Iron is an essential micronutrient for plant growth and development. In alkaline or calcareous soils, iron mainly exists in the form of highly insoluble ferric oxides, leading to severe "iron deficiency chlorosis" in crops, significantly impacting the yield and quality. Non-graminaceous plants (e.g., Arabidopsis thaliana) have evolved an iron uptake mechanism, in which root-specialized metabolites, particularly catecholic coumarins, play a crucial role. These coumarins are secreted into the rhizosphere where they strongly chelate and mobilize insoluble iron.

To investigate how root metabolic changes influence the assembly and function of the microbiome, a research team led by Dr. WANG Guodong from the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences screened 16 Arabidopsis thaliana mutants with disruptions in four specific metabolic pathways, grew them in alkaline natural soil, and analyzed their growth phenotypes, root metabolomes, and rhizosphere microbiomes. The study was published in Molecular Plant.

Researchers found that the lignin synthesis-deficient mutant cse-2 exhibited severe growth retardation and chlorosis under alkaline iron-deficient soil conditions. Metabolomic analysis showed a substantial reduction in bioactive coumarins in its roots, but a marked increase in several aromatic glycosides. Microbiome sequencing revealed that the rhizosphere of cse-2 was specifically enriched with a large number of Actinobacteria and Pseudomonadota bacteria possessing aromatic compound-degrading capabilities.

Using synthetic microbial communities co-incubated with root exudates, researchers demonstrated that microbial deglycosylation served as the core driver of the dynamic transformation of rhizosphere metabolites. Through biochemical and functional screening, they identified a key secreted β-glucosidase among the enriched microbes. This enzyme specifically and efficiently hydrolyzes plant-secreted coumarin glycosides, cleaving their glycosidic bonds to convert them into active aglycones with high iron-chelating capacity.

To validate the in vivo efficacy of this mechanism, the β-glucosidase gene was heterologously expressed in the rhizosphere probiotic strain Pseudomonas simiae WCS417r. When grown on iron-deficient medium, Arabidopsis cse-2 mutants inoculated with this engineered strain exhibited significantly increased chlorophyll content and effectively alleviated iron deficiency symptoms.

This study proposes the concept of "dynamic remodeling" of plant-microbe metabolism, elucidating an ecological model in which microbes actively "reprocess" plant metabolites to reciprocally benefit plant health. It provides new strategies for improving iron uptake efficiency in crops grown on alkaline soils, and has a value for developing functional rhizosphere microbial inoculants and breeding stress-tolerant, high-efficiency crops.