Environmental barcoding: A next generation sequencing approach to biodiversity monitoring

DNA barcoding projects are building species-specific reference libraries that will enable cheap and accurate identification of species in varied taxonomic groups and environmental settings (i.e. Zhou et al. this session). The routine workflow of barcoding is based on Sanger sequencing approach and can target single specimens. This approach is not feasible for environmental samples where mixtures of organisms are under investigation. However, recently introduced next generation sequencing technologies (i.e. Roche454 pyrosequencing) can aid in directly analyzing biodiversity in bulk environmental samples through their massively parallelized capability to read thousands of sequences from mixtures. Our work involves developing molecular tools and a dedicated bioinformatics pipeline to use sequences obtained from environmental samples using 454FLX platform for biomonitoring. We are targeting aquatic macroinvertebrates, especially mayflies (Ephemeroptera), stoneflies (Plecoptera), and caddisflies (Trichoptera) ('EPT's) because of their important role in the assessments of water quality. Our initial results on both larvae and adult samples collected from different sites suggest that environmental barcoding using 454FLX platform can provide species identities and indications of species abundances based on sequence counts obtained for each species. This work will be integrated in Environment Canada's National Biomonitoring Program (CABIN).