Terrestrial inputs of organic matter contribute greatly to the functioning of aquatic ecosystems, subsidizing between 30-70% of secondary production. This contribution of terrestrial resources is especially important in boreal lakes that are largely nutrient-poor and thus more responsive to these additions. Yet the mechanisms underlying initial processing of terrestrial resources by microbial communities at the base of lake food webs remain poorly understood. With this in mind, this thesis aims to advance our understanding of lake sediment microbial community assembly and functioning along abiotic gradients, primarily reflecting variation in terrestrial organic matter inputs that are predicted to increase with future environmental change. Chapter 1 reviews current knowledge on the terrestrial support of lake food webs and highlights gaps in understanding the factors influencing the microbial processing of terrestrial resources. It also provides an overview of metagenomics methods for microbial community analysis and their development over the course of the thesis. Chapter 2 tests how much of ecosystem functioning is explained by microbial community structure relative to other ecosystem properties such as the present-day and past environment. Theory predicts that ecosystem functioning, here measured as CO2 production, should increase with diversity, but the individual and interactive effects of other ecosystem properties on ecosystem functioning remain unresolved. Chapter 3 further questions the importance of microbial diversity for ecosystem functioning by asking whether more diverse microbial communities stabilize ubiquitous functions like CO2 production and microbial abundances through time. It also aims to identify the biotic and abiotic mechanisms underlying positive diversity-stability relationships. Chapter 4 then explores how microbial communities assemble and colonize sediments with varying types and amounts of terrestrial organic matter in three different lakes over a two-month period. Understanding how microbial communities change in relation to sediment and lake conditions can help predict downstream ecosystem functions. Finally, Chapter 5 discusses the main findings of the thesis and ends with proposed avenues for future research.