Taxonomical and functional bacterial community selection in the rhizosphere of the rice genotypes with different nitrogen use efficiencies

As the overuse of nitrogen fertilizer has caused series of environmental problems, improving the nitrogen use efficiency of rice crop has been drawing much attention. Since developing nitrogen-efficient rice genotypes is a feasible solution, illustrating the microbiological characteristics of the nitrogen-efficient rice genotypes is of great importance. We performed a field experiment, and planted 16 genotypes of rice. The nitrogen utilization efficiencies and yields of rice were examined. Real-time PCR and Illumina sequencing were employed to investigate the abundance of the nitrogen-cycle related genes and the bacterial community structure of the rhizosphere. The results revealed that rice genotypes enriched specific bacterial communities to inhabit in the rhizosphere at both the taxonomic and functional levels. The enriched bacteria were mainly involved in the functions of nitrogen transformation, ferric iron reduction, organic compound biodegradation, and sulfur transformation. We observed a strong correlation between the yield and the abundance of rhizospheric functional bacteria, especially the groups of Proteobacteria and Chloroflexi. The analysis of nitrite reductase and denitrifying genes showed that the denitrification activity in the rhizosphere inversely correlate with the efficiency of nitrogen utilization. We reason that a smaller denitrifying bacteria population leads to less the nitrogen loss in the rhizosphere, thus an increase of available nitrogen and a higher rice yield. This research revealed how functional bacteria assembled in the rhizosphere of rice genotypes with varied nitrogen use efficiencies, which may provide valuable information with regard to the improvement of nitrogen use efficiency and reduction of fertilizer application.