Analysis of structure and composition of bacterial core communities in mature drinking water biofilms and bulk water of a citywide network in Germany

Abstract

The bacterial core communities of bulk water and corresponding biofilms of a more than 20-year-old drinking water network were compared using 16S rRNA single-strand confirmation polymorphism (SSCP) fingerprints based on extracted DNA and RNA. The structure and composition of the bacterial core community in the bulk water was highly similar (>70%) across the city of Braunschweig, Germany, whereas all biofilm samples contained a unique community with no overlapping phylotypes from bulk water. Biofilm samples consisted mainly of Alphaproteobacteria (26% of all phylotypes), Gammaproteobacteria (11%), candidate division TM6 (11%), Chlamydiales (9%), and Betaproteobacteria (9%). The bulk water community consisted primarily of Bacteroidetes (25%), Betaproteobacteria (20%), Actinobacteria (16%), and Alphaproteobacteria (11%). All biofilm communities showed higher relative abundances of single phylotypes and a reduced richness compared to bulk water. Only biofilm communities sampled at nearby sampling points showed similar communities irrespective of support materials. In all of our bulk water studies, the community composition determined from 16S rRNA was completely different from the 16S rRNA gene-based community composition, whereas in biofilms both molecular fractions resulted in community compositions that were similar to each other. We hypothesize that a higher fraction of active bacterial phylotypes and a better protection from oxidative stress in drinking water biofilms are responsible for this higher similarity.

Fig 1

(A) Comparison of 16S rRNA gene-based SSCP fingerprints of bulk water and drinking water biofilm samples. STD, standards. (B) Comparative cluster analysis of 16S rRNA gene-based SSCP fingerprints of bulk water and biofilms.

Fig 2

Rank abundance plot of bulk water (gray dots) and biofilm samples (black squares) using relative band intensities from DNA-based fingerprints as a measure for relative abundance. The inset shows the regression analysis of plotted rank abundance curves. Dotted lines indicate 95% confidence bands. For bulk water, y = 5.8691^{(−0.045015x)} and R² = 0.885; for biofilm, y = 7.9153^{(−0.092472x)} and R² = 0.898.

Fig 3

(A) 16S rRNA gene-based SSCP fingerprints of biofilm samples (left side, DNA based) and 16S rRNA-based SSCP fingerprints of biofilm (right side, RNA based). (B) Comparative cluster analysis of DNA- and RNA-based SSCP fingerprints of the biofilm samples.

Fig 4

(A) Comparison of relative abundances of the major phylotypes (relative abundances above 1%) found in the bulk water communities. The left part represents the phylotypes from the DNA-based SSCP fingerprints, and the right part represents the phylotypes from the RNA-based SSCP fingerprints. The colors correspond to the major phylogenetic groups of the phylotypes. The differently hatched parts of the stacked bars represent the single phylotypes identified. (B) Comparison of relative abundances of the major phylotypes found in four selected biofilm fingerprints. The biofilms were not directly physically related. The left part represents the phylotypes from the DNA-based SSCP fingerprints, and the right part represents the phylotypes from the RNA-based SSCP fingerprints. The colors correspond to the major phylogenetic groups of the phylotypes. The differently hatched parts of the stacked bars represent the single phylotypes identified.