Total community DNA was isolated from a series of low-biomass subsurface sediments immediately after coring, either maintained as intact cores or homogenized and maintained at 17 degrees C for up to 21 weeks. Eubacterial 16S rRNA genes were recovered by PCR amplification, and full-length, cloned genes were digested with CfoI. Resulting restriction enzyme patterns were used to group clones into specific RFLP groups. The abundance and distribution of individual clones within the RFLP groups was used to assess the changes in community structure as a function of storage time and sample condition (i.e., intact versus homogenized). Ninety-eight different RFLP groups were identified in tote. Large subsets of new RFLP groups were continuously identified at increasing times post-sampling. Only 12 specific RFLP patterns were identified in both homogenized and intact samples, however, indicating that the response of these communities varied significantly between the homogenized and intact sediments. Further, a comparison of clone libraries from the multiple sample treatments provided evidence that the relative abundance of clones within specific RFLP groups reflected a change in the abundance of that specific RFLP group within the microbial community. These results support the hypothesis that both growth and resuscitational processes are responsible for post-sampling stimulation of subsurface microorganisms. These and similar approaches will further enhance our ability to more rigorously analyze the composition and structure of low-biomass (e.g., < 10(5) cells g(-1)), subsurface microbial communities.