Thursday, November 5, 2015

New paper published: Deep-sea, deep-sequencing: metabarcoding extracellular DNA from sediments of marine canyons

Getting sediment samples from a multicorer device.
by Xavier Turon

Another article with results from the ChallenGen Project is now published:

Guardiola M, Uriz MJ, Taberlet P, Coissac E, Wangensteen OS, Turon X. 2015. Deep-sea, deep-sequencing: metabarcoding extracellular DNA from sediments of marine canyons. PLoS One 10(10): e0139633. doi:10.1371/journal.pone.0139633

This is our first paper about the metabarcoding of marine communities. In this article we focus on deep-sea sedimentary communities. Samples were collected during the DOSMARES and INDEMARES projects from canyons and adjacent areas in the Catalan and Balearic Islands coasts.

This is the abstract of the article:

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.

Multidimensional Scaling (MDS) plots showing the differentiation found between the zones studied (BC, Blanes Canyon; OS, Blanes Open Slope; CC, Cap de Creus Canyon; MC, ;Menorca Canal; ST, Serra de Tramuntana Slope).