Rhizosphere effect alters the soil microbiome composition and C, N transformation in an arid ecosystem

Plants exert positive selection effect on rhizosphere microbes by influencing the nutrient conditions of the rhizosphere microenvironment, thereby changing the soil microbial structure and ecological function. In arid regions, water is the major limiting factor affecting the microbial activity and nutrient conversion. However, the effects of soil water availability on the ecological strategies and the C, N functional metabolism of desert microorganisms remain unclear. We hypothesized that soil water availability and rhizosphere effect might alter the strategy for soil C, N utilization in the arid regions. To test the hypothesis, rhizosphere and bulk soil along a gradient of soil water availability in a dry area of northwestern China were analyzed. The soil samples were collected from Reaumuria songarica, Nitraria tangutorum, and Alhagi sparsifolia and were subjected to metagenomic sequencing with a HiSeq system. The relative abundance of Gemmatimonas and Gemmatirosa increased with the increased soil water content, whereas the relative abundance of Microvirga and Nocardioides was decreased. The relative abundance of Azospirillum and Bradyrhizobium did not change with the water content as these microbial communities use limited-water, are drought-tolerant, and use inert strategies to adapt to different levels of water availability. The genes encoding ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) were more abundantly expressed in low water than in high to medium water availability (P < 0.05). The abundance of nitrate reduction genes decreased significantly with the increase in soil water availability, whereas that of denitrification genes increased. The relative abundance of the dissimilatory nitrate reduction process in the rhizosphere soil (44.83%) was significantly higher than that in the bulk soil (39.21%). It can be inferred that soil microorganisms adopt the nitrogen utilization strategy by increasing the ammonium nitrogen to mitigate reduced water availability and provide a nitrogen-rich environment to plant roots.