Applied and Environmental Microbiology最新文献

{"title":"Assessing antibacterial, antiviral, and antifungal efficacy of non-porous materials using small droplet transfer: the simulated splash method.","authors":"Alexander J Cunliffe, Emma Chareyre, Peter Askew, Gillian Iredale, Abby Marchant, James Redfern","doi":"10.1128/aem.02304-25","DOIUrl":"10.1128/aem.02304-25","url":null,"abstract":"<p><p>The transfer of microorganisms via contaminated small droplets presents a vital pathway to the spread of disease. These droplets can be expelled actively by coughing and sneezing, but also via a proxy, such as splashes from contaminated sinks and toilets. Antimicrobial materials provide a preventative approach to controlling the microbial populations on surfaces to combat this issue. However, currently, there are limited standardized testing methods for assessing the antimicrobial efficacy of surfaces using small droplets in a realistic manner. Furthermore, the impact of moisture is often overlooked in current standards. Thus, a method of assessing antimicrobial materials in realistic conditions using contaminated small droplets was developed to assess the efficacy of a given material under both wetted and dry conditions. Additionally, this method was translated to determine the impact of moisture on the antimicrobial efficacy of copper surfaces against bacteria (methicillin-resistant <i>Staphylococcus aureus</i> [MRSA] and <i>Pseudomonas aeruginosa</i>), yeast (<i>Candida albicans</i>), and viruses (bacteriophage: Φ6 and MS2). For each microorganism, stainless steel (inert) and copper (antimicrobial) surfaces were inoculated with ten 1 µL droplets of microbial inoculum and recovered at the following intervals: immediately, at the time of evaporation of the droplets on the surface (activity when droplet/moisture present), and 2 hours post-evaporation (activity when droplet/moisture absent). Reduced survival of both <i>P. aeruginosa</i> and Φ6 phage was observed on stainless steel, indicating they are inappropriate for this method, likely because of desiccation. Copper was demonstrated to have a reduced antimicrobial efficacy under lower relative humidity conditions in all cases compared to reports in the literature, highlighting the benefit of a method that assesses efficacy using approaches more aligned to real-world application of these materials, demonstrating a need for careful consideration regarding the implementation of antimicrobial materials based on methods that might not simulate end-use.IMPORTANCESmall droplet transfer represents a key pathway for microbial movement throughout the built environment, contributing to increased healthcare costs and mortality rates, particularly via healthcare-associated infections. Antimicrobial materials can provide a vital passive and low-maintenance method of microbial control within a wider infection control system. However, current standards often use either environmental conditions unrealistic to the end-use environment (e.g., relative humidity above 90% that can overemphasize the efficacy of some materials) and/or methodological specifications that increase operator variability (e.g., manual spreading of inoculum on the surface). This paper describes a method of assessing the antimicrobial efficacy of a surface under both moist and dry conditions via small droplet contamination. The method w","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0230425"},"PeriodicalIF":3.7,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101517/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147589406","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 the C9-hydrogenase for 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid (9,17-DOHNA) and the 7α-dehydratase essential for initiating β-oxidation of the B-, C-, and D-rings in steroid degradation by <i>Comamonas testosteroni</i> TA441.","authors":"Masae Horinouchi","doi":"10.1128/aem.02331-25","DOIUrl":"10.1128/aem.02331-25","url":null,"abstract":"<p><p><i>Comamonas testosteroni</i> TA441 is a model aerobic steroid-degrading bacterium whose sterane degradation pathway has been elucidated in the greatest detail to date. Similar pathways have been identified in many genera of bacteria, including both proteobacteria and actinobacteria, such as <i>Mycobacterium tuberculosis</i>. However, the genes encoding the C9-hydrogenase for 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid (9,17-DOHNA, also known as HIP) and the 7α-dehydratase essential for initiating β-oxidation of the B-, C-, and D-rings had not been identified. In this study, we identified these missing genes, located adjacent to the <i>chsE1E2H1H2ltp2</i> cluster involved in C17 side-chain degradation, and designated them <i>scdB</i> and <i>scdH</i>, respectively. This finding completes the elucidation of all degradation steps of 9,17-DOHNA prior to D-ring cleavage. AlphaFold models showed that ScdB and at least five hydrogenases/dehydrogenases involved in steroid degradation in TA441 share a similar dimer structures with Rossmann fold motif. In contrast, ScdH was predicted to form a homohexameric structure similar to ScdY and ScdN, involved in B-, C-, and D-ring degradation in TA441. Furthermore, AlphaFold modeling revealed that SteC, the dehydratase responsible for removing the C12β-hydroxyl group from 9,17-DOHNA derivatives, exhibits strong structural similarity to BaiE, the bile acid 7α-dehydratase of <i>Clostridium scindens</i> JCM 10418/VPI 12708, despite sharing only ~28% amino acid sequence identity.IMPORTANCEResearch on bacterial aerobic steroid degradation began more than 70 years ago, initially to produce intermediates for steroid drug synthesis. Recently, this field has gained renewed attention due to its implications for human health-for example, the role of cholesterol import and degradation in the persistence of <i>Mycobacterium tuberculosis</i> H37Rv within chronically infected lungs. <i>Comamonas testosteroni</i> TA441 serves as a key model organism for elucidating aerobic steroid degradation, with pathways for cleavage of the A-, B-, C-, and D-rings already well established. The functions and structures of the enzymes identified in TA441 display striking similarities to those in actinobacteria, such as <i>M. tuberculosis</i>. In this study, we identified two enzymes indispensable for initiating β-oxidation of the B-, C-, and D-rings, thereby filling the last remaining gaps for initiating this pathway. Our AlphaFold-based structural analysis of these enzymes not only provides new insights into the steroid metabolism of <i>M. tuberculosis</i> but also broadens understanding of the ecological and physiological significance of bacterial steroid degradation.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0233125"},"PeriodicalIF":3.7,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101464/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147607715","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":"Bio-Rad and QIAGEN digital PCR platforms provide equivalent quantification for wastewater-based SARS-CoV-2 surveillance.","authors":"Thomas Clerkin, Steph Smith, Kevin Zhu, Denene Blackwood, Javier Gallard-Góngora, Drew Capone, Joe Brown, Rachel T Noble","doi":"10.1128/aem.00083-26","DOIUrl":"https://doi.org/10.1128/aem.00083-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Digital PCR (dPCR) is increasingly used for wastewater surveillance due to its precision, absolute quantification, and reduced sensitivity to inhibition compared to quantitative PCR (qPCR). Although the Bio-Rad QX200 and QIAGEN QIAcuity dPCR platforms are widely adopted, their performance has not been directly compared for wastewater applications. We conducted a blinded comparison of these platforms using 93 archived wastewater influent samples from North Carolina collected in 2021-2022, spanning three orders of magnitude in SARS-CoV-2 concentration (1 × 10&lt;sup&gt;3&lt;/sup&gt;-5 × 10&lt;sup&gt;5&lt;/sup&gt; copies L&lt;sup&gt;-1&lt;/sup&gt;). Samples were stratified into low, medium, and high concentration bins and analyzed in triplicate for N1 and N2 gene targets and a bovine coronavirus processing control. Both platforms demonstrated statistically equivalent quantification across all targets, with mean differences ≤0.12 log copies L&lt;sup&gt;-1&lt;/sup&gt; (&lt;i&gt;R&lt;/i&gt;&lt;sup&gt;2&lt;/sup&gt; &gt; 0.93). Coefficients of variation were similar (3.96%-7.61%), with no significant differences across concentration bins except for N2 in the low bin (difference: 0.87 percentage points). Measurement variability correlated strongly with wastewater treatment plant site (&lt;i&gt;R&lt;/i&gt;&lt;sup&gt;2&lt;/sup&gt; = 0.89) rather than platform, indicating that sample matrix characteristics drive precision more than the analytical platform. Process limits of detection ranged from 2,160 to 2,680 copies L&lt;sup&gt;-1&lt;/sup&gt; for Bio-Rad QX200 and 5,650-9,700 copies L&lt;sup&gt;-1&lt;/sup&gt; for QIAGEN QIAcuity for N1 and N2, respectively. The Bio-Rad QX200 platform processed samples 32% faster (305 vs 435 minutes per 96 wells), while QIAGEN QIAcuity offered 29% lower consumables cost ($4.68 vs $6.11 per well). These findings support the interchangeable use of both platforms for wastewater surveillance, with platform selection based on laboratory-specific operational needs.IMPORTANCEAs wastewater-based epidemiology transitions from emergency response to sustained public health infrastructure, standardized molecular methods are essential for reliable data integration across surveillance networks. This study provides the first blinded comparison of two dPCR platforms widely deployed for wastewater pathogen surveillance in the United States. We demonstrate quantitative equivalence between Bio-Rad QX200 and QIAGEN QIAcuity platforms across three orders of magnitude in viral concentration, establishing that data from both platforms can be interpreted interchangeably for public health decision-making. This platform equivalence is critical as national surveillance systems aggregate data from diverse laboratories and as monitoring expands beyond SARS-CoV-2 to encompass additional respiratory viruses, antimicrobial resistance genes, and emerging pathogens. Our findings provide a methodological foundation for multi-platform surveillance networks and demonstrate that measurement variability is driven primarily by sample matrix characteristics rather than analytical","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0008326"},"PeriodicalIF":3.7,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147759846","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":"Efflux pump activation confers mupirocin resistance and enhances rhizosphere fitness in <i>Pseudomonas</i>.","authors":"Wen-Jie Wang, Man-Jin Wang, Wen-Jun Jiang, Li-Qun Zhang","doi":"10.1128/aem.02575-25","DOIUrl":"https://doi.org/10.1128/aem.02575-25","url":null,"abstract":"<p><p>Mupirocin (Mup) is a polyketide antibiotic for clinical methicillin-resistant <i>Staphylococcus aureus</i> treatment and agricultural biocontrol, acting by binding to IleRS to inhibit protein synthesis. Here, we demonstrate that <i>Pseudomonas viciae</i> 11K1 acquires resistance to mupirocin not through canonical mutations in <i>ileS</i>, the gene encoding the drug target, but via single-nucleotide polymorphisms (SNPs) of EmhR, a transcriptional repressor. These SNPs attenuate EmhR's DNA-binding ability, resulting in derepression of the resistance-nodulation-division (RND) efflux pump EmhABC. This leads to a 7-fold (to 800 μg/mL) increase in the mupirocin minimum inhibitory concentration and confers cross-resistance to multiple other antibiotics. Critically, 11K1 strains harboring EmhR mutations exhibit enhanced competitive fitness in colonizing wheat rhizospheres against the mupirocin-producing <i>Pseudomonas bijieensis</i> 2P24. The conservation of this regulatory mechanism in <i>Pseudomonas aeruginosa</i>, mediated by the EmhR ortholog NalD, underscores its broader biological significance. Our findings establish a direct link between efflux pump regulation and ecological adaptation, highlighting a key mechanism that contributes to environmental antimicrobial resistance and has important implications for the clinical and agricultural use of mupirocin.IMPORTANCEMupirocin and its producing <i>Pseudomonas</i> strains are widely used in both clinical and agricultural contexts, making mupirocin resistance a significant concern for public health and food security. While canonical mupirocin resistance is primarily attributed to mutations in <i>ileS</i>, the gene encoding the drug target isoleucyl-tRNA synthetase (IleRS), our study identifies a novel resistance mechanism in <i>Pseudomonas viciae</i> strain 11K1 mediated by single-nucleotide polymorphisms (SNPs) in the transcriptional repressor EmhR. These SNPs derepress the RND efflux system EmhABC and reduce intracellular mupirocin levels. This mechanism not only enhances resistance to mupirocin but also confers cross-resistance to multiple antimicrobial agents, raising the risk of multidrug-resistant strain spread. EmhR-mutant 11K1 strains exhibit enhanced rhizosphere competitiveness in the presence of mupirocin-producing <i>Pseudomonas bijieensis</i> strain 2P24, indicating an ecological fitness advantage that could promote resistant population expansion in agricultural environments. The same regulatory pathway is conserved in human pathogen <i>Pseudomonas aeruginosa</i> PAO1 via the functional ortholog NalD, suggesting that this mechanism may be widespread in <i>Pseudomonas</i>. These findings fill a critical gap in understanding non-target-based mupirocin resistance, clarify the ecological drivers of antimicrobial resistance, and offer practical insight for improving mupirocin application to limit the emergence and spread of resistant pathogens.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0257525"},"PeriodicalIF":3.7,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147760095","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 ComX-based strategy for artificially inducing competence in naturally non-transformable <i>Streptococcus parasanguinis</i>.","authors":"Hui-Ru Shieh, Yu-Shan Yen, Yu-Juan Lin, Yi-Ywan M Chen","doi":"10.1128/aem.00082-26","DOIUrl":"10.1128/aem.00082-26","url":null,"abstract":"<p><p>Many streptococci, including strains of <i>Streptococcus salivarius</i> and <i>Streptococcus parasanguinis</i>, harbor <i>com</i> genes but do not exhibit natural competence. In <i>S. salivarius</i> YS18, a chromosomal rearrangement in the 5' flanking region of <i>comX</i>, encoding σ^X, the alternative sigma factor responsible for the late <i>com</i> gene expression, was found to confer competence, whereas its parental strain 57.I was not competent. This genetic arrangement led to constitutive, high-level <i>comX</i> expression, with ComX production independent of quorum-sensing regulation. By establishing YS18 <i>comX</i> on the <i>Streptococcus-Escherichia coli</i> shuttle vector pDL278 in non-competent <i>S. parasanguinis</i> FW213, transient competence could be established, enabling mutant construction via ligation mutagenesis; thereby, bypassing the need to generate plasmids carrying mutated loci that would be introduced via electroporation. Plasmids in the mutant isolates were successfully cured by cultivation in antibiotic-free media post-mutagenesis. In conclusion, the lack of competence in <i>com</i> gene-containing streptococci may likely be due to inadequate ComX production. Given the structural conservation of ComX, constitutive <i>comX</i> expression provides a practical strategy to establish competence in non-competent streptococcal hosts.IMPORTANCEMany streptococci encode <i>com</i> genes but remain non-competent, limiting genetic manipulation. This study found that insufficient ComX production was the key barrier to competence development in these strains. However, variations in competence-stimulating peptides and σ^X-inducing peptides make optimizing <i>comX</i> expression with synthetic peptides impractical. Instead, by introducing a constitutively expressed <i>comX</i> from <i>Streptococcus salivarius</i>, a transient competence stage can be established in non-competent <i>Streptococcus parasanguinis</i>, enabling efficient mutant construction via ligation mutagenesis. This approach provides a generalizable strategy to simplify mutagenesis workflows and expands the genetic toolkit for functional studies in otherwise intractable streptococcal strains.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0008226"},"PeriodicalIF":3.7,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101493/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147472264","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":"Pathogenic effects of <i>Halomonas</i> on cyanobacteria and biocontrol potential of a deep-sea <i>Bacillus</i> strain.","authors":"Xinyi Li, Meilin Yuan, Chaomin Sun, Shimei Wu","doi":"10.1128/aem.00199-26","DOIUrl":"10.1128/aem.00199-26","url":null,"abstract":"<p><p><i>Limnospira fusiformis</i>, a nutritionally valuable cyanobacterium with significant biomanufacturing potential, faces critical challenges from pathogenic invasions. This study identified <i>Halomonas variabilis</i> 2-9 as the primary pathogen of <i>L. fusiformis</i> cultivation collapse, demonstrating broad-spectrum algicidal activity against multiple cyanobacterial species. Additionally, the algicidal substance produced by <i>H. variabilis</i> 2-9 was purified and identified as toxic dibutyl phthalate. At a concentration of 3 µg/mL, the purified algicidal substance caused 90.6% reduction in Fv/Fm within 24 h and 86% degradation of chlorophyll-<i>a</i> within 120 h. To be specific, Fv/Fm as the maximum photochemical quantum yield of photosystem II is a core indicator reflecting the photosynthetic activity and health status of spirulina. A sudden drop in Fv/Fm of spirulina indicates impaired function of Photosystem II. Therefore, the purified algicidal substance severely damaged the photosynthetic system of <i>L. fusiformis</i>. To mitigate the detrimental effects of <i>H. variabilis</i> 2-9, <i>Bacillus velezensis</i> L4 was isolated from deep-sea sediments. This strain produced an antimicrobial compound (C₃₁H₄₂O₂) that specifically inhibited <i>H. variabilis</i> 2-9 without damaging <i>L. fusiformis</i>. In co-culture experiments, <i>B. velezensis</i> L4 reversed <i>Halomonas</i>-induced algal decay, demonstrating its potential as a biocontrol agent. These findings provide both mechanistic insights into <i>Halomonas</i>-mediated cyanobacterial pathogenesis and a practical solution for sustainable aquaculture management.</p><p><strong>Importance: </strong>This study identifies <i>H. variabilis</i> 2-9 as a novel cyanobacterial pathogen that produces hazardous compound dibutyl phthalate (DBP), causing severe damage to <i>L. fusiformis</i> and exhibiting broad-spectrum algicidal activity against other cyanobacteria. The discovery of DBP-mediated pathogenesis provides crucial insights into microbial threats to aquaculture systems. Significantly, we demonstrate that <i>B. velezensis</i> L4, isolated from deep-sea environments, serves as an effective biocontrol agent through the production of a selective antimicrobial compound that specifically targets <i>H. variabilis</i> 2-9 without harming <i>L. fusiformis</i>. These findings offer both fundamental understanding of cyanobacterial disease mechanisms and a practical, sustainable solution for algal disease management.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0019926"},"PeriodicalIF":3.7,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101475/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147484245","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":"Comparison of human intestinal enteroid and zebrafish larva models for replication of human norovirus.","authors":"Sahaana Chandran, Jan Vinjé, Kimberly Huynh, Kristen E Gibson","doi":"10.1128/aem.00152-26","DOIUrl":"10.1128/aem.00152-26","url":null,"abstract":"<p><p>Human intestinal enteroid (HIE) and zebrafish larva (ZF) models support the replication of certain strains of human norovirus (HuNoV), the leading cause of viral gastroenteritis worldwide. The replication of 17 HuNoV-positive stool specimens (nine genotypes) from patients ranging from 5 months to 83 years old was evaluated in both HIE and ZF models. The yolk of 3-day post-fertilization ZF larvae was microinjected with 3 nL 10% clarified stool suspension. Each day post-infection (dpi), 10 larvae were pooled as one sample, and two specimens were collected daily until 5 dpi. Viral RNA was extracted from harvested larvae and quantified using reverse transcription (RT) droplet digital PCR. For the HIE model, J4FUT2 K1 enteroid monolayers were inoculated with 100-fold dilution of each stool specimen. Viral RNA levels were quantified at 1 and 72 h post-infection using RT real-time PCR. All genogroup (G) I specimens (<i>n</i> = 5) replicated in both models showing a 1-2.5 log increase in HuNoV RNA. Of the 12 GII specimens tested, 8 replicated in the ZF model, and 7 replicated in the HIE model. Specimens that failed to replicate in each model were not the same, although most of them were GII.4 Sydney [P16]. One additional strain, GII.17[P17], replicated only in the ZF model. Across GII strains, viral RNA increases ranged from 1.6 to 3.3 log in the ZF model and from 0.4 to 3.68 log in the HIE model. These data highlight variability in HuNoV replication efficiency across models, potentially indicating the influence of model-specific factors on replication.IMPORTANCEHuman intestinal enteroid and zebrafish larva models have been independently shown to support replication of different strains of human norovirus (HuNoV), the leading cause of viral gastroenteritis worldwide. However, whether the same HuNoV-positive stool specimens replicate similarly in both systems has not been examined. In this study, stool specimens positive for a range of HuNoV genotypes were tested in both models. While specimens from the genogroup I (GI) genogroup consistently replicated in both systems, specimens from the GII genogroup showed variable replication, with some replicating in only one model and a couple of specimens not replicating in either model. These findings demonstrate that model-specific biological factors influence HuNoV replication and highlight the significance of using complementary model systems to better understand HuNoV pathogenesis.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0015226"},"PeriodicalIF":3.7,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101513/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147589458","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":"Genetic diversification of <i>Pseudomonas fluorescens</i> maintained by multi-niche selection within biofilms.","authors":"Abigail M Matela, Colton W Siatkowski, Changhua Yan, Sachin Thiagarajan, Erin M Nawrocki, Vaughn S Cooper","doi":"10.1128/aem.02499-25","DOIUrl":"10.1128/aem.02499-25","url":null,"abstract":"<p><p>We established a research-education partnership, EvolvingSTEM, that currently provides thousands of secondary school students the opportunity to conduct authentic research experiments centered on microbial evolution each year. Providing high school students access to research experiences improves learning, can have positive and long-lasting impacts on their attitudes toward science, and gives them the opportunity to make impactful scientific contributions. Through EvolvingSTEM, students evolve populations of <i>Pseudomonas fluorescens</i> in a bead model that includes daily cycles of bacterial dispersal, attachment, and biofilm growth, and observe heritable changes in colony morphology. We sequenced the genomes of 69 evolved clones with unique colony morphologies and identified parallel mutations in genes known to regulate or affect biofilm growth (<i>wsp</i>, <i>yfiBNR</i>, <i>morA,</i> and <i>fuzY</i>). We also uncovered novel adaptations: loss-of-function mutations in phosphodiesterase PFLU0185 that did not alter colony morphology and mutations affecting periplasmic disulfide bond formation producing small colonies. PFLU0185 mutants rapidly and consistently reached high frequencies, and phenotyping revealed roles in cyclic di-GMP regulation, biofilm formation, and motility, prompting us to name this gene <i>bmo</i> (<u>b</u>iofilm and <u>mo</u>tility regulator). Competition experiments and microscopy demonstrated that <i>bmo</i> mutants are ecological generalists that compete with their ancestor and specialist mutants. Consequently, phenotypic diversity is maintained, with smooth (ancestral and <i>bmo</i>) colonies consistently outnumbering wrinkly and fuzzy variants. This study advances our understanding of biofilm genetic architecture while demonstrating that student-led research can uncover mechanisms of microbial adaptation relevant to <i>Pseudomonas</i> infection biology.</p><p><strong>Importance: </strong>Bacterial biofilms dominate microbial life; however, their evolutionary genetics remain incompletely understood. Extensive replication of biofilm selection experiments by secondary school students can provide valuable insights into mechanisms of adaptation. Notably, mutations in a conserved phosphodiesterase, PFLU0185/<i>bmo</i>, dominate evolved populations without changing colony morphology. Phenotypic assays reveal that <i>bmo</i> plays a generalist role and competes with its ancestor and other diverse, less frequent biofilm-specialist mutants, resulting in populations that have differentiated to fill multiple niches within the biofilm life cycle. This work also demonstrates the power of distributed research networks for addressing complex biological questions while promoting scientific literacy to the public.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0249925"},"PeriodicalIF":3.7,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101516/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147571794","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":"Emergence, global dispersal, and local adaptations of <i>Yersinia pestis</i>, the agent of plague.","authors":"Victoria Carcauzon, Anne Laudisoit, Philip Slavin, Steven M Goodman, Florent Sebbane, Pablo Tortosa","doi":"10.1128/aem.01658-25","DOIUrl":"10.1128/aem.01658-25","url":null,"abstract":"<p><p><i>Yersinia pestis</i>, the causative agent of plague, is a zoonotic bacterium that split at least 6,000 years ago from <i>Yersinia pseudotuberculosis</i> through plasmid acquisition, gene loss, and point mutations. These genetic events enabled a shift from the fecal-oral route to vector-borne transmission and facilitated systemic spread. In the course of its evolutionary history, <i>Y. pestis</i> has caused an unaccountable number of human outbreaks, at both regional and pandemic scales, of which three global pandemics have been documented from historical sources. The bacterium currently persists in sylvatic (enzootic) natural foci across Africa, Asia, and the Americas. Its persistence depends on the co-occurrence of reservoir hosts (mainly mammals) and competent vectors, primarily mammal ectoparasites, and their occurrence is shaped by environmental conditions. However, ecological variation among foci and limited epidemiological data still hinder our understanding of plague dynamics. This review examines the genetic evolution of <i>Y. pestis</i>, traces the bacterium's history, including its global spread, and presents the main actors of sylvatic plague involved in the bacterium's maintenance, with a special emphasis on the knowledge of vectors and hosts in countries that have reported cases of plague over the past decade. The global dispersal of <i>Y. pestis</i> has led to its adaptation to several distinct environments, highlighting the need for a comprehensive surveillance strategy for a better understanding of the ecological drivers of <i>Y. pestis</i> persistence and transmission within each of the geographical regions it is maintained in the natural environment.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0165825"},"PeriodicalIF":3.7,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101507/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147442197","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":"Continuous recirculation of hydroponic-nutrient solutions shifts bacterial communities and induces plant-defense gene expression in lettuce.","authors":"Cora M Kenderdine, Rosa E Raudales","doi":"10.1128/aem.01647-25","DOIUrl":"10.1128/aem.01647-25","url":null,"abstract":"<p><p>Biotic and abiotic factors influence bacterial communities in the rhizosphere. This project aimed to characterize bacterial communities in the lettuce rhizosphere, assess the relationships between bacteria and root rot, and evaluate the impact of reused nutrient solutions on bacterial communities. Lettuce (<i>Lactuca sativa</i> cv. Rex) was grown in deep-water culture hydroponics in reused autoclaved or non-autoclaved nutrient solutions for five cycles, with or without <i>Pythium myriotylum</i>. Bacterial composition was determined via high-throughput sequencing of the 16S rRNA gene. Quantitative real-time PCR was used to detect <i>P. myriotylum</i>. Spearman's correlation coefficient (<i>ρ</i>) was performed to assess relationships between variables. The expression of <i>PR1</i>, <i>PDF1.2</i>, and <i>LOX1</i> was quantified to determine if there were differences in plant defenses. The predominant phyla and genera across all cycles in the nutrient solution and roots were Proteobacteria (67%) and Cyanobacteria (47%) and <i>Acinetobacter</i> (13%) and <i>Ideonella</i> (22%), respectively. Bacterial communities in the nutrient solution (<i>R</i>²= 0.35) and roots (<i>R</i>²= 0.24) were significantly dissimilar between cycles. Bacterial communities were significantly dissimilar by the presence of <i>P. myriotylum</i> in nutrient solution (<i>R</i>²= 0.02) and roots (<i>R</i>²= 0.10). Bacterial correlations with health variables mostly differed by the presence/absence of <i>P. myriotylum</i>. Bacterial communities or individual bacterial isolates in recirculating hydroponic solutions that activate plant defenses resulting in the suppression or prevention of Pythium root rot in lettuce should be investigated further to be utilized as viable strains or synthesized compounds for the development of commercial products.</p><p><strong>Importance: </strong><i>Pythium myriotylum</i> is the causal agent of root rot and wilt disease, which can cause significant damage to lettuce in hydroponic systems. Root rot can be challenging to treat with traditional methods once it develops, often resulting in the destruction of the entire crop. Reused nutrient solutions have been reported to harbor microorganisms that may affect disease suppression. Examining how bacterial communities in recycled nutrient solutions change and trigger plant-defense genes may contribute to the reduction of Pythium root rot and provide chemical-free and cost-effective alternatives for soilless cultivation systems. Future studies focusing on specific microorganisms and their bioactive compounds will be essential for advancing biological control methods in hydroponic crop systems.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0164725"},"PeriodicalIF":3.7,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101472/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147442209","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}