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

Pin Su, Houxiang Kang, Qianze Peng, Wisnu Adi Wicaksono, Gabriele Berg, Zhuoxin Liu, Jiejia Ma, Deyong Zhang (), Tomislav Cernava () and Yong Liu ()
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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
Wisnu Adi Wicaksono: Graz University of Technology
Gabriele Berg: Graz University of Technology
Zhuoxin Liu: Hunan University
Jiejia Ma: Hunan University
Deyong Zhang: Hunan Academy of Agricultural Sciences
Tomislav Cernava: Graz University of Technology
Yong Liu: Hunan Academy of Agricultural Sciences

Nature Communications, 2024, vol. 15, issue 1, 1-16

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-023-44335-3

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