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Plant growth-promoting bacteria (PGPB) can effectively reduce salt damage in plants. Currently, there are many studies on the effects of PGPB on the microbial community structure of rhizosphere soil under salt stress, but fewer studies on the community structure of endophytic bacteria and fungi. We propose that inoculation of endophytic bacteria into the rhizosphere of plants can significantly affect the microbial community structure of the plant’s above-ground and underground parts, which may be the cause of the plant’s “Induced Systemic Tolerance.” The isolated endophytes were re-inoculated into the rhizosphere under salinity stress. We found that, compared with the control group, inoculation with endophytic Bacillus velezensis JC-K3 not only increased the accumulation of wheat biomass, but also increased the content of soluble sugar and chlorophyll in wheat, and reduced the absorption of Na in wheat shoots and leaves. The abundance of bacterial communities in shoots and leaves increased and the abundance of fungal communities decreased after inoculation with JC-K3. The fungal community richness of wheat rhizosphere soil was significantly increased. The diversity of bacterial communities in shoots and leaves increased, and the richness of fungal communities decreased. JC-K3 strain improved wheat’s biomass accumulation ability, osmotic adjustment ability, and ion selective absorption ability. In addition, JC-K3 significantly altered the diversity and abundance of endophytic and rhizosphere microorganisms in wheat. PGPB can effectively reduce plant salt damage. At present, there are many studies on the effect of PGPB on the microbial community structure in rhizosphere soil under salt stress, but there are few studies on the community structure changes of endophytic bacteria and fungi in plants.

As the main economic crop cultivated in the Yellow River Delta, winter jujube contains various nutrients. However, soil salinization and fungal diseases have affected the yield and quality of winter jujube. In order to use plant growth-promoting rhizobacteria (PGPR) to reduce these damages, the antagonistic bacteria CZ-6 isolated from the rhizosphere of wheat in saline soil was selected for experiment. Gene sequencing analysis identified CZ-6 as Bacillus amyloliquefaciens. In order to understand the salt tolerant and disease-resistant effects of CZ-6 strain, determination of related indicators of salt tolerance, pathogen antagonistic tests, and anti-fungal mechanism analyses was carried out. A pot experiment was conducted to evaluate the effect of CZ-6 inoculation on the rhizosphere microbial community of winter jujube. The salt tolerance test showed that CZ-6 strain can survive in a medium with a NaCl concentration of 10% and produces indole acetic acid (IAA) and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase. Studies on the inhibition mechanism of pathogenic fungi show that CZ-6 can secrete cellulase, protease, and xylanase. Gas chromatography-mass spectrometry (GC-MS) analysis showed that CZ-6 can release volatile organic compounds (VOCs), including 2-heptanone and 2-nonanone. In addition, the strain can colonize the rhizosphere and migrate to the roots, stems, and leaves of winter jujube, which is essential for plant growth or defense against pathogens. Illumina MiSeq sequencing data indicated that, compared to the control, the abundance of salt-tolerant bacteria Tausonia in the CZ-6 strain treatment group was significantly increased, while the richness of Chaetomium and Gibberella pathogens was significantly reduced. Our research shows that CZ-6 has the potential as a biological control agent in saline soil. Plant damage and economic losses caused by pathogenic fungi and salt stress are expected to be alleviated by the addition of salt-tolerant antagonistic bacteria.

Biocontrol by inoculation with beneficial microbes is a proven strategy for reducing the negative effect of soil-borne pathogens. We evaluated the effects of microbial inoculants BIO-1 and BIO-2 in reducing soil-borne wheat diseases and in influencing wheat rhizosphere microbial community composition in a plot test. The experimental design consisted of three treatments: (1) Fusarium graminearum F0609 (CK), (2) F. graminearum + BIO-1 (T1), and (3) F. graminearum F0609 + BIO-2 (T2). The results of the wheat disease investigation showed that the relative efficacies of BIO-1 and BIO-2 were up to 82.5% and 83.9%, respectively. Illumina MiSeq sequencing revealed that bacterial abundance and diversity were significantly higher ( P < 0.05 ) in the treatment groups (T1 and T2) than in the control, with significantly decreased fungal diversity in the T2 group. Principal coordinates and hierarchical clustering analyses revealed that the bacterial and fungal communities were distinctly separated between the treatment and control groups. Bacterial community composition analysis demonstrated that beneficial microbes, such as Sphingomonas, Bacillus, Nocardioides, Rhizobium, Streptomyces, Pseudomonas, and Microbacterium, were more abundant in the treatment groups than in the control group. Fungal community composition analysis revealed that the relative abundance of the phytopathogenic fungi Fusarium and Gibberella decreased and that the well-known beneficial fungi Chaetomium, Penicillium, and Humicola were more abundant in the treatment groups than in the control group. Overall, these results confirm that beneficial microbes accumulate more easily in the wheat rhizosphere following application of BIO-1 and BIO-2 and that the relative abundance of phytopathogenic fungi decreased compared with that in the control group.