Microbial ecology and metabolism in chloraminated drinking water systems

Drinking water systems are complex and multi-dimensional aquatic environments. The chemical, physical and biological factors inherent to each drinking water system drive changes in the microbial community dynamics and shape the drinking water microbiome. The complexity of interactions between these factors together with the use of differing source waters as well as the variability in treatment strategies and system design make each drinking water system unique. It is therefore important to understand the microbial ecology of drinking water systems and how the factors specific to each system shape the microbial community. The aim of this project was to understand which factors drive the microbial community dynamics of a complex, large-scale South African drinking water system, with the application of multiple disinfectant regimes (i.e., chlorination, chloramination and hypochlorination). Specific objectives included: (i) investigating the long-term spatial and temporal microbial community dynamics along the distribution system, (ii) investigating the reproducibility of the microbial community dynamics of two drinking water systems treating similar source waters and lastly, (iii) in light of the use of chloramine as a secondary disinfectant and the observed dominance of Nitrosomonas ssp., investigate microbial mediated nitrogen metabolism in the chloraminated drinking water. The large-scale drinking water system investigated in this project offered unique opportunities to explore the changes in microbial community dynamics across two drinking water treatment plants, over large distribution distances as well as through different disinfection regimes. Initially, the study conducted over a two-year period, demonstrated that substantial temporal and seasonal trends existed, specifically at individual sample locations. However, when considering the distribution system as a whole, the spatial dynamics explained more of the variation in the microbial community. In addition, the microbial community dynamics were found to be reproducible, where treatment and distribution had a similar impact on the microbial community dynamics between two systems. Similar treatment operations resulted in the development of similar microbial communities. However, the microbial communities demonstrated a differential response to chlorination, but the selection of similar taxa through distribution indicated stabilisation of the microbial community post-disinfection. Lastly, in light of the use of chloramine and based on the observed dominance of Nitrosomonas ssp., in the chloraminated sections of both the previous studies, a metagenomic approach was used to investigate the microbial mediated nitrogen metabolism. This revealed that Nitrosomonas and Nitrospira species dominated in chloraminated reservoirs and suggested that these taxa play significant roles in nitrification in chloraminated water. Furthermore, based on the dominant nitrogen transforming genes and metagenome assembled genomes, it was observed that the nitrate formed through nitrification is either reduced back to ammonia or to nitric oxide, where it may play a role in the regulation of biofilm formation. These investigations highlighted the interplay between the spatial and temporal dynamics of a large-scale drinking water system and revealed the factors that drive the changes in the microbial community through treatment and distribution. In addition, this project provided insight into the genetic network behind microbially mediated nitrogen metabolism in chloraminated drinking water and may help improve the understanding of the processes behind nitrification in systems where it is a challenge. This project contributes to the current knowledge base in this field and provides drinking water utilities with the opportunity to understand the range of mechanisms that influence the microbial community and understand the underlying contributing factors that impact microbial growth in drinking water systems.Thesis (PhD)--University of Pretoria, 2019.Microbiology and Plant PathologyPhDUnrestricte