Search Results (1,747)

Here we report the draft genome sequences of three Enterococcus faecalis strains, LAB1, LAB10, and LAB11, isolated from the pond water of a tilapia (Oreochromis niloticus) aquaculture farm at the University Nangui Abrogoua, Abidjan, Ivory Coast. These strains were previously characterised for their probiotic, plant growth-promoting (PGP), and nitrifying properties. All three strains were assigned to sequence type ST19 by multilocus sequence typing (MLST). The draft genomes of LAB1, LAB10, and LAB11 consist of 34, 35, and 34 contigs, totalling 2.94 Mb each (GC content 37.40%). Prokka annotation predicted 2872, 2873, and 2875 protein-coding sequences (CDS) for LAB1, LAB10, and LAB11, respectively. Genomic screening revealed no vancomycin resistance genes; however, tet(M) and lsa(A) resistance determinants were identified in all three strains, located on a repUS43-type plasmid replicon. Fourteen virulence factor homologs conserved in the E. faecalis reference strain V583 were detected, including Ebp pili, gelatinase (gelE), Fsr quorum-sensing system, and capsule biosynthesis genes, but no cytolysin operon was identified. Genes associated with stress tolerance (katA, sodA), bile salt hydrolysis (cbh), siderophore transport (fepC, fhuD), and ethanolamine nitrogen metabolism (eutB/eutC) were identified in all three genomes. Pan-genome analysis with the E. faecalis reference strain revealed 551 core gene clusters and 279 gene clusters exclusive to the three aquaculture isolates. Despite their high genomic similarity, we report the three genomes as distinct isolates due to observed differences in their expressed phenotypic properties. These sequences provide a genomic resource supporting the development of multifunctional probiotic consortia for integrated aquaponic systems. Full article

Cotton (Gossypium spp.) is the world’s most important fiber crop for the textile industry. Drought stress can adversely affect cotton production and quality, particularly in arid and semi-arid regions. Biochar, produced from biomass through pyrolysis, has the potential to alleviate drought stress in cotton production through improving soil properties and enhancing plant nutrition. The objectives of this study were to evaluate the effects of biochar produced from southern yellow pine (Pinus spp.) on cotton seedling emergence and growth, yield and its component traits, and fiber quality traits under field drought-stressed, arid conditions in the U.S. over two years. Six genotypes were evaluated in 2024, and three of these genotypes were evaluated following a single application of biochar at four rates (0, 6.25, 12.5, and 25.0 t ha⁻¹) applied at the beginning of the study. Significant genotypic differences were observed in both years, as expected. No genotype × biochar interaction was detected, indicating that different cotton genotypes responded similarly to biochar application. Groundcherry (Physalis acutifolia) infestation was unexpectedly higher, and cotton seedling growth was reduced in the biochar-amended plots compared with the non-biochar control in 2024, but these effects were not observed in 2025. Plots amended with 12.5 and 25.0 t ha⁻¹ biochar had significantly higher soil moisture than those receiving 0 or 6.25 t ha⁻¹ biochar. Estimated seedcotton yield was the highest in plots receiving 12.5 t ha⁻¹ biochar in both years and was significantly greater than that of the non-biochar control, with 18.3 and 8.4% increases in 2024 and 2025, respectively. Biochar had no significant effects on fiber length, uniformity, strength, elongation, and micronaire in either year, except that 6.25 and 12.5 t ha⁻¹ biochar rates increased elongation and 25.0 t ha⁻¹ biochar rate decreased micronaire. These results indicate a single biochar application had a positive, although diminishing, effect of biochar on cotton productivity during the first two years under drought stress, while having little to no effects on fiber quality. Full article

Obesity is a global metabolic disease closely associated with dyslipidemia, insulin resistance, hepatic steatosis, and chronic oxidative stress. Cydonia oblonga Miller (COM, Quince) from Xinjiang Uygur Autonomous Region of China is a traditional medicinal and edible plant rich in polyphenols, flavonoids, polysaccharides, and other bioactive constituents. Our previous studies suggested that total polyphenols of Cydonia oblonga Miller (TPCOM) may exert promising anti-obesity effects. Objective: This study aimed to investigate the therapeutic effects of TPCOM on high-fat diet-induced obese C57BL/6 mice and to explore its underlying molecular mechanisms related to glycolipid metabolism. Methods: TPCOM was extracted and purified from Xinjiang Cydonia oblonga fruits, and its total polyphenol content was determined using the Folin–Ciocalteu method. C57 mice were randomly divided into normal diet, model, and TPCOM intervention groups. After 12 weeks of high-fat diet feeding and 6 weeks of TPCOM treatment, body weight was monitored continuously. Serum levels of triglyceride (TG), total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and total antioxidant capacity (T-AOC) were measured using commercial kits. Hepatic pathological changes were observed by hematoxylin–eosin (HE) staining. Bioinformatics analyses including GO and KEGG were performed to predict key targets and pathways related to lipid metabolism. The protein expression levels of PPARGC1A, FFAR1, KLF15, Adipolin, GLUT4, and phosphorylated p38 MAPK in liver tissues were detected by Western blotting. Results: TPCOM intervention significantly reduced body weight gain in obese mice in a dose-dependent manner. Serum biochemical assays showed that TPCOM decreased TC, TG, and LDL-C levels, increased HDL-C levels, and markedly enhanced total antioxidant capacity (T-AOC). Bioinformatics analysis suggested that PPARG and FFAR1 were highly expressed in liver tissue and may participate in glucose and lipid metabolism regulation. Western blot results confirmed that TPCOM significantly upregulated the expression of PPARGC1A, FFAR1, KLF15, Adipolin, GLUT4, and phosphorylated p38 MAPK in the liver of obese mice. Conclusions: TPCOM effectively ameliorates obesity, dyslipidemia, hepatic steatosis, and oxidative stress in high-fat diet-induced obese mice. The underlying mechanism may be related to the regulation of glycolipid metabolism, mitochondrial function, insulin sensitivity, and antioxidant signaling via activating the FFAR1–PPARG–p38 MAPK axis and downstream targets including PPARGC1A, KLF15, Adipolin, and GLUT4. This study provides a scientific basis and theoretical support for the development and application of TPCOM as a natural functional ingredient in the prevention and adjuvant treatment of obesity and related metabolic disorders. Full article

First detected in environmental matrices in the early 2010s, UV-328 has aroused widespread concern due to its toxic risks to terrestrial vascular plants. However, its impacts on photosynthetic performance of bryophytes remain unclear. In this study, we exposed the moss Niphotrichum japonicum to a range of UV-328 concentrations and examined its morphological changes, oxidative stress, photosynthetic pigments, chlorophyll fluorescence kinetics, and energy allocation. Our results show that UV-328 caused dose-dependent leaf yellowing, surface shrinkage, and papillae collapse. It degraded photosynthetic pigments, disrupted chlorophyll a/b balance, and induced excess reactive oxygen accumulation. Chlorophyll fluorescence data indicated that UV-328 noticeably lowered Fv/Fm, Y(II), and qP. OJIP kinetics confirmed multi-target damage to the photosynthetic chain, including disruption of the oxygen evolving complex, decline of PSII energetic grouping, blockage of electron transfer from QA⁻ to QB, inhibition of plastoquinone pool turnover, and PSI terminal electron transport. Energy flux parameters pointed to fewer active PSII reaction centers and a higher light-harvesting load on each remaining center, which uncoupled light capture from electron transfer. The concentration that caused clear photosynthetic damage fell between 100 and 150 μM. In conclusion, UV-328 impacts moss photosynthesis through oxidative stress, structural damage, blocked electron transport, and energy imbalance. Full article

Volatile sulfur compounds (VSCs) are a subgroup of plant volatile organic compounds (VOCs) that are chemically reactive and sensory-active. In tomato (Solanum lycopersicum), sulfur-containing volatiles such as methanethiol, dimethyl sulfide, dimethyl disulfide, dimethyl trisulfide, volatile thiols, and heterocyclic sulfur compounds are of particular relevance due to their extremely low odor thresholds and strong influence on aroma perception. Beyond their sensory importance, VSCs have been shown to be involved in plant defense mechanisms, stress responses, redox homeostasis, and multitrophic interactions with microorganisms, herbivores, and neighboring plants. The formation of these structures is governed by complex interactions between sulfur assimilation pathways, lipid peroxidation processes, environmental factors, and both enzymatic and non-enzymatic reactions. The accurate characterization of VSCs remains challenging due to the following factors: their high reactivity; their low abundance; their chemical instability; and their susceptibility to oxidation. Despite the significant enhancement in detection of VSC capabilities brought about by modern analytical approaches, such as gas chromatography coupled with sulfur-selective detection and high-resolution mass spectrometry, significant methodological limitations remain. This review summarizes the current state of knowledge on the analytical challenges of VSCs in tomato plants, their biosynthesis and biological functions, mainly in the context of plant defense. Full article

Background/Objectives: Protein phosphatase type 2C (PP2C) family members are key signaling hubs in plants, but their roles in mediating the trade-off between stress adaptation and symbiotic interactions remain unclear. This study aimed to investigate the function of soybean GmPP2C113, which was identified as a potential regulator linking salt stress responses and symbiotic nodulation, in coordinating these two biological processes in soybean (Glycine max). Methods/Results: The GmPP2C113 gene was cloned, and its subcellular localization, transcriptional activity, and protein interactions were characterized. Expression patterns under salt stress and rhizobial inoculation were analyzed. The biological role of GmPP2C113 was assessed using transgenic soybean plants overexpressing GmPP2C113. GmPP2C113 was localized in the nucleus and possessed transcriptional activation capability and interacted with GmPP2C47. Its expression was strongly induced by salt stress and by rhizobial infection, with the highest levels detected in mature nodules. Overexpression of GmPP2C113 significantly enhanced salt tolerance, upregulated stress-related genes, increased nodule numbers, and promoted symbiotic nodulation under salt stress by inducing nodulation marker genes. Conclusions: These results identify GmPP2C113 as a positive modulator of salt tolerance and reveal its novel role as a molecular node that sustains symbiotic nodulation under salt stress. This provides insight into the coordinated regulation of stress adaptation and symbiosis in soybean. Full article

Nanoscale zerovalent iron (nZVI) has shown promise for soil remediation. This study examined the impact of this nanomaterial on barley and wheat grown in alkaline soil throughout a complete growth cycle, to assess its potential as a fertilizer and to understand its behavior in an uncontaminated matrix. A greenhouse experiment was conducted in which barley and wheat plants were grown in soil treated with a commercial nZVI slurry at 0 and 5% (equivalent to 0 and 8 g kg⁻¹). Physiological parameters were monitored throughout the growth cycle, and plants were harvested after five months. Biomass production, impact on root and leaf ultrastructure, and the concentrations of Fe and other nutrients were determined in several plant tissues. Soil physicochemical properties were not adversely affected by nZVI application, and an increase in Fe availability was observed regardless of the species, from 1 mg kg⁻¹ to 5.2 and 6.6 mg kg⁻¹ in barley and wheat soils, respectively. However, this increase did not translate into higher Fe accumulation in plant tissues at the end of the growth cycle, nor did it enhance plant growth in either species. Therefore, under the experimental conditions evaluated, the application of nZVI as an iron fertilizer cannot be recommended. Notably, both crops exhibited a greater sensitivity to nZVI during early stages of development, as evidenced by significant reductions in chlorophyll content and increased oxidative stress. These initial adverse effects were progressively alleviated as plant growth advanced, with no detectable alterations in cellular ultrastructure, allowing both species to complete their growth cycle. Full article

Artificial intelligence (AI) has emerged as a transformative tool for plant health monitoring, offering new opportunities for scalable, timely, and data-driven pest and disease management in agriculture. This review provides a comprehensive synthesis of AI-based methods for pest and plant disease detection, systematically organizing existing literature across sensing modalities, learning paradigms, and deployment scales. We distinguish between population-level pest monitoring, plant-centric visual inspection, and field-scale surveillance, as well as between post-symptomatic disease recognition and pre-symptomatic detection enabled by spectral imaging technologies. Beyond summarizing recent advances, this work places strong emphasis on critical analysis, discussing fundamental limitations related to data scarcity, domain shift, generalization under field conditions, and the challenge of disentangling biotic from abiotic stress factors. The review further examines the distinction between correlation-driven AI predictions and causal disease understanding, positioning AI as a complementary decision-support tool alongside established diagnostic methods. Building on these insights, we outline key future research directions, including multimodal sensor fusion, explainable and trustworthy AI, edge-based deployment for real-time monitoring, and the development of foundation models for unified agricultural intelligence. This review aims to serve as both an accessible entry point and a critical reference for advancing AI-driven plant health management. Full article

Early detection of contrasting water-stress types is important for understanding plant stress responses and improving water-stress management in forest seedlings. In this study, three-year-old Pinus tabuliformis seedlings were exposed to control (CK, 75–85% of field capacity), drought (D, 25–35% of field capacity), waterlogging (WL, water level flush with the soil surface), and water flooding (WF, water level 2 cm above the soil surface) treatments. Each treatment included 15 independent seedlings at each sampling date, resulting in 420 seedlings across four treatments and seven sampling dates. Needle water potential (Ψw), total chlorophyll content (Chl), maximum photochemical efficiency (Fv/Fm), indole-3-acetic acid (IAA), abscisic acid (ABA), and electrical impedance spectroscopy (EIS) parameters were measured to compare the temporal responses of physiological and electrical traits under different water conditions. EIS showed clear treatment-dependent changes under all stress treatments, with larger changes observed under WF and WL than under D at the treatment levels and durations evaluated in this study. Based on the present discrete sampling schedule, the real (Re) and imaginary (Im) components showed statistical separation among the four treatments in all six pairwise comparisons of the four treatments on Day 7, whereas ABA and Ψw showed separation on Day 11, Fv/Fm on Day 18, and IAA and Chl on Day 25. These results indicate that Re and Im showed treatment-dependent divergence at earlier evaluated sampling dates than the selected physiological variables. Exploratory CLAFIC analysis further indicated group-level spectral separation between CK and WL/WF on Day 3 and between CK and D on Day 7. Overall, EIS-derived features may provide useful information on early electrical responses of P. tabuliformis seedlings to contrasting water conditions. However, further validation using independent datasets, standardized measurement procedures, and field or nursery conditions is required before EIS can be applied as a practical tool for water-stress assessment. Full article

The DUF538 gene family, harboring unknown functional proteins, has been reported to take active roles in plant development and response to adversities, while few studies of genome-wide identification and functional verification have been performed in cotton. Hence, two ancestral diploid species, G. arboretum and G. raimondii, and two cultivated tetraploid ones, G. hirsutum and G. barbadense, were chosen in this study to investigate the cotton DUF538 gene family, resulting in 37, 37, 70, and 70 members identified, respectively. A phylogenetic tree was constructed on these cotton DUF538 genes, together with 22 A. thaliana ones, which were divided into seven groups unevenly distributed across nearly all chromosomes. High-degree conservatism, while rich in diversity, was separately observed in gene structure and conserved motif analyses between the same groups and different groups, and a great number of gene-replication events were detected from intraspecific and interspecific collinearity analyses, implying this was the driving force for DUF538 family expansion. Multiple cis-acting elements relevant to adversity-stress responses were found in the promoter region, which were consistent with the transcriptome expression analyses in response to low-temperature and drought stress and Verticillium wilt infection. Coincidentally, GhDUF538-7 showed the core position in the protein–protein interaction network and was identified in the overlapping region of the interval of four reported VW resistance-related QTLs. The gene function of GhDUF538-7 was verified via gene cloning, relative expression-pattern detection, and virus-induced gene silencing (VIGS) experiment. The TRV:DUF538-7 plants showed more serious VW symptoms, significantly severe disease indices, relatively higher fungal biomass, and increased brown vascular bundles compared with TRV:00 plants. Significantly lower expression levels of marker genes PR4 and MYC2 in jasmonate signaling pathways indicated GhDUF538-7 as a potentially positive regulatory factor in plant defense via hormone signal transduction. This study not only broadened the research perspective of evolution and functional differentiation of the cotton DUF538 gene family, but it also revealed the cooperative relationship between DUF538-7 and the JA pathway for further molecular mechanisms of cotton resistance to VW infection. Full article

Leaf color in tomato (Solanum lycopersicum L.) is a complex and highly informative trait that reflects pigment metabolism, chloroplast development, genetic regulation, hormonal signaling, and environmental influences. This review synthesizes current knowledge on the biological basis and diversity of tomato leaf coloration, with a particular focus on the roles of chlorophylls, carotenoids, anthocyanins, and flavonoids in generating distinct visual phenotypes. It further discusses the molecular and physiological mechanisms associated with key leaf color types, including dark green, pale green, chlorotic, purple, albino, and variegated leaves, and describes how these phenotypes develop through coordinated regulation of pigment biosynthesis, chloroplast biogenesis, and stress-responsive pathways. The review also summarizes the effects of environmental factors such as light, temperature, water availability, nutrient status, salinity, heavy metals, and biotic stress on leaf pigmentation through changes in photosynthetic efficiency and oxidative balance. In addition, hormonal regulation of leaf color is discussed with emphasis on the roles of abscisic acid (ABA), ethylene (ET), cytokinins (CKs), auxins, jasmonic acids (JA), and salicylic acid (SA) in regulating chlorophyll retention and senescence-associated color transitions. Importantly, leaf coloration functions not only as a morphological trait but also as a sensitive biomarker of plant physiological status, enabling early detection of nutrient deficiencies, abiotic stress, and disease. Recent advances in multi-omics approaches, imaging technologies, and machine learning have significantly improved the understanding of the regulatory networks controlling leaf pigmentation and their relationship with crop performance. However, important gaps remain in integrating molecular mechanisms with whole-plant and field-level responses. Future progress will depend on combining systems biology, high-throughput phenotyping, and predictive modeling to translate leaf color studies into practical applications for improving tomato productivity, stress resilience, and climate adaptation. Full article

Fungal communities associated with the phyllosphere can influence plant health, stress responses, and disease dynamics in managed crop systems. However, limited information is available on fungal microbiome structure across phyllosphere compartments of Eucalyptus cinerea cultivated for cut foliage production. In this study, fungal communities (including epiphytic and endophytic fungi) associated with leaf, stem, and bark tissues of intensively managed E. cinerea grown in Ireland were characterised using ITS amplicon sequencing. Samples were collected from five trees, with tissues pooled by compartment to generate 15 biological samples. Following quality control and denoising, 405 fungal amplicon sequence variants (ASVs) were retained for analysis. Observed richness, Shannon and Simpson indices, and Faith’s phylogenetic diversity differed among compartments, with bark exhibiting higher values than leaf and stem tissues (p < 0.05). PERMANOVA analysis indicated that both compartment (R² = 0.239, p = 0.002) and tree identity (R² = 0.451, p = 0.002) significantly influenced fungal community composition. Bark communities were dominated by Diaporthe (52.9%), Peniophora (12.8%), and Talaromyces (10.4%), whereas leaf and stem communities were characterised primarily by Vishniacozyma and Sporobolomyces. Differential abundance analysis identified 26 and 23 differentially abundant ASVs between bark and leaf, and bark and stem tissues, respectively, whereas no significant differences were detected between leaf and stem communities. Weighted UniFrac analyses further revealed separation of bark-associated communities from photosynthetic tissues. These findings demonstrate compartment-associated variation in fungal community structure within the phyllosphere of managed E. cinerea and highlight the importance of considering both host-level and tissue-level effects in plant microbiome studies. This study provides a baseline assessment of fungal assemblages associated with commercially managed Eucalyptus under Irish growing conditions and supports future investigations into the functional significance of these microbial communities for plant health and resilience. Full article

Dementia is a growing challenge for aging societies, and effective prevention depends on identifying risk factors that can be addressed early, before cognitive decline becomes clinically apparent. Declining oral and dental function, particularly tooth loss, is increasingly recognized as one such factor, and its effect on the brain extends well beyond a reduced ability to chew. This review synthesizes current evidence linking impaired oral function to cognitive decline and dementia, with a focus on nutritional and structural brain pathways. We propose that tooth loss affects the brain through two partly independent routes. The first is nutritional: tooth loss shifts the diet away from fiber- and micronutrient-rich plant foods, which may injure the brain through oxidative stress, inflammation, and gut microbiota changes; the hippocampus, a key memory region, appears especially sensitive to nutritional status. Eating alone adds a social dimension: it is associated with lower diet quality and with reduced volume in memory-related regions, an association only partly explained by diet, since the medial temporal difference persists after dietary adjustment. The second is sensory–neural: the loss of natural teeth removes sensory input from the periodontal ligament and reduces chewing, weakening signaling to the brain and its capacity for plasticity. Importantly, atrophy of the medial temporal lobe and adjacent memory-related regions, together with increased white matter damage, is detectable even in cognitively healthy older adults, and a revised Oral Frailty Five-item Checklist can identify these presymptomatic changes. Because these structural brain changes persist despite denture use and after adjusting for diet, preserving natural teeth may be an especially valuable preventive target. Overall, maintaining oral function is a promising, accessible target for dementia prevention that warrants confirmation in prospective trials. Full article

WPR (WEB1/PMI2-related) genes play a crucial role in regulating chloroplast movement and leaf coloration in plants. Previous studies have shown that these genes are implicated in leaf yellowing, both in Arabidopsis thaliana and in Paulownia fortunei following infection with Paulownia witches’ broom. To investigate the functions of the ZjWPR genes in jujube, bioinformatics methods were employed to identify the ZjWPR gene family in jujube, analyze their protein physicochemical properties, gene structure, evolutionary relationships, and cis-acting elements in this study. The results revealed that the ZjWPR gene family in jujube comprised 10 members. Phylogenetic analysis showed that WPR genes were divided into two classes, with ZjWPR genes distributed across three subgroups within Class II. Conserved motif analysis indicated that motif 2, motif 3, motif 7, and motif 8 were the most highly conserved and most genes exhibited similar structures. Cis-element analysis in their promoter suggested that ZjWPR genes were regulated by multiple hormones and were associated with stress responses such as low temperature and drought. Moreover, all ZjWPR genes contained light-responsive elements. Expression analysis of the ZjWPR gene family under Jujube Witches’ Broom (JWB) stress showed that ZjWPR4 and ZjWPR5 were significantly up-regulated in JWB-susceptible jujube cultivars following phytoplasma infection, whereas no significant changes were detected in JWB-resistant cultivars. Additionally, the expression levels of ZjWPR2, ZjWPR3, and ZjWPR6 were also altered in response to infection, suggesting their potential involvement in the response to JWB stress and the associated leaf chlorosis process. Moreover, transient overexpression of ZjWPR4 and ZjWPR5 in sour jujube leaves led to significant reductions, in critical photosynthetic parameters, including Fv/Fm, Fq′/Fm′, and ETR compared with WT, thereby reinforcing their functional contribution to JWB-associated leaf yellowing. This study provides valuable insights for further functional characterization of the ZjWPR gene family in mediating JWB-induced leaf yellowing and related metabolic pathways. Full article

Calcium (Ca²⁺) functions as a second messenger in plants, coordinating development and stress responses through cytosolic Ca²⁺ dynamics. The P-type Ca²⁺-ATPases of the ECA (P-IIA) and ACA (P-IIB) subfamilies are central to Ca²⁺ homeostasis and signal termination by extruding Ca²⁺ from the cytosol. In this study, genome-wide identification was performed to identify the P-type Ca²⁺-ATPases according to the maize B73 v5 reference genome, followed by phylogenetic, structural, chromosomal, syntenic, network, and expression analyses. Nineteen genes were identified, comprising 4 ECAs and 15 ACAs. All 19 members retained the DKTGT phosphorylation site, while the CaATP_NAI (N- terminal autoinhibitory) extension distinguished all 15 ACAs from the 4 ECAs. Collinearity analysis revealed 11 maize–rice syntenic pairs, implicating segmental duplication. ECAs were preferentially expressed in reproductive tissues, whereas ACAs were broadly expressed across vegetative organs. RNA-seq-based profiling detected distinct stress-responsive expression patterns of Ca²⁺-ATPase genes. Under abiotic stress, ZmACA12-1 was consistently upregulated under drought, ZmACA6-2 dominated the heat response, and ZmACA4-2 showed the broadest cross-stress repression. Under biotic stress, ACA members again dominated, with ZmACA1-1 being the most broadly pathogen-responsive member, ZmECA1-3 the principal ECA-class responder, and ZmACA9 exhibiting consistent pathogen-associated repression. Additionally, ZmACA12-1 and ZmACA4-4 showed genotype-dependent regulation between resistant and susceptible lines. Collectively, these candidates represent priority targets for functional validation of the calcium efflux mechanisms that underlie maize adaptation to both abiotic and biotic stresses. Full article