Microbial community dynamics within impacted coastal ecosystems

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The microbes that inhabit coastal environments are responsible for high rates of primary productivity and nutrient cycling, and are amongst the first organisms to respond to changes in their habitat. This means that microbes are often the key biological initiators of positive (eg. bioremediation) or negative (eg. algal blooms) outcomes in response to environmental perturbations associated with natural or anthropogenic disturbances. Until now, most investigations of coastal microbiology have only focused on a narrow set of organisms that indicate faecal pollution, and consequently, have overlooked the 99% of environmental microbes that are yet to be cultured. Given this shortfall in our understanding of coastal microbiology, this project aimed to identify the key environmental and biological processes that influence the microbial ecology of coastal ecosystems, including potentially harmful species. To achieve this, a 24 month, high temporal resolution sampling regime was conducted at two urban beaches that experience contrasting hydrology and exposure to anthropogenic influences. Water samples were analysed in several ways using a suite of molecular, computational and statistical approaches, to elicit patterns and interactions between climate, water chemistry and microbial community assemblages. Each of my thesis chapters focus on a particular ecological aspect of the microbial communities extracted from water collected at two beach sample locations. In Chapter 1, I provide a background and overview of microbial ecology in coastal ecosystems. In Chapter 2, the first of my data chapters, 16S rRNA sequencing was combined with threshold indicator taxa analysis and network analysis to capture the dynamics of bacteria at the community-scale, which revealed contrasting temporal patterns in whole bacterial communities, and seasonal switching between closely related taxa. Broad screening of bacterial communities also detected an interesting pattern in a population of emerging pathogens within the genus Arcobacter. This became the focus of Chapter 3, where large peaks were detected in Arcobacter abundance during inputs of stormwater and WWSO at the impacted beach, which persisted in high abundance for a further week following rainfall. In Chapter 4, the focus shifted from enteric microbes, to genes that confer resistance to antibiotics, which found 100-fold increases in several antibiotic resistance genes that were strongly correlated with potentially pathogenic enteric bacteria. In Chapter 5, this project closely tracked populations of pathogenic species within the genus Vibrio, providing new evidence that directly links blooms in pathogenic Vibrio in coastal surface waters with marine heatwave events. Overall, the findings of this project provide new and transformative insight into the microbial ecology of coastal systems, which has highlighted several potential implications for ecological and public health. Specifically, the detection of genes associated with antibiotic resistance and potential pathogens, that persist in beach water even when standard fecal indicators have diminished, has highlighted a need for broader screening tools in the monitoring and management of water quality in swimming beaches.
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