Ustiloxins are toxic cyclic peptides produced by the rice false smut fungus Ustilaginoidea virens. False smut disease turns rice grains into yellow-orange spores later turned into greenish-black smut balls, significantly reducing yield and grain quality. Due to their hydrophilic nature ustiloxins leach from spore balls and contaminate paddy soil, water, and rice products. They block eukaryotic cell division by binding tubulin and inhibit microtubule polymerization. This review provides information on advances in ustiloxin biology and control. It summarizes ribosomally synthesized and post-translationally modified peptides (RiPPs) biosynthesis and recent insights into pathway genes, regulatory networks including target of rapamycin (TOR) signaling, and comparative fungal genomics. Environmental occurrence is reviewed with emphasis on persistence in soil, water and translocation into rice grains. Ecotoxicological evidence is consolidated, spanning phytotoxicity, effects on beneficial microbes, aquatic organisms, and mammalian toxicity supported by in vivo and mechanistic studies. Progress in detection is outlined with improved LC-MS/MS, immunoassays, and emerging biosensors for field diagnostics. Management strategies are evaluated, including resistant cultivars, disease forecasting, fungicidal and biological controls, and post-harvest detoxification via enzymatic and physical approaches. A dedicated risk assessment discusses human dietary exposure, regulatory status, and the need for maximum limits. The review concludes by highlighting research priorities such as multi-omics, spread modeling, and biotechnological interventions, to close key knowledge gaps and enable effective monitoring and mitigation toward an ustiloxin-free rice agroecosystem.

Substrate composition is a primary determinant of microbial succession and functional dynamics in vermicomposting systems. However, comparative insights into how biomass pre-treatment influences microbial architecture and how different sequencing approaches capture these changes remain limited. In this study, evaluation was carried out on microbial community structure and metabolic potential in vermicompost derived from three forms of Eichhornia crassipes (water hyacinth) biomass, burnt biomass (BB), composted biomass (CB) and dry biomass (DB) using both 16S rRNA gene amplicon sequencing and shotgun metagenomics. All treatments were dominated by bacterial communities (> 97%), with Proteobacteria (Pseudomonadota), Firmicutes (Bacillota), Actinobacteria and Bacteroidota representing core phyla across substrates. However, metagenomics revealed broader domain-level coverage, detecting Archaea and Fungi that were underrepresented in 16S datasets. Substrate-specific signatures were evident such as, composted biomass exhibited enrichment of lignin degradation and carbon cycling pathways; dry biomass showed methanogenesis, fermentation and phosphate solubilization signatures; and burnt biomass was associated with nitrogen fixation and sulphur metabolism. Shannon diversity was highest in composted biomass (H' = 5.21), reflecting enhanced niche diversification during substrate maturation. Comparative analysis demonstrated that 16S rRNA sequencing effectively captured dominant bacterial structure, whereas shotgun metagenomics provided superior taxonomic resolution and direct functional inference, particularly for low-abundance and non-bacterial taxa. Notably, functional differentiation among treatments was more pronounced than broad taxonomic shifts, indicating that biomass pre-treatment exerts stronger influence on ecological function than on core community composition. These findings demonstrate that integrating taxonomic and functional metagenomics enables substrate-specific optimization of vermicompost formulations and provides a framework for designing microbiome-informed strategies for sustainable agriculture and invasive biomass valorization.

Cyanobacteria fix nitrogen and produce antioxidant metabolites, making them excellent biological resources for sustainable agriculture. Seven cyanobacterial strains, Anabaena, Westiellopsis, Nostoc, Calothrix, Phormidium, Oscillatoria, and Tolypothrix, were tested for main nitrogen metabolism enzymes (GS, NR, GOGAT, GDH) and antioxidant defense enzymes. Quantifying activities with spectrophotometric tests created a comparative biochemical profile. The results showed continuous strain differences. Phormidium sp. had the highest values for nitrogen assimilation enzymes, including GOGAT (85.9 ± 2.5 nmol NADH min[-1] mg[-1] protein), GDH (43.7 ± 1.7 nmol NAD(P)H min[-1] mg[-1] protein), and antioxidant activity, including SOD (162 ± 4.5 U mg[-1] protein) and APX (15.3 ± 0.7 nmol min[-1] mg[-1]). Anabaena sp. exhibited high GS activity (1.98 ± 0.06 U mg[-1] protein) and strong antioxidant responses (SOD 156 ± 4.2 U mg[-1] protein). Tolypothrix sp. had lower metabolic and oxidative defense capabilities, with activity levels of NR (5.8 ± 0.28 µmol NO2 [-] h[-1] mg[-1] protein) and CAT (17.4 ± 0.7 µmol min[-1] mg[-1] protein) being the lowest nitrogen metabolism and antioxidant enzymes had high positive correlations (e.g., GS-SOD: r = 0.91; NR-CAT: r = 0.88), showing that nitrogen absorption enhances oxidative stress tolerance. Cyanobacterial strains have great biochemical variety, and Phormidium sp., Anabaena sp., and Calothrix sp. are promising prospects for biofertilizer production, plant stress alleviation, and other biotechnological uses.

This study assesses the kinetics of Tandemol lubricant degradation by Pseudomonas synaxantha rhizo-25 after UV treatment and nanoparticle inclusion. The degradation efficiency was assessed in terms of the Total Petroleum Hydrocarbons (TPH) and aromatic compounds degraded in a liquid medium containing Tandemol lubricant. The medium composition was further supplemented with nanoparticles to evaluate their impact on the process. Metabolite profiling was conducted using Gas Chromatography-Mass Spectrometry (GC-MS), while transcriptomic analysis identified key enzymes involved in the degradation process. For TPH degradation, biodegradation rate (K) and half-life (t1/2) values were found to be -0.39 M-1day-1 and 10.22 days (wildtype), and 0.013 M day-1 and 9.33 days (UV-treated), respectively. For the aromatic compounds, the estimated K and t1/2 values were -63.30 M-1 day-1 and 7 h (wildtype), and -0.69 day-1 and 1.01 days (UV-treated). The nanoparticle supplemented aromatic degradation yielded K and t1/2 values of -21.01 M-1h-1 and 0.85 h (UV-treated). Aromatic compound degradation was observed to follow the meta-cleavage pathway with terminal oxidation as an activation mechanism. Oxidoreductases, namely Cytochrome P450 and Tau D/Tfd A dioxygenase, were responsible for the primary step in the degradation pathway. Overall, these results showed that the UV treatment and the inclusion of nanoparticles enhanced biodegradation efficiency towards optimum petroleum contaminant bioremediation.

Bacteriophages constitute a regulatory layer in plant-associated microbiomes that has been systematically under-characterized relative to their ecological importance. This review advances the hypothesis that phages function as metabolic switches, alternating between lytic nutrient release and lysogenic host-fitness enhancement to govern the microbial metabolic states that determine nutrient cycling, stress responses, and microbiome stability in the rhizosphere and phyllosphere. During lytic infection, phage-driven cell lysis releases dissolved organic carbon, ammonium, and phosphate through the viral shunt, redistributing microbial biomass into forms directly accessible to plant roots and surviving microbial taxa. Lysogenic integration, by contrast, delivers prophage-encoded auxiliary metabolic genes that reprogram bacterial hosts with enhanced metabolic capacity across multiple generations without immediate cell death. Environmental stressors, include drought, salinity, temperature extremes, heavy metal contamination, and pathogen pressure remodel root exudation profiles, alter microbial metabolic bottlenecks, and shift phage life-cycle decisions through quorum-sensing-responsive and SOS-dependent switching mechanisms. These phage-mediated processes have cascading consequences for plant-relevant outcomes including nutrient uptake efficiency, oxidative stress management, phytohormone signaling, and growth-defense trade-offs mediated by plant growth-promoting rhizobacteria. By integrating mechanistic evidence across abiotic and biotic stress contexts, this review proposes a phage-microbe-plant metabolic axis as a unifying framework for understanding how soil virome dynamics translate into plant physiological outcomes. Practical implications for engineering phage-informed microbiomes and developing climate-resilient agricultural systems are evaluated alongside ecological risks, knowledge gaps, and priorities for field validation, virome mapping, and predictive modeling that must be addressed before phage-based interventions can be reliably deployed in crop production.

Two pigmented bacteria strains were isolated from the Mediterranean Sea. Phylogenetic analysis revealed that both strains are affiliated with Winograsdskyella schleiferi Z215. However, in contrast to this reference strain, they can assimilate additional carbon sources such as d-mannose, l-arabinose, d-mannitol, and citrate. Zeaxanthin was identified as the major carotenoid produced by both strains, predominantly in the all-trans configuration. Carotenoid biosynthesis kinetics revealed that pigment production commenced at the early stages of growth, with maximal yields reached between 48 and 56 h (between 1 and 1.3 mg L[-1]). Specific production yields were 0.7 and 0.9 mg g[-1] for the two strains, respectively. Total carotenoid production was influenced by incubation temperature in both strains. Overall, these findings expand the scientific knowledge on carotenoid-producing marine bacteria and highlight the potential of these newly isolated strains as promising candidates for zeaxanthin biotechnological production for a wide range of novel applications ranging from feed additives to treatments for macular degeneration and melanoma.

Gut symbiotic bacteria are highly dynamic and contribute to digestion, development, immunity, detoxification, and environmental adaptation in insect hosts. In fruit-sucking moths (FSM), particularly Eudocima materna (Lepidoptera: Noctuidae), adults are destructive frugivorous pests, whereas larvae feed exclusively on toxic plants such as Tinospora cordifolia. This study investigates the gut bacterial diversity of FSM larvae, with an emphasis on their role in host plant adaptation. Nine bacterial strains were isolated, including Enterobacter hormaechei, Klebsiella aerogenes, Mammaliicoccus sciuri, Staphylococcus sciuri, Staphylococcus aureus, Staphylococcus saprophyticus, and Enterococcus gallinarum. All isolates were subjected to biochemical profiling (sugar and carbohydrate utilization) and antimicrobial susceptibility testing against 12 antibiotics. Among them, E. gallinarum (strain L4), S. sciuri, and M. sciuri exhibited anti-quorum-sensing activity. Notably, E. gallinarum played a key role in host plant digestion and was capable of degrades a ~ 45 kDa protein present in T. cordifolia leaves. GC-MS analysis of methanolic extracts of E. gallinarum revealed several bioactive compounds, including gentamicin A, cyclo (Phe-Pro), isoisopulegol, and gougerotin. Whole-genome sequencing of strain L4 identified genes encoding degradation enzymes (alcohol dehydrogenase, phosphotriesterase), multiple antibiotic resistance genes (YurZ, PptA, CatE, OadB, PycA, and Tdh), diverse metabolic pathways, and secondary metabolite biosynthesis clusters. Subsequently, digestive and detoxification enzymes were identified, including alpha-amylase, serine protease, lipase, chitinase, pectinesterase, carboxylesterase, glutathione peroxidase, and cytochrome P450. Molecular docking analysis showed strong interactions of degradation enzymes with organophosphate insecticides, with binding scores of -6.8 kcal/mol for triazophos and -5.5 kcal/mol for quinalphos. These findings highlight the multifunctional role of E. gallinarum in host plant adaptation and detoxification in FSM larvae, offering new insights into microbe-insect interactions and potential microbial-based biotechnological applications.

Fungal diseases are major constraint to global crop production, causing substantial losses and increasing reliance on chemical fungicides. Cyanobacteria offers a sustainable alternative for disease managment due to their ability to produce antifungal metabolites, including volatile organic compounds (VOCs), exopolysaccharides (EPS), and lytic enzymes. These bioactive molecules suppress phytopathogenic fungi by disrupting cell membranes, inhibiting virulence factors, inducing oxidative stress, and degrading cell wall components. Cyanobacteria also enhance plant defence responses by activating salicylic acid (SA), jasmonic acid (JA), ethylene, and nitric oxide (NO) signaling pathways, leading to upregulation of defense-related genes, including PR proteins, PAL, and WRKY transcription factors. Recent multi-omics approaches have provided valuable insights into biosynthetic gene clusters, regulatory networks, and metabolic pathways underlying cyanobacterial antifungal activity. Although laboratory evidence is encouraging, field application remains challenging by environmental variability and formulation limitations. Emerging advances in genome mining and synthetic biology may enhance the effectiveness of cyanobacterial biocontrol agents. This review highlights current progress in cyanobacteria-mediated management of fungal diseases, discusses biosafety considerations, and outlines future research directions for developing eco-friendly and sustainable crop protection solutions.

Microbial enzymes are central to numerous industrial applications, yet their large-scale production remains constrained by persistent biological and process-level limitations. These include restricted secretion capacity, insufficient operational stability, scale-up inefficiencies, and downstream processing costs that can account for 45-65% of total manufacturing expenses. This review critically examines integrated genetic, physiological, and bioprocess engineering strategies developed to overcome these interconnected bottlenecks. Comparative analysis across major enzyme classes-cellulases, proteases, lipases, and amylases-reveals both universal constraints and enzyme-specific production challenges. Quantitative benchmarks indicate that multiplex genome engineering typically delivers 3-8-fold productivity improvements in optimized strains, while adaptive laboratory evolution enhances industrial robustness by 15-30%. Process intensification and continuous production approaches reduce processing times by 40-55%, albeit with increased capital requirements, and immobilization strategies enable 50-200 operational cycles with 65-85% retention of native activity. By synthesizing advances in strain engineering, secretion optimization, fermentation design, enzyme stabilization, and downstream integration within a techno-economic framework, this review highlights how coordinated interventions yield multiplicative gains over isolated strategies. Key future directions include systems-level characterization of secretion limits, AI-assisted enzyme stability engineering, and integrated manufacturing platforms. Collectively, these insights provide practical guidance for translating laboratory advances into economically viable microbial enzyme production systems.

Monocrotophos (MCP) is a widely used insecticide in agriculture, but its high toxicity poses significant environmental and health risks. The biodegradation of monocrotophos by indigenous microbes is crucial in reducing its toxicity. The present study was aimed at assessing plant growth- stimulating factors and the biodegradable ability of monocrotophos of two indigenous soil bacterial strains, CAB1 and SD8, isolated from monocrotophos-contaminated agricultural soils in Mysuru and Mandya, Karnataka, India. Biodegradation was evaluated using spectroscopy and chromatography, with substrate degradation confirmed by the disappearance of the main peak in HPLC profiles and intermediate metabolites identified through FTIR and LC-MS analyses. Molecular characterization identified CAB1 as Stenotrophomonas pavanii (OQ861163) and SD8 as Brevibacillus parabrevis (OQ881083). Results showed that the two bacterial strains utilized MCP as their sole carbon source and exhibited biodegradation rates of 88% and 90%, respectively, under optimal conditions. Results further showed that S. pavanii CAB1 and B. parabrevis SD8 produced ammonia, IAA, catalase, and cellulase, and demonstrated phosphorus and zinc solubilization. The degradation ability of CAB1 and SD8 is attributed to the presence of the opd gene and the opdA gene. Trimethyl phosphate, dimethyl phosphate, cyclohexanone, 2- cyclohexylidene, oxalic acid, and isohexyl pentyl esters were the non-toxic intermediates produced during the biodegradation of MCP. The strains S. pavanii CAB1 and B. parabrevis SD8 can be employed, alongside a microbial consortium formulation, for the detoxification of hazardous pollutants in contaminated soils and promotion of plant growth.

Although plant-associated microbes influence plant performance and ecological adaptability, knowledge of microbial variation between the root endosphere and rhizosphere of desert relict plants remains limited. Ammopiptanthus mongolicus, a relict species native to the hyper-arid deserts of northwestern China, was used to investigate microbial community structure across ecological niches and their soil ecological responses, aiming to elucidate adaptive plant-microbe symbioses and microbial distribution patterns. Root and rhizosphere soil samples were collected from Wuhai and Alxa in July 2021 to characterize microbial assemblages. Pronounced differences in community composition were observed between niches, with significantly higher species richness and α-diversity in the rhizosphere. PCoA indicated that niche type was the primary driver of microbial differentiation, outweighing site-level effects. Although more enriched taxa occurred in the rhizosphere, differentially abundant fungal taxa were far fewer than bacterial taxa. Co-occurrence network analysis showed that positive interactions dominated microbial associations, with the rhizosphere network exhibiting greater complexity, while endosphere fungal communities showed positive associations. Six low-abundance OTUs (< 0.1%) functioned as keystone taxa supporting network stability. AP, SOC, NH4 [+]-N strongly shaped bacterial and fungal communities. Pathotrophs and saprotrophs dominated fungal guilds, whereas intracellular parasites and chemoheterotrophs prevailed among bacteria, with symbiotic fungi enriched in the endosphere.

Root rot disease incited by Rhizoctonia solani, is one of destructive soil-borne diseases which constrains faba bean (Vicia faba L.) productivity. In the present research, pathogenicity of R. solani isolates was determined and potential of putative Trichoderma species were evaluated as a biological control in both in vitro as well greenhouse conditions. The most aggressive isolate of R. solani was determined with morphological characterization and sequencing of ITS rDNA. In vitro antagonistic potential of Trichoderma atroviride and Trichoderma asperellum against R. solani was evaluated by dual culture technique, and in greenhouse trials compared with a standard fungicide recommendation for comparison of efficacy. Both Trichoderma spp., strongly inhibited mycelia growth of R. solani in vitro, with inhibition ranging from over 85% for the most effective isolates. Trichoderma spp. applied to the soil under greenhouse conditions had significant influences on these trends significantly less damping-off and root rot disease incidence with an increase in the percentage of healthy surviving plants than the infected control. T. asperellum provided more efficient disease suppression than T. atroviride, whereas the chemical fungicide resulted in the greatest reduction of disease. Furthermore, Trichoderma-treated plants had higher activities of defense-related enzymes such as catalase, peroxidase and polyphenol oxidase which indicated the induction of systemic resistance. These results indicate that Trichoderma spp., mainly T. asperellum, can be a good alternative or supplement to chemical fungicides for the integrated disease management of R. solani-mediated root rot disease in V. faba L. under field conditions.

Naringinase is an industrially important enzyme system with applications in citrus debittering, aroma enhancement, and the production of bioactive flavonoid aglycones. Accurate identification of true naringinase-producing microorganisms remains challenging due to the dual-enzyme nature of naringinase, which requires coordinated α-L-rhamnosidase and β-D-glucosidase activities. Conventional screening methods based on naringin agar or single chromogenic substrates often generate false-positive results, as they fail to distinguish partial enzyme producers from microorganisms capable of complete naringin hydrolysis. In this study, a single-plate, one-step dual chromogenic screening assay was developed for reliable identification of true naringinase producers. The method employs p-nitrophenyl-α-L-rhamnopyranoside and X-gal to simultaneously detect α-L-rhamnosidase and β-glycosidase-like activities, producing distinct yellow and blue signals, respectively. The spatial separation of these chromogenic products enables unambiguous differentiation of microbial enzymatic profiles on a single agar plate. The assay was validated using bacterial strains with known enzymatic characteristics and further confirmed by spectrophotometric enzyme assays and thin-layer chromatography. Only isolates exhibiting both chromogenic responses demonstrated complete biotransformation of naringin to naringenin. A positive correlation between chromogenic halo diameter and measured enzyme activity was also observed. The proposed assay provides a simple, reliable, and scalable platform for high-throughput screening of naringinase-producing microorganisms in applied microbiology and biotechnology.

Taxus contorta Griff., an important conifer of the Western Himalaya and a natural source of the anticancer drug Taxol, has experienced severe population decline due to overexploitation. Despite its ecological and medicinal significance, its mycorrhizal status has remained unclear, although it predominantly forms arbuscular mycorrhiza (AM), but reports of ectomycorrhizal associations also exist. In this study, mycorrhizal associations of T. contorta were examined through morpho-anatomical and molecular approaches, complemented by in-vitro mycorrhizal synthesis. Results revealed no evidence of ectomycorrhizal colonization; instead, Paris-type arbuscular mycorrhizal associations were observed, with colonization ranging from 45.54 ± 4.25% to 67.31 ± 5.71%. A total of 29 AMF species from 10 genera were identified in the rhizosphere soil, with Rhizoglomus intraradices and Glomus microcarpum as dominant taxa. The metabarcoding targeting the V4 region of the 18S rRNA gene identified 13 operational taxonomic units (OTUs) of AM fungi within T. contorta roots. Among these, three genera, Paraglomus, Glomus and Acaulospora, were identified, while more than half of the sequences could only be classified up to class level, indicating that arbuscular mycorrhizal diversity in the Himalaya remains largely unexplored. Mycorrhizal colonization peaked during active growth season, while AMF spore diversity was higher in dormant season. Both colonization and diversity were influenced by altitude, vegetation and soil properties. The dominance of specific AMF taxa suggests potential use as effective inoculants in the propagation of T. contorta in nursery, while insights into environmental influences may guide the selection of suitable sites for afforestation programs aimed at conserving this conifer.