# From metabolic fingerprints to field solutions: engineering the apple rhizosphere microbiome via host-directed Bacillus recruitment for sustainable apple replant disease control

## TL;DR

This study shows how apple trees resist replant disease by using lysine to recruit helpful bacteria, offering a sustainable solution for controlling the disease.

## Contribution

The study reveals a novel mechanism of apple replant disease resistance through lysine-mediated recruitment of protective Bacillus bacteria.

## Key findings

- Resistant apple rootstocks activate a lysine biosynthesis pathway, increasing lysine efflux and recruiting Bacillus bacteria.
- Bacillus suppresses Fusarium spore germination and mycelial growth via antifungal compounds like 2,4-di-tert-butylphenol and bacillomycin.
- Synergistic treatment of Bacillus and lysine reduces pathogenic Fusarium, enhances soil enzyme activity, and improves plant growth.

## Abstract

The rhizosphere microbiome, as the second genome of plant immunity, forms a critical ecological barrier in plant-pathogen interactions. However, its functional mechanism in resisting the replanting disease pathogenic Fusarium proliferatum MR5 in apples has not been systematically elucidated. This study employed an integrated multi-omics approach to investigate the rhizosphere mechanisms of resistant (CG935) and sensitive (M9T337) apple rootstocks, aiming to uncover the metabolic and microbial interactions underlying apple replant disease resistance.

Multiple omics joint analysis found that the infection of Fusarium proliferatum MR5 triggered the activation of a specific lysine biosynthesis pathway in resistant rootstocks, and the expression levels of key rate limiting enzymes aspartate kinase and dihydrodipicolinate synthase were significantly upregulated by 2.79 ~ 6.81 times compared to M9T337. Along with the metabolic reprogramming process, the efflux of lysine from the rhizosphere increased, and Bacillus with broad-spectrum antibacterial activity were specifically recruited, increasing its relative abundance by 40.73%. In vitro assays demonstrated that the recruited Bacillus suppressed Fusarium spore germination and disrupted mycelial growth through the production of antifungal compounds, including 2,4-di-tert-butylphenol and bacillomycin. Potted experiments have confirmed that the synergistic treatment of Bacillus and lysine significantly reduces the number of pathogenic Fusarium in the rhizosphere, increases soil enzyme activity, and reshapes a more stable rhizosphere bacterial community structure by enhancing the modularity (the degree of modularity in microbial network structure) of the microbial network. This collaborative strategy effectively alleviates the physiological damage of apple seedlings under replanting stress, resulting in a 31.18% increase in plant fresh weight. Field validation experiments further demonstrate that this strategy can promote the growth of replanted apple saplings and reduce the occurrence of apple replant disease.

Our findings elucidate an apple replant disease resistance mechanism in apple rootstocks involving lysine-mediated recruitment of protective Bacillus, which enhances rhizosphere microbiome stability and suppresses soil pathogenic Fusarium. Developed a technology for synergistic control of apple replant disease using Bacillus-lysine. The research results provide theoretical basis and practical solutions for green control of apple replant disease based on precise regulation of rhizosphere microbiome.

Video Abstract

Video Abstract

The online version contains supplementary material available at 10.1186/s40168-025-02301-9.