Vicente Gomez-Alvarez

Metagenomic Analyses of Drinking Water Receiving Different Disinfection Treatments

ABSTRACT A metagenome-based approach was used to assess the taxonomic affiliation and function potential of microbial populations in free-chlorine-treated (CHL) and monochloramine-treated (CHM) drinking water (DW). In all, 362,640 (averaging 544 bp) and 155,593 (averaging 554 bp) pyrosequencing reads were analyzed for the CHL and CHM samples, respectively. Most annotated proteins were found to be of bacterial origin, although eukaryotic, archaeal, and viral proteins were also identified. Differences in community structure and function were noted. Most notably, Legionella-like genes were more abundant in the CHL samples while mycobacterial genes were more abundant in CHM samples. Genes associated with multiple disinfectant mechanisms were identified in both communities. Moreover, sequences linked to virulence factors, such as antibiotic resistance mechanisms, were observed in both microbial communities. This study provides new insights into the genetic network and potential biological processes associated with the molecular microbial ecology of DW microbial communities.

Metagenome analyses of corroded concrete wastewater pipe biofilms reveal a complex microbial system

BackgroundConcrete corrosion of wastewater collection systems is a significant cause of deterioration and premature collapse. Failure to adequately address the deteriorating infrastructure networks threatens our environment, public health, and safety. Analysis of whole-metagenome pyrosequencing data and 16S rRNA gene clone libraries was used to determine microbial composition and functional genes associated with biomass harvested from crown (top) and invert (bottom) sections of a corroded wastewater pipe.ResultsTaxonomic and functional analysis demonstrated that approximately 90% of the total diversity was associated with the phyla Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The top (TP) and bottom pipe (BP) communities were different in composition, with some of the differences attributed to the abundance of sulfide-oxidizing and sulfate-reducing bacteria. Additionally, human fecal bacteria were more abundant in the BP communities. Among the functional categories, proteins involved in sulfur and nitrogen metabolism showed the most significant differences between biofilms. There was also an enrichment of genes associated with heavy metal resistance, virulence (protein secretion systems) and stress response in the TP biofilm, while a higher number of genes related to motility and chemotaxis were identified in the BP biofilm. Both biofilms contain a high number of genes associated with resistance to antibiotics and toxic compounds subsystems.ConclusionsThe function potential of wastewater biofilms was highly diverse with level of COG diversity similar to that described for soil. On the basis of the metagenomic data, some factors that may contribute to niche differentiation were pH, aerobic conditions and availability of substrate, such as nitrogen and sulfur. The results from this study will help us better understand the genetic network and functional capability of microbial members of wastewater concrete biofilms.

Molecular survey of concrete sewer biofilm microbial communities

The microbial composition of concrete biofilms within wastewater collection systems was studied using molecular assays. SSU rDNA clone libraries were generated from 16 concrete surfaces of manholes, a combined sewer overflow, and sections of a corroded sewer pipe. Of the 2457 sequences analyzed, α-, β-, γ-, and δ-Proteobacteria represented 15%, 22%, 11%, and 4% of the clones, respectively. β-Proteobacteria (47%) sequences were more abundant in the pipe crown than any of the other concrete surfaces. While 178 to 493 Operational Taxonomic Units (OTUs) were associated with the different concrete samples, only four sequences were shared among the different clone libraries. Bacteria implicated in concrete corrosion were found in the clone libraries while archaea, fungi, and several bacterial groups were also detected using group-specific assays. The results showed that concrete sewer biofilms are more diverse than previously reported. A more comprehensive molecular database will be needed to better study the dynamics of concrete biofilms.

Novel Microbiological and Spatial Statistical Methods to Improve Strength of Epidemiological Evidence in a Community-Wide Waterborne Outbreak

Failures in the drinking water distribution system cause gastrointestinal outbreaks with multiple pathogens. A water distribution pipe breakage caused a community-wide waterborne outbreak in Vuorela, Finland, July 2012. We investigated this outbreak with advanced epidemiological and microbiological methods. A total of 473/2931 inhabitants (16%) responded to a web-based questionnaire. Water and patient samples were subjected to analysis of multiple microbial targets, molecular typing and microbial community analysis. Spatial analysis on the water distribution network was done and we applied a spatial logistic regression model. The course of the illness was mild. Drinking untreated tap water from the defined outbreak area was significantly associated with illness (RR 5.6, 95% CI 1.9–16.4) increasing in a dose response manner. The closer a person lived to the water distribution breakage point, the higher the risk of becoming ill. Sapovirus, enterovirus, single Campylobacter jejuni and EHEC O157:H7 findings as well as virulence genes for EPEC, EAEC and EHEC pathogroups were detected by molecular or culture methods from the faecal samples of the patients. EPEC, EAEC and EHEC virulence genes and faecal indicator bacteria were also detected in water samples. Microbial community sequencing of contaminated tap water revealed abundance of Arcobacter species. The polyphasic approach improved the understanding of the source of the infections, and aided to define the extent and magnitude of this outbreak.

Impact of drinking water conditions and copper materials on downstream biofilm microbial communities and Legionella pneumophila colonization

This study examined the impact of pipe materials and introduced Legionella pneumophila on downstream Leg. pneumophila colonization and microbial community structures under conditions of low flow and low chlorine residual.

Changes in bacterial composition of biofilm in a metropolitan drinking water distribution system

This study examined the development of bacterial biofilms within a metropolitan distribution system. The distribution system is fed with different source water (i.e. groundwater, GW and surface water, SW) and undergoes different treatment processes in separate facilities.

Biofilm Community Dynamics in Bench-Scale Annular Reactors Simulating Arrestment of Chloraminated Drinking Water Nitrification

Annular reactors (ARs) were used to study biofilm community succession and provide ecological insight during nitrification arrestment through simultaneously increasing monochloramine (NH2Cl) and chlorine to nitrogen mass ratios, resulting in four operational periods (I-IV). Analysis of 16S rRNA-encoding gene sequence reads (454-pyrosequencing) examined viable and total biofilm communities and found total samples were representative of the underlying viable community. Bacterial community structure showed dynamic changes corresponding with AR operational parameters. Period I (complete nitrification and no NH2Cl residual) was dominated by Bradyrhizobium (total cumulative distribution: 38%), while environmental Legionella-like phylotypes peaked (19%) during Period II (complete nitrification and minimal NH2Cl residual). Nitrospira moscoviensis (nitrite-oxidizing bacteria) was detected in early periods (2%) but decreased to <0.02% in later periods, corresponding to nitrite accumulation. Methylobacterium (19%) and members of Nitrosomonadaceae (42%) dominated Period III (complete ammonia and partial nitrite oxidation and low NH2Cl residual). An increase in Afipia (haloacetic acid-degrading bacteria) relative abundance (<2% to 42%) occurred during Period IV (minimal nitrification and moderate to high NH2Cl residual). Microbial community and operational data provided no evidence of taxa-time relationship, but rapid community transitions indicated that the system had experienced ecological regime shifts to alternative stable states.

Bacterial composition in a metropolitan drinking water distribution system utilizing different source waters

We investigated the bacterial composition of water samples from two service areas within a drinking water distribution system (DWDS), each associated with a different primary source of water (groundwater, GW; surface water, SW) and different treatment process. Community analysis based on 16S rRNA gene clone libraries indicated that Actinobacteria (Mycobacterium spp.) and α-Proteobacteria represented nearly 43 and 38% of the total sequences, respectively. Sequences closely related to Legionella, Pseudomonas, and Vibrio spp. were also identified. In spite of the high number of sequences (71%) shared in both areas, multivariable analysis revealed significant differences between the GW and SW areas. While the dominant phylotypes where not significantly contributing in the ordination of samples, the populations associated with the core of phylotypes (1-10% in each sample) significantly contributed to the differences between both service areas. Diversity indices indicate that the microbial community inhabiting the SW area is more diverse and contains more distantly related species coexisting with local assemblages as compared with the GW area. The bacterial community structure of SW and GW service areas were dissimilar, suggesting that their respective source water and/or water quality parameters shaped by the treatment processes may contribute to the differences in community structure observed.

Resilience of microbial communities in a simulated drinking water distribution system subjected to disturbances: role of conditionally rare taxa and potential implications for antibiotic-resistant bacteria

Many US water utilities using chloramine as their secondary disinfectant have experienced nitrification episodes that detrimentally impact water quality in their distribution systems. A semi-closed pipe-loop chloraminated drinking water distribution system (DWDS) simulator was used to evaluate the biological stability of the system and describe the response of microbial communities in the bulk water (BW) and biofilm (BF) phase to a disturbance caused by changes in the operational parameters. The DWDS simulator was operated through five successive operational schemes, including an episode of nitrification, followed by a ‘chlorine burn’ by switching the disinfectant from chloramine to free chlorine. Community comparisons showed significant differences in the structure based on disinfectant and phase (e.g., BW and BF). Both disturbances created changes in the relative abundances of the core microbiome and some members of the rare biosphere (i.e., conditionally rare taxa); however, the microbial community was resilient and returned to its stable state. Genes associated with multiple antibiotic resistance mechanisms were found to be a component of the core genomes of waterborne isolates. These results provide evidence of variations in the bulk water/biofilm microbial community structure during episodes of disturbance (e.g., disinfectant switching practices, nitrification) and its recovery after disturbance.

Effect of temperature and colonization of Legionella pneumophila and Vermamoeba vermiformis on bacterial community composition of copper drinking water biofilms.

It is unclear how the water‐based pathogen, Legionella pneumophila (Lp), and associated free‐living amoeba (FLA) hosts change or are changed by the microbial composition of drinking water (DW) biofilm communities. Thus, this study characterized the bacterial community structure over a 7‐month period within mature (> 600‐day‐old) copper DW biofilms in reactors simulating premise plumbing and assessed the impact of temperature and introduction of Lp and its FLA host, Vermamoeba vermiformis (Vv), co‐cultures (LpVv). Sequence and quantitative PCR (qPCR) analyses indicated a correlation between LpVv introduction and increases in Legionella spp. levels at room temperature (RT), while at 37°C, Lp became the dominant Legionella spp. qPCR analysis suggested Vv presence may not be directly associated with Lp biofilm growth at RT and 37°C, but may contribute to or be associated with non‐Lp legionellae persistence at RT. Two‐way PERMANOVA and PCoA revealed that temperature was a major driver of microbiome diversity. Biofilm community composition also changed over the seven‐month period and could be associated with significant shifts in dissolved oxygen, alkalinity and various metals in the influent DW. Hence, temperature, biofilm age, DW quality and transient intrusions/amplification of pathogens and FLA hosts may significantly impact biofilm microbiomes and modulate pathogen levels over extended periods.