Seminar: DNA Metabarcoding

by Maria Casso

Yesterday, Xavier Turon and Owen Wangensteen participated at the seminar "DNA Metabarcoding", organised by the Biodiversity Research Institute (IRBio). DNA metabarcoding is a method to assess biodiversity which combines DNA based identification and next generation sequencing, and it can have several applications. The aim of the seminar was to show the potencial and limitations of the method.

The first lecture was Xavier's and it was an introduction about the impediments of taxonomy and how can metabarcoding methods contribute to assess biodiversity. After him, Owen talked about the specific case of metabarcoding of hard bottom marine communities. He also explained the few but critical stages of the pipeline were there isn't a consensus among scientists. It is really awesome to watch live how a new method is developing and be part of it.

The seminar took place at the School of Biology (UB). Many researchers and students attended, and some interesting questions came out. It was dense but also clarifying and motivating.

Sea stars, Sampling & Sun

by Maria Casso

Yesterday we went to Sant Feliu de Guíxols, a locality situated on the Costa Brava. We sampled some sea stars by scuba diving, from surface to 20m depth.

We were very lucky because the day was sunny and the sea was oddly calm. It is a beautiful spot, but usually, at this time of year is very difficult to find such good weather conditions. Moreover, the water was warmer than we expected (18ºC at 12m and 16ºC at 20m depth).

Lectures at the Course “New Technologies applied to the control and monitoring of invasive species”

by Xavier Turon

In October, 19 to 23, the National Parks Autonomous Agency (OAPN) organised a course on new technologies applied to the study of invasive species in Vigo (Galicia). This course was attended by staff, technicians, and rangers of the National Parks in Spain.

I was invited to give a lecture about “Genetic tools and invasive species”. It was an enjoyable experience, with interested audience that posed clever questions... and of course it was an occasion to enjoy good shellfish “mariscada” typical of Galicia’s gastronomy.

The Cíes Islands, part of the National Park of the Atlantic Islands in whose facilities the course was given. The ChallenGen project, in collaboration with the Metabarpark project, has been working on the benthic communities of these Islands.

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).

Monitoring invasive ascidians at Ebro Delta

A nice view of the bivalve culture area.

by Maria Casso

Today we went to the Ebro Delta, for monitoring the invasive ascidians at the oyster and mussel culture structures. After a week of stormy days, we had a sunny and calm monitoring day.

We want to thank the Institute of Food and Agricultural Research and Technology (IRTA) for providing the boat and skipper and collaborate in this monitoring.

Víctor Ordóñez writting down the observations.

Maria Casso and Jose Luís Costa (IRTA).