Detection and community dynamics of denitrifying bacteria in riparian buffer strips and agricultural soils

Nitrate runoff from agro-ecosystems is a major environmental concern but soil nitrogen management and nitrate reduction can be achieved through the exploitation of defined microbial activities within appropriate off-field set ups. Among these, purposely afforested buffer strips surrounding water streams can foster the reduction of nitrate loads through effective denitrification. In the present study we aimed at characterizing the variations of the denitrifyier community in relation to the hydrological regime and to compare them with those occurring in neighbouring agricultural soils. After a chemical soil characterization we assessed the denitrification potential and targeted the nirK nitrite reductase gene by DGGE analysis, band separation and sequencing. Factors affecting the phenomenon and the corresponding microbial guilds included organic carbon availability, soil depth and land use. In parallel RealTime PCR-based quantification protocols were optimized for the detection of nirK in soil bacterial communities. Standardized curves for the enumeration of gene copies per gram of soil were constructed using plasmid-cloned nirK. The dynamics of denitrifyiers fluctuation in the presence of known amounts of different organic fertilizer substrates was measured in potted soils over a two-months period. Results allowed to verify the quantitative PCR performance and to estimate the amount of soil-borne nirK-bearing genomes.