Usability evaluation of NGS for taxonomical characterization of bacterial community in freshwater biofilm. Bacterial consortia of lotic biofilm

The robust and widely applicable method for sampling of lotic microbial biofilm and further sample processing is presented including next generation sequencing of 16S rRNA gene fragment including variable regions (V4 and V5) and statistical evaluation of sequencing data for taxonomic characterization of bacterial biofilm consortia useful for aquatic ecosystem health assessment. Five artificial materials commonly used for biofilm growth (glass, stainless steel, aluminum, polypropylene, polyethylene) were tested to determine the one giving most robust and reproducible results. The effect of used sampler material on total microbial composition was not statistically significant but non-plastic materials (glass, metal) gave more stable outputs without irregularities among sample parallels. The ability of the method to differentiate among biofilm samples from localities with varying level of anthropogenic pollution was tested by the non-metric multidimensional scaling based on Bray-Curtis distance matrix. Three locations and two sampling times (spring and autumn) were compared.