The effects of enzymatic and chemical pretreatment on the DNeasy PowerWater DNA extraction protocol for DNA-based analyses of drinking water microorganisms.

Analysis of microorganisms in drinking water is useful for assessing water quality and potential public health risks. Although DNA-based analyses are widely used, DNA extraction methods are not standardized. Herein, the DNeasy PowerWater Kit was compared to a modified DNeasy PowerWater Kit protocol that employs a series of pretreatment steps. Water samples from two community water systems were collected. Biomass from each sample was concentrated onto separate filters, from which DNA was extracted using the original or the modified method. The modified method extracted significantly higher quantities of DNA (p < 0.01), but the concentrations of total bacterial biomass, total microbial biomass, Legionella spp., and Mycobacterium spp. obtained via quantitative PCR were statistically similar between the two methods (p ≥ 0.1). Vermamoeba vermiformis concentrations in both extracts were similar (p = 0.3) for one system but ~0.2 log gene copies/L greater using the modified method (p = 0.01) for the other system. The microbial communities differed significantly according to alpha and beta diversity metrics. However, operational taxonomic unit (OTU) comparisons suggest the differences were largely from OTUs of low abundance (i.e., <0.15% relative abundance), as relative abundances of most dominant and moderately abundant OTUs were similar. Overall, these results suggest that the modified method may not merit use in studies involving large numbers of samples because of the substantially greater labor and supplies requirements, although it provides marginal improvements in DNA recovery that may benefit studies of rare taxa.