DNA metabarcoding for next generation biodiversity monitoring – METABAR

One of the major hurdles in predicting how biological diversity will respond to environmental factors in the 21st century is the current limits to assemble large and standard diversity data that are repeatable over time. Sequencing technologies are currently evolving at a fast pace and should offer unique opportunities to make a significant progress for biodiversity surveys in the near future. The METABAR project proposes to combine concepts from metagenomics (analysis of cellular microbial DNA from the soil) and from the recently emerged field of DNA barcoding (use of small DNA fragments that serve to discriminate among species).
Based on recent results, we are now confident that virtually any soil contains enough extracellular DNA from decomposed tissues (even degraded and in small quantities) to be extracted, amplified, and sequenced using next generation sequencers. Second, an analysis of sequence repositories shows that, for most taxonomic groups, it is possible to find small DNA regions (ideally around 30 bp) that will efficiently discriminate across the taxa. Using this approach, we have been able to survey the recent and past diversity of plants in the arctic permafrost. We also demonstrated that such surveys are possible for temperate and tropical regions, not only for plants, but also for animal with high biomass.
The METABAR project proposes to develop innovative protocols to standardize and automate the acquisition of high-throughput biodiversity data based on environmental (extracellular) DNA samples. These novel protocols will be tested in two large-scale experiments, including broadly different environmental conditions (alpine and tropical), and taxonomic groups (plants, ants, frogs, mammals, fungi). We will then conduct an analysis of these biodiversity patterns based on ecological models bridging across species-level and community-wide approaches. In particular we will test whether patterns of spatial species turnover previously evidenced for tropical trees may also be detected for other groups. We will also contrast levels of biodiversity between pristine (or unmanaged) and disturbed (or managed) ecosystems.