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Microorganisms will be an integral part of biologically based waste processing systems used for water purification or nutrient recycling on space flights. Establishment of these systems with a defined group of microorganisms will provide a standardized means for conferring specific properties to the system. The purpose of this study was to develop microbial inocula (a defined, constructed community and an undefined community) for initiation of plant-based graywater waste processing systems. To this end, small-subunit 16S rDNA sequence analysis was used to describe the population composition of microbial communities from a plant-based graywater waste treatment system and from an industrial wastewater treatment plant (WWTP). The clonal library of organisms from the graywater-degrading rhizosphere community suggested that members of the Cytophagales and Proteobacteria phylogenetic groups dominated. The clonal library of organisms from industrial WWTP was taxonomically more diverse.