Haloxylon ammodendron and Haloxylon persicum (as sister taxa) are dominant shrubs in the Gurbantunggut Desert. The former grows in inter-dune lowlands while the latter in sand dunes. However, little information is available regarding the possible role of soil microorganisms in their habitat heterogeneity from a nutrient perspective in deserts. Rhizosphere is the interface of plant-microbe-soil interactions and fertile islands usually occur around the roots of desert shrubs. Given this, we applied quantitative real-time PCR combined with MiSeq amplicon sequencing to compare their rhizosphere effects on microbial abundance and community structures at three soil depths (0–20, 20–40, and 40–60 cm). The rhizosphere effects on microbial activity (respiration) and soil properties had also been estimated. The rhizospheres of both shrubs exerted significant positive effects on microbial activity and abundance (e.g. eukarya, bacteria and nitrogen-fixing microbes). The rhizosphere effect of H. ammodendron on microbial activity and abundance of bacteria and nitrogen-fixing microbes was greater than that of H. persicum. However, the fertile island effect of H. ammodendron was weaker than that of H. persicum. Moreover, there existed distinct differences in microbial community structure between the two rhizosphere soils. Soil-available nitrogen, especially nitrate nitrogen was shown to be a driver of microbial community differentiation among rhizosphere and non-rhizosphere soils in the desert. In general, the rhizosphere of H. ammodendron recruited more copiotrophs (e.g. Firmicutes, Bacteroidetes and Proteobacteria), nitrogen-fixing microbes and ammonia-oxidizing bacteria, and with stronger microbial activities. This helps it maintain a competitive advantage in relatively nutrient-rich lowlands. H. persicum relied more on fungi, actinomycetes, archaea (including ammonia-oxidizing archaea) and eukarya, with higher nutrient use efficiency, which help it adapt to the harsher dune crests. This study provides insights into the microbial mechanisms of habitat heterogeneity in two Haloxylon species in the poor desert soil.

This study focuses on the rhizosphere soils (0–60 cm) of H. ammodendron and H. persicum and their corresponding soil environments in the Gurbantunggut Desert. Given that N is the most crucial limiting nutrient factor for plant growth in arid area, we applied quantitative real-time PCR (qPCR) to evaluate the variations in the abundance of bacteria, eukarya, archaea and N-transforming microorganisms (N-fixing microbes, ammonia-oxidizing bacteria and ammonia-oxidizing archaea), as affected by the habitat and rhizosphere. Meanwhile, the study also evaluated compositional shifts in bacterial and eukaryal communities using MiSeq amplicon sequencing. On this basis, we compared rhizosphere effects between these two shrubs in term of microbial activity (i.e., respiration), abundance and community structure, as well as for soil properties.