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This study focuses on investigating the response mechanism of nitrogen cycling microorganisms to nitrogen addition gradients in yellow soil with and without long-term nitrogen application, in order to optimize nitrogen fertilizer management strategies in yellow soil areas. The results showed that nitrogen addition significantly affected the alpha diversity index, gene relative abundance, and species relative abundance of nitrogen cycling microorganisms in soils with a history of long-term nitrogen application. Among the treatments, high nitrogen addition contributed the most to differences in community structure. In contrast, nitrogen cycling microorganisms in soils without long-term nitrogen application exhibited weaker responses to short-term nitrogen addition. Redundancy analysis indicates that differences in soil chemical properties are important drivers of differences in soil nitrogen cycling microbial community composition, and long-term nitrogen application history determines the specificity of microbial responses to short-term nitrogen gradients.

Diatoms are environmentally responsive photosynthetic microorganisms whose growth dynamics and biosilicification processes are tightly regulated by external physicochemical conditions. However, conventional bulk cultivation and existing microfluidic platforms often fail to provide stable three-dimensional confinement together with dynamic environmental control, limiting long-term quantitative analysis at single-cell resolution. Here, we present a permeable hydrogel microreactor system integrated with microfluidic perfusion and a neural network-based image analysis workflow for on-chip investigation of diatom growth dynamics. Monodisperse alginate/carboxymethyl chitosan hydrogel microspheres were engineered to stably confine individual Cyclotella cryptica cells while permitting efficient molecular exchange. The microreactors were immobilized within a perfused microfluidic device, enabling long-term cultivation and real-time imaging under dynamically regulated conditions. Coupled with this neural network-based approach for segmentation and contour extraction, we quantitatively reconstructed single-cell growth trajectories and division events, achieving a specific growth rate of 1.874 d-1 under perfusion, which represents a 5.5-fold increase over batch controls. Furthermore, dynamic copper exposure enabled concentration-dependent stress profiling, yielding EC50 values of 8.53 μM (growth inhibition) and 7.25 μM (proliferation inhibition) at single-cell resolution. This platform offers a versatile analytical framework for resolving cellular heterogeneity and environmental responses in photosynthetic microorganisms under precisely controlled microenvironments.

Among The insects that visit Passifloras, adults of Dione juno juno lay its eggs on leaves where the recent born larva feeds and grow during great part of their life-cycle, causing important negative impact on plant development. Recently, we decided to investigate the intestinal microbiota of the larva stage of this butterfly, in order to figure out how these microorganisms interact with each other. In the present study, during one of these microorganisms isolation it was obtained the fungus Epicoccum sp. along with five bacteria. Studies toward the discover of natural substances produced by this Epicoccum using mass spectrometry (MS/MS, molecular network by GNPS) and NMR spectroscopy of isolated compounds, resulted in the annotation and identification of 11 compounds belonging to the anthraquinone class of natural products. The major isolated anthraquinones were paquibasin (1), chrysophanol (2), paquibasic acid (3), and phomarin (4), two of which (1 and 2) were tested for their activity against five putatively Bacillus bacterial strains (L-409, L-410, L-411, 412, and L-414) which were co-isolated with the fungus Epicoccum, being three bacteria susceptible, with compounds 1 and 2 shown to be the greater inhibitors, c.a. 30% of the amoxicillin potency.

Amniotic fluid sludge (AFS) is a sonographic finding associated with intra-amniotic infection and spontaneous preterm birth. The microbial composition of AFS remains poorly characterized. This systematic review and meta-analysis aimed to consolidate existing data on microbial prevalence in AFS and identify consistent microbial patterns. A systematic search of MEDLINE (PubMed), Dimensions, and OpenAlex was conducted from inception to February 11, 2026. Studies reporting the prevalence of microorganisms in AFS (minimum 10 cases) from pregnant women with AFS diagnosed via transvaginal ultrasound were included. Two reviewers independently performed screening, data extraction, and risk-of-bias assessment, with a third reviewer resolving discrepancies. Random-effects meta-analysis of proportions was used to pool overall and pathogen-specific prevalence. Four studies comprising 85 women met inclusion criteria. The pooled prevalence of any microorganism was 35% (95%CI 22-48%), with moderate heterogeneity (I2 = 36.8%). Ureaplasma spp. were the most frequently detected pathogens (pooled prevalence 17%, 95%CI 8-27%). Sensitivity analysis revealed that sampling technique was a source of heterogeneity in this dataset; excluding the single study using transvaginal amniocentesis reduced the pooled prevalence to 28% (95%CI 17-41%) and eliminated statistical heterogeneity (I2 = 0.0%). Transvaginally collected samples exhibited significantly greater microbial diversity (median 2 vs. 1 microorganism/sample, p = 0.005) and contained vaginal commensals, suggesting possible contamination. In transabdominal cohorts, the pooled prevalence of microorganisms (any) in amniotic fluid sludge was 28% (95%CI 17-41%), with Ureaplasma spp. emerging as the predominant pathogen when an infectious agent was identified. Transvaginal amniocentesis resulted in greater microbial diversity and detection of vaginal commensals, consistent with contamination. Our findings suggest that transabdominal sampling should be the preferred methodological approach for future studies of AFS microbiology.

Extreme environments such as acid mine drainage (AMD) host highly specialized microbial communities that drive profound biogeochemical cycles. Within these ecosystems, iron- and sulfur-metabolizing taxa catalyze mineral weathering, generating intense acidity and mobilizing heavy metals. However, more than 97% of these microorganisms remain uncultured "microbial dark matter," heavily restricting our understanding of extremophile metabolism and adaptation. Here we present the Microbial Biobank of AMD (mbAMD), a culturomics-derived collection of 652 isolates spanning 42 species-including 21 novel taxa-that achieves 86.7% coverage of the global AMD core microbiome. Functional validation demonstrates that 36 of these taxa possess active iron or sulfur metabolic capacities, including the discovery of the first pure cultures of acid-tolerant sulfate reducers. Comparative genomic analyses across these isolates reveal that extreme environmental adaptation is predominantly driven by pervasive horizontal gene transfer. Specifically, extremophiles preferentially acquire adaptive genes governing acid tolerance and metal resistance from phylogenetically proximal relatives rather than distant donors. These findings elucidate the modular evolutionary strategies of extremophiles and provide critical functional resources for advancing biohydrometallurgy and environmental bioremediation. This mbAMD resource will accelerate biohydrometallurgical process optimization and environmental bioremediation strategies while advancing evolutionary microbial ecology research.

Plants regulate nutrient uptake and growth by recruiting rhizosphere microorganisms via root exudates. However, a systematic understanding of how the rhizosphere core and functional microbiota jointly regulate the dynamics of carbon, nitrogen, phosphorus, and potassium across the entire plant life cycle in desert ecosystems remains limited. In this study, we asked: how does the succession of rhizosphere bacterial communities align with stage-specific nutrient demands in the desert plant Leymus racemosus? We used 16 S rRNA high-throughput sequencing to analyze the rhizosphere bacterial communities and nutrient contents of the desert plant Leymus racemosus at three growth stages (seedling, flowering, maturity) in the Kalamaili Nature Reserve, Xinjiang, China. For each stage, ten 5 × 5 m quadrats (20 m apart) were established; 6-10 healthy plants were sampled per quadrat, and rhizosphere soil from each quadrat was pooled into one composite sample (n = 10 per stage). Arthrobacter, identified as a core taxon, was associated with the stability of hydrolyzable nitrogen across all growth stages. Bacillus became the dominant genus during the flowering stage, based on correlation and functional prediction, it may contribute to nutrient supply, reflecting a potential "investment" strategy. At maturity, enhanced microbial cooperation (inferred from co-occurrence and correlation analyses) combined with reduced plant demand was associated with the accumulation of rhizosphere nutrients, possibly facilitating energy storage for subsequent growth. These findings provide a potential answer to our question, suggesting that the plant recruits distinct microbial alliances at different phenological phases-a persistent Arthrobacter-based system for nitrogen buffering, a transient Bacillus-enriched community for rapid nutrient mobilization at flowering, and a synergistic network at maturity for delayed nutrient accumulation. This study reveals the developmental dynamics of rhizosphere bacterial community assembly and nutrient regulation in L. racemosus and provides a theoretical basis for further elucidating plant-microbe interactions in desert ecosystems. However, the proposed functional roles of specific taxa are primarily derived from correlation and predictive analyses; experimental validation (e.g., strain isolation, inoculation tests, and metabolomics) is needed to establish causality.

Biodepolymerization of poly(ethylene terephthalate) (PET) plastics using microorganisms has emerged as a promising and sustainable approach for mitigating pollution caused by PET waste. In this study, Glutamicibacter mysorens ASR14, a mesophilic bacterium isolated from Kodungaiyur dumpyard (Chennai, India), showed 27.6% PET biodepolymerization in terms of weight loss in 30 d. A customized screening of 20 trials was designed using JMP statistical software to evaluate the influence of various variables. Furthermore, a Central Composite Design (CCD) of Response Surface Methodology (RSM) was adopted and validated using four variables at five levels, with 25 trials, to correlate the relationship for enhanced PET biodepolymerization. A maximum PET weight loss of 75.6% was achieved in 60 d, representing a 2.73-fold improvement compared to that under unoptimized conditions. Enzymatic assays confirmed the involvement of esterase (5,690 U/mL) and lipase (962 U/mL) activities in accelerating the breakdown of PET. The analytical characterization techniques revealed significant surface erosion, reduction in crystallinity, and high yield of terephthalic acid (TPA), which also holds potential value for biorefinery applications. This work represents the first comprehensive report on process optimization for PET biodepolymerization using G. mysorens ASR14 as a whole-cell biocatalyst. The findings establish G. mysorens ASR14 as a promising candidate for developing scalable, green bioremediation strategies.

Dry eye disease (DED) is a prevalent and multifactorial condition that significantly impacts the ocular surface, characterized by symptoms of discomfort, visual disturbance, and tear film instability. Recent research has increasingly focused on the ocular surface microbiome (OSM) and its potential role in the pathogenesis and progression of DED. The OSM consists of a diverse community of microorganisms, including bacteria, fungi, and viruses, that interact with the host to maintain ocular surface health. Dysbiosis, or the imbalance of these microbial communities, has been linked to various ocular surface disorders, including DED. This review comprehensively summarizes the current understanding of the differences in OSM between healthy individuals and patients with different types of DED, such as aqueous-deficient dry eye, evaporative dry eye, and DED associated with autoimmune conditions. Additionally, it explores the detection methods used to study the OSM, highlighting the strengths and limitations of culture-based approaches, 16 S rRNA sequencing, metagenomic shotgun sequencing, and emerging technologies like 2bRAD-M. The review also outlines future research directions, emphasizing the need for advanced multi-omics approaches, personalized microbiome-based therapies, and longitudinal studies to further elucidate the role of the OSM in DED. By enhancing our understanding of the OSM composition and function, these insights may lead to innovative diagnostic and therapeutic strategies for managing DED.

The global rise of multidrug-resistant microorganisms necessitates antimicrobial technologies that avoid the resistance mechanisms associated with conventional antibiotics and chemical disinfectants. Light-activated antimicrobial systems represent a promising alternative because they generate reactive oxygen species in situ, producing rapid and broad-spectrum pathogen inactivation through non-specific oxidative damage to multiple cellular targets. Such multitarget activity significantly reduces the probability of resistance development. Herein, the chemical synthesis, and photophysical and biological evaluation of the encapsulation of a binuclear ruthenium-platinum photosensitizer into electrospun nanofibrous membranes for antimicrobial photodynamic therapy is reported. The binuclear photosensitizer was found to produce singlet oxygen by energy transfer and superoxide through electron transfer, enabling a combined type I and type II photochemical mechanism. The complex was incorporated into electrospun nanofibrous membranes based on polyacrylonitrile and polycaprolactone, yielding high-surface-area materials. Systematic optimization of the fabrication process produced bead-free fibers with controlled morphology, while comparative analysis revealed superior photosensitizer retention and structural stability in the hydrophilic polyacrylonitrile matrix. Under visible-light irradiation, both membrane systems exhibited strong antibacterial activity against Gram-positive and Gram-negative bacteria. The presence of sodium azide increased bacterial inactivation, suggesting that the antimicrobial activity shifted from primarily singlet-oxygen-based damage to a mechanism dominated by radical-mediated oxidative stress. Durability studies under prolonged bacterial exposure demonstrated that membrane performance is governed not only by molecular photochemistry but also by matrix-dependent antifouling resilience. The polyacrylonitrile-based membrane retained structural integrity and antibacterial efficacy after aging, whereas polycaprolactone-based systems showed pronounced fouling and reduced activity. These results establish a direct link between molecular photosensitizer engineering, nanofabrication strategy, and long-term functional performance, providing a blueprint for next-generation photodynamic antimicrobial materials.

Antibiotic resistance is a global threat requiring new potential antimicrobial sources. Secondary metabolites from cold-adapted microorganisms may provide unique antimicrobial compounds. Ethyl-acetate extract of Alcaligenes pakistanensis LTP10 from Passu glacier was explored for antimicrobial potential against clinical isolates. Cytotoxicity was determined by Brine shrimp lethality assay. The extract is analyzed by LC-MS/MS and the data is processed by MZmine. Important compounds were evaluated by molecular docking and in silico study. The extract demonstrated activity against clinical isolates Staphylococcus aureus, Escherichia coli, Salmonella enterica, Pseudomonas aeruginosa, and Candida albicans with zone of inhibition ranging from 16 mm to 24 mm, with no killing of nauplii suggested non-cytotoxic nature. LC-MS/MS analysis established presence of important putative antimicrobial metabolites (E)-3-(acetyloxymethyl)-5-(2-formyl-4-hydroxy-5,5,8a-trimethyl-1,4,4a,6,7,8-hexahydronaphthalen-1-yl)pent-2-enoic acid, cyclizidine-F, neovasipyridone-G, paenibacillin-A, and tricholomenyn-A. Molecular docking study of these metabolites by AutoDock Vina against dihydrofolate reductase of S. aureus demonstrated binding affinities from -6.8 kcal/mol to -8.5 kcal/mol, while against enoyl-ACP reductase of E. coli showed binding affinity values from -6.3 kcal/mol to -7.9 kcal/mol. In silico analysis predicted considerable absorption, distribution, metabolism, excretion, safety, and druglikeness properties. These results suggest that metabolites from A. pakistanensis LTP10 possess antimicrobial potential and warrant advanced post-docking validation via molecular dynamics, free-energy, and mechanistic analyses for future antibiotic development.

As a vital carrier for the colonization and succession of diverse microbial communities, microplastics (MPs) surface form unique microplastic biofilms (MPBs) ecosystems. MPBs can enrich microorganisms involved in core nitrogen transformation processes, and the localized anoxic environment within these biofilms regulates nitrogen removal efficiency. Consequently, biofilms establish novel nitrogen transformation microenvironments within aquatic systems. Numerous studies have revealed that MPBs play a crucial role in key pathways of the nitrogen transformation. However, the potential regulatory role of MPBs in nitrogen transformation, along with the ecological risks and environmental applications arising from this process, warrants further review. A dual effect of MPBs has been identified in aquatic nitrogen transformation, presenting both ecological risks and environmental applications. MPBs promote multi-pathway coupling processes, such as nitrification and denitrification, by enriching functional microbial communities and constructing oxygen-gradient microenvironments. Incomplete denitrification and an imbalance in functional genes may significantly increase the risk of N₂O emissions from MPBs. Furthermore, biofilm succession under stress from environmental factors often accelerates the directional selection of functional communities and may alter the nitrogen balance in aquatic systems. Factors such as dissolved oxygen, DOM, and antibiotics can alter the final products of nitrogen transformation by regulating the expression of functional genes and the supply of electron donors. This paper reviews the general patterns of structural succession in MPBs, summarizes their primary ecological functions in the nitrogen transformation, and explores their underlying mechanisms from the perspective of regulation by environmental factors. The aim is to elucidate the potential impacts of MPs, as an emerging ecological niche, on nitrogen transformation processes in aquatic environments. This review deepens our understanding of nitrogen transformation functions and their environmental regulation mechanisms in MPBs, providing scientific support for aquatic environmental management and pollution control.

Coumarins represent an important class of oxygenated heterocyclic natural products widely distributed in plants, fungi, and microorganisms. Their remarkable structural diversity ranges from simple oxygenated coumarins to complex fused architectures such as pyranocoumarins, benzocoumarins, coumestans, lamellarins, and other annulated frameworks. Because many naturally occurring coumarins are available only in limited quantities from natural sources, chemical synthesis plays a crucial role in structural confirmation, biological evaluation, and the development of functional analogues. Over the past decades, significant advances have been achieved in the synthesis of coumarin-based natural products through the development of modern synthetic methodologies. These include transition-metal-catalyzed cross-coupling reactions, C-H activation strategies, oxidative annulations, multicomponent reactions, biomimetic transformations, and cascade processes that enable the rapid construction of structurally complex coumarin frameworks. This review highlights and critically examines progress in the synthesis of naturally occurring coumarins, focusing on representative total syntheses and key transformations used to assemble diverse coumarin architectures. Particular emphasis is placed on reaction design, synthetic strategy, and methodological innovations that enable efficient access to biologically significant coumarin natural products and their derivatives.

Fungal keratitis is an uncommon condition that can occur after refractive surgery. Herein, we report a case of early postoperative Aspergillus keratitis in an immunocompetent patient following photorefractive keratectomy (PRK). We report a case of a 21-year-old white man with no past ocular or systemic diseases who underwent bilateral PRK for myopia. Seven days after surgery, he presented to his surgeon, complaining of eye redness and blurred vision that had started 3 days prior. First, empirical antibiotic therapy was initiated, and antifungal agents were subsequently added based on the direct microscopic smear examination of corneal scrapings. The polymerase chain reaction test revealed an Aspergillus corneal infection, and after 7 days of antifungal treatment, significant clinical improvement was observed. This case revealed the necessity of considering atypical microorganisms, such as fungi, in the differential diagnosis of early post-PRK keratitis and highlights the role of direct smear and polymerase chain reaction tests in diagnosis, timely treatment initiation, and subsequently favorable clinical outcomes.

Antibiotics are essential chemotherapeutic agents that inhibit or destroy pathogenic microorganisms, and their development from ancient natural remedies to the discovery of penicillin in 1928 revolutionized modern medicine. Multiple major classes, including β-lactam, macrolide, tetracycline, quinolone, aminoglycoside, sulfonamide, glycopeptide, and oxazolidinone, remain central to treating bacterial infections, making accurate assessment of their quality crucial. This review summarizes key analytical methods used for determining antibiotic potency and quantifying drug levels in pharmaceutical and biological matrices. Spectroscopic techniques provide simple and cost-effective evaluation, while chromatographic methods such as RP-HPLC, UPLC, TLC and HPTLC offer high sensitivity and specificity. Because chemical assays measure potency but not biological activity, critical microbiological parameters minimum inhibitory and bactericidal concentration, mutation-prevention concentration, and related indicators provide deeper insight into bacterial susceptibility and resistance mechanisms. The review also addresses the growing challenge of antimicrobial resistance, driven by misuse and overuse of antibiotics, and outlines current methodologies such as MIC, MBC, and susceptibility testing for detecting resistance across bacterial strains. Overall, the article emphasizes the need for integrated analytical and microbiological approaches to ensure accurate antibiotic evaluation and support effective therapeutic outcomes.

Microbial enzymes play a central role in biomass valorization, and their discovery and characterization are increasingly driven by data-driven molecular approaches. However, for enzymes acting on water-insoluble polymeric substrates, enzymatic reactions are inherently confined to solid-liquid interfaces, and interfacial properties critically govern reaction efficiency and detectability. Here, we report an interfacial sensing strategy that enables ultrasensitive visual detection of microbial chitinolytic activity by exploiting a nanofibrous N-acetylchitosan hydrogel. The hydrogel consists of an entangled nanofiber network that provides a markedly increased surface area, thereby facilitating interfacial enzymatic reactions. When chitinolytic microorganisms are grown on the hydrogel surface, extracellular chitinases locally disrupt the nanofibrous network, producing nanoscale depressions that evolve into optically visible pits upon incubation. This approach enables visual detection of chitin degradation at the nanogram scale, with profilometric quantification down to ∼1 ng and naked-eye recognition at several tens of nanograms. By explicitly linking interfacial structure, surface morphology evolution, and enzymatic reaction kinetics, this work introduces a materials-based perspective that complements data-driven molecular approaches for the discovery and evaluation of microbial enzymes acting on insoluble polymeric substrates.

Sphingomonas is a dominant bacterial genus within the indigenous microbiota of plant-derived foods. S. paucimobilis, a food spoilage species and potential human pathogen, is frequently found on plant surfaces, in soils, and in freshwater environments, and raises food safety concerns. Conventional preservation strategies are often insufficient for the selective control of specific spoilage-associated microorganisms without disrupting the surrounding microbiota, underscoring the need for precision-targeted spoilage control approaches. Here, we present a peptide nucleic acid (PNA)-based antimicrobial strategy that employs antisense inhibition for selective suppression of S. paucimobilis. To enhance their cellular uptake, PNAs were conjugated with cell-penetrating peptides (CPPs), and several candidates were compared to identify the most effective delivery system. Among the tested CPPs, (KFF)3K-PNA conjugates exhibited the strongest antimicrobial activity. PNAs targeting the essential genes gyrA and rpoA showed potent sequence-specific activity, with (KFF)3K-gyrA PNAs demonstrating greater efficacy (≥0.5 μM) than (KFF)3K-rpoA PNAs (≥2 μM), whereas mismatch conjugates showed no detectable effect. Quantitative transcriptional analysis confirmed significant downregulation of target genes, particularly gyrA, after treatment. Application of (KFF)3K-gyrA PNA (2 μM) to lettuce significantly reduced discoloration and suppressed S. paucimobilis growth. These results highlight the high target specificity and antimicrobial efficacy of (KFF)3K-PNA conjugates and suggest their potential use as precision biocontrol tools for enhancing the microbial stability and shelf life of plant-derived foods.

Polyamide 4 (PA4) is a bio-based plastic with thermal stability, excellent mechanical properties, and good biodegradability in various environments. To understand the biodegradation of PA4 under natural environments, PA4-degrading microorganisms and enzymes have been investigated. Although our previous research identified the amino acid sequence and predicted the three-dimensional (3D) structure of a PA4-degrading enzyme from a marine environment (Nyl4A pa ), those of an enzyme from terrestrial environments have remained unidentified. In this study, we identified the PA4-degrading enzyme gene (nyl4Apx ) from the PA4-degrading soil bacterium Pseudoxanthomonas sp. TN-N1. In addition, nyl4Apx was successfully expressed in Escherichia coli BL21(DE3) and Brevibacillus choshinensis HPD31-SP3. The PA4-degrading activity of the enzyme secreted by recombinant B. choshinensis HPD31-SP3 reached 68.8 Δ655 nm/h/100 mL broth, representing a 2.4-fold increase compared with that produced by recombinant E. coli BL21(DE3). Based on a homology search using the amino acid sequence and predicted 3D structure of the enzyme, Nyl4A px was predicted to be composed of a substrate-binding domain, a middle domain, and a catalytic domain. Among these domains, the substrate-binding and catalytic domains of Nyl4A px are sequentially and structurally similar to those of Nyl4A pa . Furthermore, putative homologs of Nyl4A px and Nyl4A pa were found in marine-associated environmental metagenomes through BLAST searches. To our knowledge, this is the first report describing the structural properties of a PA4-degrading enzyme from a soil bacterium.