Data from: Deep-sea, deep-sequencing: metabarcoding extracellular DNA from sediments of marine canyons

Marine sediments are home to one of the richest species pools on Earth,
but logistics and a dearth of taxonomic work-force hinders the knowledge
of their biodiversity. We characterized α- and β-diversity of deep-sea
assemblages from submarine canyons in the western Mediterranean using an
environmental DNA metabarcoding. We used a new primer set targeting a
short eukaryotic 18S sequence (ca. 110 bp). We applied a protocol designed
to obtain extractions enriched in extracellular DNA from replicated
sediment corers. With this strategy we captured information from DNA
(local or deposited from the water column) that persists adsorbed to
inorganic particles and buffered short-term spatial and temporal
heterogeneity. We analysed replicated samples from 20 localities including
2 deep-sea canyons, 1 shallower canal, and two open slopes (depth range
100–2,250 m). We identified 1,629 MOTUs, among which the dominant groups
were Metazoa (with representatives of 19 phyla), Alveolata, Stramenopiles,
and Rhizaria. There was a marked small-scale heterogeneity as shown by
differences in replicates within corers and within localities. The spatial
variability between canyons was significant, as was the depth component in
one of the canyons where it was tested. Likewise, the composition of the
first layer (1 cm) of sediment was significantly different from deeper
layers. We found that qualitative (presence-absence) and quantitative
(relative number of reads) data showed consistent trends of
differentiation between samples and geographic areas. The subset of
exclusively benthic MOTUs showed similar patterns of β-diversity and
community structure as the whole dataset. Separate analyses of the main
metazoan phyla (in number of MOTUs) showed some differences in
distribution attributable to different lifestyles. Our results highlight
the differentiation that can be found even between geographically close
assemblages, and sets the ground for future monitoring and conservation
efforts on these bottoms of ecological and economic importance.