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Biological perchlorate removal using biologically active carbon (BAC) filters is a promising groundwater treatment approach. However, relatively little is known about the microbial communities responsible for perchlorate reduction in these filters. Molecular biology tools can be used to interrogate microbial communities and might be useful for tracking changes in the presence or expression of perchlorate degradation genes that could affect process performance. To assess the utility of available polymerase chain reaction (PCR) primers for genes involved in perchlorate reduction (i.e., chlorite dismutase), the microbial communities in two pilot-scale BAC filters treating perchlorate-contaminated groundwater in Rialto, California and in an enrichment culture derived from these filters were characterized. Using terminal restriction fragment length polymorphism (T-RFLP), two phylogenetic groups of known perchlorate-reducing bacteria (PRB) were putatively detected (i.e., Dechloromonas sp. and Ideonella dechloratans). Chlorite dismutase was detected in the pilot-scale filters and the enrichment culture using available primers. No known PRB that are phylogenetically distinct from those considered in the design of these available primers were detected. Thus it is likely that these available primers will be useful for interrogating the perchlorate-reducing activity of microbial communities in the BAC filters in Rialto, California. Includes 6 references.