Dataset Information

Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil.

ABSTRACT: Isolated soil DNA from an oak-hornbeam forest close to Cologne, Germany, was suitable for PCR amplification of gene segments coding for the 16S rRNA and nitrogenase reductase (NifH), nitrous oxide reductase (NosZ), cytochrome cd(1)-containing nitrite reductase (NirS), and Cu-containing nitrite reductase (NirK) of denitrification. For each gene segment, diverse PCR products were characterized by cloning and sequencing. None of the 16S rRNA gene sequences was identical to any deposited in the data banks, and therefore each of them belonged to a noncharacterized bacterium. In contrast, the analyzed clones of nifH gave only a few different sequences, which occurred many times, indicating a low level of species richness in the N2-fixing bacterial population in this soil. Identical nifH sequences were also detected in PCR amplification products of DNA of a soil approximately 600 km distant from the Cologne area. Whereas biodiversity was high in the case of nosZ, only a few different sequences were obtained with nirK. With respect to nirS, cloning and sequencing of the PCR products revealed that many false gene segments had been amplified with DNA from soil but not from cultured bacteria. With the 16S rRNA gene data, many sequences of uncultured bacteria belonging to the Acidobacterium phylum and actinomycetes showed up in the PCR products when isolated DNA was used as the template, whereas sequences obtained for nifH and for the denitrification genes were closely related to those of the proteobacteria. Although in such an experimental approach one has to cope with the enormous biodiversity in soils and only a few PCR products can be selected at random, the data suggest that denitrification and N2 fixation are not genetic traits of most of the uncultured bacteria.

SUBMITTER: Rosch C

PROVIDER: S-EPMC124007 | biostudies-literature | 2002 Aug

REPOSITORIES: biostudies-literature

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Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil.

Rösch Christopher C Mergel Alexander A Bothe Hermann H

Applied and environmental microbiology 20020801 8

Isolated soil DNA from an oak-hornbeam forest close to Cologne, Germany, was suitable for PCR amplification of gene segments coding for the 16S rRNA and nitrogenase reductase (NifH), nitrous oxide reductase (NosZ), cytochrome cd(1)-containing nitrite reductase (NirS), and Cu-containing nitrite reductase (NirK) of denitrification. For each gene segment, diverse PCR products were characterized by cloning and sequencing. None of the 16S rRNA gene sequences was identical to any deposited in the data ...[more]

PMID: 12147477

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Project description:Soil respiration in forests contributes to significant carbon dioxide emissions from terrestrial ecosystems but it varies both spatially and seasonally. Both abiotic and biotic factors influence soil respiration but their relative contribution to spatial and seasonal variability remains poorly understood, which leads to uncertainty in models of global C cycling and predictions of future climate change. Here, we hypothesize that tree diversity, soil diversity, and soil properties contribute to local-scale variability of soil respiration but their relative importance changes in different seasons. To test our hypothesis, we conducted seasonal soil respiration measurements along a local-scale environmental gradient in a temperate forest in Northeast China, analyzed spatial variability of soil respiration and tested the relationships between soil respiration and a variety of abiotic and biotic factors including topography, soil chemical properties, and plant and soil diversity. We found that soil respiration varied substantially across the study site, with spatial coefficients of variation (CV) of 29.1%, 27.3% and 30.8% in spring, summer, and autumn, respectively. Soil respiration was consistently lower at high soil water content, but the influence of other factors was seasonal. In spring, soil respiration increased with tree diversity and biomass but decreased with soil fungal diversity. In summer, soil respiration increased with soil temperature, whereas in autumn, soil respiration increased with tree diversity but decreased with increasing soil nutrient content. However, soil nutrient content indirectly enhanced soil respiration via its effect on tree diversity across seasons, and forest stand structure indirectly enhanced soil respiration via tree diversity in spring. Our results highlight that substantial differences in soil respiration at local scales was jointly explained by soil properties (soil water content and soil nutrients), tree diversity, and soil fungal diversity but the relative importance of these drivers varied seasonally in our temperate forest.

Dataset Information

Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil.

Publications

Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil.

Similar Datasets

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