroinvertebrates, fish) from a single matrix, reducing effort and cost.