Microbial mats are an extant paradigm of the earliest ecosystems. Defining the minimal ecosystem requirements necessary for the survival and proliferation of organisms is crucial in the search for extraterrestrial life and for establishing Earth-like ecosystems beyond our planet. Microbial mats are multilayered biofilms that operate as almost closed systems with persistent oxidation-reduction gradients and restricted vertical flows. Under the driving force of light the components interact and feedback flows become established. The community is the highest biological unit in an ecological hierarchy. The knowledge of the community composition is essential to understand the microbial mats dynamics. Understanding the factors that determine ecosystem stability has been one of the main challenges for ecologists. It has been pointed that both major and minor populations are important for maintaining ecosystem stability. Spirochetes represent one of the minor heterotrophic groups (ca. 1% total population) in microbial mats. However, when samples were examined with primers specific for the spirochete group, highly diverse collections of spirochete 16S rDNA were uncovered. Spirochetes may constitute a ubiquitous component of microbial mats that are linked to other microbial communities by robust trophic interactions.