Effects of soil management on structure and activity of denitrifying bacterial communities

The influx of carbon sources and energy into the grossly oligotrophic soil system is a major driving force in biogeochemical cycles. Differences in these inputs due to the ground-covering plants and agriculture practices, likely influence the activity of the microbial communities. Previously, we have shown that the extent and degree of active bacterial diversity in soils are clearly affected by the type of management. In the present study we have evaluated the effects of different soil managements (tilled vineyard, grass-covered vineyard, temporary grassland, pasture, cork oak forest) on the diversity and activity of denitrifying bacterial species. Total DNA and RNA were directly extracted from soil sampled in two different seasons, spring and autumn. Genes and transcripts for two nitrite reductases (nirS and nirK), nitric oxide reductases (qnorB) and nitrous oxide reductase (nosZ) were used as PCR targets of denitrifying bacteria. Denaturing Gradient Gel Electrophoresis (DGGE) results showed a high abundance and wide distribution of bacterial denitrifiers in soil, while denitrifying gene expression was detected in few species or groups of species. A distinct seasonal shift was evident in denitrifying active communities, that also showed a significant variation depending on soil variables such as texture, pH and organic carbon. DGGE band sequence analysis revealed similarities between sequences found in our soil and those belonging mainly to α and β-Protebacteria division. However, several sequences were not related to any known denitrifying species. The applied RT-nested PCR approach has proven to have the potential to provide information on diversity of active denitrifying bacterial communities and on where and when these bacteria express their ability within the soil.