Applied and Environmental Microbiology, April 2001, p. 1893-1901, Vol. 67, No. 4
0099-2240/01/$04.00+0 DOI: 10.1128/AEM.67.4.1893-1901.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
Center for Microbial Ecology1 and Department of Microbiology and Molecular Genetics,2 Michigan State University, East Lansing, Michigan 48824-1325; School of Oceanography, University of Washington, Seattle, Washington 982953; and Landeskriminalamt Schleswig-Holstein, 24116 Kiel, Germany4
Received 17 August 2000/Accepted 19 December 2000
Steep vertical gradients of oxidants (O2 and
NO3
) in Puget Sound and Washington
continental margin sediments indicate that aerobic respiration and
denitrification occur within the top few millimeters to centimeters. To
systematically explore the underlying communities of denitrifiers,
Bacteria, and Archaea along redox gradients at
distant geographic locations, nitrite reductase (nirS) genes and bacterial and archaeal 16S rRNA genes (rDNAs) were PCR amplified and analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis. The suitablility of T-RFLP analysis for
investigating communities of nirS-containing denitrifiers was established by the correspondence of dominant terminal restriction fragments (T-RFs) of nirS to computer-simulated T-RFs of
nirS clones. These clones belonged to clusters II, III, and
IV from the same cores and were analyzed in a previous study (G. Braker, J. Zhou, L. Wu, A. H. Devol, and J. M. Tiedje, Appl.
Environ. Microbiol. 66:2096-2104, 2000). T-RFLP analysis of
nirS and bacterial rDNA revealed a high level of functional
and phylogenetic diversity, whereas the level of diversity of
Archaea was lower. A comparison of T-RFLPs based on the
presence or absence of T-RFs and correspondence analysis based on the
frequencies and heights of T-RFs allowed us to group sediment samples
according to the sampling location and thus clearly distinguish Puget
Sound and the Washington margin populations. However, changes in
community structure within sediment core sections during the transition
from aerobic to anaerobic conditions were minor. Thus, within the top
layers of marine sediments, redox gradients seem to result from the
differential metabolic activities of populations of similar
communities, probably through mixing by marine invertebrates rather
than from the development of distinct communities.
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