'Dolomite lime effects on acid forest soils: traditional and molecular approaches

The study of biogeochemical processes in soil has long been restricted by the techniques available for investigating the micro-organisms concerned. In particular, isolated nitrifying bacteria are not active in culture media below pH 5.5-6.0, and it is not clear to what extent these strains, if at all, are active in the acid soils of temperate forests. Since DNA/RNA based microbiological techniques do not require isolation of bacterial strains, they provide a new, powerful approach to gain insight into the nitrification process. We therefore combined the use of a large scale field experiment and laboratory soil incubations with molecular analysis of the nitrifying bacterial community to investigate the effect of dolomite lime on the nitrification process in the soil of the Belgian Ardenne.
In this area, soils are naturally poor in magnesium and liming at moderate doses has been suggested to alleviate soil acidification and nutritional deficiencies. However, possible side effects needed to be evaluated, in particular on the nitrification process. As nitrification may be linked to soil acidification, cation leaching, aluminium mobilisation and N2O emission, increased knowledge is essential when evaluating effects of global environmental change and management strategies on forest ecosystems. The effects of dolomite lime (3-5 T/ha) were investigated at the watershed (80 ha, mainly Picea abies), plot (Quercus petraea and Picea abies stands) and laboratory level. Runoff chemistry, soil solution, net nitrate production in the laboratory and the community structure of ammonium oxidising bacteria (by PCR amplification of 16S-RNA genes, Denaturing Gradient Gel Electrophoresis - DGGE, sequence analysis and hybridisation) were analysed.
In the watersheds, consequences on runoff water chemistry were minor. However, in the plot study, soil solution nitrate concentrations were significantly increased through liming in the Quercus plots. Increased net nitrification in the Quercus stand was confirmed by potential net nitrification measurements in the laboratory, whereas soil pH rose in both stands. The impact of liming on potential net nitrification was not related to a shift in the 16S rDNA DGGE community profile of ammonia-oxidising bacteria. The DDGE profile, combined with hybridisation and sequencing of cut out bands revealed a dominance of Nitrosomonas europea-like sequences and a minor presence of Nitrosospira cluster 2-like sequences. These results contrast with several reports suggesting a dominance of Nitrosospira-like organisms among ammonia oxidiser communities in acid soils. Our study reflects the great potential of combining new molecular techniques with conventional methods for improving our knowledge on the ecology of biogeochemical processes.