The project begins!

The first months of the Metabarpark Project have been devoted to the setup of methods and protocols. We have been using samples from the Catalan and Balearic shores for the trials.

We have collaborated with Dr. Pierre Taberlet and his team at the Laboratory of Ecologie Alpine in Grenoble to apply methods developed for terrestrial soils to marine communities

We have amplified a fragment of the 18S rDNA using universal primers developed at LECA. The sequencing has been done using an Illumina MiSeq. We obtained >3 milion reads from 80 samples. The reads were processed using the OBITools pipeline, and ca. 1000 Molecular Taxonomic Units (MOTUs, our surrogate for species) were identified. Downstream analyses have revealed that the communities can be thoroughly inventoried, and that differences in composition (presence-absence) and in abundance (using read number as a proxy) can be detected between communities and localities using this method.

In a second trial we used a different extraction protocol (with lysis step) and combined amplification of DNA and amplification of cDNA obtained from RNA in the samples. We also tested an improved set of primers. The sequencing this time yielded 5 milion reads and 2700 MOTUs.
These trials allowed us to choose the best reagent kits and protocols for the study of the samples of the Parks. We are currently working in a set of primers to amplify the mitochondrial COI gene for comparison with the 18S nuclear gene, but we are having trouble in finding universal primers for sequence lengths adequate for Illumina sequencing. We will see if we succeed!