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Microbiome homeostasis on rice leaves is regulated by a precursor molecule of lignin biosynthesis

Author

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  • Pin Su

    (Hunan Academy of Agricultural Sciences)

  • Houxiang Kang

    (Chinese Academy of Agricultural Sciences)

  • Qianze Peng

    (National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City
    Hainan University)

  • Wisnu Adi Wicaksono

    (Graz University of Technology)

  • Gabriele Berg

    (Graz University of Technology
    Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB)
    University of Potsdam)

  • Zhuoxin Liu

    (Hunan University)

  • Jiejia Ma

    (Hunan University)

  • Deyong Zhang

    (Hunan Academy of Agricultural Sciences
    National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City
    Hainan University)

  • Tomislav Cernava

    (Graz University of Technology
    University of Southampton)

  • Yong Liu

    (Hunan Academy of Agricultural Sciences)

Abstract

In terrestrial ecosystems, plant leaves provide the largest biological habitat for highly diverse microbial communities, known as the phyllosphere microbiota. However, the underlying mechanisms of host-driven assembly of these ubiquitous communities remain largely elusive. Here, we conduct a large-scale and in-depth assessment of the rice phyllosphere microbiome aimed at identifying specific host-microbe links. A genome-wide association study reveals a strong association between the plant genotype and members of four bacterial orders, Pseudomonadales, Burkholderiales, Enterobacterales and Xanthomonadales. Some of the associations are specific to a distinct host genomic locus, pathway or even gene. The compound 4-hydroxycinnamic acid (4-HCA) is identified as the main driver for enrichment of bacteria belonging to Pseudomonadales. 4-HCA can be synthesized by the host plant’s OsPAL02 from the phenylpropanoid biosynthesis pathway. A knockout mutant of OsPAL02 results in reduced Pseudomonadales abundance, dysbiosis of the phyllosphere microbiota and consequently higher susceptibility of rice plants to disease. Our study provides a direct link between a specific plant metabolite and rice phyllosphere homeostasis opening possibilities for new breeding strategies.

Suggested Citation

  • Pin Su & Houxiang Kang & Qianze Peng & Wisnu Adi Wicaksono & Gabriele Berg & Zhuoxin Liu & Jiejia Ma & Deyong Zhang & Tomislav Cernava & Yong Liu, 2024. "Microbiome homeostasis on rice leaves is regulated by a precursor molecule of lignin biosynthesis," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-023-44335-3
    DOI: 10.1038/s41467-023-44335-3
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    1. Tomislav Cernava, 2024. "Coming of age for Microbiome gene breeding in plants," Nature Communications, Nature, vol. 15(1), pages 1-3, December.

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