Shangdong Yang

To elucidate genotype-associated differences in rhizosphere microbial community assembly, this study compared the microbiomes of three Fusarium wilt-resistant and three susceptible watermelon cultivars using amplicon sequencing. Results revealed distinct bacterial and fungal community structures between the two groups. Notably, resistant cultivars harbored a higher number of unique operational taxonomic units and displayed greater fungal richness compared to their susceptible counterparts. Beyond taxonomic composition, co-occurrence network analysis demonstrated that the fungal community within the resistant group exhibited a more highly connected network topology. Additionally, functional prediction highlighted significant divergence in potential functional profiles, including variations in Forms_Biofilms and Contains_Mobile_Elements . Collectively, these findings demonstrate that rhizosphere microbial composition, diversity, and network complexity are closely linked to watermelon resistance phenotypes. This comprehensive characterization of genotype-driven microbiome variation offers a critical basis for understanding plant–microbe interactions and their potential to enhance plant health. IMPORTANCE: Fusarium wilt is one of the most destructive diseases affecting watermelon production worldwide, yet the role of soil microbes in helping plants resist this disease has remained unclear. This study shows that disease-related;resistant watermelon plants naturally recruit a richer and more cooperative community of beneficial microbes around their roots. These microbes may help protect the plant by improving nutrient use, forming biofilms that enhance microbial stability, and competing with or inhibiting harmful pathogens. In contrast, susceptible plants rely on only a few protective microbes, making their root environment less stable and more vulnerable to infection. By revealing how plant genetics shape the assembly and function of root-associated microbial communities, this work provides a scientific foundation for developing microbiome-based strategies-such as microbial inoculants or breeding for microbiome‑friendly cultivars-to improve crop resilience and reduce reliance on chemical pesticides.

Maize (Zea mays L.) is a globally significant cereal of wide nutritional diversity, yet how host genetics, the kernel endophytic microbiome, and metabolic fluxes interact remains unclear. We integrated targeted carotenoid quantification, 16S rRNA and ITS amplicon sequencing, and untargeted metabolomics comparing yellow and white maize kernels. Yellow maize accumulated substantially more lutein (up to 5.45 μg/g) and zeaxanthin (up to 15.30 μg/g) than white maize, which contained only trace amounts. Host genotype shaped the microbiome: bacterial diversity was comparable, yet fungal alpha diversity was higher in yellow maize. Tepidiamorphus and Fusarium were enriched in yellow maize, whereas Pseudomonas and Aspergillus dominated white kernels. Untargeted metabolomics identified 315 differential metabolites (lipids, organic acids, phenylpropanoids); active KEGG pathways included phenylalanine, tyrosine, and tryptophan biosynthesis, hormone signaling, and ABC transporters. These findings reveal an interplay between host secondary metabolism and the endophytic microbiome, offering targets for precision breeding and biofortification.

Sex expression in cucumber ( Cucumis sativus L.) is a critical agronomic trait governing fruit yield and cultivation efficiency. Although its genetic and hormonal regulation is well-characterized, the role of endophytes and their metabolic interplay remains largely unexplored. In this study, an integrated approach, combining high-throughput sequencing of endophytic bacteria and fungi with untargeted metabolomics was conducted to investigate differences in endophytic community structure between gynoecious versus monoecious cucumbers. We found that gynoecious plants harbored bacterial communities with significantly higher richness, evenness, and a greater number of unique operational taxonomic units (OTUs) than monoecious plants, whereas fungal diversity was not significantly different. Although Proteobacteria, Actinobacteriota, and Firmicutes were dominant in both genotypes, gynoecious were uniquely enriched in Verrucomicrobiota and Myxococcota, while Patescibacteria characterized monoecious. LEfSe analysis identified Myxococcota and Bdellovibrionota as key biomarkers in gynoecious cucumbers, implying a potential for enhancing pathogen suppression. Functional prediction indicated that gynoecious-associated microbiota possessed stronger capacities for hydrocarbon degradation and iron respiration, whereas the microbiota-associated communities were enriched in pathways for nitrogen and nitrate respiration. Metabolomic analyses revealed pronounced genotype-dependent differences, including tryptophan metabolism, plant hormone signal transduction, linoleic and linolenic acid metabolism, and indole alkaloid biosynthesis were significantly upregulated in gynoecious root. Meanwhile, key metabolites, such as L-tryptophan, tryptamine, serotonin, indole-3-acetic acid, jasmonic acid, and salicylic acid were also accumulated at higher levels in gynoecious roots. Furthermore, correlation network analysis revealed stronger associations between specific microbial taxa and hormone- or defense-related metabolites in gynoecious plants compared to monoecious plants.

Loess, calcareous, and laterite soils are common in Guangxi, southern China, where tomatoes are widely cultivated. To understand how these soil types affect tomato growth and the associated microbial communities, we analyzed soil fertility and the rhizosphere microbiome. Tomatoes in calcareous soil exhibited higher β-glucosidase activity and microbial biomass carbon, whereas those in laterite soil showed increased acid phosphatase activity and microbial biomass phosphorus. Actinobacteriota, Proteobacteria, and Acidobacteriota were the dominant bacterial phyla across all soils, while Ascomycota and Basidiomycota predominated among fungi. Each soil type hosted distinct microbial communities: loess was enriched with the bacterial genera Ramlibacter and Bradyrhizobium and the fungus Alternaria ; calcareous soil favored the bacterium Rubrobacter and the fungus Fusarium , and laterite supported bacteria such as Bacillus and Sphingobium , along with the fungus Curvularia . Given its higher phosphorus availability and the presence of beneficial microbes like Bacillus , laterite soil appears to provide a more favorable environment for tomato cultivation compared to loess and calcareous soils. IMPORTANCE: Soil type is a critical but often overlooked factor influencing tomato productivity in southern China, where diverse soils such as loess, calcareous soil, and laterite are extensively cultivated. Understanding how these soils shape rhizosphere microbial communities and soil nutrient dynamics is essential for improving crop performance. This study provides the first comparative assessment of tomato-associated microbiomes across these major soil types in Guangxi. Our findings reveal that each soil fosters distinct microbial assemblages and enzyme activities, with laterite particularly enriched in beneficial taxa such as Bacillus and associated with enhanced phosphorus availability. These insights highlight the importance of soil-specific microbial processes in supporting tomato growth and offer a scientific basis for selecting and managing soils to optimize productivity. The results also contribute to broader efforts to harness rhizosphere microbiomes for sustainable agricultural improvement.

Endophytic microbiome and metabolome are known to influence plant physiology, but their specific roles in fruit flavor development remain poorly understood. To explore microbial and metabolic factors linked to distinct flavor phenotypes, we compared stem endophytic microbiome composition and untargeted metabolomes between melon (Cucumis melo, CM) and bitter gourd (Momordica charantia, MC). Our goal was to identify candidate taxa, metabolites and pathways potentially related to sweetness and bitterness. Results showed that fungal diversity and richness were significantly higher in CM than in MC. CM stems were characterized by enrichment of Ascomycota and unique dominance of Sphingomonas, whereas MC exhibited significant enrichment of Botryosporium and a higher relative abundance of Bacteroidota. Metabolomic and pathway analyses revealed that CM displayed upregulation of phenylalanine, tyrosine and tryptophan biosynthesis, flavonoid biosynthesis, and cofactor biosynthesis, along with accumulation of sweet-enhancing metabolites such as naringin dihydrochalcone. By contrast, MC showed elevated activity in plant hormone signal transduction and higher levels of (S)-abscisic acid and dihydrozeatin. This study demonstrates distinct stem endophytic microbiomes and metabolomes between melon and bitter gourd, and highlights candidate functional microorganisms, key metabolites and metabolic pathways that correlate with sweetness and bitterness phenotypes. Further experimental validation is needed to confirm the causal roles of these candidates. These findings provide new insights into the mechanisms underlying melon sweetness and bitter gourd bitterness, and lay a methodological foundation for multi-omics investigations and the future development of microbiome- or metabolite-based strategies for modulating fruit quality and flavor.

Cucumber sex expression is a key agronomic trait determining yield, but whether its formations is related to rhizosphere soil microbes remains poorly understood. This study compared the soil microbial community structures in rhizosphere between gynoecious and monoecious cucumbers to identify potential associations. The results showed that bacterial genera including Sphingomonas , and other unclassified taxa, were significantly enriched in the rhizosphere of the gynoecious plants. In contrast, members of Rokubacteriales and other taxa were significantly enriched in rhizosphere of monoecious cucumbers. For fungi, genera such as Aspergillus , Plectosphaerella , and Chaetomella were enriched in rhizosphere of gynoecious plants. Conversely, Trichoderma , Emericellopsis , Collariella , and Cordana were significantly enriched in monoecious cucumbers. Correlation network analysis revealed that the rhizosphere microbial network (especially the bacterial community) was more stable and displayed greater interspecific cooperation in monoecious cucumbers. Functional prediction revealed that multiple nitrogen-cycling processes of bacterial communities, including nitrification, aerobic nitrite oxidation, nitrite and nitrate ammonification, aerobic ammonia oxidation, and arsenate respiration were detected in rhizosphere of the gynoecious cucumbers. By contrast, hydrocarbon degradation functions, particularly those for aromatic and aliphatic non-methane hydrocarbons were significantly enriched in rhizosphere of monoecious cucumbers. Moreover, the rhizosphere of gynoecious plants harbored a higher abundance of saprotrophic and symbiotrophic fungi but a lower abundance of pathotrophic fungi compared with monoecious cucumbers. These findings demonstrate that the composition and potential functions of the rhizosphere microbiota differ between gynoecious and monoecious plants, indicating that soil microbes in rhizosphere play a role in the sex expression of cucumber varieties.

To investigate light quality how to shape phyllosphere microbial communities on crop leaves, we analyzed the microbiota of lettuces grown under five light treatments: nature light (CK), Red light (RL), Yellow light (YL), Blue light (BL) and white light (WL) using high-throughput sequencing. The results revealed that light quality significantly altered both bacterial and fungal compositions in the lettuces phyllosphere. At the genus level, in comparison with nature light (CK), RL and YL enriched bacterial genera, such as Rothia , Bradyrhizobium , and fungal genera, such as Cladosporium , Phialosimplex . Notably Rickettsia was uniquely enriched under RL, along with fungal genera Trametes and Ramichloridium . Similarly, YL specifically enriched bacterial genera Hyphomicrobium and Novosphingobium , fungal genera Myrothecium , Talaromyces and Sporobolomyces . In contrast, Exiguobacterium and Cystobasidium were enriched across CK, BL, and WL treatments, while Rhodococcus and Pseudocercospora were uniquely abundant under WL treatment. Function prediction further indicated that symbiotrophic fungi were significantly enriched under RL, whereas WL promoted the proliferation of potentially pathogenic bacteria and fungi (e.g., Pseudocercospora ). Collectively, these findings demonstrate that light quality is a key driver of phyllosphere microbial assembly in lettuce. provide new insights into light-driven microbial assembly on lettuce leaves and set the stage for functional studies on plant-microbe interactions under controlled light spectra.