Community structure of denitrifiers, bacteria, and archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes - PubMed (original) (raw)

Community structure of denitrifiers, bacteria, and archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes

G Braker et al. Appl Environ Microbiol. 2001 Apr.

Abstract

Steep vertical gradients of oxidants (O(2) and NO(3)(-)) 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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Figures

FIG. 1

FIG. 1

Locations and water depths of the sampling stations at Puget Sound and the Washington margin.

FIG. 2

FIG. 2

Profiles of the oxidants oxygen, nitrate, nitrite, and ammonium within sediment cores from Puget Sound (Carkeek) and the Washington margin (cores 301, 306, and 304).

FIG. 3

FIG. 3

Total numbers of T-RFs derived from amplified nirS genes and 16S rDNAs (Bacteria and Archaea) within sediment samples from Puget Sound (C/1 to C/3) and the Washington margin (301/1 to 301/6; 306/1 to 306/5; 304/1 to 304/3). Total numbers were calculated from cleavages with three restriction endonucleases.

FIG. 4

FIG. 4

Relative abundances of T-RF of amplified nirS genes (A) and 16S rDNAs of Bacteria (B) and Archaea (C) within sediment samples from Puget Sound (C/1 to C/3) and the Washington margin (301/1 to 301/6; 306/1 to 306/5; 304/1 to 304/3). Diagrams show results after cleavage with _Hha_I (nirS), _Hae_III (Bacteria), and _Hha_I (Archaea). Numbers on top of the columns indicate the numbers of detectable T-RFs for individual samples. Numbers in the keys indicate the lengths of the T-RFs in base pairs for fragments with a relative abundance of more than 2%.

FIG. 5

FIG. 5

Relationship of T-RFLPs of amplified nirS genes and 16S rDNAs (Bacteria and Archaea) within sediment samples from Puget Sound (C/1 to C/3) and the Washington margin (301/1 to 301/6; 306/1 to 306/5; 304/1 to 304/3). Dendrograms calculated from the presence and absence of peaks (A) and correspondence analysis using combined results from three individual cleavages (B) are shown. Dim, dimension.

FIG. 6

FIG. 6

Comparison of T-RFs of amplified nirS genes to nirS clone fragments from in silico digestion of sequences from marine sediment samples. T-RFs were detected in sediment samples from Puget Sound (C/1) and the Washington margin (304/1); cloned nirS fragments were obtained from environmental DNA extracts from the same core. Shaded peaks and arrows indicate clones corresponding to T-RFs. x axis, size (base pairs); y axis, relative fluorescence units.

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