Applied and Environmental Microbiology最新文献

{"title":"<i>Clostridium butyricum</i>-derived extracellular vesicles alleviate ETEC K88-induced intestinal injury by regulating Wnt/β-catenin signaling and gut microbiota.","authors":"Huiru Chen, Ningtao Chen, Shuang Liang, Lingyan Ma, Nana Jing, Yingping Xiao, Ying Ren, Haiqin Wu","doi":"10.1128/aem.00424-26","DOIUrl":"10.1128/aem.00424-26","url":null,"abstract":"<p><p>Probiotic-derived extracellular vesicles (EVs) serve as crucial mediators that alleviate intestinal barrier dysfunction. As a well-established probiotic, <i>Clostridium butyricum</i> (<i>Cb</i>) has been shown to ameliorate ETEC K88-induced intestinal injury. Nevertheless, the potential role of <i>Cb</i>-derived EVs (CbEVs) in ETEC K88-induced intestinal injury has not yet been elucidated. This study showed that CbEVs effectively ameliorated ETEC K88-induced ileal injury, as evidenced by improved ileal morphology and reduced levels of proinflammatory cytokines, diamine oxidase, and malondialdehyde. Mechanistically, CbEVs activated Wnt/β-catenin signaling, thereby accelerating the renewal of intestinal epithelial cell lineages, which is pivotal for maintaining intestinal homeostasis. In parallel, they also reshaped the ileal microbiota by restoring microbial balance. Collectively, these findings demonstrated that CbEVs alleviated ETEC K88-induced ileal barrier dysfunction by coordinating the restoration of intestinal stem cell (ISC) activity and gut microbiota composition, providing a theoretical basis for developing CbEV-based strategies to prevent ETEC-induced intestinal barrier dysfunction in both humans and animals.IMPORTANCEETEC infection-induced intestinal injury continues to pose a significant threat to human and livestock health, while effective preventive strategies remain limited. This study demonstrates that extracellular vesicles derived from the probiotic <i>Clostridium butyricum</i> accelerate intestinal epithelial regeneration by activating Wnt/β-catenin signaling and restoring gut microbiota homeostasis, thereby conferring protection against ETEC-induced intestinal injury. These findings provide a solid scientific basis for the development of <i>Clostridium butyricum</i>-derived extracellular vesicles as a promising non-viable probiotic (postbiotic) strategy to prevent intestinal infections, thereby offering a safer and more stable alternative to live bacteria in functional foods and feed additives.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0042426"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599551/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148838766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Light-induced carotenogenesis enhances growth and high hydrostatic pressure tolerance in a deep-sea bacterium by reducing intracellular ROS.","authors":"Jin Lin, Xue-Gong Li, Wei-Jia Zhang, Hai-Rong Fang, Guan-Yuan Zhang, Long-Fei Wu","doi":"10.1128/aem.00658-26","DOIUrl":"10.1128/aem.00658-26","url":null,"abstract":"<p><p>Deep-sea hydrothermal vents emit geothermal light, yet its ecological role in shaping microbial adaptation remains largely unexplored. To investigate this, we designed a custom cultivation system that simultaneously applies high hydrostatic pressure (HHP) and light and used it to isolate 12 bacterial strains from active chimney fragments collected at the Kairei hydrothermal field. All 12 isolates exhibited enhanced growth under light exposure. Among them, strain SY138, identified as a novel <i>Microbacterium</i> species, was selected for mechanistic investigation. Our results demonstrate that light exposure directly induces carotenoid biosynthesis in SY138, which in turn reduces intracellular reactive oxygen species (ROS) levels. Inhibition of carotenoid synthesis using fosmidomycin abolished both the ROS-lowering effect and the light-dependent growth promotion, confirming that carotenoids are essential for this physiological response. Notably, while HHP severely inhibited growth by elevating intracellular ROS, light-induced carotenogenesis effectively counteracted this oxidative stress and alleviated HHP-induced growth inhibition. Collectively, these findings uncover a previously unrecognized adaptive strategy, wherein deep-sea hydrothermal vent bacteria exploit geothermal light as an environmental signal to activate carotenoid-based antioxidant defenses, thereby enhancing their survival under HHP conditions. This study highlights a previously underappreciated role of light in microbial stress tolerance in extreme deep-sea ecosystems.IMPORTANCEDeep-sea hydrothermal vents harbor thriving ecosystems under extreme pressure and perpetual darkness, yet they have long been considered to be driven solely by chemosynthesis. The discovery of geothermal light has raised fundamental questions regarding its ecological role. Using a specialized cultivation system that simulates <i>in situ</i> high pressure and illumination, we isolated multiple light-responsive bacterial strains from a deep-sea vent, substantially expanding the known diversity of such microorganisms. Using <i>Microbacterium</i> sp. SY138 as a model, we uncovered a previously unrecognized adaptive strategy: these bacteria exploit light not as an energy source but as an environmental cue to preemptively activate carotenoid-based antioxidant defenses. This light-induced mechanism counteracts oxidative stress imposed by high pressure, a ubiquitous deep-sea stressor. Our findings reveal an unexpected interplay between light and pressure in the deep-sea environment, suggesting that light sensing could represent a more widespread and ecologically significant adaptive trait than previously recognized.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0065826"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599544/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148838886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of genes promoting fitness of a plant-associated <i>Salmonella</i> Choleraesuis strain on alfalfa sprouts during cold storage.","authors":"Maximilian Beck, Laura Führer, Steffen Porwollik, Weiping Chu, Verena Hohenester, Irmak Sah, Michael McClelland, Claudia Guldimann, Irene Esteban-Cuesta","doi":"10.1128/aem.00604-26","DOIUrl":"10.1128/aem.00604-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Consumption of sprouted seeds, such as alfalfa sprouts, has increased in recent years due to their nutritional value and antioxidant content. However, these products have repeatedly been implicated in outbreaks of foodborne pathogens, including &lt;i&gt;Salmonella enterica&lt;/i&gt;. Although host-adapted &lt;i&gt;Salmonella&lt;/i&gt; serovars are less frequently associated with foodborne illness, infections caused by these serovars often result in invasive and severe outcomes, highlighting the importance of understanding their persistence in food production systems. Moreover, the variability among &lt;i&gt;Salmonella&lt;/i&gt; serovars requires characterization beyond the most prevalent types to support the development of precision food safety strategies effective across the diversity of serovars capable of contaminating fresh produce. Here, a plant-internalized &lt;i&gt;Salmonella&lt;/i&gt; Choleraesuis strain was used as a model to investigate persistence mechanisms on alfalfa sprouts. A bar-coded transposon mutant library comprising approximately 33,000 unique insertions was generated, along with a collection of individual insertion mutants. These resources were used to identify genetic determinants contributing to strain fitness on sprouts under abusive cold storage (8°C) simulating commercial shelf-life environments. Genome-wide analyses identified negative selection for mutants with insertions in &lt;i&gt;eda&lt;/i&gt;, &lt;i&gt;fabF&lt;/i&gt;, &lt;i&gt;lpp1_2&lt;/i&gt;, &lt;i&gt;pnp&lt;/i&gt;, &lt;i&gt;stpA&lt;/i&gt;, &lt;i&gt;SCHChr_03621&lt;/i&gt;, and two intergenic regions. Competition assays confirmed fitness defects associated with &lt;i&gt;eda&lt;/i&gt;, encoding a key enzyme of the Entner-Doudoroff pathway; &lt;i&gt;mnmG&lt;/i&gt;, encoding a tRNA modification enzyme involved in translational fidelity; and &lt;i&gt;fabF&lt;/i&gt;, involved in fatty acid biogenesis. These findings provide a genome-wide perspective on mechanisms enabling persistence on sprouts of a plant-associated, host-adapted &lt;i&gt;Salmonella&lt;/i&gt; strain during cold storage and inform risk assessment and intervention design within precision food safety frameworks.IMPORTANCEFood safety strategies are frequently based on knowledge derived from well-studied, epidemiologically relevant &lt;i&gt;Salmonella&lt;/i&gt; serovars, yet many less frequent types still pose a risk to consumers and may contaminate fresh produce. Different &lt;i&gt;Salmonella&lt;/i&gt; serovars may vary in the relative contribution of persistence mechanisms. Recognizing these differences is essential for improving precision food safety efforts, particularly for foods such as sprouts that are repeatedly linked to outbreaks. This study highlights that less-studied serovars can rely on both shared survival strategies and unique traits that might otherwise not be captured by current control approaches. By demonstrating that strain diversity influences persistence on fresh produce, this work supports the development of precision food safety strategies that address a broader spectrum of &lt;i&gt;Salmonella&lt;/i&gt;, thereby improving risk assessment and helping to better protect public ","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0060426"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599476/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148700566","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chemotypic diversity of the fungus <i>Epichloë brachyelytri</i> symbiotic with the wild forest grass <i>Brachyelytrum erectum</i>.","authors":"Padmaja Nagabhyru, Simona Florea, Huazhen Liu, Pradeep Kachroo, Patrick J Calie, Carolyn A Young, Christopher L Schardl","doi":"10.1128/aem.00754-26","DOIUrl":"10.1128/aem.00754-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Many cool-season grasses (Poaceae subfam. Poöideae) host seed-transmissible symbionts (endophytes) in the fungal genus &lt;i&gt;Epichloë&lt;/i&gt;, which can produce diverse alkaloids that protect against invertebrate and, in some cases, vertebrate herbivores. Rarely have population surveys been conducted to assess comprehensive alkaloid profiles and diversity of &lt;i&gt;Epichloë&lt;/i&gt; in wild grasses. In this study, we surveyed &lt;i&gt;Brachyelytrum erectum&lt;/i&gt;, which is a woodland grass in an early-diverging lineage of Poöideae, and commonly symbiotic with &lt;i&gt;Epichloë brachyelytri&lt;/i&gt;. Analytical methods based on high-resolution UHPLC-MS/MS were refined to provide rapid, comprehensive detection, and quantitation of &lt;i&gt;E. brachyelytri&lt;/i&gt; alkaloids, for six &lt;i&gt;B. erectum&lt;/i&gt; populations in Kentucky. Chemotypes were identified with two or three of the alkaloids &lt;i&gt;exo&lt;/i&gt;-1-acetamidopyrrolizidine (&lt;b&gt;1&lt;/b&gt;), chanoclavine (&lt;b&gt;2&lt;/b&gt;), and peramine (&lt;b&gt;3&lt;/b&gt;). Both &lt;b&gt;1&lt;/b&gt; and &lt;b&gt;2&lt;/b&gt; are known as intermediates in biosynthetic pathways to more complex alkaloids, and chemotypes having both &lt;b&gt;1&lt;/b&gt; and &lt;b&gt;2&lt;/b&gt; as pathway end-products are novel. Such chemotypes were also identified in other species, and phylogenetic analysis indicated their multiple origins by a combination of convergent evolution, possible horizontal gene transfer, and interspecific hybridization. Alkaloid levels were comparable between most populations and at most plant developmental stages. Levels of &lt;b&gt;3&lt;/b&gt; were compared between &lt;i&gt;E. brachyelytri&lt;/i&gt; variants with and without &lt;b&gt;1&lt;/b&gt;, providing evidence for competition between the pathways in young shoots, but not in older leaves or seeds. Furthermore, levels of &lt;b&gt;1&lt;/b&gt; and &lt;b&gt;2&lt;/b&gt; were moderate to high compared with their respective alkaloid classes in other grass-&lt;i&gt;Epichloë&lt;/i&gt; symbiotic systems. We conclude that production of the alkaloids likely represents an important metabolic investment by &lt;i&gt;E. brachyelytri&lt;/i&gt;.IMPORTANCEDefensive mutualisms, symbioses of hosts with organisms that defend them against parasites or predators, play important ecological roles. A widespread example is protection of cool-season grasses by symbiotic &lt;i&gt;Epichloë&lt;/i&gt; species, which are fungi that transmit in seeds and produce several kinds of anti-insect alkaloids. Profiles of alkaloids evolve due to shifting balances of their benefits and the costs of producing them. In this study, &lt;i&gt;Epichloë brachyelytri&lt;/i&gt; symbiotic with the wild forest grass &lt;i&gt;Brachyelytrum erectum&lt;/i&gt; produced three alkaloids, of which two have been rarely reported. Furthermore, variations in its alkaloid profiles and quantities of each alkaloid at different plant growth stages and tissues suggested that occasional loss of its most abundant alkaloid can be adaptive due to the metabolic load of producing it. Although rare, similar alkaloid profiles were identified in several other species in which they arose by a combination of convergent evolution, possible horizontal gene transfer,","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0075426"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599531/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148759276","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic traits, transcriptional responses, and metabolic activities determine functional divergence in mineral dissolution between <i>Priestia megaterium</i> PMA2-2 and <i>Priestia flexa</i> PMD1-1.","authors":"Wen Dong, Sheng-Zhi Zhang, Duo Yu, Qi Sheng, Lin-Yan He, Xia-Fang Sheng","doi":"10.1128/aem.01201-26","DOIUrl":"10.1128/aem.01201-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Priestia&lt;/i&gt; strains are gram-positive bacteria and globally distributed in mineral-rich environments. However, the functional divergence in mineral dissolution and its molecular drivers among &lt;i&gt;Priestia&lt;/i&gt; strains remains poorly understood. Here, we employ comparative phenotypic and multi-omics analyses to decipher the molecular mechanisms for divergent mineral dissolution phenotypes between the efficient mineral-dissolving &lt;i&gt;Priestia megaterium&lt;/i&gt; PMA2-2 and the inefficient mineral-dissolving &lt;i&gt;Priestia flexa&lt;/i&gt; PMD1-1. Compared to PMD1-1, PMA2-2 exhibited significantly enhanced biotite dissolution, medium acidification, polysaccharide production, and biofilm formation on the biotite surface. Genomic analysis revealed that PMA2-2 harbored more genes associated with organic acid metabolism, biofilm formation, and EPS biosynthesis than PMD1-1. Transcriptomic and metabolomic analyses linked PMA2-2's enhanced biotite-dissolution phenotype to the coordinated upregulation of genes located on both its chromosome and plasmids, and enhanced production of exometabolites involved in organic acids, proton efflux, biofilm formation, polysaccharide production, amino acid metabolism, cell wall components, and flagellar assembly. Furthermore, genes involved in environmental sensing (including two-component systems and quorum sensing) and nutrient transport systems (ABC transporters) were also upregulated in PMA2-2. Genomic conservation analysis of PMA2-2 revealed that the genes responsible for efficient mineral dissolution are widespread and phylogenetically conserved across the &lt;i&gt;Priestia&lt;/i&gt; genus. These core mineral dissolution-related genes were responsive to a range of silicate and oxide minerals (biotite, potassium-feldspar, olivine, and hematite). Our findings establish a genotype-to-phenotype map for mineral dissolution, providing new insights into the functional divergence in mineral dissolution between &lt;i&gt;Priestia&lt;/i&gt; strains PMA2-2 and PMD1-1, as well as the molecular mechanisms that facilitate these processes.IMPORTANCETo date, the molecular mechanisms underlying the functional divergence in mineral dissolution in gram-positive &lt;i&gt;Priestia&lt;/i&gt; strains are largely unexplored. This study characterizes the mechanisms involved in functional divergence in biotite dissolution between two closely related strains of &lt;i&gt;Priestia&lt;/i&gt;, one an efficient mineral-dissolving strain (PMA2-2) and the other an inefficient mineral-dissolving strain (PMD1-1). The coordinated upregulation of genes and exometabolites associated with organic acid and polysaccharide production, proton efflux, biofilm formation, cell wall components, as well as environmental sensing and nutrient transport systems may be responsible for PMA2-2's enhanced biotite dissolution phenotype. The multiple genes associated with efficient mineral dissolution by PMA2-2 are widespread and conserved among &lt;i&gt;Priestia&lt;/i&gt; strains. Furthermore, a range of silicate and oxide minerals induce","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0120126"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599522/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148700524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Research progress on nanomaterials in promoting phage function and application.","authors":"Yi Jin, Zhu Chen, Yiping Wang, Bingqing Xu, Mengye Ma, Jieting Pan, Xingyu Li, Qun Chen, Xibang Liu, Lijian Ding, Liming Jiang","doi":"10.1128/aem.01244-26","DOIUrl":"10.1128/aem.01244-26","url":null,"abstract":"<p><p>Phages, as viruses capable of specifically infecting and lysing bacteria, demonstrate significant therapeutic potential in addressing the escalating challenge of antibiotic resistance. However, their clinical application faces multiple limitations, including poor <i>in vivo</i> stability, rapid clearance by the immune system, narrow host range, induction of bacterial resistance, limited efficacy against biofilms, and intracellular bacteria, which severely constrain therapeutic outcomes. Traditional formulation approaches are insufficient to overcome these challenges, making it crucial to explore novel strategies that enhance phage functionality. In recent years, nanomaterials have emerged as innovative solutions through their unique physicochemical properties, offering new perspectives for optimizing phage therapy. This review systematically summarizes and evaluates the latest research progress on various nanomaterials in enhancing phage stability, detection sensitivity, targeted delivery efficiency, and antibacterial efficacy, aiming to provide theoretical references and practical insights for overcoming existing limitations in phage therapy and developing more effective and reliable phage-nanomaterial combination antimicrobial strategies.IMPORTANCEDespite increasing interest in phage-nanomaterial systems, the literature in this emerging field remains highly fragmented. Existing studies have explored various nanomaterials to address distinct limitations of phage therapy. These investigations have largely proceeded in parallel across different material platforms, including polymer nanomaterials, liposomes, metal nanomaterials, magnetic nanomaterials, and others, targeting functional outcomes such as stability, detection sensitivity, targeted delivery, and antibacterial efficacy, among others. A systematic synthesis that consolidates these scattered findings and provides a coherent framework across different enhancement strategies is currently lacking. This review contributes to addressing this gap by categorizing recent advances according to the enhanced phage function, summarizing key strategies and mechanisms reported to date, and offering an integrated reference to guide the rational design of phage-nanomaterial combination strategies.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0124426"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599530/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148700585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A pathway for complete mineralization of the ambergris constituent (-)-Ambrox in <i>Sphingomonas</i> sp.","authors":"Tina Haupt, Felix Flachsmann, Gerhard Brunner, Yumiko Weiner-Sekiya, Lucas Hortencio, Cyrille Jarin, Patrick Robe, Alessio Fonzo, Francis Voirol, Eric Eichhorn, Andreas Natsch","doi":"10.1128/aem.00876-26","DOIUrl":"10.1128/aem.00876-26","url":null,"abstract":"<p><p>(-)-Ambrox, the smelling principle in ambergris of sperm whales, is a saturated polycyclic terpenoid ether with multiple tertiary and quaternary centers. Despite these structural features, it is readily biodegradable and thus represents an interesting case to understand the degradation pathway of a complex, saturated polycyclic terpene. We isolated two <i>Sphingomonas</i> spp. strains from activated sewage sludge capable of rapidly mineralizing (-)-Ambrox. The structures of seven isolated metabolites were determined by 2D-NMR, and further metabolite structures were proposed based on their exact masses. The use of two ¹³C-labeled substrates allowed completing the hypothesis for the biodegradation pathway. Biodegradation starts by oxidation of the α-C(4)-methyl group, followed by hydroxylation of the adjacent C(5)-angular CH-group, which allows opening of ring A by a unique retro-aldol process. β-Oxidation leads to a C11 metabolite, which is further degraded to a C6 δ-lactone. This metabolic fate is conserved among strains. The structure-biodegradation relationship indicates that only natural (-)-Ambrox and related labdanoids were mineralized, but not enantiomers and epimers. For both strains, the complete genome was sequenced; for one strain, a fosmid library was prepared, and the gene for the first oxidation step was cloned. The activity for the following step was located on a fosmid in a non-adjacent genomic region, indicating that this pathway is dispersed over the genome. This detailed study provides unique insights into the complex biodegradation pathway of the poorly studied class of saturated polycyclic terpenoids.</p><p><strong>Importance: </strong>For complex, polycyclic natural substrates such as sesquiterpenes and diterpenes, there is little knowledge on biodegradation pathways, except for the elucidated steroid degradation pathways. This study presents key steps in the biodegradation pathway for (-)-Ambrox, a natural constituent of the sperm whale secretion ambergris, which was found to be readily biodegradable, despite a polycyclic ring system with multiple tertiary and quaternary carbon centers. This may be one of the first detailed studies on the biodegradation pathway of a polycyclic natural sesquiterpenoid.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0087626"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599519/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148672960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The iron paradox and particle size sensing: transcriptomic response of <i>Enterococcus faecalis</i> to non-nutritive minerals.","authors":"Luhan Li, Jianchao Zhang, Sumin Qu, Zhiying Zhou, Beibei Wang, Haitao Wu, Zilin Guo, Lin Shi, Bohao Yin, Xiangyu Zhu, Yuebo Wang, H Henry Teng","doi":"10.1128/aem.00954-26","DOIUrl":"10.1128/aem.00954-26","url":null,"abstract":"<p><p>Minerals are known to influence microbial metabolism as nutrient sources or redox partners, yet whether chemically inert, non-nutritive minerals can regulate microbial physiology, and through what mechanisms, remains poorly understood. Here, we used transcriptomics to investigate the response of <i>Enterococcus faecalis</i> to Al₂O₃ and SiO₂ particles spanning nanoscale to millimeter scale. Mineral exposure triggered extensive transcriptional reprogramming across hundreds of differentially expressed genes. Notably, a massive upregulation of iron acquisition genes (log₂FC range from 3.8 to 4.2) concurrent with oxidative stress defenses (catalase, thiol peroxidase, and NADH oxidase) is suggestive of an \"iron paradox,\" which is potentially attributable to mineral-mediated nutrient sequestration and steric hindrance of membrane transporters alongside interfacial reactive oxygen species generation. To adapt, <i>E. faecalis</i> orchestrated a coordinated metabolic shift, repressing serine catabolism (log₂FC = -2.7) while investing nitrogen into glutathione biosynthesis (cystathionine synthase genes, log₂FC = 3.7). Correlation analysis identified an o<i>mpR</i>-s<i>igV</i> axis through which <i>E. faecalis</i> discriminates mineral particle size, with nanoscale particles eliciting stronger transcriptional responses than their larger counterparts. This stress response additionally upregulated virulence-associated genes and antibiotic resistance genes without direct antimicrobial selection pressure. These findings suggest that non-nutritive minerals shape microbial physiology through physical and surface-chemical cues independent of their nutritional value, highlighting the need for further exploration of the non-nutritional functions of minerals in microbial ecology.IMPORTANCEEven in the absence of utilizable nutrients, non-nutritive minerals such as Al₂O₃ and SiO₂ can profoundly influence the transcriptional responses of <i>Enterococcus faecalis</i>. Using transcriptomic sequencing, we show that these inert minerals regulate microbial transcription, enhancing iron acquisition, oxidative stress repair, pathogenicity, and antibiotic resistance. Mineral-mediated transcriptional control is driven primarily by physical contact, surface chemistry, and particle size sensing, rather than conventional metabolic interactions. These findings identify inert minerals as signaling molecules that actively modulate microbial transcription, playing a proactive role in microbial evolution and environmental adaptation. This study redefines inert minerals as active carriers of transcriptional regulation, filling a critical gap in geomicrobiology and providing new insights into microbial environmental responses, biogeochemical cycling, and the mechanisms underlying microbial functional evolution and maintenance.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0095426"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599488/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148787592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Seasonal dynamics of microbial communities and potential human pathogens in <i>Crassostrea hongkongensis</i> and ambient water in southern China.","authors":"Xiaoxia Liu, Xianyu Wang, Haipeng Zhu, Wenqi Chen, Xin Hong, Yi Wan, Jiaomei Huang, Chunsheng Liu","doi":"10.1128/aem.01056-26","DOIUrl":"10.1128/aem.01056-26","url":null,"abstract":"<p><p>Oysters are a popular raw seafood worldwide, yet their contamination with human pathogens poses substantial public health risks. However, the seasonal dynamics of host-associated microbiota and the environmental drivers of pathogen accumulation in <i>Crassostrea hongkongensis</i> remain poorly understood. Here, we conducted 16S rRNA amplicon sequencing to profile the gill and intestinal microbiota of <i>C. hongkongensis</i>, sampled quarterly over a 1-year period in Beihai and Zhanjiang, southern China. A pronounced divergence in oyster-associated bacterial communities was observed between the two locations in December. Key bacterial families, such as Lachnospiraceae and Muribaculaceae, showed significant temporal fluctuations in abundance, suggesting their potential role in maintaining bacterial community stability within oysters. These microbial shifts were significantly correlated with environmental parameters such as chlorophyll <i>a</i> and pH. In parallel, we used plate counting to quantify five foodborne pathogens and total viable counts. Vibrios were more frequently detected in oyster tissues than in ambient seawater. Pathogen-associated amplicon sequence variants exhibited a strong response to variations in pH and chlorophyll <i>a</i>, whereas the abundance of culturable <i>Vibrio vulnificus</i> was significantly negatively correlated with temperature and nitrate. The integration of high-throughput sequencing and culture-based methods provides comprehensive insights into the dynamics of pathogenic bacteria within oysters under natural mariculture settings. This study offers valuable ecological insights into the interactions within the oyster-associated microbial ecosystem, contributing to a deeper understanding of its dynamics and implications for public health.</p><p><strong>Importance: </strong>Mariculture of <i>Crassostrea hongkongensis</i> serves as a critical interface between coastal ecology and public health, yet seasonal dynamics of its microbiome and core stabilizing taxa remain poorly understood in subtropical aquaculture. This study identified Acetobacteraceae, Lachnospiraceae, Prevotellaceae, and Muribaculaceae as key families associated with seasonal microbiome stability in <i>C. hongkongensis</i>, highlighting their potential contribution to community resilience. It further revealed that <i>Vibrio</i> species detection was negatively correlated with temperature. These findings advance our understanding of interactions between the oyster microbiome and the environment, and provide a theoretical basis for improving oyster health management and promoting sustainable aquaculture practices.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0105626"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148878738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Trichoderma reesei</i> Nsd3 transcription factor: pleiotropic roles in development, stress response, secondary metabolism, and cellulase production.","authors":"David Batista Maués, Lucas Matheus Soares Pereira, Andrei Stecca Steindorff, Amanda Cristina Campos Antoniêto, Rafael Silva-Rocha, Marcelo Damário Gomes, Zachary A Lewis, Roberto N Silva","doi":"10.1128/aem.00865-26","DOIUrl":"10.1128/aem.00865-26","url":null,"abstract":"<p><p><i>Trichoderma reesei</i> is known for its ability to secrete high amounts of cellulases, enzymes of fundamental importance in generating products from lignocellulosic biomass. Diverse signaling pathways and transcription factors (TFs) control the cellulolytic repertoire in <i>T. reesei</i> to ensure correct adaptation to the environment. Here, we analyzed RNA-Seq data and identified a new potential regulator of cellulase production in <i>T. reesei</i>: a novel TF named Nsd3, a homolog of NsdC from <i>Aspergilli</i>. Deletion of <i>nsd3</i> reduced vegetative growth and conidiation on solid medium. Phenotypic characterization of the Δ<i>nsd3</i> strain showed that it is more sensitive to osmotic stress, but more resistant to cell wall and oxidative stresses. Our results showed that Nsd3 is a repressor of cellulase expression by directly regulating key genes in the cellulolytic pathway, an unreported role for this TF in fungi. Loss of <i>nsd3</i> leads to a faster and more robust induction of cellulolytic genes, and higher cellulase and hemicellulase activities. Transcriptional profiling by RNA-Seq, chromatin accessibility profiling by ATAC-Seq, and protein-DNA interaction assays showed that sugar transporters are important targets of Nsd3 during cellulase expression regulation. Combined with microscopy and gene expression analyses, the ATAC-Seq data also highlighted Nsd3 as a central regulator of cell wall remodeling and organization. Furthermore, the transcriptomics also showed that Nsd3 regulates genes involved in secondary metabolism. These results showed that Nsd3 regulates several physiological processes and provide novel insights into the regulatory system of cellulases in <i>T. reesei</i> that can be used in the design of high-performance strains for biorefinery.IMPORTANCE<i>Trichoderma reesei</i> is a key player in the production of hydrolytic enzymes for the degradation of lignocellulose biomass, and transcription factors are important targets for genetic engineering to construct cellulase-hyperproducing strains. Here, we identified the transcription factor Nsd3 and characterized its role as a regulator of cellulase production in <i>T. reesei</i>. We applied two powerful genomics methods (transcriptome sequencing and chromatin accessibility sequencing) to unravel the global role of Nsd3 and its regulatory mechanism. Nsd3 participates in various biological processes in <i>T. reesei</i>, including cell wall remodeling, calcium metabolism, and secondary metabolism, in addition to regulating the expression of sugar transporters. Protein-DNA interaction assays demonstrate that Nsd3 acts through important genes to regulate cellulase expression, including ace4, crt1, stp1, and cel1b. Our study provides mechanistic insights about how Nsd3 regulates diverse physiological processes in <i>T. reesei</i>. This work also applied ATAC-Seq for the first time to study chromatin accessibility in <i>T. reesei</i>.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0086526"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599534/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148886196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}