The rhizosphere microbiome, known as the plant’s “second genome”, is vital for plant growth and health. As a staple crop for nearly half of the global population, rice yield directly impacts food security. The tiller number, a core agronomic trait determining rice yield, is regulated by genetic and various environmental factors. For decades, whether and how rhizosphere microbial communities participate in regulating tiller formation, along with its molecular mechanisms, has remained an unresolved mystery. Answering this question will be a groundbreaking advancement for microbial agriculture and crop-sustainable production.

Scheme of microbial metabolite cyclo(Leu-Pro) mediated rice tillering regulation mechanism

Associate Professor Ancheng Huang’s research group from the Department of Biology at the Southern University of Science and Technology (SUSTech), in collaboration with the research groups of Professor Yang Bai from Peking University, Professor Jiayang Li from Yazhouwan National Laboratory and the Institute of Genetics and Developmental Biology (IGDB) of the Chinese Academy of Sciences (CAS), Professor Chengcai Chu from South China Agricultural University, and Professor Song Gao from Sun Yat-sen University, have uncovered—for the first time—how the functional and molecular mechanisms by which the rhizosphere microbiome regulates rice tillering.

This milestone study in plant-root microbiota interactions employed a suite of interdisciplinary approaches to map the microbial influence on tillering. Leveraging extensive microbial resources to identify key strains governing tillering, their findings established a closed-loop circuit from data mining to mechanistic and functional decoupling. This work signifies a paradigm shift in plant-microbiome research from descriptive science to mechanistic understanding and bioengineering applications, which provides scientific and technological support for crop yield enhancement and global food security.

Their paper, entitled “Root microbiota regulates tiller number in rice”, has been published in the top journal Cell.

Based on genomic data from 182 rice varieties, the research team detected a significant connection between the rhizosphere microbiome and rice tiller number through association study between tillering phenotypes and rhizosphere microbiome data. The rhizosphere microbiome demonstrated substantial explanatory power (28.2%) for tiller number variation, while the interaction effect between the microbiome and plant genotype accounted for 79.9% of the total genotypic explanatory capacity. Linear regression analyses showed that both α-diversity (Shannon index) and β-diversity (PCo1) of the rhizosphere microbial community were significantly associated with tiller number. Across two independent experimental field environments, the team identified 12 bacterial genera significantly correlated with tiller number, including seven positively correlated and five negatively correlated genera.

Utilizing the in-house rice rhizosphere bacteria library, the researchers screened key bacterial strains from tiller-associated genera and conducted functional validation under both laboratory and field conditions. Results demonstrated that Roseateles R780 and Piscinibacter R1801 significantly promoted tillering, while Exiguobacterium R2567, Burkholderia R2488, and Pleomorphomonas R1405 markedly inhibited tillering. To investigate whether the regulatory effects on tillering depend on the strigolactone (SL) phytohormone pathway, the team analyzed SL biosynthesis and signaling status under bacterial treatments and performed phenotypic validation using SL biosynthesis mutants (d27) and signaling mutants (d14). The study revealed that Roseateles R780 and Exiguobacterium R2567 regulate tillering via the rice SL pathway but employ distinct mechanisms. The promotion effect of Roseateles R780 requires both SL biosynthesis and signaling, whereas the inhibitory effect of Exiguobacterium R2567 primarily relies on SL signaling.

To investigate the mechanism by which Exiguobacterium R2567 inhibits tillering, they first determined that certain microbial bioactive compounds were responsible for this regulation. They subsequently isolated a bioactive molecule, S6, which was structurally characterized via LC-MS and NMR as the cyclic dipeptide cyclo(Leu-Pro). A series of experiments demonstrated that cyclo(Leu-Pro) mimics strigolactone (SL) function by promoting OsD53 protein degradation, thereby suppressing rice tillering. Molecular interaction assays (MST, BLI, YLG) and protein crystallography revealed that the binding site of OsD14 for cyclo(Leu-Pro) overlaps extensively with that of the SL analog rac-GR24. Genetic evidence confirmed that cyclo(Leu-Pro) loses its ability to regulate OsD53 protein levels and tillering in the d14 mutant.

In summary, cyclo(Leu-Pro) mimics strigolactone (SL) function by directly binding to the SL receptor OsD14 and activating SL signaling, thereby suppressing rice tillering. This discovery challenges the conventional understanding that endogenous plant hormones like SL solely regulate tillering, demonstrating that microbial metabolites can similarly and precisely manipulate this critical agronomic process in rice.

Researcher Associate Jingying Zhang from IGDB, CAS and Peking University; Professor Bing Wang, Dr. Haoran Xu, Ph.D. candidate Weidong Liu, and Dr. Jinwei Wei from IGDB, CAS; Ph.D. candidate Jingwei Yu from SUSTech; Dr. Qiuxia Wang from Sun Yat-sen University; and Professor Dr. Hong Yu from Yazhouwan National Laboratory are the co-first authors of this study. Professors Yang Bai, Jiayang Li, Chengcai Chu, Ancheng Huang, and Song Gao are the corresponding authors.

Paper link: https://www.cell.com/cell/fulltext/S0092-8674(25)00351-4

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