Objectives In this paper, we studied the effects of two bacteria strains on the growth of apple seedlings and the soil biological environment, aiming to provide a green biological control measure to alleviate apple replant disease.

Methods A pot experiment was conducted using soil collected from a 32-year apple orchard. We rejuvenated and processed Malus hupehensis Rehd., Penicillium commune D12 (R1), and Lactobacillus reuteri (R2) into fermentation products with an active bacteria population of ≥2×10⁹ CFU/mL and ≥3×10⁹ CFU/mL, respectively. The four treatments were no strain control (CK), applying R1, R2, and their mixture in a 1:1 (R3) ratio. Soil samples were collected on the 38, 69, and 100 days after application to determine enzyme activities. The samples collected at 100 days post-application were used to determine bacteria and fungi. Simultaneously, apple seedling growth, root respiration rate, and preserved enzyme activities were measured.

Results The growth of Malus hupehensis Rehd. seedlings were promoted under the three fermentation products treatments. The seedlings biomass was in the order R3 >R1 >R2 >CK. At 100 days, the plant height, ground diameter, fresh weight, dry weight, and root respiration rate of R3 were 7.7%, 17.4%, 50.82%, 37.5%, and 17.04% higher than CK, respectively. The fermentation products increased the activities of soil enzymes to different degrees. Compared with CK, R3 increased the activities of soil urease, phosphatase, and invertase by 66.67%, 34.24%, and 25.49%, respectively. The fermentation products promoted the antioxidant enzyme activity in the roots of Malus hupehensis Rehd. seedlings. R3 increased the activities of SOD, POD, and CAT, by 29.19%, 92.62%, and 39.59% on the 100th day, respectively. PCoA analysis and cluster analysis showed that the application of fermentation products impacted the replanted soil fungal community. The effects of single fermentation product treatment (R1 and R2) and mixed fermentation products treatment (R3) on the replanted soil fungal community differed. Applying the fermentation products increased the number of cultivable bacteria and decreased the number of cultivable fungi in soil. The relative abundance of Humicola and Mortierella in R3 soil increased by 73.61% and 137.72%, while Fusarium and Alternaria decreased by 52.48% and 73.35%, respectively. The biomass, root respiration rate, and root enzyme activity of Malus hupehensis Rehd. seedlings were significantly positively correlated with soil urease activity. Further, the ground diameter had a significant negative correlation with the number of fungi, Fusarium, Alternaria, and Cladosporium.

Conclusions The application of Penicillium commune D12 and Lactobacillus reuteri fermentation products could promote the growth of Malus hupehensis Rehd. seedlings, increase root respiration rate, SOD, POD and CAT activities, and soil enzyme activities. It improves the replanted soil microbial community structure and makes the soil environment conducive to plant growth. Therefore, the fermentation products could be an effective measure to prevent and control the apple replant disease.