Merging imaging technologies and metabarcoding to assess Rhizaria abundances, diversity and contribution to the silicon cycle in the Mediterranean Sea

Siliceous Rhizaria (polycystine radiolarians and phaeodarians) are significant contributors to carbon and silicon biogeochemical cycles. Considering their broad taxonomic diversity and their wide size range (from a few micrometres up to several millimetres), a comprehensive evaluation of the entire community to carbon and silicon cycles is challenging. Here, we assess the diversity and contribution of silicified Rhizaria to the global biogenic silica stocks in the upper 500 m of the oligotrophic North-Western Mediterranean Sea using both imaging (FlowCAM, Zooscan and Underwater Vision Profiler) and molecular tools and data. While imaging data revealed that the most abundant organisms were the smallest, molecular results showed that the largest Rhizaria had the highest relative abundances. While this seems contradictory, relative abundance data obtained with molecular methods correlated well with the total biovolume of the organisms. This result reflects a potential link between gene copies number and the volume of a given cell allowing reconciling molecular and imaging data. Using abundance data from imaging methods we estimate that siliceous Rhizaria accounted for up to 6% of the total biogenic silica biomass of the siliceous planktonic community in the upper 500m of the water column. <br> Here you will find all scripts used in this study dealing with the metabarcoding data (processing raw sequencing results, ASV clustering, plotting and other analyses) and the resulting processed ASV table to build figure 3C. Scripts are named in order of execution and commented to ease their reusability. The ASV table gathers the abundances of the ASVs selected to recreate the figure 3 (panel C) from the paper described above. The table has the following structure divided by columns: -sequence: The sequence of the ASV -ASV: the identification of the ASV -taxonomy: the associated PR2 taxonomy -total_presence: the number of samples that the ASV is present in -total_abundance: the total number of reads of the ASV -the remaining columns are the specific samples <br> <br> <br>