Publications: Peer-reviewed journal articles (by staff)
Assessment of the metabarcoding approach for community analysis of benthic-epiphytic dinoflagellates using mock communities
Smith KF, Kohli GS, Murray SA, Rhodes LL 2017b. Assessment of the metabarcoding approach for community analysis of benthic-epiphytic dinoflagellates using mock communities. New Zealand Journal of Marine and Freshwater Research 51(4): 555-576.
DOI link here
In this study, we assessed the use of DNA metabarcoding as a method for biodiversity assessment of benthic-epiphytic dinoflagellate communities and for detecting rare, toxin-producing taxa. Mock communities and three primer pairs were used to establish the recovery of species signal and quantitative representation of species in the samples, as well as to determine primer biases, bioinformatic filtering steps, and threshold levels. Samples were analysed using high-throughput sequencing Illumina™ MiSeq technology. We did not find a relationship between read number and cell abundance for all treatments. However, the method was extremely sensitive, with two of the primer pairs detecting a single cell representing less than 0.001% of the cells in the sample. Benthic and epiphytic dinoflagellate communities were also collected from the Bay of Islands (Northland, New Zealand). Dinophyceae species richness was much higher when samples were analysed using metabarcoding than when analysed by microscopy, and we detected several new taxonomic records for New Zealand.