We have used molecular biological methods to study the distribution of microbial small-subunit rRNAs (SSU rRNAs), in relation to chemical profiles, in offshore Lake Michigan sediments. The sampling site is at a depth of 100 m, with temperatures of 2 to 4°C year-round. RNA extracted from sediment was probed with radiolabeled oligonucleotides targeting bacterial, archaeal, and eukaryotic SSU rRNAs, as well as with a universal probe. The coverage of these probes in relation to the present sequence database is discussed. Because ribosome production is growth rate regulated, rRNA concentrations are an indicator of the microbial populations active in situ. Over a 1-year period, changes in sedimentary SSU rRNA concentrations followed seasonal changes in surface water temperature and SSU rRNA concentration. Sedimentary depth profiles of oxygen, reduced manganese and iron, and sulfate changed relatively little from season to season, but the nitrate concentration was approximately fivefold higher in April and June 1997 than at the other times sampling was done. We propose that sediment microbial SSU rRNA concentrations at our sampling site are influenced by seasonal inputs from the water column, particularly the settling of the spring diatom bloom, and that the timing of this input may be modulated by grazers, such that ammonia becomes available to sediment microbes sooner than fresh organic carbon. Nitrate production from ammonia by autotrophic nitrifying bacteria, combined with low activity of heterotrophic denitrifying bacteria in the absence of readily degradable organic carbon, could account for the cooccurrence of high nitrate and low SSU rRNA concentrations.Molecular microbiological methods based on nucleic acid (RNA and DNA) extraction can yield information about the in situ distribution and activities of multiple microbial groups simultaneously from a relatively small volume of sample. They are especially useful for sediments, where numerous different species are present and chemical composition and microbial populations can change on a scale of millimeters to centimeters. Molecular methods are also free of the well-known biases associated with traditional culture-based approaches, such as the preferential recovery of species that are well adapted to laboratory conditions, although issues such as extraction efficiency have yet to be fully resolved.In this study, we have used oligonucleotide probes to characterize small-subunit rRNAs (SSU rRNAs) extracted from sediments at an offshore Lake Michigan site. SSU rRNA is an essential component of the ribosome, the RNA-protein complex responsible for protein synthesis in both prokaryotes and eukaryotes. rRNA-encoding genes (rDNAs) from thousands of species have now been sequenced and used to infer phylogenetic relationships based on nucleotide sequence divergence (67). Because the ribosome content generally increases with growth rate (reviewed in reference 33) and decreases with starvation (see, e.g., references 14, 23, and 46), rRNA quantitation by oligonucleotide prob...