Flavones enrich rhizosphere Pseudomonas to enhance nitrogen utilization and secondary root growth in Populus

Jiadong Wu, Sijia Liu, Haoyu Zhang, Sisi Chen, Jingna Si, Lin Liu, Yue Wang, Shuxian Tan, Yuxin Du, Zhelun Jin, Jianbo Xie () and Deqiang Zhang ()
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Jiadong Wu: Beijing Forestry University
Sijia Liu: Beijing Forestry University
Haoyu Zhang: Beijing Forestry University
Sisi Chen: Beijing Forestry University
Jingna Si: Beijing Forestry University
Lin Liu: Beijing Forestry University
Yue Wang: Beijing Forestry University
Shuxian Tan: Beijing Forestry University
Yuxin Du: Beijing Forestry University
Zhelun Jin: Beijing Forestry University
Jianbo Xie: Beijing Forestry University
Deqiang Zhang: Beijing Forestry University

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract Plant growth behavior is a function of genetic network architecture. The importance of root microbiome variation driving plant functional traits is increasingly recognized, but the genetic mechanisms governing this variation are less studied. Here, we collect roots and rhizosphere soils from nine Populus species belonging to four sections (Leuce, Aigeiros, Tacamahaca, and Turanga), generate metabolite and transcription data for roots and microbiota data for rhizospheres, and conduct comprehensive multi-omics analyses. We demonstrate that the roots of vigorous Leuce poplar enrich more Pseudomonas, compared with the poorly performing poplar. Moreover, we confirm that Pseudomonas is strongly associated with tricin and apigenin biosynthesis and identify that gene GLABRA3 (GL3) is critical for tricin secretion. The elevated tricin secretion via constitutive transcription of PopGL3 and Chalcone synthase (PopCHS4) can drive Pseudomonas colonization in the rhizosphere and further enhance poplar growth, nitrogen acquisition, and secondary root development in nitrogen-poor soil. This study reveals that plant-metabolite-microbe regulation patterns contribute to the poplar fitness and thoroughly decodes the key regulatory mechanisms of tricin, and provides insights into the interactions of the plant’s key metabolites with its transcriptome and rhizosphere microbes.

Date: 2025
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DOI: 10.1038/s41467-025-56226-w

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