Introduction: Trifoliate orange (Poncirus trifoliataL. Raf) and “Ziyang Xiangcheng” (Citrus junos Sieb. ex Tanaka) are the predominant rootstocks for lemon production in China, exhibiting distinct adaptations to soil pH and differential impacts on plant resilience. As pivotal mediators of scion-soil interactions, rootstocks have emerged as key research targets for their regulatory potential in rhizosphere microbial communities and metabolites.Methods: Pot-cultured systems were established with lemon (Citrus × limon “Eureka”) saplings grafted onto trifoliate orange (PTL) and “Ziyang Xiangcheng” (CJL) rootstocks. Integrated metagenomic and GC-MS metabolomic approaches were employed to analyze rhizosphere microbial communities and metabolites.Results: The results demonstrated no significant difference in rhizospheric microbial α-diversity (richness) between PTL and CJL, although PTL exhibited higher evenness. β-Diversity and LEfSe analysis revealed significant structural divergence in communities. A total of 15 differentially enriched genera across three phyla were identified, among which Pseudomonas, Cupriavidus, and Burkholderia in CJL, along with Sphingobium in PTL, exhibited strong effects. Random forest modeling identified 15 key differential metabolites, with 4 significantly upregulated in CJL and 11 in PTL. Microbial-metabolite correlation and GSEA analysis uncovered 10 core pathways involving genetic information processing, energy metabolism, environmental adaptation, and disease resistance mechanisms. Soil analysis showed CJL significantly surpassed PTL in organic matter content, catalase activity and plant height, whereas PTL exhibited superior cellulase, sucrase and urease activities. Mechanistically, PTL appears to recruit Pseudomonas mediterranea via 1-Monostearin secretion to activate glycerolipid metabolism, enhancing drought tolerance. Its caffeate and salicyl alcohol-β-glucoside secretions potentially mobilize Sphingobium and Ensifer adhaerens to regulate amino sugar metabolism, promoting carbon sequestration and root defense. Conversely, CJL likely employs L-alanine exudation to recruit Pseudomonas putida, triggering exopolysaccharide biosynthesis through arginine-proline metabolism as a key tolerance mechanism (such as drought tolerance and alkali tolerance)Discussion: The findings elucidate rootstock-specific modulation of rhizosphere microecosystems, highlighting distinct microbial-metabolite interactions and tolerance mechanisms. These results provide theoretical support for precision rootstock selection and microbiome engineering to advance sustainable citrus production.

Background: Lemon peels are crucial quality traits and important sources of nutraceuticals. However, the regulation of peel development remains largely misunderstood. Here, we delved into the dynamic molecular mechanisms that control smooth lemon peel formation through transcriptomics and metabolomics analyses of developing peels at five different stages, including C1 (30 DAF, day after flowering), C2 (60 DAF), C3 (90 DAF), C4 (120 DAF), and C5 (150 DAF). Results: Our analyses revealed that peel development is stage-specifically regulated, with the transition from stage C2 to stage C3 being the most critical period. Notably, major metabolic adjustments and transcriptional switches occurred between C2 and C3. Particularly, phytohormones and their related genes, flavonoids, terpenoids, phenolic acids, vitamin C, and citric acid were down-regulated at stage C3. Differentially expressed genes between the transition from C2 to C3 were mainly enriched in hydrolase activity, nucleic acid binding transcription, transcription factor activity, sequence-specific DNA binding and pathways such as plant hormone signal transduction, starch and sucrose metabolism, MAPK signaling pathway-plant, plant-pathogen interaction, and circadian rhythm-plant biosynthesis. Plant hormone signaling was crucial for peel development process. Specifically, we found that crosstalks between jasmonic acid, abscisic acid, salicylic acid, gibberellic acid, and ethylene dynamically and coordinately regulate peel development process. ABC transporter family genes and green-degrading promoting genes, including protein SGR1 ( LOC18041639 ), ervatamin-C ( LOC18051181 ), and many ethylene-responsive transcription factors were significantly induced from C2. Furthermore, we screened out stage-specific most regulated genes. Conclusions: Our findings offer molecular understanding of peel formation process and fundamental resources for the functional dissection of its regulatory networks and for genomics-assisted control of peel shape and fruit quality in lemon.

Background: The Orah mandarin is an economically important variety of Citrus reticulata for citrus growers in Yunnan Province, China. Generally, the fruit peel is smooth, an attractive feature for consumer preferences. Recently, rough peels have been observed in several orchards, making the fruit aesthetically less desirable. Little is known about the mechanism of rough skin development. Methods: In this study, we used global metabolomics and a comparative transcriptomic approach to characterize the differences between smooth (CK) and rough (CP) Orah mandarin peels. Results: Our results indicate that CP fruits have a significantly larger diameter, peel weight and thickness, total soluble solids, and titratable acid content compared to CK. Metabolomic analysis detected 810 metabolites, of which 192 were differentially accumulated in CP and CK. CP is characterized by higher levels of flavonoids, amino acids and derivatives, terpenoids, and alkaloids. We also report nine compounds detected exclusively in CP, including dambonitol, 3-methyl-L-histidine, deacetylnomilinic acid, obacunoic acid, and 6-O-acetylarbutin. The transcriptome results showed that the expression of genes enriched in flavonoids, lipid, and amino acid metabolism and related pathways were consistent with the metabolome profiles. We also discuss the possible involvement of phytohormones in peel roughening. Conclusions: Overall, we present, for the first time, a detailed comparative metabolome and transcriptome profile in smooth and rough Orah mandarin peels. Our data and discussion highlight the potential mechanisms and provide a theoretical basis for the improvement of rough peel Orah mandarins.