Metatranscriptomic profiling across the salinity graident of the Tamar estuary, Southwest UK. A Biogeochemical Assessment of a Temperate Estuarine System: Nitrifier Ecology and Gene Expression Profiling Across the Tamar Estuary, UK.

Estuarine ecosystems are dynamic interfaces between riverine and marine environments, acting as critical biogeochemical hotspots. The convergence of steep physiochemical gradients and substantial nutrient influxes creates unique niches that foster rich tapestries of microbially-mediated biogeochemical transformations. These systems are pivotal in the cycles of key elements such as carbon, nitrogen, sulphur, and phosphorus, which are integral to maintaining ecological balance and supporting the rich biodiversity of coastal regions. This study investigates the biogeochemical activities of microbial communities across the freshwater-saltwater interface of the Tamar Estuary, Southwest UK. By integrating 16S rRNA gene amplicon sequencing with catalysed reporter deposition fluorescence in situ hybridisation and incubation experiments, we explore the composition, distribution and activity of aquatic ammonia oxidising microorganisms within the TE, shedding light on both the ecology and functionality of this still poorly understood group within the ecosystem. In addition, we conduct a comprehensive metatranscriptomic analysis of the microbial communities residing across the estuary, highlighting the biogeochemically relevant processes that are active from river to sea. Through this work, we demonstrate that ammonia oxidising communities within the system exhibit strong patterns of spatiotemporal heterogeneity, with ammonia oxidising archaea and Betaproteobacterial ammonia oxidising bacteria differentially dominating temporally, with both increasing in abundance with salinity. Additionally, we find little correlation between their abundance and ammonia oxidisation rates across the system, highlighting the complexity of physiochemical parameters influencing their activity. Furthermore, our metatranscriptomic profiling revealed that photosynthesis and primary production by microeukaryotes, such as Thalassiosirales and Mammiellales, is the transcriptionally dominant process within the ecosystem. Bacterial groups such Rhodobacterales and Flavobacteriales appeared to be key players in organic matter cycling, whilst acting as significant players in other biogeochemical processes. This study sheds light on the dynamics of the microbially-mediated biogeochemical cycling processes occurring within the Tamar estuary and deepens our understanding of these complex and critical ecosystems.