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Factors affecting community structure and connectivity within systems are crucial for provision of microbial ecosystem-services (e.g., soil nitrogen cycling), but what these factors are and how they are affected by land-use and management is poorly understood. Biogeochemical cycles are disrupted in agricultural-systems, providing an excellent opportunity to investigate the roles of management and land-use in shaping microbial communities and ecosystem function. We investigated soil ammonia oxidisers under different cropping practices and within a nearby grassy woodland; representing a gradient of physical/chemical disturbance. Land-use and management practices resulted in significant differences in community structure. Major differences in system connectivity were observed between land-uses, but not within management practices, indicating that land-use change is the major driver of ecosystem change, rather than management within land-uses. Agricultural ammonia oxidiser communities appeared to be less well connected and rely less on biotic interactions than those in natural systems, perhaps a reflection of the extent to which natural feedback loops are disturbed in managed systems. Smaller, but significant, differences were also evident between management treatments. Despite differences in community structure and connectivity there was, however, no significant effect on potential N-cycle rates, indicating that although land-use and management impacts may drive community changes, these do not necessarily translate into changes in functional capacity. [ABSTRACT FROM AUTHOR]