The agricultural microbial resources team at the Institute of Agricultural Resources and Regional Planning (IARRP), CAAS, recently conducted a study focusing on beneficial Pseudomonas fluorescens. They systematically elucidated a new mechanism by which the two-component system GacS regulates two key downstream pathways involved in the remodeling of rhizosphere microbial communities and microbial competition. Findings were published under the title "A GacS-mediated regulatory framework coordinates bacterial competition and rhizosphere microbiome remodeling in Pseudomonas fluorescens" in the leading microbiology journal, Microbiome, which has a five-year average impact factor of 18.5.

Pseudomonas is the second largest genus of cultivable bacteria, and fluorescent Pseudomonas is a typical type of Plant Growth-Promoting Rhizobacteria (PGPR) known for its characteristics of antagonizing pathogens, inducing plant resistance, promoting plant growth, and improving plant health. Current research into PGPR mostly focuses on the function of individual genes, lacking a systematic understanding of how these genes synergistically act to regulate the multi-interface interactions among the environment, microbes, and plants. In this study, researchers systematically analyzed 16 genes associated with protein secretion, signal regulation, and antimicrobial metabolism in Pseudomonas fluorescens. The team knocked out these genes individually and systematically compared each mutant for motility, biofilm formation, plant immune stimulation, as well as changes in soil and rhizosphere microbial communities. The study found that the global regulator GacS acts as a "master switch," coordinating two key downstream pathways, GacS-FliC and GacS-Phl, to participate in rhizosphere microbial community remodeling and bacterial competition. On one hand, GacS modulates the expression of flagellin-encoding gene fliC, altering bacterial motility and plant immune responses, and enriching beneficial taxa such as Devosia to reshape rhizosphere microbial community structure. On the other hand, GacS controls the phl biosynthetic gene cluster to promote the production of the antimicrobial metabolite 2,4-diacetylphloroglucinol (2,4-DAPG). This metabolite directly reduces the abundance of another major beneficial microbial group in the soil — Streptomyces — thereby reshaping the microbial interaction landscape. In vitro validation showed that Pseudomonas fluorescens has a broad-spectrum inhibitory capability against the genus Streptomyces, and this effect mainly depends on the GacS-Phl pathway.

The study is reportedly the first to analyze the functional regulatory network of important genetic elements of PGPR from the "environment-microbe-plant" tri-interaction interface. Moreover, it proposes a synergistic action model of "global regulatory factor-functional gene cluster-environmental response". This deepens the understanding of how beneficial microbes coordinate various ecological functions such as their own motility, plant immune stimulation, and antimicrobial substance synthesis, thereby influencing the processes of rhizosphere microbial communities. This provides a theoretical basis for the targeted optimization of beneficial microbes and the rational design of synthetic microbial communities.

The paper's co-first authors are Wang Jing, an assistant researcher at the IARRP, and Luo Yuan, an IARRP graduate who currently works at the Suzhou School of the High School Affiliated to Renmin University of China. Researcher Wei Hailei is the corresponding author. Assistant researcher Ma Yinan from the Biotechnology Research Institute of CAAS, associate researcher Li Junzhou from IARRP, and Professor Zhang Liqun from China Agricultural University participated in the work. The study was supported by the National Key Laboratory of Efficient Utilization of Dryland and Semi-arid Arable Land, the Beijing Rural Revitalization Agricultural Science and Technology Project (NY2401090200), and the Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences (CAAS-CSCB-202401).  

DOI : 10.1186/s40168-026-02557-9