Relative abundance of denitrifying and dinitrogen-fixing bacteria in layers of a forest soil

Abstract

The populations of N(2)-fixing and denitrifying bacteria in an acid forest soil near Cologne were characterized by gene probing. The DNA isolated from the soil for this purpose was suitable for DNA-DNA hybridization using 0.4-0.7-kb probes targeting denitrification enzymes, dinitrogenase reductase (nifH) and eubacterial 16S rRNA. The densitometrical comparison of band intensities obtained in these Southern hybridizations indicated that the highest number of total bacteria, of denitrifying and N(2)-fixing microorganisms always occurred in the upper ( approximately 5 cm) soil layer. The concentration of all these organisms decreased in parallel with the soil depth. The soil investigated was rich in nitrate in all layers, and the availability of nitrate apparently did not govern the distribution of denitrifying and N(2)-fixing bacteria in this soil. Soil cores investigated in the laboratory formed N(2)O on addition of nitrate irrespective of the presence of C(2)H(2). Hybridization intensities, with a gene probe for the 16S rRNA, and MPN numbers were generally higher in soil samples taken from the roots of plants than in the bulk soil. There was no selective enrichment of denitrifying or N(2)-fixing bacteria at the roots. The data obtained by hybridizing isolated soil DNA generally matched previous results obtained with culturable bacteria.

Long-term experimental warming alters nitrogen-cycling communities but site factors remain the primary drivers of community structure in high arctic tundra soils

“…However, Braker et al (2001) used an alternative denitrification marker (nirS) to investigate changes in community structure in ocean sediment cores based upon the transition to an anaerobic environment and as depth increased only a slight decrease in denitrifier diversity was detected in deeper samples even though a strong redox gradient was present. Enzyme analysis and gene probing of forest soils have also shown that denitrifier abundance decreases with depth despite lower levels of oxygen in deep samples (À25 cm) that should favor anaerobes (Mergel et al, 2001;Rö sch et al, 2002). Our findings are not inconsistent with these studies, although we did not measure absolute abundance of nosZ or nifH.…”

New Method of Denitrification Analysis of Bradyrhizobium Field Isolates by Gas Chromatographic Determination of 15 N-Labeled N 2

“…Most denitrifying bacteria reduce the electron acceptors sequentially as NO 3 Ϫ 3 NO 2 Ϫ 3 NO 3 N 2 O 3 N 2 , and each step of these reactions is catalyzed by specific respective reductases (31). To evaluate denitrification capability, the acetylene inhibition assay (30) has been widely used in pure cultures (13) as well as for environmental samples such as soils (8,14,27) and water (24) because of sensitivity and atmospheric N 2 contamination (13). In this assay, the excess of N 2 O emission in the presence of acetylene over the level of N 2 O emission in the absence of acetylene is regarded as the N 2 evolution (because acetylene inhibits N 2 O reductase).…”

Determination of Denitrification Genes Abundance in Environmental Samples

“…For denitrifying bacteria, oligomer microarrays of different molecular sizes have been developed for assessing narG, nirK, nirS, and nosZ diversity and distribution [18,68,112,115,131]. Microarray-based whole-genome hybridization has also been used as a technique to detect and identify microorganisms in environmental samples [132].…”