Applied and Environmental Microbiology, September 2001, p. 3908-3922, Vol. 67, No. 9
0099-2240/01/$04.00+0 DOI: 10.1128/AEM.67.9.3908-3922.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.


andCivil Engineering Department, Northwestern University, Evanston, Illinois 602081; Center for Great Lakes Studies, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 532042; and Department of Biology, Central Michigan University, Mount Pleasant, Michigan 488593
Received 13 February 2001/Accepted 21 June 2001
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.
Present address: Pacific Northwest National Laboratories, Richland,
WA 99532.
Present address: Department of Geology and Geophysics, University
of Wisconsin, Madison, WI 53706.
§
Present address: Engineering Sciences Department, EAWAG, CH8600
Dübendorf, Switzerland.
Present address: Jet Propulsion Laboratory, California Institute
of Technology, Pasadena, CA 91109.
#
Present address: Civil and Environmental Engineering, University of
Washington, Seattle, WA 98195-2700.
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