Municipal wastewater treatment removes carbon and nutrients from sewage by harnessing a dense microbial community in a biological treatment process. The dynamics of the viral community structure and function through wastewater treatment is not well understood. Viruses are expected to play critical roles in biological wastewater treatment because they are highly abundant, exhibit complex host interactions ranging from predatory to symbiotic, and accelerate host evolution. The lack of rigorous

more »

... hods for isolating viral communities from environmental samples and quantitative methods for measuring and interpreting viral metagenomes has hindered our understanding of the roles of viruses in the environment, in general, and biological wastewater treatment, in particular. The overall goal of this dissertation research was to develop and apply metagenomic and in silico approaches to explore viral community dynamics through biological wastewater treatment and probe the roles that viruses play on the dissemination and emergence of antibiotic resistance. This dissertation developed rigorous methodologies for studying environmental viromes. To address the issue of virus enrichment from environmental samples, an ultrafiltration approach was compared with an iron chloride flocculation method. Next, to measure the absolute abundances of target viruses in wastewater samples before and after treatment, a rigorous quantitative viral metagenomic method was developed. Specifically, dsDNA and ssDNA standards were added to viral DNA extracts to relate relative and absolute abundances. A bioinformatic pipeline, QuantMeta, was developed to calculate concentrations of targets (e.g., contigs or sequences from databases) and assess target-specific detection thresholds and detect and correct non-specific mapping and assembly errors. QuantMeta was applied to quantitative viromes from wastewater samples and improved quantification confidence and accuracy. QuantMeta is not specific to wastewater viromes and is applicable to whole metagenomes [...]