Search results for "metabarcoding approaches"

Re-Clustering tool using an Open-Reference method that improves OTU definition

2019

International audience; 1.Environmental microbial communities are now widely studied using metabarcoding approaches, thanks to the democratization of high‐throughput DNA sequencing technologies. The massive number of reads produced with these technologies requires bioinformatic solutions to be treated. A key step in the analysis is to cluster reads into Operational Taxonomic Units (or OTUs) and thus reduce the amount of data for downstream analyses. Due to the important impact of the clustering method on the quantity and quality of OTUs, finding an equilibrium between the reliability and time‐consuming nature of the chosen strategy is a real challenge. The present article proposes a new pos…

Assessing the effect of chromium pollution on benthic foraminiferal community: morphological vs. environmental metabarcoding approaches

The purpose of this experimental study is to assess the impact of different concentrations of chromium (Cr) through time on the diversity of cultured benthic foraminifera combining two morphological approaches for the identification of living specimens that are Rose Bengal (RB) staining and CellTracker Green (CTG) labelling as well as environmental DNA and RNA metabarcoding. Seven tanks/aquaria with different concentrations of Cr in water, namely 100 ppt, 1 ppb, 10 ppb, 100 ppb, 1 ppm and 10 ppm plus the control were used. A mesocosm was extracted from each tank at pre-established time (1 week, 2 weeks, 4 weeks 6 weeks and 8 weeks). Morphological analyses produced 6 datasets based on staini…