Search Results (4,525)

The ascomycete fungus Clonostachys rosea is a promising biocontrol agent against root-knot nematodes. To develop a more effective and stable biocontrol strategy, we rationally constructed a co-culture system by partnering C. rosea with the plant growth-promoting bacterium Bacillus velezensis. Through systematic optimization of the medium and inoculation protocol, the co-culture demonstrated significantly enhanced performance, achieving 95.3% mortality of Meloidogyne incognita juveniles, a 78.0% increase in tomato shoot dry weight, and 69.2% disease control efficacy in pot trials. Metabolomic profiling indicated that the co-culture triggered a distinct metabolic profile compared to the respective monocultures. The enhanced efficacy was associated with the accumulation of two functional metabolite groups. First, the co-culture synergistically accumulated direct-effect compounds with reported nematicidal (e.g., daidzin, L-tryptophan) and plant-growth-promoting (e.g., isopentenyladenine, melatonin, and indole-3-propionic acid) activities. In parallel, L-proline emerged as a critical microbial interaction modulator. Targeted quantification showed a clear proline abundance gradient: highest in the C. rosea monoculture, intermediate in co-culture, and lowest in the B. velezensis monoculture. This gradient suggests that proline produced by C. rosea is likely utilized by B. velezensis, a finding further supported by the observation that proline enhanced bacterial biofilm formation and upregulated the matrix genes epsC and tasA. Accordingly, the co-culture itself formed significantly more robust biofilms. Thus, the enhanced biocontrol can be attributed to synergistic metabolite accumulation together with proline-mediated fitness gains in the bacterial partner, establishing a metabolic basis for rationally engineering microbial consortia. Full article

Yam end black disease (YEBD) is a devastating soil-borne disease that severely compromises the yield of Chinese yam (Dioscorea opposita Thunb.). Despite its agricultural importance, the etiological agents and molecular mechanisms underlying YEBD remain poorly understood. In this study, we employed an integrated multi-omics approach, combining transcriptomics and microbiome analysis, to dissect the host responses and microbial shifts associated with YEBD. De novo transcriptome assembly revealed significant enrichment of differentially expressed genes involved in polyamine metabolism and hormone signaling pathways. Microbiome profiling identified a substantial increase in nematodes (Meloidogyne spp.) in diseased samples, which correlated negatively with the beneficial fungus Cladosporium. Bacterial community analysis showed an increase in Proteobacteria and Bacteroidetes and a decrease in Actinobacteria and Firmicutes in YEBD-affected roots. Notably, the rhizosphere microbiome was less affected than the endophytic community, suggesting that internal microbial dysbiosis plays a critical role in disease progression. These findings provide new insights into the interactions among yam, nematodes, and microbes, offering potential strategies for biocontrol and disease management. Full article

The valorization of agricultural and other waste residues into biochar represents a promising strategy for sustainable waste management and environmental remediation within a circular economy framework. Engineering multifunctional biochars like agricultural waste-derived biochars (AWDBs) exhibit tunable physicochemical properties governed by feedstock characteristics and thermochemical conversion conditions, enabling their application across water, soil, and sediment systems. While extensive research has demonstrated the effectiveness of biochar in isolated environmental compartments, natural systems function as interconnected water–soil–sediment continua, where pollutants, nutrients, and organic matter dynamically interact. This review critically synthesizes recent advances in the production, properties, and environmental applications of biochars, with a particular focus on their multifunctional performance in coupled environmental systems. Mechanistic insights into contaminant sequestration, nutrient cycling, and microbial interactions across media are discussed, alongside evidence of synergistic and antagonistic effects arising from cross-media processes. Despite significant progress, major knowledge gaps persist, including limited integrated multi-medium studies, lack of standardized assessment methodologies, insufficient understanding of long-term biochar stability, and challenges associated with field-scale implementation. Future research directions are proposed to address these limitations through standardized protocols, engineered multifunctional biochars, long-term monitoring, and policy integration. Advancing a system-based perspective is essential to unlock the full potential of agricultural waste-derived biochars for sustainable and scalable environmental remediation. Full article

Silicon has long been recognized as a beneficial element in plant biology. Recent advances in nanosilicon technology have revealed its transformative potential in legume-rhizobia symbiosis. This review synthesizes current knowledge on how silicon and SiO₂ nanoparticles (Si-NPs) influence nodulation, microbial metabolism, and soil–plant interactions. We highlight emerging evidence that Si-NPs enhance symbiotic signaling, strengthen infection pathways, and mitigate oxidative stress, thereby supporting nitrogen fixation efficiency. Beyond the rhizosphere, nanosilicon improves soil structure, microbial diversity, and plant resilience under abiotic stress, offering a multifaceted approach to sustainable agriculture. The novelty of this review lies in its integrative perspective, connecting molecular mechanisms with ecological impacts and climate-smart applications. By examining Si-NPs across three domains—soils, rhizosphere metabolites, and plants—we provide a framework for understanding their role in enhancing productivity while reducing environmental costs. Importantly, we identify critical research gaps, including the need for standardized application protocols, large-scale field validation, sustainable nanosilicon production, and robust regulatory frameworks. These insights position nanosilicon as a promising tool for advancing legume productivity, reducing reliance on synthetic fertilizers, and contributing to global food security. This review underscores silicon’s potential not only as a plant nutrient but also as a strategic agent in climate-resilient agriculture. Full article

In forest ecosystems, rhizodeposition can lead to significant differences in the availability of soil carbon (C), nitrogen (N), and phosphorus (P) between rhizosphere and bulk soils. Soil stoichiometry affects microbial and enzyme nutrient content and determines the abundance and composition of microbes and thus regulates microbial carbon use efficiency (CUE). However, how soil stoichiometry—particularly its variation between the rhizosphere and bulk soil—regulates microbial CUE by shaping microbial biomass, extracellular enzyme stoichiometry, and community composition remains insufficiently quantified. Here, through the C:N, C:P, and N:P ratios for available soil nutrients, microbial biomass, and extracellular enzyme activities—(β-1,4-glucosidase (BG), β-1,4-N-acetylglucosaminodase (NAG), leucine aminopeptidase (LAP), and acid phosphatase (ACP))—and the composition and activity of microbial communities (based on sequencing of bacterial 16S rRNA and fungal ITS genes) in the rhizosphere and bulk soils of five temperate forest ecosystems in northeastern China, we aimed to unravel their integrated effects on microbial CUE. Results indicated that soil C, N, and P and their stoichiometry, microbial community composition, and microbial CUE were significantly different between rhizosphere and bulk soils among all tree species. The disproportionate variation in soil nutrient pools between the rhizosphere and non-rhizosphere regions has led to a stoichiometric imbalance. There was higher microbial CUE in the rhizosphere soil than that in the bulk soil among all tree species. However, the effect pathways of tree species on microbial CUE in the rhizosphere and bulk soils differed. The structural equation model (SEM) further suggested that tree species affected microbial CUE through distinct pathways in different soil compartments. In the rhizosphere, the effect was directly driven by available nutrient stoichiometry. In bulk soil, it was jointly mediated by both available nutrients and microbial biomass stoichiometry. These findings demonstrate that root rhizodeposition shapes microbial carbon cycling by altering soil stoichiometric imbalances, which can strengthen the current understanding of plant–microbe–soil interactions in temperate forests. Full article

Safe drinking water and microbial inactivation from surfaces and devices are among the World Health Organization’s priorities. Plasma-activated water (PAW) inactivates microorganisms mainly by producing radicals (hydroxyl radicals, superoxide, nitrogen oxide, etc.), which form secondary reactive species like nitrates, nitrites, hydrogen peroxide, etc., from the air–liquid interface, where the plasma interacts with the water. A plasma arc device for water treatment with enhanced arc length was constructed at the Andronikashvili Institute of Physics (TSU) and used in the study. PAW’s antibacterial efficacy has been evaluated against Gram-negative E. coli and remarkably stress-resistant Gram-positive B. pumilus. This study identifies reactive oxygen (hydrogen peroxide and superoxide anions) and nitrogen species (total nitrate and nitrite ions) in plasma-activated water, analyzing their potential impact on antioxidant enzyme activity and their relationships with bacterial cell viability. B. pumilus exhibits greater resistance to plasma-activated water as a disinfectant compared to E. coli. Catalase is more effective than superoxide dismutase in protecting cells from external oxidative stress, based on the two antioxidant enzymes studied. Full article

Against the backdrop of global climate change, climate warming and increasing nitrogen deposition are profoundly altering carbon (C) and nitrogen (N) cycling in terrestrial ecosystems. Short-term observations are critical for capturing the initial response trajectories of soil C-N dynamics to environmental stress, providing timely insights into early-stage adaptation mechanisms that underpin long-term ecosystem stability. This study investigated the interactive effects of these drivers on soil C and N transformation rates, component dynamics, and their coupling relationships in a warm steppe and a warm shrub grassland within the forest–steppe ecotone of northwestern Liaoning Province. We employed field-controlled experiments using open-top chambers for warming in combination with four nitrogen addition gradients. Results showed warming plus high N addition increased soil total N but reduced net N mineralization, supporting the “N saturation hypothesis”. Though N addition generally suppressed the C conversion rate, low-level N (5 g N m⁻² a⁻¹) mitigated C loss and enhanced it under warming. Soil organic C and microbial biomass C drove C transformation. Warm shrub grassland’s stable mineral-associated organic C pool rose 640.5% (stronger resilience), while warm steppe’s C/N turnover depended on seasons (greater vulnerability); C/N transformations were synchronized in the steppe but independent in shrubland. Full article

Cadmium (Cd) contamination of agricultural soils threatens crop productivity and food safety by disrupting physiological and molecular processes in plants. Increasing evidence indicates that epigenetic regulation, including DNA methylation, histone modifications, and emerging epitranscriptomic marks such as RNA methylation, plays a crucial role in coordinating plant responses to Cd stress. In parallel, plant-associated microbiomes have emerged as influential modulators of metal uptake, antioxidant capacity, hormone signaling, and stress resilience. Yet the mechanisms by which microbiome-derived signals intersect with host chromatin and transcriptome regulation under Cd exposure remain poorly understood. This review synthesizes current knowledge on plant epigenetic responses to Cd stress and critically examines how microbial metabolites, phytohormones, and redox-active compounds shape plant regulatory networks. Network-based ecological studies reveal that increased microbial community complexity and cooperative interactions are consistently associated with reduced Cd accumulation and enhanced plant performance, suggesting that microbial organization itself may represent an additional regulatory layer influencing plant responses. Despite compelling conceptual links, direct experimental evidence connecting microbiome signals to stable epigenetic or epitranscriptomic reprogramming under Cd stress remains limited. To date, only limited experimental studies have demonstrated causal relationships between microbial cues and host DNA or RNA methylation dynamics in Cd-exposed plants, highlighting clear mechanistic potential while also underscoring remaining knowledge gaps. By integrating physiological, ecological, and chromatin-level perspectives, this review identifies key unanswered questions and outlines future research directions to establish causal links between microbial community dynamics, epigenetic regulation, and long-term Cd stress adaptation in plants. Full article

Rosacea is increasingly recognized as a complex inflammatory disorder extending beyond isolated cutaneous pathology, involving dysregulated interactions between the skin, gastrointestinal system, and central nervous system. The skin–gut–brain axis has emerged as a relevant conceptual framework for understanding this multifactorial disease, integrating gut microbiota dysbiosis, neuroimmune signaling, autonomic nervous system dysfunction, and stress-related mechanisms. The aim of this narrative hypothesis-driven overview is to reframe rosacea as a neuroimmune disorder in which central nervous system involvement plays an active regulatory role, rather than as a purely peripheral or dermatological condition. We synthesize the mechanistically relevant evidence linking gastrointestinal inflammation and microbial imbalance with neurogenic inflammation, mast cell activation, sebaceous gland dysfunction, and aberrant innate immune responses in the skin, with particular emphasis on neurovascular and trigeminal pathways. A key novelty of this perspective lies in highlighting brain-centered mechanisms, including central sensitization, autonomic dysregulation, and stress-related neural modulation, as integral components of the skin–gut–brain axis in rosacea. By integrating peripheral and central processes, we propose rosacea as a model condition for studying neuroimmune dysregulation across interconnected regulatory systems. Finally, we discuss the clinical and translational implications of this framework and outline future research directions, focusing on autonomic regulation, patient stratification, and personalized, multidisciplinary therapeutic approaches. Full article

Background: Cultivation environments impose distinct abiotic and biotic stresses that act as primary drivers reshaping the metabolic profile and microbiome assembly of medicinal plants. This study investigates the impact of simulative habitat versus arched greenhouse cultivation on the synthesis of bioactive ginsenosides and the associated root microbiome structure in Panax ginseng. Methods: A combined metabolomics and microbiomics approach was applied to compare ginsenoside accumulation and rhizosphere microbial community composition under the two cultivation modes. Results: Ginseng from simulative habitat cultivation exhibited significantly higher ginsenoside content, particularly ginsenoside Re, compared to arched greenhouse cultivation, with this advantage being more pronounced in long-term cultivation. Microbiome profiling revealed that specific taxa, including Bradyrhizobium, were strongly enriched in simulative habitats and positively correlated with enhanced ginsenoside accumulation, suggesting a microbiome-mediated mechanism for metabolic plasticity. In contrast, arched greenhouse cultivation was associated with a more complex microbial structure characterized by increased negative interactions, which may compromise metabolic quality. Conclusions: These findings, utilizing multi-omics correlations, provide a theoretical basis for optimizing Panax ginseng quality through ecological cultivation strategies that leverage stress-responsive microbe–metabolite interactions. Full article

Staphylococcus aureus, particularly its multidrug-resistant strains, poses a critical biological hazard throughout the global food supply chain, underscoring the need to transition from inert petroleum-based packaging to active, biodegradable alternatives. This review presents a comprehensive analysis of the structure function relationships and interfacial interaction mechanisms that govern polysaccharide-, protein-, and lipid-based films designed for the targeted inhibition of S. aureus. We critically evaluate the extent to which the intrinsic molecular features—such as the polycationic charge density of chitosan and the amphiphilic self-assembly of fatty acids—determine baseline antibacterial activity. A key contribution of this work is the elucidation of three synergistic pathways: physical barrier effects, chemical interference, and biological regulation. Furthermore, we discuss how composite systems, such as polysaccharide lipid hybrids and protein nanomaterial scaffolds, exploit charge complementarity and controlled-release kinetics to surpass the performance limitations of single-component materials. Finally, we address the critical trade-offs between mechanical integrity and antimicrobial efficacy, proposing a roadmap for intelligent, stimuli-responsive packaging that is capable of responding to microbial metabolic cues. Overall, this review provides a theoretical foundation for the rational design of high-performance biodegradable films to safeguard global food safety. Full article

Global wetlands play a significant role as “blue carbon sinks”. Despite their relatively small coverage, they have enormous potential for carbon capture and sequestration, and also serve as an important natural source of atmospheric carbon dioxide (CO₂) and methane (CH₄). Wetland ecosystems are characterized by complex microbial interactions that mediate carbon (C) cycling processes, and also directly influence the dynamic changes of CO₂ and CH₄, underscoring the crucial role of microorganisms in these systems. Understanding the ecological significance of these gases and their response mechanisms to environmental changes is vital for mitigating the greenhouse effect and conserving ecosystems. This paper reviewed the major environmental challenges facing wetlands globally, such as salinization, over-fertilization, heavy metal input, and microplastic pollution, all influenced by human activities. Additionally, it examined their impact on microbial interactions that mediate the carbon cycle and related greenhouse gas emissions. This review highlighted the crucial role of microorganisms in these cycles and provided a microbial ecological perspective and theoretical foundation for promoting sustainable development and reducing greenhouse gas emissions in wetland areas. Full article

Background: High-fat diet-induced metabolic disorders are associated with trimethylamine (TMA)/trimethylamine N-oxide (TMAO), whose production is linked to gut microbial choline metabolism. However, changes in specific gut microbiota under a high-fat diet and the relationship between these changes and choline in TMA/TMAO production remain unclear. Methods: A total of 48 7-week-old male C57BL/6J mice were subjected to one-week acclimatization feeding, and then randomly divided into four groups (12 mice per group) to establish a 2 × 2 factorial design animal experiment: the control group (CON, basal diet), the choline-supplemented control group (CON + C, basal diet supplemented with 1% choline), the high-fat diet group (HF, high-fat diet), and the high-fat plus choline group (HF + C, high-fat diet supplemented with 1% choline). The experiment lasted for 9 weeks, during which dynamic monitoring of TMAO levels in mice was performed in the first 4 weeks. At the ninth week, the mice were sacrificed and samples were collected for subsequent assays, including the concentrations of TMA and TMAO in serum, colonic contents and feces; the pathological morphology of liver tissue, adipocyte staining characteristics and serum biochemical parameters; and the expression levels of key genes and proteins in liver, small intestine and colon tissues. Meanwhile, metagenomic analysis was conducted on colonic contents, combined with machine learning to predict the correlation between gut microbiota and TMA. In addition, gene cloning, multiple sequence alignment, molecular simulation and in vitro culture experiments were carried out to verify the TMA-producing function of the target strain. Results: This study elucidated that high-fat diet and high choline exert a significant interaction in TMA/TMAO production through a 2 × 2 animal experiment; meanwhile, the significantly increased TMA/TMAO levels co-induced by the two factors further exacerbate metabolic disorders. Notably, through combined metagenomics and machine learning, we identified Serratia marcescens as the primary TMA-producing microorganism under high-fat/choline diet induction. In vitro cultures simulating the intestinal environment revealed that the TMA conversion ability of Serratia marcescens is time-dependent, reaching 60 ± 2.49% after 24 h of anaerobic culture with choline chloride. Multiple sequence alignment and molecular simulation further demonstrated that the CutC enzyme of Serratia marcescens has a conserved amino acid sequence and high affinity for choline. Conclusions: We uncovered a two-factor synergistic effect of a high-fat/choline diet on TMA/TMAO, and for the first time identified the genus Serratia as a TMA-producing bacterium. These findings provide a new potential target for intervening in metabolic disorders mediated by high-fat diet-induced TMAO elevation. Full article

Chilli pepper agroecosystems (Capsicum annuum L.) are increasingly threatened by cadmium (Cd) contamination, with emerging climatic stressors such as drought further exacerbating risks to food safety and crop productivity. This review synthesizes current evidence on microbiome-mediated Cd phytostabilisation in chilli pepper, with a particular focus on the roles of capsaicinoids and cultivar-specific genetic regulation in shaping rhizosphere microbial communities. Existing studies demonstrate that capsaicinoid-rich cultivars selectively recruit specialized rhizosphere microbes, enhancing root-level Cd sequestration and achieving Cd retention efficiencies of approximately 40–55%, thereby substantially restricting Cd translocation to edible fruit tissues. Multi-strain plant growth-promoting rhizobacteria (PGPR) consortia, especially when combined with structured organic amendments, have been reported to reduce fruit Cd and nickel (Ni) accumulation by more than 87% in contaminated soils. These responses are regulated by pungency-associated genetic loci, including Pun1 (pungency locus 1) and Pun4 (pungency locus 4) genes, which influence secondary metabolism and microbial assembly under metal stress conditions. The review highlights key knowledge gaps regarding the long-term stability of engineered rhizobiomes, the in situ dynamics of the Capsicum volatilome as a microbial recruitment signal, and the interactive effects of Cd contamination and drought in field environments. Overall, this synthesis provides a mechanistic framework for deploying high-pungency cultivars and microbiome-based strategies to improve Cd phytostabilisation, with important implications for sustainable chilli production in drought-prone, metal-contaminated agroecosystems. Full article

Marine fish communities in the Yangtze River Estuary and Adjacent East China Sea (YRE-ECS) are subject to complex environmental gradients; however, their multidimensional assembly mechanisms remain insufficiently resolved. Here, we integrated environmental DNA (eDNA) metabarcoding, co-occurrence network analysis, and environmental profiling to examine fish community structure across vertical layers, hydrographic zones, and seasons. Vertically, surface communities dominated by pelagic-associated Perciformes and Clupeiformes showed more variable assembly patterns, whereas bottom communities enriched in Gobiiformes and Pleuronectiformes were more strongly associated with temperature and dissolved oxygen. Horizontally, among three zones delineated by salinity and hydrographic characteristics, the Mixed Transitional Water (MTW) supported the most diverse and interactive assemblages and functioned as an ecological connector between estuarine (EHSW) and offshore (OWSW) waters. Seasonally, community structure shifted markedly: spring communities exhibited higher diversity and denser trophic networks supported by zooplankton-rich, phototrophic plankton (e.g., Arthropoda, Bacillariophyta), whereas autumn communities were simpler, dominated by Chlorophyta and microbial taxa, with fish assemblages showing increased modularity and reliance on fewer planktonic groups. This seasonal pattern suggests a transition from diversified energy pathways to more constrained trophic coupling. βNTI and Mantel analyses jointly revealed a stratified environment-response-feedback framework driving community differentiation through combined stochastic and deterministic mechanisms. These findings highlight the importance of integrated spatial-temporal monitoring and suggest that protecting transitional zones and spring food-web integrity is critical for ecosystem resilience in the YRE-ECS. Full article