Influence of rhizosphere microbiome diversity on plant pathogen dynamics and biocontrol success

• Main Author: Nishisaka, Caroline Sayuri
• Publication Date: 2025
• Format: Doctoral thesis
• Language: eng
• Source: Biblioteca Digital de Teses e Dissertações da USP
• Download full: https://www.teses.usp.br/teses/disponiveis/11/11138/tde-03062025-160814/
• topic: Bioinoculant; Bioinoculante; Diluição para extinção; Dilution-to-extinction; Disease suppressiveness; EPS/TasA; EPS/TasA; Genoma; Genome; Rhizosphere; Rizosfera; Supressão de doenças

Soil microbiome is vital for plant health, influencing nutrient cycling, growth promotion, and disease suppression. The rhizosphere, where plant roots interact with soil microorganisms, plays a crucial role in this process. Microorganisms in this region can promote plant growth, protect against pathogens, and enhance plant resilience. The effectiveness of microbial inoculants in the rhizosphere is influenced by soil microbial diversity, as soils with low diversity may facilitate inoculant establishment, while high diversity can create competitive barriers. Plus, understanding the role of microbial genes, such as EPS and TasA from Bacillus subtilis strain UD1022, in biofilm formation and microbial recruitment is key to optimizing biocontrol strategies. The objectives of this study were to investigate the effect of soil microbial diversity on the bioinoculant establishment, assess the impact of Pseudomonas inefficax strain CMAA1741 on plant growth and disease suppression, characterize bacterial genomes for plant growth promotion and biocontrol genes mining, and explore the role of EPS and TasA genes in Bacillus subtilis colonization. The researchers employed a dilution-to-extinction method to create soil microbial diversity gradients, ranging from natural soil to fully autoclaved soil, for the assessment of disease severity, plant growth, and microbiome composition. Genomic sequencing was used to characterize the genomes of the interested rhizosphere bacteria Pseudomonas inefficax strain CMAA1741, isolated from wheat landraces. Additionally, the role of exo-polymeric genes, EPS and TasA, in Bacillus subtilis strain UD1022 was analyzed using mutant models to evaluate their effect on microbiome assembly. Inoculation with Pseudomonas inefficax strain CMAA1741 significantly reduced disease severity caused by Bipolaris sorokiniana, particularly in low-diversity soils. Furthermore, Bacillus subtilis exo-polymeric genes, particularly EPS and TasA, were found to be critical for rhizosphere colonization and the assembly of beneficial microbial communities. Inoculation with wild-type Bacillus subtilis strain UD1022 led to more pronounced effects on microbial community structure in soils with lower microbial diversity. The findings highlight the significant role of microbial diversity and functional traits in enhancing biocontrol efficacy, promoting plant growth, and shaping rhizosphere microbiome. The research emphasizes the potential of using microbial interactions and functional genes to develop sustainable, microbiome-based strategies for improving crop productivity, pathogen management, and resilience in agricultural systems.