Applied and Environmental Microbiology最新文献

{"title":"Cystathionine β-synthase TtCbs1 from <i>Tetrahymena thermophila</i> catalyzes the synthesis of CdS quantum dots for methyl orange decolorization.","authors":"Wenliang Lei, Juan Liu, Jing Xu, Wei Wang","doi":"10.1128/aem.01255-25","DOIUrl":"https://doi.org/10.1128/aem.01255-25","url":null,"abstract":"<p><p>Cystathionine β-synthase (CBS) is a pivotal enzyme in the transsulfuration metabolic pathway, catalyzing the synthesis of H₂S and cystathionine. These metabolites mediate stress responses and maintain cellular redox homeostasis. In <i>Tetrahymena thermophila</i>, <i>TtCBS1</i> expression was upregulated under cadmium stress, with cysteine further enhancing its transcription. The recombinant His-TtCbs1 protein was expressed in <i>Escherichia coli</i> and purified by affinity chromatography. The His-TtCbs1 catalyzed the synthesis of monodisperse cadmium sulfide quantum dots (CdS QDs) in cysteine and Cd²⁺ solutions. The QDs exhibited an average diameter of 3.51 nm, with size increasing over reaction time. Fourier-transform infrared spectroscopy revealed characteristic amide I (1,640 cm⁻¹) and amide II (1,520 cm⁻¹) peaks, confirming interactions of CdS and the protein. Cysteine and glutathione stabilized the CdS QDs in the solution. Under UV light irradiation, the CdS QDs decolorized 91% of methyl orange. This study shows that CBS from protists mitigates cadmium toxicity by synthesizing CdS QDs. The biosynthesized CdS QDs also function as effective biocatalysts for the decolorization of organic dyes.</p><p><strong>Importance: </strong>The significant upregulation of <i>TtCBS</i>1 in <i>Tetrahymena thermophila</i> under cadmium stress indicates that this enzyme is a key player in the organism's defense mechanism against cadmium toxicity. Cadmium sulfide (CdS) nanoparticles were synthesized using the TtCbs1 single-enzyme system <i>in vitro</i>. Cysteine and glutathione play a critical role in controlling the growth of biosynthetic CdS particle size. Understanding the precise mechanisms by which cysteine and glutathione control particle size could lead to the development of more precise and efficient biomineralization processes. The synthesized CdS quantum dots exhibited significant photocatalytic activity. This work highlights the potential of cystathionine β-synthase from protists in metal detoxification and environmental remediation.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0125525"},"PeriodicalIF":3.7,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145129942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel homoarginine-containing cyclic peptide pioamide with selective antipseudomonal activity isolated from the nematode symbiont <i>Photorhabdus khanii</i>.","authors":"Yu Imai, Sangkeun Son, Miho Sasaki, Libang Liang, Michael F Gates, Meghan Ghiglieri, Takeshi Shimosato, Chandrashekhar Honrao, Xiaoyu Ma, Jason J Guo, Kim Lewis","doi":"10.1128/aem.01123-25","DOIUrl":"https://doi.org/10.1128/aem.01123-25","url":null,"abstract":"<p><p>Gram-negative bacteria harbor an outer membrane that physically protects them from the penetration of antibiotics into the cells. This barrier makes it challenging to develop antibiotics that effectively kill Gram-negative pathogens. The entomopathogenic bacterium <i>Photorhabdus</i> species produces various bioactive molecules and is receiving attention as an attractive source of novel antibiotics. We identified a novel antipseudomonal antibiotic, pioamide, from the culture supernatant of <i>Photorhabdus khanii</i> HGB1456, a strain that produces darobactin, which selectively kills Gram-negative bacteria. Pioamide, a pentapeptide antibiotic with a molecular weight of 704, exhibits selective activity against <i>Pseudomonas aeruginosa</i> but does not exhibit any activity against other bacteria or human cell lines. Whole-genome sequencing of spontaneous pioamide-resistant mutants of <i>P. aeruginosa</i> revealed mutations in <i>pmrB</i>, which encodes a two-component regulatory system response regulator that modifies the lipopolysaccharide composition in Gram-negative bacteria, conferring pioamide resistance to <i>P. aeruginosa</i>. Furthermore, the susceptibility of both <i>P. aeruginosa</i> PAO1 and the mutant strain PΔ6-Pore, which overexpresses porins and lacks six efflux pumps, to pioamide was identical, indicating that porins and the efflux pump exert no significant effect on the activity of pioamide. These results suggest that pioamide either targets the cell surface of <i>P. aeruginosa</i> or is incorporated via a species-specific uptake mechanism. Our findings highlight the potential of <i>Photorhabdus</i> strains as an attractive source for the discovery of antibiotics active against Gram-negative pathogens.</p><p><strong>Importance: </strong>The rise of multidrug-resistant Gram-negative bacteria is a growing threat to global public health. Narrow-spectrum antibiotics minimize disruption of the host microbiota and reduce the risk of resistance development in off-target bacteria. In the field of antibacterial discovery, developing compounds effective against <i>Pseudomonas aeruginosa</i> remains particularly challenging. Although <i>Photorhabdus</i> species are known to produce various antibiotics, their potential remains largely underexplored. In this study, we applied differential screening to a highly concentrated culture extract of <i>Photorhabdus khanii</i> HGB1456 and discovered pioamide, a novel cyclic peptide with unusual selective activity against <i>P. aeruginosa</i>. Mutations in pmrB confer pioamide resistance to <i>P. aeruginosa</i>. However, the mechanism of action is distinct from that of colistin, which also involves resistance conferred by <i>pmrB</i> mutations. These findings underscore the untapped potential of <i>Photorhabdus</i> species as an attractive source of species-specific antibiotics and highlight the utility of differential screening for discovering compounds with targeted antibacterial activity.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0112325"},"PeriodicalIF":3.7,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145129958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fecal microbiota transplantation alleviated heat-induced colonic tissue damage, epithelial apoptosis, and oxidative stress.","authors":"Xiyu Liu, Chuchu Liu, Xiaoli Qian, Shiqing Zhang, Zhenghong Yao, Yanxi Chai, Qianhan Shi, Wenwen Yang, Qingxian Wang, Lina Zhang, Xiang Zeng, Cuiqing Liu, Yue Wu, Qinghua Sun","doi":"10.1128/aem.00976-25","DOIUrl":"https://doi.org/10.1128/aem.00976-25","url":null,"abstract":"<p><p>Exposure to high ambient temperatures can cause significant damage to the gastrointestinal tract; however, the therapeutic potential of fecal microbiota transplantation (FMT) in this context remains largely unexplored. We investigated whether FMT could alleviate heat-induced colonic injury in C57BL/6J mice. Mice were randomly divided into four groups: normal control (22°C only), normal-FMT (NF, 22 °C+ FMT), heat exposure (HE, 39°C only), and HE-FMT (HF, 39°C + FMT). The HE and HF groups were exposed to 39°C for 2 hours daily over 15 consecutive days. FMT (100 µL/day) was administered by oral gavage to the NF and HF groups for 15 days, starting after the first HE. Our results showed that FMT significantly modulated gut microbiota composition, increasing the relative abundance of <i>Alistipes</i>, <i>Citrobacter</i>, <i>Parasutterella</i>, <i>Bifidobacterium, Lachnospiraceae_UCG-001</i>, <i>Raoultella</i>, <i>Woeseia</i>, <i>Prevotellaceae_UCG-001,</i> and <i>Christensenellaceae,</i> while decreasing <i>Clostridium_sensu_stricto_1</i>, <i>Eubacterium_xylanophilum_group</i>, <i>Clostridioides</i>, <i>Bilophila</i>, <i>GCA-900066575,</i> and <i>Peptococcus</i>. Notably, FMT markedly restored epithelial integrity and enhanced mucus production, as shown by hematoxylin-eosin and periodic acid-Schiff staining. Moreover, FMT attenuated heat-induced epithelial cell apoptosis, evidenced by reduced apoptotic cells and downregulation of mitochondrial apoptotic markers, including Bax, Bak, cleaved Caspase-3, cleaved Caspase-9, and the phospho-P53/P53 ratio. In addition, FMT mitigated oxidative stress induced by HE, indicated by decreased 3-nitrotyrosine levels and normalization of antioxidant-related proteins, such as <i>Nrf2</i>, <i>Sod1</i>, <i>Cat</i>, and <i>Gpx4</i>. Collectively, these findings demonstrate that FMT alleviates heat-induced colonic injury by restoring mucosal barrier integrity, inhibiting apoptosis, and reducing oxidative stress, highlighting its potential as a promising therapeutic strategy for heat-related gastrointestinal disorders.</p><p><strong>Importance: </strong>This study is the first to demonstrate the protective role of fecal microbiota transplantation (FMT) against heat-induced colonic injury in a mouse model. We show that FMT mitigates colonic damage by restoring gut microbiota balance, preserving mucosal barrier integrity, inhibiting epithelial cell apoptosis, and reducing oxidative stress. These findings underscore the essential role of the gut microbiota in maintaining intestinal homeostasis under heat stress and highlight the therapeutic potential of microbiota-targeted strategies, such as FMT, in preventing or treating heat-related intestinal injury.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0097625"},"PeriodicalIF":3.7,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145129879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microeukaryotic habitat specialists exhibit stronger determinism and biodiversity-nutrient cycling relationship than generalists in a subtropical river.","authors":"Lu Li, Huihuang Chen, Weidong Chen, Jun Yang","doi":"10.1128/aem.01364-25","DOIUrl":"https://doi.org/10.1128/aem.01364-25","url":null,"abstract":"<p><p>Microeukaryotic generalists and specialists exhibit varying levels of environmental sensitivity, which contribute differently to community dynamics and are important for aquatic ecosystem functioning. However, the community assembly, co-occurrence network, and impacts of microeukaryotic generalists and specialists' diversity on ecosystem functions remain poorly understood in riverine ecosystems. Here, we investigated the microeukaryotic generalists and specialists along a subtropical river. Our results showed that specialists were more controlled by deterministic processes compared with generalists. Co-occurrence network analysis revealed that microeukaryotic specialists were more interconnected and contributed more to maintaining network stability. More importantly, microeukaryotic specialists also played disproportionately important roles in maintaining nutrient cycling. Overall, our results elucidated the different ecological responses of microeukaryotic generalists and specialists and emphasized the important roles of microeukaryotic specialists in maintaining ecosystem stability and functions, thus providing a new perspective to better understand the significance of specialists in riverine ecosystems.</p><p><strong>Importance: </strong>The underlying community assembly mechanisms and biodiversity-nutrient cycling (BNC) relationships of microeukaryotic generalists and specialists remain unknown in riverine ecosystems. Here, we found that microeukaryotic habitat specialists, compared with generalists, exhibited stronger deterministic processes and contributed more to maintain co-occurrence network stability, suggesting that specialist communities were more vulnerable to environmental disturbances than generalists. Furthermore, we found specialists exhibited stronger BNC relationships, indicating specialists with narrow distribution seem to have greater capacity to support ecosystem functions. Overall, this study expands the current understanding of assembly mechanisms and BNC relationships in microeukaryotic generalists and specialists.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0136425"},"PeriodicalIF":3.7,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145124033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Erratum for Kaur et al., \"Pseudogenes and host specialization in the emergent bacterial plant pathogen <i>Xylella fastidiosa</i>\".","authors":"Navdeep Kaur, Neha Potnis, Leonardo De La Fuente","doi":"10.1128/aem.01781-25","DOIUrl":"https://doi.org/10.1128/aem.01781-25","url":null,"abstract":"","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0178125"},"PeriodicalIF":3.7,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145123971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Contribution of UbrA, a ubiquitin ligase essential for Arg/N-degron pathway, to peptidase gene expression in <i>Aspergillus oryzae</i>.","authors":"Waka Muromachi, Mao Ohba, Yasuaki Kawarasaki, Youhei Yamagata, Mizuki Tanaka","doi":"10.1128/aem.00813-25","DOIUrl":"https://doi.org/10.1128/aem.00813-25","url":null,"abstract":"<p><p>The degradation of intracellular proteins by N-degron pathways depends on their N-terminal amino acids. In budding yeast, the Arg/N-degron pathway controls the expression of dipeptide/tripeptide transporter gene by degrading a transcriptional repressor. However, there is no detailed information on the N-degron pathway in filamentous fungi, and its role in regulating microbial nitrogen metabolism is unclear. Here, we demonstrated that the E3 ubiquitin ligase, UbrA, which is required for the Arg/N-degron pathway, regulates peptidase gene expression in the filamentous fungus <i>Aspergillus oryzae</i>. Using ubiquitin-fused green fluorescent protein as a reporter, we showed that the Arg/N-degron pathway in <i>A. oryzae</i> is similar to that in budding yeast. Disruption of <i>ubrA</i> significantly reduced the activities of acidic endopeptidase and carboxypeptidase in submerged culture using soy protein as the nitrogen source. In addition, <i>ubrA</i> disruption dramatically reduced the mRNA expression of the major endopeptidase and carboxypeptidase genes but increased alkaline peptidase production. Moreover, <i>ubrA</i> disruption reduced the expression levels of dipeptidyl-peptidase and tripeptidyl-peptidase genes and dipeptide/tripeptide transporter genes. This regulation was independent of PrtR, the transcription factor regulating a broad range of extracellular peptidase genes. Our data showed that UbrA is involved in the expression of various peptidase genes in concert with dipeptide/tripeptide transporter genes.</p><p><strong>Importance: </strong>Peptidases produced by <i>Aspergillus oryzae</i> are important in the production of Japanese fermented foods and are used as industrial enzymes for various food-processing and pharmaceutical applications. The expression of dipeptide/tripeptide transporter gene in budding yeast is controlled by a positive feedback mechanism through the dipeptide-mediated activation of the E3 ubiquitin ligase, Ubr1, which is essential for the Arg/N-degron pathway, which determines the lifetime of intracellular proteins. In this study, we demonstrated that <i>A. oryzae</i> UbrA (an ortholog of yeast Ubr1) regulates peptidase gene expression in addition to dipeptide/tripeptide transporter genes. Disruption of <i>ubrA</i> decreases the expression of major acidic peptidase genes and increases the expression of alkaline peptidase gene. In addition, the expression levels of dipeptide/tripeptidyl peptidase genes and dipeptide/tripeptide transporter genes were reduced by <i>ubrA</i> disruption. These results suggest that UbrA regulates the expression of various peptidase genes to facilitate positive feedback of dipeptide/tripeptide transporter genes.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0081325"},"PeriodicalIF":3.7,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145124018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Community and functional stability in a working bioreactor degrading 1,4-dioxane at the Lowry Landfill Superfund Site.","authors":"Jessica L Romero, Jack H Ratliff, Christopher J Carlson, Daniel R Griffiths, Christopher S Miller, Annika C Mosier, Timberley M Roane","doi":"10.1128/aem.00574-25","DOIUrl":"https://doi.org/10.1128/aem.00574-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;1,4-dioxane (dioxane) is an emerging contaminant that poses risks to human and environmental health. Bacterial dioxane degradation is increasingly being studied as a method to remove dioxane from contaminated water. However, there is a lack of studies on microbial community structures and functions within efficient, large-scale, biodegradation-based remediation technologies. The Lowry Landfill Superfund Site (Colorado, USA) uses an on-site, pump-and-treat facility to remove dioxane from contaminated groundwater by biodegradation. Here, 16S rRNA gene and shotgun metagenomic sequencing were used to describe microbial community composition, soluble di-iron monooxygenase (SDIMO) alpha hydroxylases, and potential for dioxane degradation and horizontal gene transfer in bioreactor support media from the facility. Support media showed diverse microbial communities dominated by Nitrospiraceae, Nitrososphaeraceae, and Nitrosomonadaceae. &lt;i&gt;Pseudonocardia&lt;/i&gt; was also detected, suggesting a potential presence of known dioxane-degraders. Candidate SDIMOs belonged mostly to Group V, followed by Groups IV, II, and I (based on read depth). The most abundant Group V clade contained 38 proteins that were phylogenetically related to DxmA-like proteins, including that of &lt;i&gt;Pseudonocardia dioxanivorans&lt;/i&gt; CB1190 (a known dioxane degrader). Seventeen Lowry contigs containing DxmA-like proteins contained protein-coding genes potentially involved in chemical degradation, transcriptional regulation, and chemical transport. Interestingly, these contigs also included evidence of potential horizontal gene transfer, including toxin-antitoxin proteins, phage integrase proteins, putative transposases, and putative miniature inverted-repeat transposable elements. These findings improve our understanding of potential dioxane biodegradation mechanisms in a functioning remediation system. Further studies are needed to definitively confirm microbial activity and enzymatic activity toward dioxane removal in this site.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;As an environmental contaminant, 1,4-dioxane poses risks for water quality and human health. Used as a solvent and chemical stabilizer in a variety of manufacturing and industrial applications, microbiological methods of detoxification and mitigation are of interest. The degradation of 1,4-dioxane by the bacterium &lt;i&gt;Pseudonocardia&lt;/i&gt; spp. is the best understood example; however, these studies are largely based on single isolate, bench-scale, or &lt;i&gt;in silico&lt;/i&gt; experiments. Consequently, a knowledge gap exists on bacterial degradation of 1,4-dioxane at environmentally relevant concentrations using functioning remediation technologies at scale. This study addresses this gap directly by describing microbial taxa, enzymes, and potential horizontal gene transfer mechanisms associated with an active treatment plant located on a 1,4-dioxane-impacted U.S. Environmental Protection Agency (EPA) superfund site. As 1,4-dioxane contami","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0057425"},"PeriodicalIF":3.7,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145124021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of isolates used in bacterial-based strategies for accelerated carbonation of lime mortars.","authors":"Franco Grosso Giordano, Quinten Mariën, Nele De Belie, Carlos Rodriguez-Navarro, Nico Boon","doi":"10.1128/aem.00683-25","DOIUrl":"https://doi.org/10.1128/aem.00683-25","url":null,"abstract":"<p><p>Portland cement largely replaced hydraulic lime over the past century because of its rapid hardening. Achieving earlier hardening in lime through faster carbonation is thus essential to help overcome one of lime's limiting qualities. Here, we isolated two alkaliphilic bacteria, <i>Shouchella clausii</i> and <i>Shouchella patagoniensis,</i> from a lime mortar wall. <i>S. clausii</i> was then further grown in high pH (>11) by adaptive laboratory evolution to acclimate a third isolate. Bacterial suspensions of all three isolates were followed for 14 days in serum bottles at pH 11, and gas composition of the headspace, intact/damaged cell populations, and pH were measured. In parallel, lime mortar samples were incubated in a closed environment with bacterial suspension of the isolates and analyzed with thermogravimetric analysis after 7 and 14 days to quantify carbonation. <i>S. patagoniensis</i> produced more CO₂, close to the estimated maximum CO₂ uptake rate of lime, and carbonated the lime mortars to a larger extent than the other isolates. Finally, the bacterial suspensions were directly mixed with lime. A linear and homogeneous carbonation of the paste samples was measured compared to water-based pastes, and the development of Liesegang patterns was observed upon phenolphthalein spreading. All this indicated that the organic addition altered the carbonation dynamics of the material, although bacteria did not accelerate carbonation relative to media alone and inhibited it relative to water-based paste. Still, a relationship between bacterial activity, CO₂ emission, and carbonation rate was established, but practical aspects of bacterial delivery into lime must be addressed.IMPORTANCEPortland cement is the dominant binder used in most construction today, but until last century, lime was the ubiquitous construction material. The increase in use of cement has sprung from its higher strength and faster hardening; yet, lime still remains a relevant material, particularly in masonry structures and the built heritage. As such, novel lime materials are necessary to tackle some of the current limitations of lime, such as earlier hardening, which would not only make lime easier to work with but would also limit failure due to environmental conditions. As existing strategies to speed up lime hardening have had limited uptake due to their reliance on expensive and often toxic chemicals, the need for novel solutions is in place. We show that bacterial-based strategies could be a viable option to go beyond the limitations of current strategies, but limitations are in place.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0068325"},"PeriodicalIF":3.7,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145123992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA adenine methylation influences gene expression and biofilm formation in <i>Streptococcus mutans</i>.","authors":"Haowei Zhao, Delphine Dufour, Niki Ghobaei, Laurent Bozec, Céline M Lévesque","doi":"10.1128/aem.01094-25","DOIUrl":"https://doi.org/10.1128/aem.01094-25","url":null,"abstract":"<p><p><i>Streptococcus mutans</i>, a key oral pathogen, utilizes quorum sensing to regulate biofilm formation-a major virulence factor in the development of dental caries (tooth decay). Our recent research uncovered a complex interplay between the CSP-ComDE quorum sensing pathway and the Type II DpnII restriction-modification (R-M) system in <i>S. mutans</i>. The DpnII R-M system methylates adenine at 5'-GATC-3' sites and cleaves unmethylated DNA, significantly influencing foreign DNA acquisition and gene expression. In this study, we investigated the impact of a ΔRM mutant, which lacks adenine methylation, on biofilm formation. The ΔRM mutant formed fragile biofilms that easily detach from surfaces, with significantly reduced exopolysaccharide content and increased extracellular DNA, which appears to be associated with membrane vesicle production rather than cell lysis. RNA-seq analysis revealed only few differentially expressed genes directly involved in biofilm formation, such as <i>gtfC</i>, suggesting that the biofilm defect may result from indirect effects or alternative regulatory mechanisms. Notably, the downregulation of mutanobactin-related genes and upregulation of genes involved in <i>de novo</i> purine nucleotide biosynthesis point to novel pathways influenced by DNA methylation. These findings contribute to a deeper understanding of the multifactorial nature of biofilm formation and the role of epigenetic modifications in microbial behavior.</p><p><strong>Importance: </strong>This study highlights the critical role of DNA methylation in regulating biofilm formation and virulence in <i>Streptococcus mutans</i>. By examining the interplay between adenine methylation, extracellular DNA (eDNA), membrane vesicles (MVs), and glucan production, we provide new insights into the complex biology of biofilm development. Our findings challenge traditional views by emphasizing the importance of MVs and eDNA in maintaining biofilm integrity. Understanding these epigenetics modifications not only advances our knowledge of microbial regulation but also identifies novel targets for antimicrobial therapy. Since adenine methylation is rare or absent in mammalian cells, targeting this modification presents a promising strategy to disrupt biofilm formation and combat bacterial infections. The insights gained from this study may inform the development of innovative approaches to manage biofilm-associated infections and improve oral health outcomes.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0109425"},"PeriodicalIF":3.7,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145124028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacterial generalists and fungal specialists play important roles in maintaining community stability and regulating microbial diversity of the algae-associated microbiome throughout the growth cycle of <i>Alexandrium pacificum</i>.","authors":"Yanlu Qiao, Lingzhe Wang, Shuo Wang, Shijie Li, Feng Wang, Bo Wang, Siheng Lin, Yuyang Liu","doi":"10.1128/aem.01359-25","DOIUrl":"https://doi.org/10.1128/aem.01359-25","url":null,"abstract":"<p><p>The algae-associated microbiome represents a consortium that has been chronically domesticated by specific algae, maintaining a close relationship with the host population. Although the microbes associated with dinoflagellates have garnered significant attention in recent years, the interactions and contributions of microbial generalists and specialists through the growth cycle of a bloom-forming dinoflagellate remain largely unexplored. Herein, the ecological and evolutionary characteristics of free-living generalists and specialists within bacterial and fungal communities were investigated during the growth process of <i>Alexandrium pacificum</i> cultured in the laboratory for years without antibiotic treatment. From an ecological perspective, bacterial generalists and fungal specialists dominated the community, indicating different microbial niche patterns between the bacterial and fungal consortia. Furthermore, microbial specialists were more susceptible to disturbance from algal proliferation, as evidenced by greater community dissimilarity and determinacy-dominated assembly processes. Compared with their counterparts, the molecular networks of bacterial generalists and fungal specialists were more complex and robust, suggesting that they significantly contributed to resistance to environmental stress and functional maintenance. Evolutionarily speaking, bacterial generalists and fungal specialists showed much higher diversification potential, and others featured higher extinction rates. Despite these differences, a continuous transition from the former two to their counterparts was observed, alleviating the \"Matthew effect\" in the biological world for ecological trade-offs. Collectively, these findings emphasize that bacterial generalists and fungal specialists play important roles in maintaining community stability and regulating microbial diversity during the growth process, which expands the current understanding of the maintenance mechanisms of the diversity and community of phytoplankton-associated microbes in the face of disturbance from bloom-forming dinoflagellates.IMPORTANCELike the microbes residing in the rhizosphere and human gut, bacteria that coexist chronically with microalgae exemplify a relationship, forming potentially intimate partnerships with the host. However, studies on the ecological significance of algae-associated microbiomes with different niches under the interference of bloom-forming species are still lacking. This work investigated the ecological interactions and contributions of generalists and specialists within algae-associated bacterial and fungal communities across the growth cycle of <i>Alexandrium pacificum</i> for the first time. These results increase the understanding of the microbial ecology of algae-associated microbes in the context of interference from the proliferation of harmful algal bloom species.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0135925"},"PeriodicalIF":3.7,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}