Environmental gradients exist at global and local scales and the variable conditions they encompass allow the coexistence of different microbial assemblages. Studying gradients and the selection forces they enclose can reveal the spatial succession and interactions of microorganisms and, therefore, how they are assembled in functionally stable communities. By combining high-throughput sequencing technology and laboratory experimental approaches, I investigated the factors that influence the microbial community assemblages in two types of environmental gradients in the Red Sea. I have studied the communities in the chemoclines occurring at the transition zones along the interfaces between seawater and the Deep Hypersaline Anoxic Brines (DHABs) at the bottom of the Red Sea. Across these chemoclines salinity increases of 5-10 times respect to the overlying seawater. I compared the microbial community diversity and metabolisms in the chemoclines of five different DHABs, finding different microbial community compositions due to the different DHABs characteristics, but the same succession of metabolisms along the five interfaces. From the Suakin Deep brine, I assembled the genome of a novel bacterial phylum and revealed the metabolic features that allow this organism to cope with the challenging variable conditions along the chemocline. In an alternative environmental system, I studied the effect of different thermal regimes on the microbiome of coastal sediment exposed to different yearly ranges of temperature variation. Sediment bacterial communities living under larger temperature variations are more flexible and can grow under a larger range of thermal conditions than communities experiencing narrower temperature ranges. My results highlight the large metabolic flexibility of microorganisms and their capacity to efficiently self-organize in complex functional assemblages under extreme ranges of environmental conditions.