Application of N 2 -fixing Paenibacillus triticisoli BJ-18 changes the compositions and functions of the bacterial, diazotrophic, and fungal microbiomes in the rhizosphere and root/shoot endosphere of wheat under field conditions

From 2015 to 2018, we continuously applied the diazotroph Paenibacillus triticisoli BJ-18 as an inoculant to soil cropped winter wheat under field condition. Based on 16S rRNA, nifH, ITS, and shotgun metagenome sequencing, we investigated the influences of diazotroph on the composition and function of the bacterial, diazotrophic, and fungal communities in the rhizosphere and root/shoot endosphere of wheat in 2018. P. triticisoli BJ-18 significantly increased soil total N, available P, organic matter, nitrogenase activity, and wheat yield. The diversities of the rhizospheric bacterial community were higher in the inoculation treatment than the non-inoculation treatment, while the relative abundances of rhizospheric fungal, endospheric bacterial, and diazotrophic communities were lower in the inoculation treatment. Paenibacillus became dominant in the rhizosphere and root, and also the relative abundance of indigenous diazotrophs was increased by inoculation. The microbial inoculation also significantly increased the relative abundances of indigenous plant growth-promoting microbes (Bacillus, Klebsiella, and Podospora) but decreased the relative abundances of indigenous pathogenic fungi (Alternaria). Notably, some nitrogenase gene abundances were significantly enriched by inoculation. These results demonstrated that P. triticisoli BJ-18, acting as a keystone species, can change (optimize) the composition and function of plant microbiome to promote plant growth and productivity.