The ecological interaction of plants and bacteria was studied in a peat-based sediment subjected to long-term fertilization with nitrogen and phosphorus at Twin Cays, Belize. The main purpose of this research was to better understand the functional relationship among microorganisms, mangrove trees and sediment geochemistry in mangrove sediments. Specifically, the variability of broad bacterial community structure, the bacterial carbon source utilization patterns, the spatial and temporal dynamics of nitrogen-fixing populations, and the molecular diversity of nitrogen fixers were studied. A combination of molecular and chemical techniques combined with statistical tools was used for the identification of key biological and environmental factors directly controlling the community structure of microorganisms in mangrove sediments. Results showed that mangrove trees strongly affect the activity and community composition of N₂ fixers, but not the whole bacterial community (based on PLFAs) or taxonomic traits (based on phylogenetic analysis). In most cases roots were inversely related to N₂ fixation rates and N₂ fixers (community composition), primarily under fertilized conditions. The functional relationship among microorganisms, plants and sediment geochemistry in Belize showed that bacteria rely on degrading organic matter from mangroves as a primary source for carbon, and that mangrove roots do not confer a stable microenvironment that promotes stability and persistence in microbial populations. Effects of the long-term fertilization with N or P on bacteria and N ₂ fixers revealed that effects depend on the initial conditions prior to disturbance, and that effects include changes in microbial metabolic pathways and in community composition patterns of microbial functional groups. Remarkably, variability of bacteria and N₂ fixers in mangrove sediments was observed in response to natural environmental conditions and also to fertilization. A wide range of physiological adaptations of N₂ fixers (primarily sulfate reducers) to a large heterogeneity of microenvironments is a strategy ensuring important biogeochemical processes for the whole ecosystem's functioning in highly dynamic environments such as mangroves. This research further explored the complexity in the ecology of marine microorganisms over different temporal and spatial scales, an important step to better understand the link between microbial communities and the biogeochemistry of sediments in coastal environments.