Rhizosphere microorganisms are key regulators of plant growth, stress tolerance, and secondary metabolism. However, whether soil microbial communities influence lutein and zeaxanthin biosynthesis in maize remains unclear. Analysis of rhizosphere microbial communities revealed that maize varieties rich in lutein- and zeaxanthin harbored greater soil microbial diversity and richness compared to common varieties. Distinct bacterial taxa enriched in these rhizospheres included the phylum Methylomirabilota and the genera Xanthobacteraceae, MB-A2-108, Rokubacteriales, and Acidothermus. Specific fungal genera comprised Didymella, Coprinellus, Trichoderma, Clonostachys, Poaceascoma, Arachniotus, Monocillium, along with several unclassified taxa within Chytridiomycota, Pleosporales, GS13, Agaricomycetes, Polyporales. Most of these specific bacterial and fungal genera correlated positively 0with lutein and zeaxanthin contents. Our findings demonstrate that rhizosphere microbial community composition differs in high-lutein and zeaxanthin maize variety, suggesting a potential association between maize genotype, rhizosphere microbiota, and carotenoid accumulation.

(1) Background: The rhizosphere microbiome, as the “second genome” of plants, plays a crucial role in nutrient acquisition, stress resistance, and soil health maintenance. Polyploidization is a key breeding strategy for watermelon: triploids are valued for seedlessness and high stress resistance, while tetraploids serve as important parental materials for triploid hybridization. However, how ploidy level (diploid, triploid, tetraploid) shapes the micro-ecological environment and microbial community assembly remains unclear. This study aims to elucidate the link between ploidy and rhizosphere microbiota, providing a theoretical basis for optimizing breeding and cultivation practices. (2) Methods: High-throughput sequencing (Illumina MiSeq PE300 for bacteria, PE250 for fungi) targeting the bacterial 16S rRNA gene (primers 338F/806R) and fungal ITS region (primers ITS1F/ITS2R) was used to analyze rhizosphere microbial communities of diploid (HLL40-3), triploid (Guixi No.5), and tetraploid (MT410n-1) watermelons. Alpha diversity (Shannon/Chao1/ACE/Simpson), beta diversity (PCoA/PLS-DA), taxonomic composition (phylum/genus level), and functional prediction (PICRUSt2/Tax4Fun/FUNGuild) were performed to compare differences among groups. (3) Results: Triploid watermelons exhibited significantly higher bacterial and fungal alpha diversity (Shannon/Chao1) than diploid and tetraploid varieties. Beta diversity analysis confirmed distinct separation of microbial communities across ploidy levels ( p < 0.05). Taxonomically, diploid rhizospheres were enriched in Proteobacteria, Melanconiella, and Hypomyces ; triploids were enriched in Bacteroidota, Microvirga , Mortierellomycota, Cercophora , and Neocosmospora ; tetraploids were specifically enriched in Patescibacteria , Gaiella , Trichoderma , and Papiliotrema . Functional prediction showed diploids were dominated by plant/wood saprotrophs; triploids harbored diverse functional guilds (animal pathogens, endophytes, soil saprotrophs, etc.); tetraploids had the highest relative abundance of undefined saprotrophs. (4) Conclusions: Ploidy level is a key determinant of watermelon rhizosphere microbial structure and function. Triploid watermelons assemble a more diverse and functionally versatile microbial community through selective recruitment, which may contribute to their superior agronomic traits. These findings deepen our standing of plant-microbe interactions and provide new insights for integrating polyploid breeding with rhizospheric microecological regulation in sustainable watermelon production.

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.

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.

ABSTRACT 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.

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.

【Objective】Plum (Prunus salicina Lindl.) , a woody plant of the Rosaceae family, is rich in organic acids, vitamins, carotenoids, proteins, and mineral elements such as iron and calcium. The Zhenzhu Li plum cultivated in Tian′e County, Guangxi, is an important local economic crop. However, leaf blight severely affects its yield and fruit quality, posing a major challenge to the sustainable development of the plum industry. Field observations revealed that the Mihuang Li cultivar exhibits strong resistance to leaf blight, whereas Zhenzhu Li is susceptible. This study aims to compare the rhizosphere microbial community compositions as well as the functional differences between the resistant (Mihuang Li, TA) and susceptible (Zhenzhu Li, TB) cultivars under the same environmental conditions, aiming to elucidate the mechanisms underlying the high disease resistance of Mihuang Li and to identify potential antagonistic microorganisms, thus providing theoretical and technical support for developing an ecological control system against plum leaf blight.【Methods】The experiment was conducted in a Zhenzhu Li plum orchard in Tian′e County, Hechi City, Guangxi. Rhizosphere soil samples were collected from three healthy trees per cultivar (TA and TB) around the canopy drip line in four directions. Samples were processed for DNA extraction, and high-throughput sequencing of bacterial 16S rRNA (V3-V4 region) and fungal ITS regions was performed on the Illumina MiSeq PE300 platform (Majorbio BioPharm Technology Co., Ltd., Shanghai, China) . PCR amplicons were purified, quantified, and sequenced (2 × 300 bp) . Data were analyzed using QIIME for diversity metrics, PICRUSt2 for COGbased bacterial functions, FUNGuild for fungal guilds, and IBM SPSS Statistics 21 for statistical comparisons (Duncan′s multiple range test, P＜0.05) .【Results】At the bacterial phylum level, the dominant phyla in the TA rhizosphere were Proteobacteria, Actinobacteriota, Acidobacteriota, and Chloroflexi, with Verrucomicrobiota and WPS-2 uniquely detected in TA. In contrast, TB was dominated by Actinobacteriota, Proteobacteria, Acidobacteriota, and Chloroflexi, with Bacteroidota and Methylomirabilota uniquely detected. At the genus level, TA showed higher relative abundances of Bradyrhizobium and Acidothermus, whereas TB was enriched in Arthrobacter. For fungi, TA was dominated by Ascomycota, Basidiomycota, and Mortierellomycota, while Rozellomycota was uniquely detected in TB. At the genus level, Trichoderma, Apiotrichum, and Solicoccozyma were detected only in TA, whereas TB showed higher relative abundances of Fusarium, Neocosmospora, and Chordomyces. COG-based functional prediction showed that TA had higher relative abundances of functional categories related to cell motility, secondary metabolite biosynthesis, lipid metabolism, and energy production and conversion, whereas TB exhibited higher abundances of categories associated with cytoskeleton formation, RNA processing, carbohydrate metabolism, and defense mechanisms. FUNGuild analysis revealed that TA rhizosphere fungi were mainly classified as saprotrophic guilds, while TB harbored a higher proportion of plantpathogenic guilds.【Conclusion】The rhizosphere microbial community of the resistant cultivar Mihuang Li (TA) differs significantly from that of the susceptible cultivar Zhenzhu Li (TB) in both composition and predicted function. TA harbors beneficial microorganisms such as Bradyrhizobium and Trichoderma, which exhibit strong saprotrophic activity and potential antagonism against pathogens, as well as enrichment in metabolic pathways related to energy production and secondary metabolism. These features may contribute to enhanced host resistance by maintaining rhizosphere ecological balance and suppressing pathogen colonization. In contrast, the TB rhizosphere community is dominated by potential pathogens (Fusarium, Gibberella) and decomposers, making it more prone to disease occurrence. Overall, this study reveals the potential role of rhizosphere microbial communities in the formation of leaf blight resistance in P. salicina, providing theoretical support for the screening of antagonistic microbes and the development of microbe-based disease control strategies in plum orchards.

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.

Endophytic microbial communities and leaf metabolites dynamically respond to light quality, yet their coordinated patterns remain poorly understood in horticultural system. Here, we systematically investigated the endophytic microbial composition and metabolic profiles of lettuce leaves exposed to white (W), red (R), blue (B), and yellow (Y) light, compared with natural light (CK). Endophytic bacterial diversity increased significantly under all artificial light treatments, whereas endophytic fungal diversity decreased. At the phylum level, Actinobacteriota, Bacteroidota, and unclassified_k__Fungi were consistently enriched across W, R, B and Y groups, with Actinobacteriota showing significantly higher relative abundance than in CK. Notably, Cyanobacteria, Deinococcota, and Nitrospirota emerged as dominant phyla specifically enriched under W, B, and Y light treatments, respectively. At the genus level, Bradyrhizobium, Rothia, and Bacillus all showed increased abundance under artificial light conditions. Furthermore, Methyloversatilis, Mycobacterium, Aquabacterium, Delftia, Curvularia, Aspergillus, and Phialosimplex served as biomarker genera characteristic of W, R, B, and Y treatments, respectively. Metabolomic analysis revealed distinct pathway enrichment and differential metabolite profiles across all light treatment relative to CK. Each spectrum uniquely modulated phenylpropanoid biosynthesis, flavonoid metabolism, and amino acid metabolism, resulting in differential accumulation of antioxidant and defense-related compounds. These findings demonstrate that light quality drives pronounced shifts in both endophytic microbial community structure and leaf metabolic profiles. The coordinated restructuring of the microbiome and metabolome provides mechanistic insights into light-dependent metabolic regulation in lettuce.

Endophytic microbiome and metabolome are closely related to the plant resistance. Unravelling the compositional features of the endophytic microbiome and metabolome can help to understand plant resistant mechanisms. This study investigates the resistant mechanisms of leaf blight-resistant plum cultivars through comparative analysis of endophytic microbiome and metabolome features between leaf blight resistant (Mihuang Plum, RP) and susceptible (Pearl Plum, SP) cultivars. The results showed that higher microbial diversity and richness could be detected in RP cultivar than those of SP cultivar. Meanwhile, the endophytic bacterial genera, such as 1174-901-12, Sneathia, Gardnerella, Bacteroides, Prevotella, Fastidiosipila, and the endophytic fungal genera, Paramycosphaerella, Epicoleosporium, Zasmidium, and Zeloasperisporium were enriched in the RP cultivar. Moreover, in comparison with SP cultivar, Flavonoid biosynthesis, Isoflavonoid biosynthesis, Phenylalanine metabolism, Phenylpropanoid biosynthesis, and Nucleotide metabolism showed high expression levels in RP cultivar, and the contents of (-)-Naringenin, 4-Coumaric acid, Epicatechin, Genistein, M-Coumaric acid, Dihydrokaempferol, and 4-Hydroxycinnamic acid were also significantly higher in RP cultivar. Our findings had revealed that significant differences of endophytic microbiome and metabolome features could be found between leaf blight resistant (Mihuang Plum, RP) and susceptible (Pearl Plum, SP) cultivars. Meanwhile, positive correlations between potential functional microorganisms, metabolites and leaf blight resistant plum cultivar also had been identified. In future research, a deeper exploration of these microbial communities and metabolites is warranted to fully understand their functional roles in the resistance mechanisms. Identifying the specific microbial taxa and metabolites that contribute to leaf blight resistance could provide valuable insights into their potential applications in biological control. By harnessing these natural microbial and metabolic resources, it may be possible to develop sustainable, eco-friendly strategies for managing leaf blight, ultimately reducing the dependency on chemical pesticides.

To screen out the bio-control soil microorganisms for preventing melon wilt, soil microbial compositions in rhizospheres between wilt-resistant and susceptible melon varieties were analyzed. The results showed that the soil fungal richness in rhizospheres of wilt-resistant melon varieties (MT) was significantly higher than that of wilt-susceptible melon varieties (MS). Additionally, in comparison with MS, soil bacterial compositions, such as Proteobacteria, Bacteroidota, Acidibacter, Streptomyces, etc., and the soil fungal compositions, such as Penicillium, Derxomyces, Aspergillus, and Talaromyces, enriched; also, Trichoderma, Gibellulopsis, and Pseudallescheria decreased in rhizospheres of wilt-resistant melon varieties (MT). Moreover, Mycothermus, Zopfiella, and Cladorrhinum were the unique soil-dominant fungal genera in rhizospheres of MT. All the above results suggested that the soil bacterial communities, such as Proteobacteria, Bacteroidota, Acidibacter, Streptomyces, etc., and the soil fungal communities, such as Penicillium, Derxomyces, Aspergillus, Talaromyces Mycothermus, Zopfiella, and Cladorrhinum, could be speculated as the potential soil bio-control microorganisms for preventing melon wilt.

The structure of endophytic microbial communities and metabolic functions differ significantly among plant varieties with different resistance levels. Currently, there is a lack of research articles that combine microbiomics and metabolomics to explore the mechanism of resistance to wilt disease in watermelon. To seek out the antagonistic microorganisms and metabolites against watermelon wilt from different watermelon varieties, we investigated the characteristics of endophytic microbial communities, metabolic features and functions in the roots of wilt–resistant (RW) and susceptible (SW) watermelon varieties. The results suggested that significant differences of endophytic microbial communities and metabolites could be found in the roots between RW and SW. Meanwhile, the endophytic bacterial genera such as Chryseobacterium, Pseudomonas, Delftia, Lechevalieria, unclassified_f__Methylophilaceae, Tahibacter, and the endophytic fungal genera, unclassified_p__Basidiomycota, Neocosmospora, unclassified_f__Lasiosphaeriaceae, Edenia were the unique dominant bacterial and fungal genera in the roots of RW, respectively. Additionally, the differential metabolites, including Galactinol, Sucrose, Stachyose, Coniferyl Aldehyde, Coniferin, 5–Hydroxyconiferyl alcohol, 4–Coumaryl alcohol, 3–Hydroxybenzoic Acid, and the metabolic pathways including Galactose metabolism, Phenylpropanoid biosynthesis, Phenylalanine, tyrosine and tryptophan biosynthesis significantly upregulated in wilt resistant watermelon varieties. This study systematically reveals, for the first time, the synergistic defense mechanisms between root endophytic microbiome and metabolome during Fusarium wilt resistance formation in watermelon. Significantly, we have identified potential functional microorganisms, key metabolites, and critical pathways that actively contribute to these defense mechanisms. However, the specific functions of these potential antagonistic microorganisms and metabolites still need further validation. These findings provide a novel perspective for crop disease resistance research, transcending the limitations of traditional single-factor analytical paradigms, while establishing a methodological foundation for developing multi-omics integrated approaches in crop disease resistance regulation strategies.

The fruit set in the Cucurbitaceae family is a critical determinant of fruit production and development. However, limited information is available regarding the regulatory mechanisms relating to pumpkin fruit sets. To elucidate the interplay between pumpkin fruit setting and endophytic microorganisms, we conducted a comparative analysis of the endophytic microbiota and metabolite profiles in the stems of naturally pollinated and non-pollinated pumpkin using microbiome and untargeted metabolomics approaches. The results showed that both the alpha- (reduced by 18.33∼21.88 % and 16.63∼24.08 %) and beta-diversities (reduced by 12.40 % and 40.00 %) of endophytic microorganisms (bacteria and fungi) in stems of pollinated pumpkins were significantly reduced which were significantly reduced compared to those in non-pollinated pumpkins. Meanwhile, in comparison with pollinated pumpkins, the deficiency of endophytic bacterial genera that regulate endogenous hormones and metabolites, such as Pantoea, Staphylococcus, Brevundimonas, Tatumella, and Gluconobacter, and the weak metabolic pathways, viz, the relatively stable homeostasis, such as flavone and flavonol biosynthesis, alanine, aspartate, and glutamate metabolism, and phenylpropanoid biosynthesis in stems of non-pollinated pumpkin were important reasons why fruits could not bear fruits without pollination. All above results reveal that endophytic microorganisms are closely related to the growth and development of pumpkins, also, the endophytic microbial community structures in stems of pumpkins can be reshaped by man-made measures, such as pollination.

Lotus root texture significantly influences consumer preferences and market value, yet the role of endophytes in determining the distinct mealy (ML) and crunchy (CL) textural properties remains unclear. This study aimed to clarify the relationship between endophyte composition and metabolic characteristics underlying the texture differences between ML and CL lotus root varieties. Two lotus root varieties (ML and CL) were analyzed for endophytic microbial communities using high-throughput sequencing methods. Metabolite profiling of cellulose, starch, pectin, soluble sugars, and proteins was conducted using standard biochemical assays. The findings revealed higher cellulose, starch, and pectin content in mealy lotus root (ML) varieties than those in crunchy lotus root (CL) varieties. Additionally, the functions of cellulose-degrading and protein-producing microorganisms, such as Firmicutes, Bacteroides, Exiguobacterium, Bradyrhizobium, and Basidiomycota, were primarily enriched in the ML varieties. In contrast, the CL varieties had specific dominant endophytic bacterial genera, such as Myxococcota, Geobacter, Paludibacteraceae, Rhodocyclaceae, Comamonadaceae, Micromonosporaceae, Sideroxydans, Bacillus, Lactococcus, Oxalobacteraceae, and Treponema. These results indicate that different endophytes are associated with the development of mealy and crunchy properties. Understanding these microbial–metabolic relationships offers practical implications for selective breeding and agricultural management aimed at texture improvement. Future research should elucidate the specific metabolic pathways regulated by these endophytes to facilitate targeted agricultural interventions.

Late blight caused by the oomycete Phytophthora infestans poses a severe threat to global tomato (Solanum lycopersicum L.) production. While genetic resistance forms the cornerstone of disease control, the mechanisms underlying cultivar-specific resistance, particularly their interactions with rhizosphere microbiomes, remain poorly understood. To elucidate the mechanisms of tomato cultivar resistance to late blight and screen out antagonistic microorganisms against P. infestans, we investigated the microbial compositions in the rhizospheres of tomato cultivars with different late blight-resistance levels under both natural and P. infestans-inoculated conditions. Considerable differences in soil microbial diversity and composition of rhizospheres were found between late blight-resistant and -susceptible tomato cultivars. Under natural conditions, the resistant tomato cultivar exhibited higher bacterial diversity and lower fungal diversity than that of the susceptible cultivar. Additionally, after P. infestans inoculation, both the resistant and susceptible cultivars showed enrichment of microorganisms with potential antagonistic effects in the rhizospheres. Among them, bacterial genera, such as Pseudomonas, Azospirillum, and Acidovorax, and fungal genera, including Phoma, Arthrobotrys, Pseudallescheria, and Pseudolabrys, were enriched in the rhizospheres of the late blight-resistant tomato cultivar. In contrast, bacterial genera, including Flavobacterium, Pseudolabrys, and Burkholderia-Caballeronia-Paraburkholderia, and the Trichoderma fungal genus were enriched in the rhizospheres of the late blight-susceptible tomato cultivar. Simultaneously, the enrichment of pathogenic microorganisms, such as Neocosmospora and Plectosphaerella, was also detected in the rhizospheres of the susceptible tomato cultivar. Moreover, no enrichment of pathogenic microorganisms occurred in the late blight-resistant tomato cultivar after P. infestans inoculation. These findings suggest that these traits serve as effective defense mechanisms against pathogen invasion in resistant tomato cultivar. Overall, this study provides a comprehensive analysis of the rhizosphere microbial community structures in late blight-resistant and -susceptible tomato cultivars under natural conditions and their response following pathogen inoculation. Additionally, potential antagonistic microorganisms against late blight were also identified. The findings offer valuable insights for effective late blight management in tomatoes and contribute to the development of sustainable agricultural practices.

To investigate the relationship between the rhizosphere microbial community structure and lotus root texture, the biological properties, and the rhizosphere microbial composition of mealy (ML) and crunchy lotus (CL) varieties were all analyzed using traditional and high-throughput sequencing technologies. The results showed that the ML varieties exhibited significantly lower moisture but higher starch contents than those of CL. Meanwhile, the rhizosphere fungal richness of ML was also significantly higher than that of CL. Moreover, the relative abundances of bacterial phyla and genera, such as Nitrospirota, Bacteroidota, Proteobacteria, and Bacillus, alongside fungal phyla and genera, i.e., Ascomycota and Emericellopsis, were enriched in rhizosphere of ML compared to CL. Functional prediction also revealed that elevated nitrogen cycling, polysaccharide degradation and cellulose breakdown functions could be detected in ML, potentially driving starch accumulation and cell wall modification. These results suggest that rhizosphere microbial composition, particularly nitrogen-cycling bacteria and lignocellulose-degrading fungi, may contribute to texture formation between texture-differentiated lotus root varieties.

Sugarcane smut, caused by the fungus Sporisorium scitamineum, is a devastating disease that limits sugarcane production and causes significant yield losses worldwide. This urgent threat highlights the critical need for novel sustainable control strategies. While utilizing beneficial plant-associated microbes shows promise for enhancing disease resistance, the contribution of the sugarcane rhizosphere microbiome in smut resistance remains poorly understood. In this study, rhizosphere microbial communities of sugarcane cultivars with contrasting resistance to smut were comparatively analyzed using high-throughput amplicon sequencing of the 16S rRNA gene and ITS region. Analysis of microbial co-occurrence networks analysis revealed that the resistant cultivars maintained more complex and stable networks than the susceptible cultivars. The rhizosphere microbiome of smut-resistant cultivars was predominantly enriched in beneficial genera such as Trichoderma, Penicillium, Talaromyces, Psathyrella, and Sphingomonas whereas that of susceptible cultivars contained more Streptomyces and Gibberella. Functional prediction also revealed distinct metabolic functions between the two microbiomes. These findings demonstrate that network stability and enrichment of antagonistic microbes constitute key determinants of rhizosphere-mediated smut resistance. Our study provides critical insights for developing microbiome-driven breeding strategies and biological control measures against this economically important disease.

To explore how endophytic microbial compositions in amaranth roots are influenced by various fertilization methods and to determine whether these microbes are associated with amaranthin formation, we conducted an analysis of the endophytic microbial community structure. The roots of amaranth plants subjected to different fertilization treatments—conventional fertilization without potassium (NP), conventional fertilization without phosphorus (NK), conventional fertilization without nitrogen (PK), and balanced fertilization (NPK)—were examined. The results showed that the proportions of Streptomyces, Actinospica, and Burkholderia-Caballeronia-Paraburkholderia in the amaranth roots under the balanced fertilization (NPK) treatment were all greater than those in the amaranth roots under the nitrogen (PK), phosphorus (NK), and potassium (NP) deficiency fertilization treatments. In contrast, the proportions of Phenylobacterium, Acrocalymma, Neocosmospora, Fusarium, Acidovorax, Gibellulopsis, Cladosporium, Dactylonectria, and Gibberella in the amaranth roots under the nutrient deficiency fertilization (NP, NK, and PK) treatments were higher than those in the amaranth roots under the balanced fertilization treatment. Additionally, a significantly positive correlation was found between Streptomyces and the amaranthin content. Furthermore, Acrocalymma, Neocosmospora, and Fusarium exhibited significantly negative correlations with the amaranthin content. The above results suggested that endophytes could easily colonize in amaranth roots as beneficial microorganisms under balanced fertilization conditions. In other words, the balanced fertilization (N, P and K fertilizers are 188.0, 53.0 and 50.0 kg·hm−2, respectively) could recruit more beneficial endogenous microorganisms in amaranth roots for improving their growth and quality.

Wood vinegar promotes crop growth and improves soil fertility and health. It is important to explore the mechanism by which wood vinegar promotes tomato growth under the continuous cropping system. Four wood vinegar treatments, i.e., the sterilized deionized water only (control, CK), and 300 times (A), 600 times (B) and 900 times (C) dilutions were set up, and the endophytic microbial compositions in the roots of tomatoes under the continuous cropping system using wood vinegar dilutions were analyzed. The results showed that the root morphological indices of tomatoes grown under continuous cropping systems were improved by different wood vinegar applications. In comparison with the CK, 600 times wood vinegar dilution increased the endophytic bacterial (and fungal) Shannon and ACE indices by 14.04

The synthesis of betalain using microorganisms is an innovative developmental technology, and the excavation of microorganisms closely related to betalain can provide certain theoretical and technical support to this technology. In this study, the characteristics of soil microbial community structures and their functions in the rhizospheres of white-fleshed dragon fruit (Hylocereus undatus) and red-fleshed dragon fruit (Hylocereus polyrhizus) were analyzed. The results show that the soil bacterial and fungal compositions in the rhizospheres were shaped differently between H. undatus and H. polyrhizus. Bacterial genera such as Kribbella and TM7a were the unique dominant soil bacterial genera in the rhizospheres of H. undatus, whereas Bradyrhizobium was the unique dominant soil bacterial genus in the rhizospheres of H. polyrhizus. Additionally, Myrothecium was the unique dominant soil fungal genus in the rhizospheres of H. polyrhizus, whereas Apiotrichum and Arachniotus were the unique dominant soil fungal genera in the rhizospheres of H. undatus. Moreover, TM7a, Novibacillus, Cupriavidus, Mesorhizobium, Trechispora, Madurella, Cercophora, and Polyschema were significantly enriched in the rhizospheres of H. undatus, whereas Penicillium, Blastobotrys, Phialemonium, Marasmius, and Pseudogymnoascus were significantly enriched in the rhizospheres of H. polyrhizus. Furthermore, the relative abundances of Ascomycota and Penicillium were significantly higher in the rhizospheres of H. polyrhizus than in those of H. undatus.