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Background and Aims <p>Soil sickness caused by long-term monoculture severely limits the productivity of <i>Lycium barbarum</i>, yet the microbial mechanisms underlying its alleviation remain poorly understood.</p> Methods <p>We integrated field soil surveys, controlled pot experiments, amplicon sequencing, microbial isolation, and inoculation assays to evaluate how organic fertilization alters rhizosphere microbial communities, plant–soil feedback (PSF), and soil-borne pathogen dynamics in <i>L. barbarum</i> monoculture soils.</p> Results <p>Organic fertilization significantly improved seedling growth, particularly in soils exhibiting negative PSF, and induced marked shifts in rhizosphere microbial composition. These changes included a reduced abundance of pathogenic <i>Fusarium</i> and enrichment of potentially beneficial taxa such as <i>Bacillus</i>, <i>Streptomyces</i>, and <i>Penicillium</i>. Random forest modeling identified <i>Bacillus</i> and <i>Streptomyces</i> as key positive predictors of plant biomass and PSF strength. In-vitro confrontation assays and inoculation experiments across multiple field soils further confirmed that these taxa exhibit antagonistic activity against <i>Fusarium</i> and synergistically enhance plant performance. Notably, organic fertilizer extracts did not directly stimulate plant growth or suppress <i>Fusarium</i>, but selectively promoted the proliferation of <i>Bacillus</i> and <i>Streptomyces</i> isolates.</p> Conclusion <p>Together, these results demonstrate that organic fertilization alleviates soil sickness primarily by inducing microbiome-mediated community reassembly, rather than through nutrient supplementation alone or direct chemical suppression of pathogens. This reassembled rhizosphere microbiome enhances soil-borne pathogen suppression and restores plant–soil feedbacks, contributing to improved soil biological function in perennial monoculture systems.</p>

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Organic fertilization alleviates soil sickness in monoculture systems by driving pathogen-suppressive rhizosphere community assembly

  • 期刊论文

  • 发表日期：

    2026年3月10日

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  • Tong Peng,
  • Chuanji Zhang,
  • Xiaoqi He,
  • Zhenyu Cheng,
  • Junjie Li,
  • Yanfang Song,
  • Ziyu Liu,
  • Meiyun Pu,
  • Yi Yan,
  • Panshuai Fei,
  • Yurong Bi,
  • Xiaofan Na

摘要

Background and Aims

Soil sickness caused by long-term monoculture severely limits the productivity of Lycium barbarum, yet the microbial mechanisms underlying its alleviation remain poorly understood.

Methods

We integrated field soil surveys, controlled pot experiments, amplicon sequencing, microbial isolation, and inoculation assays to evaluate how organic fertilization alters rhizosphere microbial communities, plant–soil feedback (PSF), and soil-borne pathogen dynamics in L. barbarum monoculture soils.

Results

Organic fertilization significantly improved seedling growth, particularly in soils exhibiting negative PSF, and induced marked shifts in rhizosphere microbial composition. These changes included a reduced abundance of pathogenic Fusarium and enrichment of potentially beneficial taxa such as Bacillus, Streptomyces, and Penicillium. Random forest modeling identified Bacillus and Streptomyces as key positive predictors of plant biomass and PSF strength. In-vitro confrontation assays and inoculation experiments across multiple field soils further confirmed that these taxa exhibit antagonistic activity against Fusarium and synergistically enhance plant performance. Notably, organic fertilizer extracts did not directly stimulate plant growth or suppress Fusarium, but selectively promoted the proliferation of Bacillus and Streptomyces isolates.

Conclusion

Together, these results demonstrate that organic fertilization alleviates soil sickness primarily by inducing microbiome-mediated community reassembly, rather than through nutrient supplementation alone or direct chemical suppression of pathogens. This reassembled rhizosphere microbiome enhances soil-borne pathogen suppression and restores plant–soil feedbacks, contributing to improved soil biological function in perennial monoculture systems.