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Crop microbiome responses to pathogen colonisation regulate the host plant defence

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Abstract

Aims

Soil-borne pathogens severely damage the yield and quality of crops worldwide. Plant and soil microbiomes (e.g. in the rhizosphere) intimately interact with the plant, the pathogen and influence outcomes of disease infection. Investigation of how these microbiomes respond to disease infection is critical to develop solutions to control diseases.

Methods

Here, we conducted a field experiment and collected healthy and crown rot disease infected (caused by Fusarium pseudograminearum, Fp) wheat plants. We investigated their microbiomes in different compartments, plant immune responses and interactions with the pathogen (Fp) aiming at advancing our knowledge on microbiome-mediated regulation of plant responses to pathogens.

Results

We found that Fp colonised wheat plants significantly in terms of relative abundances, accounting for 11.3% and 60.7% of the fungal communities in the rhizosphere and roots, respectively. However, Fp presented with a small fraction of the leaf microbiome, up to 1.2%. Furthermore, Fp-infection led to significant changes in the composition of microbiomes in the rhizosphere and root while had little impact on leaves. We further found that wheat defence signalling pathways, microbiomes and the pathogen intimately correlated with each other in structural equation modelling. As such, we also identified ecological clusters explained changes in the wheat defence signalling pathways. Lastly, microbial co-occurrence network complexity was higher in Fp-infected plants relative to healthy plants, suggesting that Fp-infection may have led to changes in the wheat microbial community structure.

Conclusions

We provide novel evidence that soil-borne diseases disrupt belowground plant microbiomes influencing the responses of plant immunity to pathogens.

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Data availability

The 16S rRNA and ITS gene amplicon sequences associated with this study have been deposited in the NCBI SRA under accession: PRJNA436828.

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Authors and Affiliations

  1. Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2753, Australia

    Hongwei Liu, Juntao Wang, Haiyang Zhang, Jiayu Li & Brajesh K. Singh

  2. School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia

    Hongwei Liu

  3. Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012, Sevilla, Spain

    Manuel Delgado-Baquerizo

  4. Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, 41013, Sevilla, Spain

    Manuel Delgado-Baquerizo

  5. Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, 2753, Australia

    Brajesh K. Singh

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  1. Hongwei Liu
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  2. Juntao Wang
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  3. Manuel Delgado-Baquerizo
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Contributions

H.L., J.L. and B.S. conceptualized the idea; H.L., J.W., M.D.B., and H.Z. analysed the data; HL did the writing with all authors having critically revised the manuscript.

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Correspondence to Hongwei Liu or Brajesh K. Singh.

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The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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Liu, H., Wang, J., Delgado-Baquerizo, M. et al. Crop microbiome responses to pathogen colonisation regulate the host plant defence. Plant Soil 488, 393–410 (2023). https://doi.org/10.1007/s11104-023-05981-0

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