Rhizosphere microbiome influences fruit quality in citrus

Fruit quality is shaped by both crop genetics and cultivation environments, with soil conditions driving rhizosphere microbiome assembly. While rhizosphere microbes are known to enhance nutrient utilization and plant metabolism, their direct contribution to fruit quality regulation remains poorly understood. In this study, we demonstrate that the Satsuma mandarin (Citrus unshiu Marc.) and Navel orange (Citrus sinensis L. Osbeck) rhizosphere microbiome influence fruit sugar concentration, a key determinant of fruit quality. The rhizosphere core microbiota and soil mineral nutrients were positively correlated with fruit quality indices. Fruit quality-correlated bacterial operational taxonomic units (OTUs) explained an average of 32.6% of the observed variation in quality parameters. Inoculation with three bacterial strains (affiliated with Burkholderia, Pseudomonas, Rhizobium) and two bacterial consortia significantly increased fruit sugar concentrations. Metagenomic analysis linked sugar-associated microbes to iron (Fe) utilization, revealing genomic enrichment of siderophore biosynthesis gene clusters. Consistently, the selected bacterial strains exhibited siderophore secretion capabilities, increased leaf Fe content by 23.3-47.8% in citrus rootstock. Further field application of chelated-Fe fertilizer also increased fruit sugar concentration. Collectively, our results revealed an influence of the rhizosphere microbiome on fruit quality that is related to Fe acquisition optimization and subsequent sugar accumulation in citrus.