Bioregenerative components for advanced life support (ALS) systems will need to be reliable and stable for long-duration space travel. To examine the stability and resilience of microbial communities that recover nutrients from inedible wheat residues, we maintained 4 bacterial strains in mixed communities for 7 weeks. After 3 weeks of incubation, aeration was stopped for several days. Although the abundance of each isolate declined during the perturbation, all strains persisted throughout the experiments. However, only 80% of functions lost during perturbation were recovered afterward. Thus, persistence of strains in a community did not guarantee the persistence of metabolic functions which those strains could perform. Niche partitioning of the heterogeneous molecules in the wheat residue apparently contributed to stable coexistence of the 4 strains. A different community, composed of 4 isolates from a hydroponic study grown under either simulated microgravity or 1×g control conditions in a comparatively homogeneous 1/2-TSB medium, was less stable. Increased diversity of microbial strains and complexity of the substrates upon which they were maintained seemed to increase the stability of microbial communities in ALS bioreactors.