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Bio-fertilizer Amendment Alleviates the Replanting Disease under Consecutive Monoculture Regimes by Reshaping Leaf and Root Microbiome


Replanting disease is a growing problem in intensive agricultural systems. Application of bio-fertilizer containing beneficial microbes contributes to disease suppression and is a promising strategy to control replanting disease. However, the effect of both replanting disease and bio-fertilizer amendment on the assembly of crop microbiota in leaves and roots and their relationships to crop yield and quality remains elusive. In these experiments, roots and leaves of Radix pseudostellariae were collected from different consecutive monoculture and bio-fertilizer amended fields, and the associated microbiota were characterized by bacterial 16S rRNA gene sequencing and quantitative PCR. Consecutive monoculture altered the bacterial community structure and composition and significantly increased the abundance of potential pathogenic Ralstonia and Fusarium oxysporum in leaves and roots. Furthermore, bio-fertilizer application alleviated replanting disease by decreasing the pathogen load, increasing the potential beneficial genera Pseudomonas, Streptomyces, Paenibacillus, and Bradyrhizobium. The proportion of positive correlations in the co-occurrence network of bio-fertilizer application was the highest, implying that bio-fertilizer potentially enhanced ecological commensalism or mutualism of the bacterial community across the two compartments. Structural equation models indicated that bio-fertilizer had a positive and indirect effect on both yield and quality by shaping the leaf microbiota and the root microbiota. Our findings highlight the role of leaf and root microbiota on replanting disease, showing that bio-fertilizer contributes to alleviating replanting disease by improving microbe–microbe interactions.

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Data Availability

All data generated or analyzed were included in this manuscript and the supporting information.


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We thank the National Science Foundation of China and the Project Funded by China Postdoctoral Science Foundation for providing the funds used in this work.


This work was supported by National Science Foundation of China (U1205021, 82003884, 81573530), and the Project Funded by China Postdoctoral Science Foundation (No. 2019M650150).

Author information




WX Lin and HM Wu conceived the study; HM Wu wrote the paper. HM Wu, JY Wang, XJ Qin and J Chen performed experiments; HM Wu and Z Zhang performed the statistical analyses; LK Wu and S Lin were involved in soil sampling. C Rensing and WX Lin have revised the manuscript. All authors discussed the results and commented on the manuscript.

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Correspondence to Zhen Zhang, Christopher Rensing or Wenxiong Lin.

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Wu, H., Zhang, Z., Wang, J. et al. Bio-fertilizer Amendment Alleviates the Replanting Disease under Consecutive Monoculture Regimes by Reshaping Leaf and Root Microbiome. Microb Ecol (2021).

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  • Soil sickness
  • Phyllosphere
  • Crop microbiome
  • Allelopathy
  • Sustainable agriculture