Comparison of materials for rapid passive collection of environmental DNA

Brief description

Passive collection is an emerging sampling method for environmental DNA (eDNA) in aquatic systems. Passive eDNA collection is inexpensive, efficient, and requires minimal equipment, making it suited to high density sampling and remote deployment. Here we provide the raw sequence data and final data tables produced from an experiment where we compared the effectiveness of nine membrane materials for passively collecting fish eDNA from a 3 million litre marine mesocosm. We submerged materials (cellulose, cellulose with 1% and 3% chitosan, cellulose overlayed with electrospun nanofibers and 1% chitosan, cotton fibres, hemp fibres and sponge with either zeolite or active carbon) for intervals between five and 1080 minutes. We show that for most materials, with as little as five minutes submersion, mitochondrial fish eDNA measured with qPCR, and fish species richness measured with metabarcoding, was comparable to that collected by conventional filtering. Furthermore, PCR template DNA concentrations and species richness were generally not improved significantly by longer submersion. The associated manuscript is published in Molecular Ecology Resources.
Lineage: The data was produced using DNA metabarcoding amplification for fish detection. One-step quantitative polymerase chain reactions (qPCR) were performed in duplicate for each sample using 2 µL of extracted DNA and a mitochondrial DNA 16S rDNA universal primer set targeting fish taxa (16SF/D
5ʹ GACCCTATGGAGCTTTAGAC 3ʹ and 16S2R-degenerate 5ʹ CGCTGTTATCCCTADRGTAACT 3ʹwith a 178-228 bp amplicon size; Berry et al. 2017, Deagle et al. 2007), with the addition of fusion tag primers unique to each sample that included Illumina P5 and P7 adaptors.