Rivers and their adjacent riparian zones are locations of high levels of biodiversity and are well known for their enhanced rates of important biogeochemical processes. Despite their small total area, rivers contribute disproportionally to regional carbon fluxes and riparian zones are hotspots of terrestrial denitrification. Microorganisms drive these biogeochemical processes as well as serve as the basis of brown food webs and contribute to physical processes such as sediment flocculation and soil aggregation. Despite the importance of microbial communities in rivers and riparian systems, they are relatively understudied in comparison to other riverine organisms. This doctoral work investigates microbial community structure and function at the aquatic/terrestrial interface. First, a theoretical work based on the newly proposed concept of microbial community coalescence explores the potential consequences of environmental mixing on lotic and riparian microbial community structure. This work takes a catchment-scale perspective of microbial community assembly across ecosystem boundaries. Next, results of a field study conducted across nine rivers in the UK are presented, providing insight about the influence of chemical, hydrological and spatial drivers on sediment fungal community structure. This provides a sub-catchment scale view of lotic fungal diversity. The final chapter details results of an experimental study investigating the influence of collembolans, ubiquitous soil organisms, on the production of the greenhouse gas N2O. This work explores the effects of biotic-scale processes on ecosystem functioning. We reviewed field studies investigating environmental mixing processes and found evidence that environmental mixing influences microbial community structure in some compartments, such as headwaters and estuaries. The application of the microbial community coalescence concept in rivers may increase the amount of variance explained between observed local communities. Despite a rich body of literature about lotic fungal decomposer communities inhabiting leaf litter, very few studies investigated general fungal diversity. Our investigation of sediment fungal communities revealed highly diverse communities that were differentiated by underlying geology. Hydrological and chemical variables explained some of the differences between microbial communities, while spatial variables were less important. Finally, we conducted an experimental study to investigate the microbial-driven process of denitrification – an anaerobic nitrogen cycling process that produces N2 and N2O, a greenhouse gas. We found the different species of the ubiquitous soil organism Collembola affect the proportion of N2O that is produced as an end-product of denitrification and that this is related to shifts in soil nitrate concentrations. Together, this work reports findings from several under-investigated areas of microbial structure and functioning in rivers, soils and across their interface at three different scales. Our results provide insight about patterns of riverine microbial biodiversity through application of a new conceptual framework that may improve explanatory power and through a field investigation that reveals the relative importance of spatial and environmental drivers. Our field investigation was one of the first studies in Europe to apply next-generation sequencing to general fungal communities in rivers. We also provide evidence that denitrification is impacted by the presence of soil microarthropods, organisms with highly diverse communities in riparian zones. As riverine systems are simultaneously vital for ecosystem function and highly threatened by anthropogenic activity, there is an urgent need for fundamental knowledge of lotic biodiversity patterns and their relationship with function to inform conservation and restoration efforts.
