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Microbial monitoring by instrumental methods will become more necessary as manned spaceflight missions increase in length. Permanently manned space station or lunar bases have potential for microbial problems that we cannot foresee until we begin to monitor activities of organisms in each unique environment. These microbial communities could impair crew health, equipment performance, life science experiments and environmental control systems. The environmental factors that influence each organism's ability to survive, grow, and reproduce on earth can have new influences in variable or reduced gravity. The combination of environmental factors has the potential to produce changed interactions in the microbial communities. Different species may dominate, adapt, or regress in ways we cannot predict from today's information. Microbial instrumentation is being developed for in-situ study and eventual online control monitoring in spaceflight applications.