The MIRADA project was launched in the fall of 2007 to establish a Microbial Biodiversity Survey and Inventory across all 13 of the major aquatic (marine and freshwater) Long Term Ecological Research (LTER) sites in the NSF US LTER Program. The long-term objective of our study is to document and describe baseline diversity and relative abundance data for both common and rare members of microbial communities and to relate this diversity to the underlying physical and chemical environment. Our project employs a new, high-throughput DNA pyrosequencing technology based on the sequencing of small-subunit ribosomal RNA gene hypervariable regions, that will allow for discovery of novel microbial diversity in the bacterial, archaeal and eukaryal domains of life and enable us to examine whether or not biogeographical patterns exist for microbial populations. Biodiversity in general, and microbial biodiversity in particular is important because microorganisms help shape Earth’s habitability by orchestrating the major carbon transformations, biogeochemical cycles, and input into atmospheric composition. Radical fluctuations in microbial populations caused by changes in the environment pose irreversible threats to our quality of life and the entire biosphere. Our initial results confirm the widespread occurrence of the “Rare Biosphere” of many diverse taxa in a community dominated by few major groups. The resulting data will directly benefit participating LTERs that actively communicate results to policy makers, natural resource managers, the broader scientific community and the general public. We conclude that our approach will serve as a model for future microbial inventories that are global in scope.