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Analysis of the Differences in Rhizosphere Microbial Communities and Pathogen Adaptability in Chili Root Rot Disease
Qiuyue Zhao1,2, Xiaolei Cao1, Lu Zhang1
1Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi 832003, China.
Microorganisms
|August 28, 2025
Summary
Crop rotation in chili cultivation improves soil health by enriching beneficial bacteria and suppressing pathogens, reducing root rot incidence. This strategy optimizes soil microbial communities for sustainable agriculture.
Area of Science:
- Agricultural Science
- Soil Microbiology
- Plant Pathology
Background:
- Continuous cropping of chili peppers leads to soil health degradation and reduced yields.
- Crop rotation is a potential strategy to improve soil microbial environments and disease management.
- The impact of crop rotation on the diversity of rhizosphere microbial communities in chili cultivation remains unclear.
Purpose of the Study:
- To investigate the effects of chili-cotton crop rotation (CR) versus continuous chili cropping (CC) on rhizosphere soil microbial community composition and characteristics.
- To determine how CR influences the abundance of beneficial and pathogenic microorganisms in chili soil.
- To provide insights into microbial-based soil management strategies for chili cultivation.
Main Methods:
- High-throughput sequencing was employed to analyze bacterial and fungal communities in rhizosphere soil.
- Principal Component Analysis (PCA) was used to compare community structures between CC and CR treatments.
- Linear Discriminant Effect Size (LEfSe) analysis identified differentially abundant taxa.
Main Results:
- CR treatment altered soil microbial community structure, reducing bacterial alpha diversity but having less impact on fungal diversity.
- CR increased the relative abundance of beneficial bacteria (e.g., *RB41*, *Lactobacillus*, *Bacillus*) and decreased pathogenic fungi (e.g., *Alternaria*, *Fusarium*).
- CC favored the enrichment of pathogens, while CR promoted beneficial bacteria, including those suppressing root rot pathogens like *Fusarium solani* and *F. oxysporum*.
Conclusions:
- Chili-cotton crop rotation enhances soil health and reduces root rot incidence by modulating the soil microbial community structure.
- CR increases beneficial bacteria and suppresses key fungal pathogens, offering a sustainable approach to chili cultivation.
- The findings support the use of crop rotation as a scientific basis for microbial-based soil management in chili farming.
