Frontiers In Plant Science[JOURNAL]
Sun
200 papers
Metabolic reprogramming of tomato roots during rhizobacteria-mediated defense against : modulation by gold nanoparticle conjugation.
Ali N, Haje Dashti N, Raju AI
Front Plant Sci · 2026 · PMID 42389137 · Full text
Rhizobacteria-induced systemic resistance (ISR) is an established strategy for enhancing plant tolerance to biotic stress, yet its metabolic consequences under nanoparticle-assisted delivery remain poorly understood. Her...
Rhizobacteria-induced systemic resistance (ISR) is an established strategy for enhancing plant tolerance to biotic stress, yet its metabolic consequences under nanoparticle-assisted delivery remain poorly understood. Here, we investigated metabolic reprogramming in tomato roots ( L.) challenged with the pathogen following treatment with PGPR strain (Sr) applied either alone or conjugated to phycosynthesized gold nanoparticles using . Bionanogold synthesis was confirmed by UV-Visible surface plasmon resonance (~534 nm). Successful conjugation with (Sr-AuNPs) was validated via TEM, FTIR, dynamic light scattering (size increase from 78.15 ± 10.89 nm to 90.96 ± 1.96 nm), zeta potential (-28.56 mV), and ICP-MS, indicating stable nanoparticle-bacteria association. The integrated metabolic fingerprinting of tomato root exudates obtained from GC-MS, LC-MS/MS, and H NMR data was normalized and autoscaled prior to multivariate analysis. The variations in metabolic signatures associated with tomato roots under different treatments- control (T1), rhizobacteria (T2: Sr+Ep), rhizobacteria conjugated with nanoparticles (T3: Sr-AuNPs+Ep), and pathogens (T4: Ep) were characterized and distinguished by multivariate analysis. Various metabolites with distinct signatures were observed among the different treatments through one-way ANOVA test with FDR adjustment. These included LC-MS/MS m/z 338.33 (putative signature 13-docosenamide or Tentative lipid amide (C22), long chain lipid-associated ions (m/z 337.06), derivatives of Benzoic acid, oleanitrile and H NMR peaks related to lipid, Citrate/succinate, and oxygenated compounds. Pathway topology analysis revealed that the TCA cycle, Flavonoid biosynthesis, glyoxylate and dicarboxylate metabolism, and Cutin/Suberin/Wax biosynthesis were some of the more significant pathways represented in the detected metabolite data set. These pathway-level associations should be regarded as preliminary indications of functional relationships among the detected metabolites, rather than direct or conclusive evidence of pathway activation or metabolic flux changes. FTIR analysis further supported treatment-associated biochemical variation in root exudates. Collectively, the nanoparticle-conjugated rhizobacterial treatment was associated with a metabolite profile distinct from both the pathogen-only and rhizobacteria-only treatments. This provides a preliminary metabolomic framework for understanding nano-enabled plant-microbe interactions under biotic stress.
Evaluation of uncharacterized quinoa ( Willd.) accessions for salinity tolerance during seedling emergence and early growth.
Suthar JD, Ganjegunte GK, Hashimi R
Front Plant Sci · 2026 · PMID 42389136 · Full text
INTRODUCTION: Salinity stress is a major constraint to crop establishment and productivity in arid and semi-arid regions, necessitating the identification of salt-tolerant crops and accessions. METHODS: This greenhouse s...
INTRODUCTION: Salinity stress is a major constraint to crop establishment and productivity in arid and semi-arid regions, necessitating the identification of salt-tolerant crops and accessions. METHODS: This greenhouse study assessed the salinity tolerance of 22 quinoa ( Willd.) accessions, including uncharacterized accessions, seedling emergence, and early seedling growth under six irrigation water salinity levels (ECiw ≈ 1, 3, 6, 9, 12, and 15 dS m). A completely randomized design with three replications was employed. Salinity tolerance was assessed using the salinity tolerance index (STI) and membership function value (MFV), and accessions were classified through hierarchical cluster analysis. RESULTS: Increasing salinity significantly reduced seedling emergence, delayed emergence, and decreased growth and biomass (P ≤ 0.01). At 15 dS m, emergence declined by 66.7%, and biomass decreased by more than 90%. Salinity altered ion accumulation, increasing Na and Ca concentrations while decreasing K concentration and the ionic ratios (K/Na and Ca/Na). Among the accessions, PI 634923 exhibited the highest salinity tolerance, followed by PI 698783, PI 698773, PI 698780, and PI 698775. Biomass-related traits showed stronger associations with overall tolerance than seedling emergence traits. The threshold salinity corresponding to 50% STI was estimated at approximately 10.5 dS m for seedling emergence and the early growth stage. DISCUSSION: Overall, the study reveals substantial genetic variability in quinoa and identifies promising accessions for saline environments. The inclusion of previously uncharacterized germplasm provides novel insights into breeding programs and supports the development of climate-resilient cropping systems.
Leguminous green manure enhances soil quality and plant productivity in coal mine reclaimed lands: a decade-long field study.
Dong Y, Quan YJ, Zhang HF … +10 more , Yang Y, Xue DH, Bo HJ, Bo JH, Zhang BH, Jin DS, Zhang WJ, Zhang Q, Xu MG, Wang W
Front Plant Sci · 2026 · PMID 42389135 · Full text
Green manure planting is a commonly used environmentally friendly and sustainable field management practice in resource-constrained agricultural ecosystems. However, the effects of green manure on soil quality and plant...
Green manure planting is a commonly used environmentally friendly and sustainable field management practice in resource-constrained agricultural ecosystems. However, the effects of green manure on soil quality and plant production in coal mine reclamation agroecosystems remain unclear. In this study, a decade-long legume cultivation experiment was conducted to evaluate the effects on soil aggregate structure, nutrients, microbial diversity, and plant productivity. The experiment was established at the Gujiao long-term monitoring site of Shanxi Agricultural University and included three treatments: natural restoration, alfalfa planting and villose vetch planting. Compared with the control, legume planting-particularly alfalfa-significantly increased plant biomass and the accumulation of soil organic carbon (SOC) and total phosphorus. Specifically, in the 0-20 cm soil layer under the RAF treatment, SOC and TP contents increased by 23.84% and 47.17%, respectively. Moreover, alfalfa planting enhanced the proportion of aggregates larger than 0.25 mm by 36.56% in wet sieving. Interestingly, continuous legume forage cultivation significantly improved soil aggregate stability. Moreover, alfalfa planting increased bacterial diversity, stimulated the accumulation of lignin-derived compounds, and resulted in the highest acid-formaldehyde ratio, indicating that alfalfa planting increased lignin degradation capacity and provided beneficial nutrients for reclaimed soil. Variance partitioning analysis indicated that both soil physicochemical properties and the microbial community structure co-driven plant biomass variations. These findings clarify the mechanisms by which legume cultivation improves soil quality, enhances microbial diversity, and increases biomass production. In conclusion, this study supports the application of leguminous green manure as a natural solution for coal mine land reclamation, contributing to soil quality improvement and fostering sustainable development in postmining ecosystems.
Nano-zeolite-coupled biochar-based phosphorus fertilizer enhances soil phosphorus availability and leaf phosphorus concentration in Moso bamboo forests.
Xie J, Liu J, Jiang Z … +4 more , Xiao M, Zhou J, Yu B, Li Y
Front Plant Sci · 2026 · PMID 42389134 · Full text
INTRODUCTION: Phosphorus (P) availability is a major constraint on nutrient management in acidic Moso bamboo (Phyllostachys edulis) forests, where conventional P fertilizers are prone to rapid fixation by soil minerals....
INTRODUCTION: Phosphorus (P) availability is a major constraint on nutrient management in acidic Moso bamboo (Phyllostachys edulis) forests, where conventional P fertilizers are prone to rapid fixation by soil minerals. Biochar-based P fertilizers can help retain P in soil. Yet it is still unclear whether they can sustain soil P availability and support plant P nutrition over time in acidic forest soils. METHODS: Here, we carried out a 24-month field trial in a subtropical Moso bamboo forest. We compared three P fertilizer treatments: conventional phosphorus fertilizer (CP), biochar-based phosphorus fertilizer (BP), and nano-zeolite-coupled biochar-based phosphorus fertilizer (NBP). Soil P fractions, microbial biomass P, and leaf P concentration were investigated. RESULTS AND DISCUSSION: Compared with the CP treatment, the BP and NBP treatments increased soil pH and retained more P in labile and moderately labile pools. The NBP treatment exhibited the strongest positive effects on soil P availability, particularly after 24 months. At this time, NBP reduced the accumulation of HCl-P, a relatively poorly available inorganic P fraction, while maintaining more P in accessible forms, including HO-P, NaHCO-P, NaHCOP, and NaOH-P. Beyond these physicochemical changes, NBP also enhanced biological P cycling, as indicated by increased microbial biomass P, gene abundance, alkaline phosphatase activity, and leaf P concentration. These results suggest that NBP improved P supply through both microbial P retention and organic P mineralization. Overall, the nano-zeolite coupling enhanced the capacity of biochar-based P fertilizer to alleviate soil acidity and sustain P availability through these combined physicochemical and biological processes. The results obtained in this study reveal that NBP is a promising strategy for improving soil P availability and sustaining P nutrition in acidic Moso bamboo forest soils.
From the field to the pot: phenological, agronomic, and cookability traits of common beans ( L grown in contrasting climatic regions in Uganda.
Nanyonjo AR, Lan Y, Brhane H … +4 more , Geleta M, Nkalubo ST, Nakimbugwe D, Kuktaite R
Front Plant Sci · 2026 · PMID 42389133 · Full text
INTRODUCTION: Common beans ( L.) phenotypic characteristics, cooking quality, and resilience to climate change are pivotal in making varietal choices of this crop in Uganda. METHODS: This study evaluated 247 common bean...
INTRODUCTION: Common beans ( L.) phenotypic characteristics, cooking quality, and resilience to climate change are pivotal in making varietal choices of this crop in Uganda. METHODS: This study evaluated 247 common bean genotypes across two climate-diverse regions, Mubuku (883 mm precipitation) and Namulonge (1300 mm precipitation), with 199 genotypes evaluated for phenological, agronomic, and cookability characteristics. RESULTS: The mixed model analysis indicated significant differences in both genotype and genotype x environment effects for days to flowering and maturity, number of pods per plant, 100-seed weight, seeds per pod, and per plant (P < 0.001). The environment significantly influenced days to flowering and maturity (P < 0.001), while the genotype affected cooking time (P < 0.05), but not water absorption capacity. Significantly longer cooking time (75 minutes, P < 0.05) for red color seeds and shorter cooking time (62 minutes, P < 0.05) for white color seeds were found compared to the mean. The medium-seed-size genotypes had the shortest cooking time. Meanwhile, both the medium and large-seed-size genotypes exhibited high yields. Seven genotypes (NAROBEAN6, SMR48, SCR60, SCR45, SCN20, KND100, SCN744), which showed superior performance based on best linear unbiased predictor values for the traits studied, should be further tested across multiple climates and considered in common bean improvement programs. DISCUSSION: The phenotypic trait, 100-seed weight, is important particularly when breeding for yield and cooking time. This study uniquely highlights the common bean genotypes that might be critically important in drought-stress environments and for the improvement of food security in Uganda and Africa at large.
Identification of EMS-induced sesame (.) mutants with improved low-temperature tolerance during germination and early seedling growth.
Tahri N, Louafi B, Kouighat M … +2 more , Mikou K, Nabloussi A
Front Plant Sci · 2026 · PMID 42389132 · Full text
Sesame ( L.) is a valuable oilseed crop in Morocco, but its cultivation is strictly constrained by sensitivity to low temperatures during early-season sowing. Traditionally sown in June, advancing the sowing date to Apri...
Sesame ( L.) is a valuable oilseed crop in Morocco, but its cultivation is strictly constrained by sensitivity to low temperatures during early-season sowing. Traditionally sown in June, advancing the sowing date to April would allow farmers to capitalize on residual spring rainfall, significantly reduce irrigation dependency, and improve the crop productivity. However, this strategy exposes germinating seeds to sub-optimal soil temperatures (10-15 °C night minima). Mutation breeding via ethyl methanesulfonate (EMS) offers a powerful approach to generate novel genetic variability for abiotic stress tolerance. This study aimed to identify EMS-induced sesame mutants exhibiting superior germination and early seedling growth performance under progressive low-temperature stress conditions. Germination and seedling growth traits were assessed under controlled conditions. Low temperature stress induced highly significant genotypic variation (p<0.001) for all traits except for root and plumule length. At the coldest regime (24 °C/12 °C), mutants ML2-37 and ML2-72 maintained significantly higher germination percentages compared to the cold-sensitive mutant US1-2. The tolerant mutants exhibited faster germination rates, shorter mean germination times, superior root-shoot ratios, and higher seedling vigor indices. The mutants ML2-37 and ML2-72, demonstrating promising low-temperature tolerance during the critical germination phase, represent valuable genetic resources for developing early-sowing, climate-resilient sesame cultivars. However, since the present study was conducted exclusively under controlled laboratory conditions, the findings should be supported by an extensive field validation across multiple sites and seasons in order to confirm their agronomic performance and yield stability under real early-spring sowing conditions.
Synergistic role of plant growth-promoting rhizobacteria and fungi in biofertilizer development for chilli ( L.): mechanistic and functional insights.
Gehlot P, Yadav J, Jain T
Front Plant Sci · 2026 · PMID 42389131 · Full text
Agricultural sustainability is increasingly threatened by the excessive use of chemical fertilizers, which has led to soil degradation, nutrient imbalance, and ecological disturbances, necessitating the development of ec...
Agricultural sustainability is increasingly threatened by the excessive use of chemical fertilizers, which has led to soil degradation, nutrient imbalance, and ecological disturbances, necessitating the development of eco-friendly alternatives. Biofertilizers based on plant growth-promoting microorganisms (PGPM), particularly plant growth-promoting rhizobacteria (PGPR) and plant growth-promoting fungi (PGPF), have emerged as promising tools for enhancing crop productivity while maintaining soil health. Chilli ( L.), an economically important spice crop, is often constrained by nutrient deficiencies, declining soil fertility, and disease pressure, which significantly affect its yield and quality. This review critically examines current advances in the mechanistic and functional roles of PGPR and PGPF in sustainable chilli cultivation, with particular emphasis on microbial-mediated nutrient mobilization, including nitrogen fixation, phosphate solubilization, phytohormone production, enzymatic activities, and biocontrol mechanisms. Emerging evidence suggests that microbial consortia involving bacterial and fungal inoculants establish synergistic interactions that enhance nutrient availability, improve root architecture, and increase plant tolerance to biotic and abiotic stresses more effectively than single inoculants. Additionally, microbial traits such as siderophore production, and antagonistic potential further contribute to enhanced plant growth, nutrient-use efficiency, and yield stability. Particular attention is also given to recent developments in consortium-based biofertilizer formulations, including carrier selection, inoculant stability, microbial survival, and field-level applicability. Collectively, the available literature indicates that integrated PGPR-PGPF biofertilizer approaches represent a promising strategy for improving chilli productivity, reducing dependency on chemical fertilizers, and promoting long-term soil health and sustainable agricultural resilience.
A prebiotic-based biostimulant enhances growth parameters, photosynthetic efficiency, and grain yield in rice ( ssp. ).
Medina-Jiménez K, Hale B, Cerquera-Hernández C … +2 more , Gesto-Borroto R, Lorence A
Front Plant Sci · 2026 · PMID 42389130 · Full text
Biostimulants constitute an emerging class of biological inputs with potential to boost crop yield in a sustainable manner. However, such products must be tested rigorously to unravel complex and oftentimes discrete mode...
Biostimulants constitute an emerging class of biological inputs with potential to boost crop yield in a sustainable manner. However, such products must be tested rigorously to unravel complex and oftentimes discrete modes of action, which is crucial for optimizing product placement and maximizing grower return on investment. This study combined high-throughput phenotyping of seedling establishment, assessment of vegetative and reproductive development, and quantification of photosynthetic efficiency to determine the impact of FoliarBlend, a prebiotic-based biostimulant, on the rice var. Kitaake (Oryza sativa ssp. japonica) from seed germination through seed production. Automated, non-invasive phenotyping revealed that FoliarBlend-treated seedlings displayed consistently elevated projected leaf area, convex hull area, caliper length, and compactness from 5 to 14 days after germination (DAG). The treatment did not introduce additional physiological stress, as evidenced by levels of chlorophyll fluorescence, relative water content, and estimation of chlorotic leaf surface area. Manual phenotyping from 21 to 82 DAG revealed that FoliarBlend application had paradoxical effects on vegetative and reproductive development, decreasing leaf and tiller number while increasing plant height, panicle number, above and belowground biomass, and ultimately grain yield. Furthermore, assessment of photosynthetic parameters highlighted improved Photosystem II (PSII) efficiency and chlorophyll content in treated plants from 49 to 82 DAG, along with an elevation in the quantum yield of non-regulated energy dissipation in PSII. These outcomes indicate that FoliarBlend positively impacts rice seedling establishment, reproductive growth, photosynthetic efficiency, and grain yield under controlled conditions, posing significant implications for enhancing rice production.
Replacing nitrogen fertilizer with organic alternatives changes the soil microbial community diversity in Northwest China's arid farmland, leading to increased potato yields.
Shi X, Zhang Y, Xu B … +9 more , Qin Y, Chen Y, Yu J, Liu K, Wu L, Liang J, Jin Z, Fan M, Jia L
Front Plant Sci · 2026 · PMID 42389129 · Full text
Northwest China, a major potato-producing region, relies heavily on chemical nitrogen fertilizers to maintain yields. In this arid area with limited rainfall and low soil organic matter, however, excessive nitrogen use i...
Northwest China, a major potato-producing region, relies heavily on chemical nitrogen fertilizers to maintain yields. In this arid area with limited rainfall and low soil organic matter, however, excessive nitrogen use impairs soil structure and disturbs nutrient balance, ultimately degrading soil quality and undermining sustainable agriculture. Therefore, understanding whether organic fertilizers can replace chemical nitrogen to improve soil quality and stabilize yields is essential. In this study, we applied six fertilization treatments and used 16S rRNA and ITS high-throughput sequencing to analyze potato rhizosphere microbial communities. We found that replacing 60% of chemical nitrogen with organic fertilizer was the optimal strategy for potato production in this arid region; this substitution increased potato yields by 8.23% compared with chemical fertilizer alone. This substitution also significantly reduced soil bulk density, enhanced the formation and stability of soil water-stable aggregates, and increased the levels of total nitrogen (TN), soil organic carbon (SOC), ammonium (NH-N), and nitrate (NO-N). Organic fertilizer had a more pronounced effect on bacterial diversity than fungal diversity, notably boosting the populations of Proteobacteria and Actinobacteria. The fungal community was primarily composed of Ascomycota and Basidiomycota. Key factors influencing bacterial community changes included SOC, NH-N, NO-N, and pH, while SOC and the carbon-to-nitrogen (C:N) ratio mainly affected the fungal community. In summary, substituting nitrogen fertilizers with organic alternatives can enhance soil physical and chemical properties, boost potato yields, and significantly alter the rhizosphere microbial community structure. This provides a scientific foundation for mitigating soil quality degradation in northern China's arid regions and promoting sustainable and efficient fertilization practices.
Evolutionary and functional analysis of ARF and Aux/IAA gene families reveals their roles in sugar metabolism and watermelon domestication.
Zhengwei S, Kenea FT, Gang C … +7 more , Dongdong Y, Mengli C, Yushi Z, Xuqiang L, Hongju Z, Nan H, Wenge L
Front Plant Sci · 2026 · PMID 42389128 · Full text
Auxin signaling, mediated by auxin response factors (ARFs) and Aux/IAA proteins, is central to plant development; however, its role in regulating fruit quality traits-particularly soluble sugar and organic acid metabolis...
Auxin signaling, mediated by auxin response factors (ARFs) and Aux/IAA proteins, is central to plant development; however, its role in regulating fruit quality traits-particularly soluble sugar and organic acid metabolism-remains largely unexplored in Cucurbitaceae crops. To address this gap, we integrated comparative genomics, metabolomics, and transcriptomics to elucidate the evolutionary conservation and functional specialization of and gene families in cucurbit fruit quality regulation. We identified 157 and 275 genes across eight cucurbit species, revealing extensive evolutionary conservation under predominant purifying selection (Ka/Ks < 0.6). Despite this constraint, domestication-driven functional divergence was evident: comparative metabolomic and population genomic analyses of wild watermelon ancestors ( and ) and cultivated accessions showed that glucose and fructose contents increased sharply during the to transition, whereas sucrose accumulation rose later during the shift from seed-type to landrace watermelons. Four candidate genes (, , , and ) exhibited significant allelic differentiation during this early sugar-accumulation transition and remained stably fixed in subsequent domestication stages, directly linking evolutionary signatures with functional outcomes. Exogenous auxin treatment increased glucose and fructose by 23-35% while reducing malate by 18%, confirming that auxin signaling reprograms carbon partitioning toward hexose accumulation. Transcriptome profiling revealed that most genes peaked during early fruit development (10-22 days after pollination), coinciding with metabolic shifts in sugar and organic acid accumulation. Promoter analysis uncovered conserved cis-regulatory elements associated with fruit development across watermelon, cucumber, and melon, suggesting shared regulatory logic. Collectively, this study provides the first integrated evidence that and gene families coordinate fruit quality metabolism in cucurbits through evolutionarily conserved regulatory architecture with lineage-specific functional adaptations. These findings establish a molecular framework for cucurbit quality improvement, offering candidate targets for marker-assisted selection or genome editing to enhance fruit sweetness and flavor.
Identification of rice genotypes for reproductive stage heat tolerance and yield stability through multi-trait and multivariate analysis.
Jasmin A, Rajendran K
Front Plant Sci · 2026 · PMID 42389127 · Full text
CONTEXT: High temperature during the flowering phase is a major constraint to stable rice productivity. Heat tolerance cannot be explained solely by yield, as yield is affected by several interacting traits. Therefore, a...
CONTEXT: High temperature during the flowering phase is a major constraint to stable rice productivity. Heat tolerance cannot be explained solely by yield, as yield is affected by several interacting traits. Therefore, an integrated multi-trait evaluation is essential to identify rice genotypes with superior performance under heat stress. OBJECTIVE: The research was designed to identify high-yielding, heat-tolerant rice genotypes and the key traits contributing to yield maintenance under heat stress. METHODS: A total of 80 rice accessions, comprising 45 landraces and 35 improved cultivars, were evaluated across four field environments using an alpha-lattice design across two cropping seasons under normal and heat-stress conditions during 2024-2025. Twenty morphological, physiological, and phenological traits were recorded. Pooled analysis of variance, correlation analysis, path coefficient analysis, principal component analysis, cluster analysis, and Multi-Trait Genotype-Ideotype Distance Index (MGIDI) analysis were performed, while a trait-wise heat tolerance index was applied to examine genotype performance under heat stress conditions. RESULTS: Pooled ANOVA revealed evident impacts of genotype, environment, and genotype × environment interaction for all traits, indicating substantial genetic variability and contrasting responses to heat stress. High temperature during the reproductive stage adversely affected reproductive and yield-associated traits, with the largest reductions noticed in single plant yield, panicle weight, number of filled grains per panicle, spikelet fertility, and productive tillers. Trait-wise, HTI showed considerable diversity among genotypes, with TKM 9, TRY 1, PR 128, TPS 5, and TRY 5 recording superior performance in single-plant yield. Correlation and path coefficient analyses highlighted harvest index, panicle weight, productive tillers, number of grains per panicle, and filled grains per panicle as major contributors for yield maintenance under stress, whereas delayed flowering and high leaf temperature were unfavorable. Principal component analysis revealed that reproductive efficiency and grain formation explained more variation in heat tolerance than vegetative vigor, while cluster analysis identified Cluster III as the most promising group with superior genotypes under heat stress. MGIDI-based ranking further recognized TRY 1, RNR 15048, TPS 5, Indhurani, and Anna R 4 as promising multi-trait genotypes. CONCLUSIONS: Heat tolerance in rice is governed by multiple interacting traits rather than yield alone. Integrating trait-based analysis with trait-wise HTI and MGIDI improves the identification of superior genotypes under field conditions. The identified genotypes and key traits offer valuable resources for breeding heat-tolerant rice under increasing temperature stress.
Effect of partial substitution of chemical fertilizer with organic manure combined with biochar on lettuce yield, soil properties and leaf metabolism.
Li P, Li S, Li Z … +1 more , Dabu X
Front Plant Sci · 2026 · PMID 42389126 · Full text
The co-application of biochar and organic fertilizer with chemical fertilizer is considered an important strategy for improving soil functions and vegetable quality. In this study, a field experiment was conducted with f...
The co-application of biochar and organic fertilizer with chemical fertilizer is considered an important strategy for improving soil functions and vegetable quality. In this study, a field experiment was conducted with four treatments under equal total nutrient input: chemical fertilizer alone (T1), 50% substitution of chemical fertilizer nutrients with organic manure (T2), chemical fertilizer plus biochar (T3), and 50% substitution of chemical fertilizer nutrients with organic manure plus biochar (T4). The objective of this study was to investigate the effects of organic fertilizer and biochar application on lettuce yield, soil physicochemical properties, and leaf metabolomic profiles, thereby providing a scientific foundation for reducing chemical fertilizer inputs, enhancing fertilizer use efficiency, and improving vegetable quality. The results showed that, compared with T1, treatments T2, T3, and T4 increased soil organic matter, pH, available nitrogen, phosphorus, and potassium contents, as well as lettuce yield and nutrient uptake to varying degrees, with T4 exhibiting the most pronounced overall effects. Metabolomic analysis revealed that the application of organic fertilizer and biochar significantly up-regulated phenolic acids and flavonoids in lettuce leaves and promoted the enrichment of pathways associated with secondary metabolite accumulation, such as phenolic acid biosynthesis and sulfur metabolism. Correlation analysis further indicated that the changes in leaf metabolites were significantly correlated mainly with soil organic matter, pH, and available potassium. KEGG enrichment analysis uncovered differential impacts of the fertilization treatments on metabolic pathways: organic fertilizer primarily affected the tyrosine metabolism pathway, biochar mainly influenced nitrogen metabolism-related pathways (involving zeatin and amino acids), whereas the combination of organic fertilizer and biochar predominantly affected pathways including phenolic acid biosynthesis and sulfur metabolism. In conclusion, from a metabolomics perspective, this study revealed the metabolic pathway division of labor and synergistic effects of organic fertilizer and biochar in regulating secondary metabolism in lettuce, and preliminarily established associations between soil physicochemical factors and leaf metabolites, providing new insights into the quality improvement mechanism of organic substitution combined with biochar.
An image-based phenotyping system for hydroponic maize seedling roots based on DB-UNet and customized skeleton-based analysis.
Guo Y, Huang Y, Zhu C … +6 more , Tian L, Zhang J, Li Y, Liu Y, Wu H, Fu X
Front Plant Sci · 2026 · PMID 42389125 · Full text
Root phenotype is a key agronomic trait affecting maize growth and development. observation and high-precision root phenotypic analysis provide important support for monitoring maize growth. Traditional root phenotyping...
Root phenotype is a key agronomic trait affecting maize growth and development. observation and high-precision root phenotypic analysis provide important support for monitoring maize growth. Traditional root phenotyping methods lack monitoring capabilities, and existing models have limited accuracy in root segmentation. To address these issues, we developed a crop root phenotyping system integrating crop cultivation and data collection. We also proposed a DB-UNet model for hydroponic maize root segmentation. DB-UNet builds a CNN-ViT dual-branch parallel structure during encoder downsampling level. The lightweight ViT branch uses sequential downsampling to achieve global topological dependency modeling while reducing computational costs. An attention fusion module dynamically calibrate dual-branch features weights, achieving complementary fusion of local root edge details and global context information. we constructed a mixed loss function combining Dice loss, Focal loss, and structural consistency KL loss to solve class imbalance, hard sample segmentation, and semantic divergence of dual-branch features. On our custom hydroponic maize root dataset, DB-UNet achieved an mIoU of 91.02%, an FG IoU of 82.78%, and a Centerline-Dice of 97.72%.Compared to classic UNet, mIoU, FG IoU, and Centerline-Dice increased by 0.92%, 1.84%, and 1.99%, respectively. Plant-level five-fold cross-validation further showed that DB-UNet maintained stable segmentation performance across different plant-level partitions. Based on DB-UNet segmentation results, we propose a custom skeleton-based algorithm for multi-trait root phenotyping, enabling the extraction of total root length and root branch points. Root area is calculated from binary mask pixel statistics. Compared to the traditional Zhang-Suen algorithm, the average relative error of root length measurement is reduced to 3.14%, which is 8.42 percentage points lower than the traditional method. Furthermore, we analyzed relationships between segmentation accuracy metrics and phenotypic relative errors. Higher segmentation quality generally led to lower phenotypic relative errors and more reliable trait measurements. In particular, Centerline-Dice was closely associated with root length estimation, whereas pixel-level segmentation consistency was more closely related to root area measurement. Pearson and Spearman correlation analyses showed a strong positive correlation between maize plant height and total root length, with coefficients of 0.8466 and 0.8634, respectively.
Differences in carbon sequestration capacity, rhizosphere microorganisms and metabolic functions among different herbaceous plants.
Zhou Y, Bian P, Yang C … +3 more , Qu J, Wang H, Gao W
Front Plant Sci · 2026 · PMID 42389124 · Full text
Mitigating the rapid increase in global CO₂ concentrations necessitates a deeper understanding of plant-microbe symbiotic carbon sequestration. While previous research has predominantly focused on woody plants, the carbo...
Mitigating the rapid increase in global CO₂ concentrations necessitates a deeper understanding of plant-microbe symbiotic carbon sequestration. While previous research has predominantly focused on woody plants, the carbon sequestration potential and mechanisms of herbaceous plants and their rhizosphere microbiomes remain largely underexplored. To address this gap, this study employed metagenomic technology to systematically investigate the carbon sequestration capacities and metabolic mechanisms of seven plant species and their rhizosphere soil microorganisms. Plant physiological measurements were integrated with microbial functional profiles predicted via PICRUSt2. The results show that the rhizosphere soil microbial communities generally possess functional genes for carbon decomposition and carbon fixation, providing evidence for the coupling of intracellular decomposition and synthesis metabolism in microorganisms. Notably, Spearman correlation analysis established a direct statistical link between plant physiological performance and specific microbial metabolic pathways. These findings demonstrate a functional coupling between plant physiology and rhizosphere microbial carbon metabolism. By linking plant phenotypes to microbial gene pathways, this study reveals that herbaceous plants and their rhizosphere microbiomes form an integrated carbon sequestration system. Therefore, leveraging such plant-soil interactions offers a promising strategy to enhance ecosystem carbon sinks and mitigate rising atmospheric CO₂.
Co-application of leguminous and non-leguminous green manures enhances subsequent wheat yield stability in saline-alkali soils.
Zhang M, Yu R, Cao J … +7 more , Li W, Tang S, Chen Z, Liu H, Wang X, Cai J, Zhang H
Front Plant Sci · 2026 · PMID 42389123 · Full text
The incorporation of green manure into cropping systems is recognized as an effective practice for improving environmental sustainability, particularly in irrigated agroecosystems such as the Hetao Irrigation District. H...
The incorporation of green manure into cropping systems is recognized as an effective practice for improving environmental sustainability, particularly in irrigated agroecosystems such as the Hetao Irrigation District. However, the effect of green manure as a preceding crop in regulating subsequent wheat productivity and soil functioning in saline soils under limited nitrogen (N) inputs remains insufficiently understood. To address this gap, a 9-year field experiment was conducted to evaluate the effects of green manure types (non-leguminous feed rape (GMR), leguminous hairy vetch (GMV), and their combined application (GMRV) and N application rates (N150, 150 kg N per ha; N0, no N input) on multi-year spring wheat yield, soil ecosystem multifunctionality (EMF), and microbial resource limitation. The results showed that only green manure types had significant influence on subsequent yield and stability except for year. Compared with GMR, the GMRV treatment increased average yield by 17.2% under N150 and enhanced yield stability by 21.7% and 22.2% under N150 and N0, respectively. In addition, GMRV markedly enhanced soil organic carbon (SOC), enzyme activities, and EMF across both the wheat-growing and green manure seasons. Positive relationships were observed among SOC, total nitrogen (TN), EMF, and crop yield. Microbial communities were primarily constrained by C and N availability. GMRV reduced the microbial C limitation during the green manure season, while GMV alleviated the microbial C limitation at spring wheat season. In conclusion, the combined application of leguminous and non-leguminous green manure improved crop productivity and soil functioning by promoting SOC accumulation, nutrient availability, and ecosystem multifunctionality, while alleviating microbial resource constraints. This approach offers a promising pathway for reducing nitrogen fertilizer dependence in saline agroecosystems such as the Hetao Irrigation District.
Phylogenomics, divergence time estimation, and biogeography of species from Kazakhstan using plastome sequence analysis.
Almerekova S, Yermagambetova M, Alikhanova A … +3 more , Yerbolatov D, Osmonali B, Turuspekov Y
Front Plant Sci · 2026 · PMID 42389122 · Full text
INTRODUCTION: The genus Tourn. ex L. (Iridaceae Juss.) comprises more than 300 accepted species distributed across the Northern Hemisphere and widely valued for its medicinal and ornamental significance. However, is a...
INTRODUCTION: The genus Tourn. ex L. (Iridaceae Juss.) comprises more than 300 accepted species distributed across the Northern Hemisphere and widely valued for its medicinal and ornamental significance. However, is a taxonomically complex genus with controversial circumscription and unresolved phylogenetic relationships, emphasizing the need for comprehensive systematic studies. METHODS: In this study, plastomes of 14 species collected in Kazakhstan were sequenced, assembled, and annotated. Comparative genomic analyses, divergence time estimation, and biogeographic reconstruction were performed based on complete plastome data. RESULTS: All plastomes exhibited the typical quadripartite circular structure, with genome sizes ranging from 150, 612 bp () to 155, 046 bp (). The gene content was highly conserved among the studied species, with 133 genes identified, including 87 protein-coding genes (PCGs), 38 tRNA genes, and eight rRNA genes. Among these, eight PCGs (, and ), seven tRNA genes (, and ), and all four rRNA genes (, and ) were duplicated. Ten highly variable regions were identified, namely , and , most of which were located in the large single-copy region. A total of 2, 401 simple sequence repeats (SSRs) were detected across the 14 plastomes, with an average of 171.5 SSRs per species. Mononucleotide repeats were the most abundant type, accounting for 65.7% of all SSRs, with a strong bias toward A/T motifs. Phylogenetic analyses resolved three major clades corresponding to the subgenera , , and . Molecular dating suggested that originated approximately 49.31 Ma (95% CI: 40.13-59.60 Ma), with crown group diversification beginning around 41.43 Ma (95% CI: 33.97-50.97 Ma). Ancestral area reconstruction indicated a combined Eastern Asia-Central Asia origin for the genus. DISCUSSION: Overall, this study provides comprehensive plastome-based insights that may contribute to resolving phylogenetic relationships, improving population genetic studies, and elucidating the evolutionary history and biogeography of .
LSL-YOLO11n: a YOLO11n-based model for maize leaf disease detection in complex field environments.
Yang C, Feng Q, Mai J … +4 more , Zhang R, Chong N, Ru Z, Liang T
Front Plant Sci · 2026 · PMID 42382414 · Full text
Maize leaf diseases in field environments often exhibit large variations in lesion scale, irregular morphology, blurred boundaries, and complex backgrounds. These factors pose challenges for existing detection models, pa...
Maize leaf diseases in field environments often exhibit large variations in lesion scale, irregular morphology, blurred boundaries, and complex backgrounds. These factors pose challenges for existing detection models, particularly in detecting small lesions and achieving precise bounding-box localization. To address these issues, this study proposes LSL-YOLO11n, a maize leaf disease detection model based on the YOLO11n framework. The proposed model improves feature representation, localization quality modeling, and bounding-box regression to enhance disease detection performance under complex field conditions. Experiments were conducted on a dataset containing 15,119 images and 29,366 annotated instances across eight categories, including seven maize disease categories and healthy leaves. To evaluate the effectiveness of the proposed model, ablation experiments, comparative experiments with mainstream object detection models, and visual detection analyses were carried out. The ablation results show that the improved components contribute positively to the overall detection performance. LSL-YOLO11n achieves a Precision of 84.4%, Recall of 73.9%, and mean Average Precision (mAP) of 83.3%, which is 3.1 percentage points higher than that of the baseline YOLO11n model. Compared with YOLOv8n, YOLOv9t, YOLOv10n, and YOLOv12n, the proposed model improves mAP by 4.7, 3.3, 5.3, and 10.9 percentage points, respectively. The visual detection results further indicate that LSL-YOLO11n performs more stably in complex backgrounds and small-lesion scenarios. These findings provide technical support for rapid maize disease recognition and intelligent field monitoring.
Patterns of plastid gene evolution: identifying candidate genes for plastid-nuclear incompatibility across the Campanulaceae.
Scoffield B, López-Caamal A, Galloway LF … +1 more , Barnard-Kubow KB
Front Plant Sci · 2026 · PMID 42382413 · Full text
Most protein complexes within the chloroplast consist of both plastid and nuclear-encoded subunits. This integration leads to potential coevolution between the genomes, with disruption of coevolution a potential cause of...
Most protein complexes within the chloroplast consist of both plastid and nuclear-encoded subunits. This integration leads to potential coevolution between the genomes, with disruption of coevolution a potential cause of plastid-nuclear incompatibility (PNI). Both plastid-nuclear coevolution and PNI have been found across many, sometimes overlapping, lineages of flowering plants. However, drawing a direct connection between these two phenomena has been difficult as the underlying genetics of PNI have been determined in only a handful of cases. The goal of this study was to identify candidate plastid genes contributing to the PNI observed in by analyzing patterns of evolution in plastid genes from the two most divergent lineages of as well as species across the Campanulaceae. Photosynthetic genes exhibited low rates of nucleotide substitution and dN/dS ratios indicating purifying selection, while several genes/gene families related to gene regulation and proteostasis (, , ) exhibited elevated rates of nucleotide substitution and dN/dS ratios indicating relaxed or positive selection. The genes are the most likely candidates for contributing to the PNI in due to their high dN/dS ratios in both lineages and an increased rate of sequence evolution in and its close relatives. These results suggest that disruption of plastid translation could be a mechanism for intraspecific PNI in this species.
Assembly and comparative analysis of the complete mitochondrial genome of .
Xu J, Mo X, Zhang J … +2 more , Yuan L, Xu G
Front Plant Sci · 2026 · PMID 42382412 · Full text
INTRODUCTION: , a distinctive ornamental plant native to the subtropical Himalayas, is valued for its unique hat-shaped calyces, strong adaptability, and ecological significance in slope restoration and nectar provision....
INTRODUCTION: , a distinctive ornamental plant native to the subtropical Himalayas, is valued for its unique hat-shaped calyces, strong adaptability, and ecological significance in slope restoration and nectar provision. Its phylogenetic position within Lamiales has remained controversial due to limited molecular evidence. Although earlier studies have successfully elucidated its chloroplast (cp) genome, the complete mitochondrial (mt) genome remains uncovered. METHODS: This study undertook the sequencing, assembly, and comprehensive analysis of the complete mt genome of . RESULTS: The mt genome of is a circular DNA molecule measuring 405,461 bp in length with a GC content of 46.00%. It contains 36 protein-coding genes (PCGs), three ribosomal RNAs (, , ) and 33 transfer RNAs. The mt genome is rich in repetitive sequences; a total of 550 interspersed repeats were identified, including 300 palindromic repeats (54.55%) and 250 forward repeats (45.45%), without inverted or complementary repeats. Additionally, 79 simple sequence repeats (SSRs) were detected, with tetranucleotide repeats (AAAG/CTTT) being the most abundant. Codon usage analysis revealed a preference for A/U-ending codons, and the codon GCU (Ala) exhibited the highest relative synonymous codon usage (RSCU) value of 1.57. A total of 565 RNA editing sites (all C-to-U conversions) were predicted, with the majority (80.71%) potentially leading to increased protein hydrophobicity. Six cp plastid DNAs were identified in the mt genome, indicating intracellular gene transfer events. Most mt genes are under strong purifying selection (Ka/Ks < 1), while nucleotide diversity analysis showed that had the highest diversity (Pi = 0.06444) and the lowest (Pi = 0.00305). Phylogenetic analysis based on 14 shared mt PCGs placed within Lamiaceae, forming a well-supported clade with , , , and (bootstrap = 100%). Collinearity analysis revealed extensive genome rearrangements among related species, and gene content analysis indicated the loss of , and as well as duplications of , and . DISCUSSION: Understanding the mt genome characteristics of is critical for elucidating its phylogenetic placement and genetic background. The results of this study serve as a foundation for future genetic, evolutionary, and breeding studies of this ornamental and potentially medicinal species.
Genotypic resilience and fruit quality responses of tomato ( L.) in progressive salinity stress across diverse cultivation conditions.
Singh N, Talwar D, Singh K … +5 more , Babanjeet, Jindal SK, Singh J, Mahala P, Verma J
Front Plant Sci · 2026 · PMID 42382411 · Full text
Tomato is a worldwide significant vegetable crop mainly grown for its nutritional and nutraceutical value, but its productivity is severely constrained by soil salinity. This study aimed to evaluate the performance of 20...
Tomato is a worldwide significant vegetable crop mainly grown for its nutritional and nutraceutical value, but its productivity is severely constrained by soil salinity. This study aimed to evaluate the performance of 20 tomato genotypes with graded salinity (0-6 dS m) in both field and pot conditions. The experiment was conducted using a split-plot design with salinity levels as main plots and genotypes as subplots, replicated thrice over two growing seasons. Genotypic variations were apparent as PTNI-203, PTNI-202, and PTNI-8 exhibited better vegetative development, earlier flowering, larger fruit, and dense pericarp thickness under high salinity. Root fresh and dry weights were maximized in PTNI-11, PTNI-25, and PTNI-20, indicating good osmotic adjustment and salt-tolerant processes. Physiological and biochemical profiling further revealed substantial genotypic variation in osmolyte accumulation, pigment stability, and membrane integrity under saline conditions. These genotypes also recorded 30%-40% higher proline, 15%-20% higher protein content, and membrane stability indices above 85. The total yield was reduced gradually with the salinity, and the tolerant genotypes (PTNI-203, PTNI-8, and PTNI-202) maintained higher yield (524-540 q acre), representing 55%-65% higher productivity than susceptible genotypes under 6 dS m. Rank analysis supported the fact that genotype was the major factor that determined growth and productivity traits with salinity imposing secondary inhibitory effects. This study provides practical insights into genotype-specific adaptation to salinity stress and identifies promising tomato lines for sustaining productivity and contributing to climate-resilient horticultural practices. The identified genotypes can serve as promising candidates for cultivation and breeding programs in salt-affected regions.
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