Coastal-estuarine microbiology explored: Community dynamics, biogeochemical processes and cell specific targeting of nitrogen cyclers

Abstract

Coastal-estuarine environments hold critical importance across ecological, biogeochemical, and socioeconomic domains. The nutrient-rich conditions, sharp physiochemical gradients, and overall dynamic complexity of these regions foster a rich diversity of microorganisms- an unseen but integral component of coastal-estuarine biogeochemistry and food webs. Over a third of the globe’s population reside within 100 km of a coastline, and as such these environments are under severe strain from anthropogenic activities. Despite their known critical importance in these ecosystems, and the implications that their activity have for the health of global oceans, how microbial communities will respond to these changing environments is still poorly understood.

In this thesis, I conduct a detailed investigation into the microbial ecology and biogeochemistry of the Tamar Estuary, southwest UK. Utilising 16S and 18S rRNA gene amplicon sequencing, I offer a comprehensive analysis of both prokaryotic and microeukaryotic communities within this ecosystem. My research reveals that these communities exhibit significant spatiotemporal heterogeneity, with physicochemical factors such as salinity, temperature, and nutrient loading playing integral roles in shaping their diversity and composition. Furthermore, I delve into the ecology and activity of ammonia-oxidising microorganisms, demonstrating the complexity of this biogeochemically crucial yet phylogenetically diverse group. Alongside this, I conduct an extensive metatranscriptomic analysis of these communities, revealing that photosynthesis-driven primary productivity is the predominant process within this ecosystem. Additionally, I assess the effectiveness of DAF-FM diacetate, an intracellular nitric oxide-detecting probe, for specifically targeting active marine nitric oxide cycling microorganisms. I highlight the probe's limitations for this specific purpose and outline areas of future development. Overall, this thesis casts fresh light on the complex microbiology of estuarine ecosystems and the factors driving the distribution, dynamics and activities of these pivotal yet often unseen organisms.

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ORCID for Phyllis Lam: orcid.org/0000-0003-2067-171X

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