16S rDNA analysis for characterization of denitrifying bacteria isolated from three agricultural soils

• Published in: FEMS microbiology ecology 2000-12, Vol.34 (2), p.121-128
• Main Authors: Chèneby, Dominique, Philippot, Laurent, Hartmann, Alain, Hénault, Catherine, Germon, Jean-Claude
• Format: Article
• Language: English
• Subjects: 16S rDNA; Agronomy. Soil science and plant productions; Amplified ribosomal DNA restriction analysis; Animal, plant and microbial ecology; Bacillus; Biochemistry and biology; Biological and medical sciences; Burkholderia; Chemical, physicochemical, biochemical and biological properties; Denitrification; Denitrifier; Frateuria; Fundamental and applied biological sciences. Psychology; Life Sciences; Microbial ecology; Microbiology; Microbiology and Parasitology; Phylogenetic diversity; Physics, chemistry, biochemistry and biology of agricultural and forest soils; Pseudomonas; Ralstonia; rRNA genes; Soil; Soil science; Streptomyces; Xanthomonas
• ISSN: 0168-6496; 1574-6941
• DOI: 10.1016/S0168-6496(00)00080-5

Bacteria capable of denitrification are spread among phylogenetically diverse groups. In the present investigation, molecular methods (amplified ribosomal DNA restriction analysis (ARDRA) and partial 16S rDNA gene sequencing) were used to determine the genetic diversity of culturable denitrifying soil bacteria. The purpose of this work was to study the microbial density and diversity of denitrifying communities isolated from two luvisols and a rendosol. The denitrifying bacterial density was significantly higher in the two luvisols (3×10 6 and 4×10 6 bacteria g −1 dry soil) than in the rendosol (4×10 5 bacteria g −1 dry soil). Denitrifying isolates from soils were grouped according to the similarity of their restriction patterns into 26 ARDRA types. Interestingly ARDRA analysis suggests that some denitrifying isolates are specific to a soil type while others seem to be geographically widespread. The number of individual isolates found in each ARDRA type appeared to be highly variable between the two sampling dates but some denitrifying types were capable of persisting in soil. The tree obtained from the partial sequences revealed five major branches exhibiting highest identity to the following genera: (i) Burkholderia-Ralstonia, (ii) Pseudomonas, (iii) Xanthomonas-Frateuria, (iv) Bacillus and (v) Streptomyces. Our 16S rDNA-based analysis clearly reveals broad diversity exceeding that previously described in the literature.