Microorganisms, including bacteria, cyanobacteria, microalgae, and various fungi and fungal-like organisms (e.g., Peronsporomycetes), are critical components of all communities today. These organisms certainly performed similar functions in the past, and were responsible for the evolution and sustainability of ancient ecosystems in activities ranging from decomposition to nutrient cycling. Unfortunately, however, relatively little is known about how precisely the individual groups of microorganisms functioned in the geologic past. In this research program, various microorganisms that are three-dimensionally preserved in Early Devonian to Late Carboniferous cherts will be investigated. The Devonian and Carboniferous are important periods of geologic time in which all major lineages of vascular land plants (except angiosperms) and the fundamental architectural principles of their body plan (e.g., roots, shoot axis, leaves) evolved. As a result of this increased plant diversity, the number of ecologically distinct (micro-) habitats increased drastically, which, in turn, has resulted in the evolution of new and specific plant-microbe interactions (e.g., leaf endophytism). Because both microbes and their hosts are preserved in chert, these associations provide an extraordinary opportunity to document the diversity of microbes through an important segment of geologic time, and also to study a number of complex interactions that were critical in the functioning of the ancient terrestrial ecosystems. Some of these interactions include parasitism, saprophytism, and various degrees of mutualistic association. To accomplish the goals of this research agenda an international team was assembled that has expertise with both fossil and extant microbes. The project will encompass four interrelated themes: 1) documenting overall microbe diversity, 2) examining diversity through segments of geologic time in which there are well known host plants, 3) characterizing certain types of mutualistic (mycorrhizal) fungi based on spore wall features used with extant glomeromycoytan fungi, 4) documenting microbe interactions based on host responses. The utilization of structurally preserved organisms is the only method available to directly investigate complex interactions that existed between various microbes and their fossil hosts. Documenting these microorganisms, their associations, and interactions with other organisms will make it possible to trace co-evolutionary trends that can be used together with modern approaches to investigate the evolutionary history of certain types of biological and ecological processes that sustain and drive terrestrial ecosystems.