Intercropping is widely used as an important means to promote crop productivity; but the underpinning mechanisms of rhizosphere soil microbial processes in shaping soil phosphorus (P) bioavailability under cotton-based intercropping systems have not been investigated in arid northwest China. Therefore, taking cotton-maize intercropping as an example, biologically based P (BBP) and metagenomics methods were used to investigate changes of soil P bioavailability, microbial community and functional P-cycling genes in the rhizosphere. Three treatments were cotton monoculture, maize monoculture and cotton-maize intercropping. We found that rhizosphere soils from cotton-maize intercropping exhibited higher soil organic matter (SOM), available P (AP), and alkaline phosphatase (ALP) than those of crop monocultures (p < 0.05). The change of bioavailable-P fractions in the order HCl-P > Citrate-P > Enzyme-P > CaCl2-P, and higher mount of CaCl2-P, Citrate-P and Enzyme-P were observed in soil samples from cotton-maize intercropping. These results indicated that P bioavailability were improved after two crops intercropping. The dominate soil microbial community from all treatments belonged to the phyla Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi and Gemmatimonadetes. In addition, we observed that the expression of functional genes which involved in soil microbial inorganic phosphate transportation (phoR), inorganic phosphate solubilization (phoD, glpA, glpK, glpQ), phosphate ester mineralization (gcd, ppk, ppx), and phosphate ester mineralization (pstABC, pit) were also up-regulated in cotton-maize intercropping (p < 0.05). Redundancy analysis showed that SOM, CaCl2-P and AP significantly correlated genes gcd, ppx, pstABC, pit, and phoD, suggesting that SOM, CaCl2-P and available P are important factors in influencing expression of these P-cycling functional genes. It is concluded that cotton-maize intercropping increased P bioavailability via changing rhizosphere soil microbial composition and functional genes.
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