PhD ThesisClimate change, population growth and increasingly strict environmental regulation means the
global water industry is currently facing an unprecedented coincidence of challenges (Palmer,
2010). Better microbial ecology could significantly contribute, since explicitly engineering and
maintaining efficient and functionally stable microbial communities would allow existing assets to
be optimised and their robustness improved. Given its role in natural systems viral infection could
be an important, yet overlooked, factor. Here we attempt to address this lacuna, particularly
within activated sludge systems.
To facilitate this process we developed, optimised and validated a flow cytometry method,
allowing rapid (relative to other methods), accurate and highly reproducible quantification of total
free viruses in activated sludge samples (mixed liquor (ML)). Its use spatially identified viruses are
highly abundant, with concentrations ranging from 0.59 - 5.14 × 109 viruses mL-1 across 25
activated sludge plants.
Subsequently we applied this method to ML collected from one full- and twelve replicate lab-scale
activated sludge systems respectively. At both scales viruses in the ML were shown to be both
abundant and temporally/spatiotemporally dynamic, thus ever present across activated sludge
systems. Through statistical inference they were shown to be associated (positively) with total
host (bacterial) abundance, with microbial community structure and with a systems function (the
removal of COD and NH4
+
-N from influent wastewaters), whilst exogenous factors, particularly
those involved in adsorption processes, played an important role in their dynamics.
Evidence of predator-prey dynamics between a subset of measured viruses and a key functional
group (ammonia oxidising bacteria (AOB)) within the full-scale system is also presented, whilst a
detailed examination of all garnered abundances highlights the relative abundance of viruses, as
reported in marine systems, declined with increasing host density. Finally preliminary
metagenomic data shows wastewater viromes are largely phylogenetically and functionally
uncharacterised, yet relative abundances of known viruses vary throughout the wastewater
treatment stream.
Considering the evidence presented viruses appear to play a more central role in the dynamics of
activated sludge systems than hitherto realised and thus should be considered more frequently
when assessing the key factors governing bacterial abundance, community composition and
functional stability
