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

Abstract

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 (N 2 O) or dinitrogen (N 2 ) 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 on...

Response of denitrification genes nirS, nirK, and nosZ to irrigation water quality in a Chinese agricultural soil

“…In this study, there was lower nirS gene abundance than nirK in all samples, which was consistent with some previous studies (Hai et al 2009;Yoshida et al 2009). The abundance of nosZ gene was the highest one among the three functional genes in this study.…”

“…Wolsing and Prieme (2004) found that fertilization with mineral fertilizer and cattle manure caused a shift in the community structure of denitrifiers in an agricultural soil. More recently, it was reported that organic fertilizers (manure, straw) increased the abundance of both nirK and nirS genes in a tropical agro-ecosystems (Hai et al 2009). These studies indicated that the abundance and community structure of the soil denitrifiers were influenced by N availability, carbon availability, moisture, pH, and management practices, and these different functional genes could respond differently to environmental changes.…”

Land-use systems affect Archaeal community structure and functional diversity in western Amazon soils

“…Interestingly, Yrjala et al (2004) showed that the addition of ashes to the soil microcosm leads to significant changes in the archaeal community. In this context, it is also important to consider that different plant development stages, litter quality and historical soil management practices can influence the diversity and community structure of soil-inhabiting Archaea (Hai et al, 2009;Su et al, 2010).…”

Chemistry and Microbial Functional Diversity Differences in Biofuel Crop and Grassland Soils in Multiple Geographies

“…For instance, we observed some significant differences among the N-cycling genes for the sorghum crop and grassland sites for nitrogen fixation, nitrification, and denitrification. Interestingly, effects of N fertilization have been reported to impact the number of copies of nifH genes in the rhizosphere of sorghum [46], numbers of ammonia-oxidizing bacteria denitrifiers [47], numbers of plant growth-promoting rhizobacteria in sorghum soils [48], and abundance of ammonia oxidizers and denitrifiers in maize soils [49]. The lower microbial gene diversity in sorghum soil samples was not restricted to genes within the carbon cycling, nitrogen cycling, phosphorus utilization, and sulphur utilization.…”

“…Using the GeoChip FGA approach, which is based on DNA probes for functional microbial genes rather than for specific taxa, we observed some significant differences among the N cycling genes for nitrogen fixation, nitrification, and denitrification. In addition to the known effects of N fertilization on soil microbial communities [46][47][48][49], other factors reported to influence microbial composition and activities in soils include plant species and genotype, soil type, soil structure and pH, and the interactions and feedback between plants and soils [37][38][39][40][41][42]. Use of the GeoChip 4.0 allowed us to look for microbial gene diversity and abundance differences among diverse geographic samples across multiple gene categories that related to important ecosystem processes such as C, N, P, and S cycling.…”