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. 2015 Jun 12:5:10044.
doi: 10.1038/srep10044.

Diversity and functions of bacterial community in drinking water biofilms revealed by high-throughput sequencing

Yuanqing Chao  1 , Yanping Mao  2 , Zhiping Wang  3 , Tong Zhang  2
Affiliations

Diversity and functions of bacterial community in drinking water biofilms revealed by high-throughput sequencing

Yuanqing Chao et al. Sci Rep. .

Abstract

The development of biofilms in drinking water (DW) systems may cause various problems to water quality. To investigate the community structure of biofilms on different pipe materials and the global/specific metabolic functions of DW biofilms, PCR-based 454 pyrosequencing data for 16S rRNA genes and Illumina metagenomic data were generated and analysed. Considerable differences in bacterial diversity and taxonomic structure were identified between biofilms formed on stainless steel and biofilms formed on plastics, indicating that the metallic materials facilitate the formation of higher diversity biofilms. Moreover, variations in several dominant genera were observed during biofilm formation. Based on PCA analysis, the global functions in the DW biofilms were similar to other DW metagenomes. Beyond the global functions, the occurrences and abundances of specific protective genes involved in the glutathione metabolism, the SoxRS system, the OxyR system, RpoS regulated genes, and the production/degradation of extracellular polymeric substances were also evaluated. A near-complete and low-contamination draft genome was constructed from the metagenome of the DW biofilm, based on the coverage and tetranucleotide frequencies, and identified as a Bradyrhizobiaceae-like bacterium according to a phylogenetic analysis. Our findings provide new insight into DW biofilms, especially in terms of their metabolic functions.

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Figures

Figure 1
Figure 1
Relative distribution of 454 reads at the phylum level, as classified by RDP Classifier at a confidence threshold of 80%, for the 6 DW biofilm samples. The number of reads that were annotated to the Bacteria domain was designated as 100%.
Figure 2
Figure 2
Relative distribution of 454 reads among families of the Proteobacteria phylum, classified by RDP Classifier, for the 6 DW biofilm samples. The families that accounted for greater than 0.5% of reads in at least one sample are shown in the figure. The clustering among samples was generated according to Gower distance using the PAST software (v 1.99).
Figure 3
Figure 3
Top 10 most abundant genera in the 60, 120, and 180 d (A), and the PE and SS (B) biofilm samples. The left segments represent the DW biofilm samples, and the right segments represent the top 10 genera in each biofilm. In the inner layer, each different colour represents a different sample or genus, and the numbers beside the axis indicate the relative abundances of the corresponding samples or genera. The width of the ribbons connecting the sample and genus segments indicates the relative abundances of the corresponding genera in the accordant biofilm samples. In the outer layer of the arc for the sample segments, the different colours represent the top 10 most abundant genera in each sample, with the percentages of reads presented in descending order. For the genus segments, the outer layer illustrates the distribution of the specific genera in each DW biofilm sample.
Figure 4
Figure 4
Principal component analysis of 3 typical aquatic ecosystems according to the percentage of annotated reads/tags in the SEED subsystems. The red star indicates the DW biofilm metagenome analysed in the present study. The metagenomes of the ocean, fresh water and DW samples were analysed by using the publicly available data on MG-RAST. The information for these ecosystems is provided in Table S6.
Figure 5
Figure 5
KEGG network of GSH metabolism, constructed by using 1,205 bacterial species (non-redundant) in KEGG. Network A contains the abundances of annotated enzymes detected in the DW biofilm metagenome. Network B contains the numbers of annotated enzymes (ORFs) detected in the draft genome.
Figure 6
Figure 6
Relative abundances of genes related to the SoxRS system, the OxyR system and RpoS regulated genes (A), and EPS production and degradation (B), in the DW biofilm metagenome. Here, CMPA represents CMP-N-acetylneuraminate and GALNS represents N-acetylgalactosamine 6-sulfate sulfatase.
Figure 7
Figure 7
Phylogenetic tree of the draft genome and typical species in genera of the order Rhizobiales. The annular sector outlined by the blue dashed line indicates the cluster containing the draft genome. The blue arrows indicate the bacterial species that belong to the family Bradyrhizobiaceae. The 16S rRNA genes were compared by ClustalW multiple alignment. The phylogenetic tree was generated by the neighbour-joining method, with 1,000 of bootstrap replications, using the MEGA software (v 5.05).
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