Evaluation of water sampling methodologies for amplicon-based characterization of bacterial community structure

Reduction in costs of next-generation sequencing technologies has allowed unprecedented characterization of bacterial communities from environmental samples including aquatic ecosystems. However, the extent to which extrinsic factors including sampling volume, sample replication, DNA extraction kits, and sequencing target affect the community structure inferred are poorly explored. Here, triplicate 1, 2, and 6. L volume water samples from the Upper Mississippi River were processed to determine variation among replicates and sample volumes. Replicate variability significantly influenced differences in the community α-diversity (P = 0.046), while volume significantly changed β-diversity (P = 0.037). Differences in phylogenetic and taxonomic community structure differed both among triplicate samples and among the volumes filtered. Communities from 2. L and 6. L water samples showed similar clustering via discriminant analysis. To assess variation due to DNA extraction method, DNA was extracted from triplicate cell pellets from four sites along the Upper Mississippi River using the Epicentre Metagenomic DNA Isolation Kit for Water and MoBio PowerSoil kit. Operational taxonomic units representing ≤. 14% of sequence reads differed significantly among all sites and extraction kits used, although differences in diversity and community coverage were not significant (P ≥. 0.057). Samples characterized using only the V6 region had significantly higher coverage and lower richness and α-diversity than those characterized using V4-V6 regions (P <. 0.001). Triplicate sampling of at least 2. L of water provides robust representation of community variability, and these results indicate that DNA extraction kit and sequencing target displayed taxonomic biases that did not affect the overall biological conclusions drawn.