In Beijing, the Agricultural Microbial Resources Team at the Institute of Agricultural Resources and Regional Planning (IARRP) — part of the Chinese Academy of Agricultural Sciences — recently systematically analyzed the distribution, structure, and evolutionary mechanisms of the type III secretion system (T3SS) in rhizosphere Pseudomonas fluorescens. The study, entitled "Type III secretion system diversity in the Pseudomonas fluorescens species complex", was published in the prestigious academic journal New Phytologist.

T3SS is a critical molecular apparatus used by many Gram-negative pathogens to interact with their hosts. However, T3SS has also been found in numerous rhizosphere-associated Pseudomonas fluorescens in recent years. Over five years, the research team isolated 2,633 strains of fluorescent Pseudomonas from 114 rhizosphere soil samples collected across 48 different crops across 15 provinces, autonomous regions, and municipalities in China. Using specific probes, they screened out 110 strains carrying T3SS-related genes. Through whole-genome sequencing, they systematically analyzed the genomic characteristics of 43 T3SS-positive Pseudomonas fluorescens strains and constructed a database comprising 88 T3SS-positive strains by integrating public databases. The study revealed six Rsp types are distributed across seven subgroups of the Pseudomonas fluorescens species complex,. Further phylogenetic and comparative genomic analyses indicated that multiple independent horizontal gene transfer events significantly contributed to the dissemination and evolution of T3SS — highlighting that its spread and functional differentiation are driven by ecological niche adaptation. Functional analysis revealed that T3SS-positive strains generally possess plant growth-promoting and disease-preventing functional modules, with some Rsp T3SS can induce plant cell death responses. Moreover, the representative strains of Rsp I and Rsp II retain the ability to translocate effector proteins.

The study is said to challenge the traditional view of T3SS as an exclusive pathogenic weapon — systematically revealing its widespread distribution and high phylogenetic diversity among beneficial rhizosphere Pseudomonas fluorescens. It is viewed as enhancing the understanding of the evolutionary mechanisms of functional genes in rhizosphere microorganisms — and lays a theoretical foundation for distinguishing between "pathogenic" and "symbiotic" functions in microbe-plant interactions. Additionally, the research is said to provide significant insights into safety assessments, precise screening, and the genetic improvement of beneficial Pseudomonas fluorescens strains — and lays an important foundation for the targeted regulation of plant-microbe interactions. 

Liao Kaiji, a doctoral student at the IARRP, is the first author of the paper, with researcher Wei Hailei as the corresponding author. Doctoral student Luo Yuan and researcher Zhuang Qiguo from the Sichuan Provincial Academy of Natural Resource Sciences contributed to parts of the work. The research was supported by the national key laboratory of efficient utilization of arid and semi-arid farmland in northern China. It was also supported by the special support fund for basic research of central public-interest scientific research institutes.

Link: https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.71510