This study aimed to optimize the sampling strategy for environmental DNA (eDNA) metabarcoding targeting prokaryote, protistan, and metazoan life compartments in deep-sea sediment and aboveground water samples. For sediment, we evaluated the effect of sieving sediment to separate size classes and avoid biomass biases, and compared results to inventories obtained through DNA directly extracted from 10 g of sediment. For water, we evaluated the performance of two sampling devices: 7.5 L sterile sampling boxes and a newly developed high-throughput in situ pump. We applied these four sampling methods on a deep-sea site and evaluated resulting biodiversity inventories targeting metazoans (18S V1-V2, COI), but also prokaryotes (16S V4-V5) and unicellular eukaryotes (18S V4).

The data associated to this work can be found following the DOI link below, with raw sequencing data in the data/dna-sequence-raw folder, taxonomic assignment databases in the data/sequence-set-nucleic-acid folder, and all analyses outputs can be found in the /operation folder.

The bioinformatic scripts can be downloaded from: https://gitlab.ifremer.fr/abyss-project