Quantification of Key Genes Steering the Microbial Nitrogen Cycle in the Rhizosphere of Sorghum Cultivars in Tropical Agroecosystems

The effect of agricultural management practices on geochemical cycles in moderate ecosystems is by far better understood than in semiarid regions, where fertilizer availability and climatic conditions are less favorable. We studied the impact of different fertilizer regimens in an agricultural long-term observatory in Burkina Faso at three different plant development stages (early leaf development, flowering, and senescence) of sorghum cultivars. Using real-time PCR, we investigated functional microbial communities involved in key processes of the nitrogen cycle (nitrogen fixation, ammonia oxidation, and denitrification) in the rhizosphere. The results indicate that fertilizer treatments and plant development stages combined with environmental factors affected the abundance of the targeted functional genes in the rhizosphere. While nitrogen-fixing populations dominated the investigated communities when organic fertilizers (manure and straw) were applied, their numbers were comparatively reduced in urea-treated plots. In contrast, ammonia-oxidizing bacteria (AOB) increased not only in absolute numbers but also in relation to the other bacterial groups investigated in the urea-amended plots. Ammonia-oxidizing archaea exhibited higher numbers compared to AOB independent of fertilizer application. Similarly, denitrifiers were also more abundant in the urea-treated plots. Our data imply as well that, more than in moderate regions, water availability might shape microbial communities in the rhizosphere, since low gene abundance data were obtained for all tested genes at the flowering stage, when water availability was very limited.Land degradation is one of the most serious threats to food production on the African continent. Soil erosion, nutrient depletion, low organic matter content, and unfavorable pH values are some of the reasons for a deficient soil fertility (30), mainly in Central African countries. Combined with high variability and irregular distribution of rainfall, these factors contribute to negative nutrient balances. For example, 4.4 million tons of nitrogen (N) are lost per year in African soils, but only 0.8 million tons are reapplied by fertilization (12, 34). Since nitrogen is a key nutrient determining the productivity of agroecosystems (7, 11, 43), it is of central importance to optimize the nitrogen balance in these countries, mainly by steering the genetic resources of soil microbes in a way that losses of applied nitrogen are minimized and biological nitrogen fixation is increased. The aim should be to obtain a highly efficient nitrogen turnover, with leaching of nitrate and losses of gaseous products such as nitrous oxide (N₂O) or dinitrogen (N₂) as low as possible.Despite the importance of this issue, not much data are available on microbial community structure and function related to the nitrogen cycle in agroecosystems of Central Africa, and scenarios from moderate climatic regions cannot simply be transferred to tropical agroecosystems. Furthermore, the few studies published thus far only investigated effects of agricultural management on a single process of the nitrogen turnover (18, 20, 32) and ignore the fact that nitrogen turnover is a network of closely interlinked processes.Therefore, we sought to investigate the effects of different fertilizer regimens on multiple transformation processes within the nitrogen cycle in agroecosystems from semiarid areas in Central Africa. We investigated nitrogen dynamics on a full-cycle approach, including the most important steps in well-aerated agricultural soils (nitrification, denitrification, and nitrogen fixation). We hypothesized that each fertilizer regimen results in typical abundance pattern of the functional populations. While in moderate agroecosystems the plant (respectively, the plant development stage and the plant performance) plays an important role in shaping microbial community structure and function in the rhizosphere, we further postulated that nitrogen turnover and the corresponding populations are also influenced by the availability of water in semiarid soils. To test these hypotheses on a molecular basis, we quantified bacterial genes encoding the nitrogenase reductase (nifH), ammonia monooxygenase (amoA), and nitrite reductase (nirK and nirS), as well as archaeal amoA genes, by real-time PCR and linked the data to soil properties and grain yield.