The agricultural microbial resources team from the Institute of Agricultural Resources and Regional Planning (IARRP), CAAS, recently revealed some major findings. The team systematically characterized the secretome of the type III secretion system in beneficial Pseudomonas fluorescens, uncovering the molecular mechanism behind its functional shift from a "pathogenic weapon" to a "rhizosphere colonization tool". The findings were published in the authoritative journal Microbiological Research under the title "Multi-omics insights reveal a divergent type III secretion system-associated secretome in plant growth-promoting rhizobacterial Pseudomonas fluorescens". 

The type III secretion system (T3SS) reportedly acts as a "dedicated injector" for many Gram-negative pathogens, delivering effector proteins into plants and playing a critical role in the pathogenic process. Through systematic research, the agricultural microbial resources team discovered that many beneficial Pseudomonas fluorescens in the plant rhizosphere also possess a similar T3SS, but yet its secretome and biological functions remained poorly understood.. By using the biocontrol strain Pseudomonas fluorescens 2P24 as a model, the team integrated bioinformatics, transcriptomics, and secretomics analyses and found that this strain had lost most canonical T3SS effector proteins. Furthermore, compared to the dozens of effector proteins in pathogens, it retained only two homologous proteins. Functional validation of one homolog, HopM1, revealed that it had lost its pathogenic activity. Transcriptomic analysis showed that under plant root signal induction, the key T3SS regulator RspL could reprogram nearly one-third of the bacterial genes, promoting energy metabolism pathways, while inhibiting motility and signaling pathways. Functional validation indicated that RspL significantly enhanced the colonization of the strain in the plant rhizosphere. Secretomics analysis demonstrated that the T3SS acts as a "sorter", exporting various metabolic enzymes to modify the rhizosphere microenvironment while restricting the release of motility-related proteins such as flagellar proteins, aiding in stable colonization on the root surface. Using multi‑omics approaches, the study screened and validated two T3SS‑dependent secreted metabolic enzymes, laying a theoretical foundation for further elucidating the mechanism of the T3SS in beneficial Pseudomonas fluorescens in the rhizosphere.

Model diagram illustrating rhizosphere adaptation of Pseudomonas fluorescens 2P24 via the RspL‑T3SS module.

Co-first authors of the paper are Wang Jing, assistant researcher at the IARRP; Hou Jiawei, PhD candidate at the College of Life Sciences, Shanxi University; and Luo Yuan, PhD from RDFZ Suzhou School (a graduate of the IARRP). Jia Baolei, a researcher at Xianghu Laboratory, and Wei Hailei, a researcher at the IARRP, are the corresponding authors. The research was supported by the Beijing Rural Revitalization Agricultural Science and Technology Project (NY2401090200), the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (CAAS-CSCB-202401), and the Special Project of the National Key Laboratory for Efficient Utilization of Dryland and Semi-arid Arable Land in Northern China (G2026-05-10). 

doi: 10.1016/j.micres.2026.128738