This technical platform has been set up to allow ecologists to perform large-scale analysis of environmental DNA via a metabarcoding approach. DNA metabarcoding refers to high throughput DNA-based identification of multiple species from environmental DNA. The main applications consist in diet analysis from feces, in biodiversity assessment using soil or water samples, and in palaeo-environment reconstruction using lake sediments and permafrost samples.
The eDNA platform is composed of three pre-PCR extraction rooms dedicated to feces, soil, and ancient DNA, and to several post-PCR rooms dedicated to the purification and the titration of PCR products. The next generation sequencing on Illumina platforms (HiSeq or MiSeq) is outsourced.
Beside the basic equipment (centrifuges, vortex, etc.), the eDNA platform is equipped with a 96 pipetting head (see pictures below) and two PCR machines with each two 384 heads. This allows the set up, the amplification, and the purification of more than 4500 PCR per day.
When carrying out large-scale sampling (soil or feces), the eDNA platform possesses all the equipment that can be transported and installed in the field to allow DNA extraction straight after the sampling, and to bring back the DNA on the extraction columns (see pictures below). Using this approach, large-scale extractions have been carried out in French Guiana, in China, and in South Africa.
The personnel involved in the eDNA platform has all the competences in designing new metabarcodes and testing them in silico, in designing the experiments (how many samples, how many sequence reads, how many positive and negative controls, how to produce a reference database, etc.), in carrying out the experiments at the bench, and in analyzing the output of the next generation sequencers (using a collection of program developed within the eDNA platform, and specifically dedicated to DNA metabarcoding ; http://metabarcoding.org/obitools).