Ecosystems are subjected to seasonal environmental changes and species are adapted to cycles of natural disturbance and recovery. While models have been developed to examine the impact of environmental change on ecosystem function, studies are just beginning to address the complexity and contribution of the microbiome to ecosystem stability. In this study, we examined a hypersaline microbial mat ecosystem located on San Salvador Island, Bahamas. This semi-closed ecosystem is subjected to predictable seasonal environmental disturbances, serving as an excellent platform to test the relationship of microbial diversity and ecosystem stability.