Microbial approaches for monitoring the ecological condition of aquatic environments

Anthropogenic activities often result in the release of multiple stressors in the aquatic environment. These include pollution due to industrial effluents, sewage, mining, urbanization and agriculture. These stressors not only impact the ecological health of the water ecosystems but also diminish their benefits to society. While it has been well documented that human activities can reduce fish abundances and affect the algal bloom, theyalso affect the benthic communities which underpin ecosystem condition, including microbial organisms. Microorganisms, specifically bacteria, are some of the first responders to environmental perturbation and are of critical importance for ecosystem function. They facilitate many of the processes mediating ecosystem services such as nutrient cycling, disease causation and suppression and pollutant removal. Their structure and function establish how and to what extent disturbances alter the environment. Recent technological advances combined with a substantial reduction in the costs of DNA sequencing now allows microbial ecologists to access an enormous amount of data, transforming our capacity to investigate the composition and dynamics of complex microbial communities that inhabit aquatic environments. However, there is still a paucity in the understanding of how common stressors such as chemical, including nutrients and metals; and biological including sewage, alter bacterial communities. This includes determining whether there are predictable changes in composition. Consequently, there is an opportunity to demonstrate the potential use of microbial communities to monitor aquatic ecosystems, combining new approaches, that are unique to microbiome studies, and standard practices, that are broadly used to monitor aquatic environments. This research examined aquatic microbial communities subjected to anthropogenic pressures from two aspects. The first is examining inputs of exogenous bacteria into aquatic systems, specifically, those derived from sewage both locally and globally. The second by studying the composition patterns and connectivity with co-occurrence networks analysis within bacterial communities of coastal water column endogenous bacteria. This thesis demonstrates that microbial tools can not only be used to examine the input of human activities on the ecosystembut also, conversely how humans impact those microorganisms naturally residing in the system. Collectively, the research emphasises the need to include microbial communities in aquatic biomonitoring, providing managers and end-users with a new range of tools to assist in the protection of the social, economic and ecological values that water bodies provide.