Applied and Environmental Microbiology最新文献

{"title":"Detection of biofilms on explanted urinary incontinence slings and their relationship with pain, exposure, or urinary tract complications.","authors":"Nazish Abbas, Thomas Willmott, Paul M Campbell, Gurdeep Singh, Maya Basu, Fiona Reid, Cecile El Chami, Andrew J McBain","doi":"10.1128/aem.00735-26","DOIUrl":"10.1128/aem.00735-26","url":null,"abstract":"<p><p>Midurethral slings (MUS) are synthetic mesh implants used to treat stress urinary incontinence in women. Positioned via retropubic or transobturator approaches, they support the mid-urethra to maintain closure during increases in intra-abdominal pressure. Although generally effective, long-term MUS complications have been associated with chronic inflammation, pain, and infection, with explanted slings often showing bacterial colonization. The underlying mechanisms remain unclear, particularly the role of microbial biofilms. We examined the presence and characteristics of biofilms on MUS removed for various complications to better inform clinical management. MUS samples (<i>n</i> = 112) from 52 women were imaged using confocal laser scanning microscopy following application of a eubacterial FISH probe, TOTO-1, and DAPI. Biofilms were detected on all samples, forming dense bacterial aggregates along mesh fibers. The vaginal portions of the MUS demonstrated higher biofilm volumes than retropubic or obturator regions. However, mesh exposed through vaginal tissue did not show increased bacterial load. When all samples were analyzed, no significant differences in biofilm volume were observed between complication types, including chronic pain, vaginal or lower urinary tract perforation, and recurrent incontinence. While biofilms were universally present, greater volumes in the vaginal region did not correlate with worse clinical outcomes. These findings suggest a threshold between benign colonization and clinically significant infection. Variation in bacterial composition, rather than biofilm quantity, may influence host response and the development of mesh-related complications.</p><p><strong>Importance: </strong>Biofilms are common on explanted midurethral slings, but their volume does not predict complications. These findings suggest that bacterial composition and host response, rather than bacterial load, drive mesh-related morbidity. Understanding these factors may improve mesh design and guide strategies to prevent infection and chronic complications.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0073526"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148721175","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":"Exploring <i>Lachancea thermotolerans</i> biodiversity: insights into lactic acid production and carbon metabolism in response to oxygen availability.","authors":"Theo R Jacobs, Mathabatha E Setati, Carole Camarasa, Benoit Divol","doi":"10.1128/aem.01155-26","DOIUrl":"10.1128/aem.01155-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Lactic acid production by &lt;i&gt;Lachancea thermotolerans&lt;/i&gt; offers a promising biological strategy to restore wine acidity often compromised by climate change, yet this metabolic trait remains highly variable and poorly controlled. This study systematically evaluated the impact of controlled oxygenation regimes on fermentation performance and primary metabolism in three genetically distinct &lt;i&gt;L. thermotolerans&lt;/i&gt; strains. Oxygen availability drastically altered metabolic fluxes. Under continuous aerobic conditions, carbon was redirected toward biomass formation (9- to 13-fold increase), with reduced ethanol and lactic acid yields, as well as increased succinic acid, acetoin, and 2,3-butanediol, whereas fully anaerobic conditions lowered fermentation performance but substantially increased lactic acid. These results confirmed that &lt;i&gt;L. thermotolerans&lt;/i&gt; is a weakly Crabtree-positive yeast with mixed respiratory-fermentative metabolism. Carbon redistribution under aerobic conditions was not fully compensated by measured metabolites, resulting in substantially decreased carbon recovery (~70%) and suggesting undetermined respiratory CO&lt;sub&gt;2&lt;/sub&gt; production alongside diversion of carbon toward undetermined intracellular components. This imbalance was supported by a decline in cell density following peak growth, consistent with potential redox imbalance or oxidative stress. Lactic acid production occurred primarily under oxygen limitation, independent of ethanol formation, indicating a regulated, facultative adaptive response rather than a constitutive fermentation product. Strain-dependent differences further revealed distinct carbon allocation strategies. While oxygen strongly influenced metabolic behavior, pulse strategies showed limited, condition-dependent effects, highlighting the importance of timing and intensity for modulating lactic acid production. Overall, oxygen is a powerful lever to modulate metabolic fluxes in &lt;i&gt;L. thermotolerans&lt;/i&gt;, but its application for predictable bio-acidification requires further optimization.IMPORTANCEWine acidity is increasingly difficult to maintain under climate change, creating a need for reliable biological solutions. Some strains of &lt;i&gt;Lachancea thermotolerans&lt;/i&gt; can produce lactic acid during fermentation, but this metabolic trait is inconsistent and difficult to control. This study shows that oxygen availability is a key factor shaping how this yeast uses carbon, shifting it between growth and lactic acid production. Under the continuous aerobic condition, carbon flux was redirected toward biomass, whereas the fully anaerobic condition favored lactic acid production but reduced fermentation performance. Importantly, pulsed oxygen additions did not provide consistent control of lactic acid production, but they revealed trends that highlight the importance of timing and intensity. These findings show that lactic acid production is a flexible response to environmental conditions rather than a c","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0115526"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599520/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148672890","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":"Influenza A deletion-containing viral genome production is altered by metabolites, metabolic signaling molecules, and cyanobacterial extracts.","authors":"Ilechukwu Agu, Suzanna Y Gomez, Ivy R José, Samuel L Díaz-Muñoz","doi":"10.1128/aem.01232-26","DOIUrl":"10.1128/aem.01232-26","url":null,"abstract":"<p><p>RNA virus infections generate abundant non-standard viral genomes that have been associated with milder clinical outcomes, leading to research into harnessing them as novel antivirals. We recently showed that altering host cell metabolism away from pro-growth pathways using alpelisib increased the production of influenza A nonstandard viral genomes (specifically deletion-containing viral genomes, DelVGs). To uncover more drugs that could induce increased DelVGs, we subjected influenza infections (A/H1N1 and A/H3N2) to a screen of metabolites, metabolic signaling molecules, and cyanobacterium-derived biologics, and quantified DelVGs and total viral genomes using long-read sequencing. We show that metabolites and signaling molecules of host cell central carbon metabolism can significantly alter DelVG production early in influenza A infection. Adenosine emerged as a potent inducer of defective viral genomes, significantly amplifying DelVG production across both subtypes. Insulin had similar effects, albeit subtype-specific, predominantly enhancing polymerase segment DelVGs in A/H3N2 infections. Tricarboxylic acid (TCA) cycle inhibitors, 4-octyl itaconate and UK5099, along with the purine analog favipiravir, increased total viral genome production across subtypes. Cyanobacterial extracts primarily affected DelVGs and total viral genome production in A/H3N2 infections, with a specific, almost complete shutdown of influenza antigenic segments. These results suggest new avenues for antiviral intervention, including host metabolic pathways (PI3K-AKT, Ras-MAPK pathways, TCA, and purine-pyrimidine) and cyanotherapeutics that affect DelVG production. Our study advances our fundamental understanding of DelVG production mechanisms and highlights the potential of targeting host metabolism to develop broad-spectrum influenza therapeutics.IMPORTANCEAntivirals currently available for flu infections lack effectiveness or face rapid emergence of antiviral resistance. Flu infections naturally produce nonstandard viral genomes, which interfere with viral reproduction and lead to milder clinical outcomes. Here, we test drugs that alter the host metabolism to induce influenza infections to produce more of this \"natural antiviral.\" We find that molecules generated from human metabolism, particularly adenosine, can increase these deletion-containing viral genomes (DelVGs) and also find evidence that biological extracts from cyanobacteria have antiviral effects. Our findings suggest that the social interactions observed between defective and full-length viral genomes depend not only on the viral actors but can also be altered by the stage provided by the host. Our findings have potential applications to increasing DelVG production for research or industrial uses; employing metabolites as biomarkers for flu infection severity; and using drugs to alter host metabolism to steer influenza infections to milder outcomes.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0123226"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599498/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148787581","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 characterization and phage cocktail suppression of a multidrug-resistant <i>Vibrio sinaloensis</i> isolate from diseased shrimp.","authors":"Zhongfeixue Wang, Jiulong Zhao, Chengcheng Li, Yufei Yue, Zengmeng Wang, Linkai Ou, Yantao Liang, Min Wang, Yongyu Zhang","doi":"10.1128/aem.00680-26","DOIUrl":"10.1128/aem.00680-26","url":null,"abstract":"<p><p><i>Vibrio sinaloensis</i> has been reported in association with disease events in aquaculture, yet its genomic features and non-antibiotic suppression strategies remain largely unexplored. Here, we report genomic characterization of a multidrug-resistant <i>V. sinaloensis</i> strain, ZZ006, isolated from diseased shrimp and evaluate phage-mediated suppression of this strain <i>in vitro</i>. The ZZ006 genome harbors multiple putative virulence-associated secretion systems and antimicrobial resistance genes, suggesting chromosomal carriage of traits potentially relevant to host association and antimicrobial tolerance. Using this isolate and its phage-resistant derivatives as hosts, we isolated and characterized three novel bacteriophages (VS1, VS2, VS3) with complementary infection strategies. Their combined application efficiently suppressed ZZ006 growth <i>in vitro</i> and reduced the emergence of phage-resistant populations compared with individual phages. Whole-genome resequencing of cocktail-resistant isolates revealed recurrent mutations in pilus- and pseudopilin-associated genes, consistent with receptor-level phage resistance. This study provides genomic characterization of an aquaculture-associated <i>V. sinaloensis</i> isolate and establishes an <i>in vitro</i> framework for phage cocktail suppression and resistance-evolution analysis, supporting future evaluation of phage-based biocontrol in aquaculture-relevant settings.</p><p><strong>Importance: </strong><i>Vibrio sinaloensis</i> has been detected in diseased aquaculture animals, and multidrug-resistant isolates may complicate disease management. By integrating genomic analysis with experimental phage therapy, this work characterizes a multidrug-resistant <i>V. sinaloensis</i> isolate from diseased shrimp and evaluates <i>in vitro</i> phage-mediated suppression of this isolate and its phage-resistance evolution. These findings offer actionable solutions for mitigating antibiotic resistance and enhancing sustainability in aquaculture systems.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0068026"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148787472","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":"Characterization of vaginal lactobacilli from South African women toward the development of a biotherapeutic to optimize the vaginal microbiome.","authors":"Jenna Wilson, Aleya Sarah Amir Hamzah, Christine Jordan, Joshua A Hayward, Brian R Kullin, Monalisa T Manhanzva, David Tyssen, Celia Mehou-Loko, Andrea G Abrahams, Nina Radzey, Rushil Harryparsad, Bahiah Meyer, Anna C Hearps, Mark Ziemann, Hilton Humphries, Pamela Mkhize, Linda-Gail Bekker, Jo-Ann S Passmore, Heather B Jaspan, Anna E Sheppard, Gilda Tachedjian, Lindi Masson","doi":"10.1128/aem.00566-26","DOIUrl":"10.1128/aem.00566-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;HIV remains among the world's most serious healthcare challenges, with adolescent girls and young women in sub-Saharan Africa at particularly high risk of infection. Bacterial vaginosis (BV) is a key risk factor for HIV acquisition; however, current treatment strategies are limited. Optimal vaginal lactobacilli protect against BV and HIV, largely through immunoregulatory and antimicrobial activities mediated in part by lactic acid. Toward the development of a live biotherapeutic for African women, we sampled 181 isolates of vaginal lactobacilli from 25 BV-negative South African women. Fifty isolates were selected for evaluation of inflammatory responses using vaginal epithelial cells, D- and L-lactate, lactic acid production, and culture acidification. Aside from a single &lt;i&gt;Ligilactobacillus salivarius&lt;/i&gt; strain, &lt;i&gt;Lactobacillus crispatus&lt;/i&gt; isolates acidified the culture media the most and produced the most D- and L-lactic acid. Inflammatory cytokine responses to different strains of lactobacilli were variable, with &lt;i&gt;Lb. crispatus&lt;/i&gt; eliciting the lowest levels of cytokine production, while some strains induced substantial inflammatory responses. When all properties were evaluated collectively, &lt;i&gt;Lb. crispatus&lt;/i&gt; strains exhibited the most desirable biotherapeutic characteristics. Whole genome sequence analysis of 10 &lt;i&gt;Lb. crispatus&lt;/i&gt; isolates led to the identification of putative bacteriocins and intact prophage sequences in all isolates, while no antimicrobial resistance elements were detected. Importantly, the majority of &lt;i&gt;Lb. crispatus&lt;/i&gt; isolates were more closely related to one another than to isolates from other geographical regions. This supports the need for live biotherapeutics to be tailored for the population of intended use.IMPORTANCEHIV remains highly prevalent in sub-Saharan Africa, particularly among adolescent girls and young women. Bacterial vaginosis (BV), characterized by the loss of protective lactobacilli, affects approximately one in four women in this region and increases HIV susceptibility. However, effective and durable therapeutics are lacking. Live biotherapeutics containing beneficial lactobacilli represent a promising treatment strategy, yet there are no approved products including strains isolated from African women, despite well-established geographic variation in vaginal microbiome composition. Through the characterization of 50 vaginal &lt;i&gt;Lactobacillus&lt;/i&gt;, &lt;i&gt;Limosilactobacillus,&lt;/i&gt; and &lt;i&gt;Ligilactobacillus&lt;/i&gt; strains from 25 BV-negative South African women, we demonstrate substantial strain-level variation in live biotherapeutic-relevant properties. Some isolates produced minimal lactic acid or induced marked inflammatory responses, highlighting the importance of rigorous strain selection. Notably, whole genome sequencing revealed that South African &lt;i&gt;Lactobacillus crispatus&lt;/i&gt; strains had distinct genomes compared to isolates from other regions, providing evidence that vaginal live bi","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0056626"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599504/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148787488","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":"Fine-scale structural diversification among closely related <i>Legionella pneumophila</i> isolates from a bath-associated environmental reservoir.","authors":"Naoki Nakajima, Michio Jinnai, Aya Okamura, Yoshimi Date, Ichiro Furukawa","doi":"10.1128/aem.01127-26","DOIUrl":"10.1128/aem.01127-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Legionella pneumophila&lt;/i&gt; populations within environmental reservoirs can exhibit genomic diversity, complicating source attribution during outbreak investigations. Core genome single-nucleotide variant (cgSNV)-based approaches are widely used for identifying closely related lineages during molecular epidemiological investigations; however, they primarily focus on nucleotide-level variation and may overlook structural variation among closely related isolates. In this study, we investigated genomic diversity among clinical and environmental &lt;i&gt;L. pneumophila&lt;/i&gt; isolates obtained during an epidemiological investigation of a legionellosis case. By analyzing multiple colonies isolated from individual samples, we integrated cgSNV analysis with comparative genome structural analysis to characterize insertion sequence (IS)-mediated structural variation within a highly related population. A total of 138 serogroup 1 isolates belonging to sequence type 138 were analyzed. cgSNV analysis revealed that clinical isolates formed a clonal lineage, whereas environmental isolates from the same bath system exhibited substantial diversity despite differing by no more than 20 cgSNVs. Complete genome analysis of 48 representative isolates demonstrated nearly identical genome synteny with limited large-scale rearrangements. In contrast, IS insertion patterns showed considerable variability, particularly for IS256, which exhibited extensive diversity in insertion sites across isolates. Differences in IS insertion patterns were observed even among isolates sharing identical cgSNV genotypes, indicating that IS-mediated structural variation can occur independently of core genome SNV variation. More than half of the coding sequence differences relative to the reference genome were associated with IS insertion sites, predominantly IS256-associated events. These findings suggest that closely related &lt;i&gt;L. pneumophila&lt;/i&gt; populations within environmental reservoirs undergo fine-scale diversification associated with dynamic IS activity.IMPORTANCEIn this study, we analyzed a large collection of &lt;i&gt;Legionella pneumophila&lt;/i&gt; isolates obtained from a patient and a bath-associated environmental source and identified extensive insertion sequence-associated structural variation even among isolates sharing highly similar core genome single-nucleotide variant genotypes. Despite this structural diversification, the closely related isolate population retained highly conserved genome organization and broadly similar insertion sequence distribution patterns, supporting the interpretation that it remained highly clonal rather than undergoing large-scale genomic divergence. These findings highlight the importance of analyzing multiple colonies from individual samples to better characterize within-source population diversity. They further indicate that structural genome variation, particularly mobile insertion sequences such as IS256, provides complementary resolution beyond conven","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0112726"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599499/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148838966","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":"Rapid detection of cultivated truffle fungi (<i>Tuber</i>) from truffles and ectomycorrhizal root tips using loop-mediated isothermal amplification.","authors":"Alassane Sow, Andrew Cooper, Inga Meadows, Gregory Bonito, Matthew E Smith","doi":"10.1128/aem.01559-26","DOIUrl":"10.1128/aem.01559-26","url":null,"abstract":"<p><p>Truffle fungi, such as <i>Tuber melanosporum</i> and <i>T. aestivum</i>, are prized luxury food products that have been historically cultivated in Mediterranean regions of Europe. Recent advances in truffle cultivation have led to the establishment of productive truffle orchards in North America, South America, China, and Australia. Despite these advances, a consistent issue has been the introduction and accidental cultivation of non-target truffle species. Non-target truffle species (e.g., <i>T. indicum</i> and <i>T. brumale</i>) often morphologically resemble target species (e.g., <i>T. melanosporum</i>) and may unintentionally be included as an inoculum and introduced to seedlings. Detecting inoculum and seedling contamination is difficult and often relies on inconsistent morphological analyses or labor-intensive and time-consuming PCR-based methods. Furthermore, quantitative PCR (qPCR) assays have only been developed for <i>T. melanosporum</i> and <i>T. aestivum,</i> leaving truffle growers without rapid tools to detect important contaminants such as <i>T. brumale</i>. Here, we develop a rapid loop-mediated isothermal amplification (LAMP) assay to detect three globally cultivated <i>Tuber</i> species (<i>T. melanosporum</i>, <i>T. borchii</i>, and <i>T. aestivum</i>) and the most common introduced contaminant species (<i>T. brumale</i>). The assays presented here are sensitive to at least 10^-3 ng of DNA and are species-specific. These assays should be of special interest to both truffle orchard owners and truffle testing facilities given the low time commitment, high sensitivity, high specificity, and cost comparable to PCR and qPCR-based approaches.</p><p><strong>Importance: </strong>Despite the global success of truffle cultivation, the accidental cultivation of undesirable truffle species has been a persistent issue. To address this issue, we developed four loop-mediated isothermal amplification (LAMP) assays for the rapid detection of <i>Tuber aestivum</i>, <i>T. borchii</i>, <i>T. brumale,</i> and <i>T. melanosporum</i> from ectomycorrhizal root tips and truffle fruiting bodies. These assays are alternatives to the widely used <i>T. aestivum</i> and <i>T. melanosporum</i> qPCR assays and are the first rapid detection assays for <i>T. borchii</i> and <i>T. brumale</i>.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0155926"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599548/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148838874","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":"Aerobic dissimilatory nitrate reduction to ammonium in <i>Streptomyces hydrogenans</i> EM-F5: metabolic insights, physiological activity, and driving factors.","authors":"Manman Zhang, Jiachen Wang, Dandan Li, Tengxia He, Pan Wu","doi":"10.1128/aem.01039-26","DOIUrl":"10.1128/aem.01039-26","url":null,"abstract":"<p><p>Dissimilatory nitrate reduction to ammonium (DNRA) can retain nitrogen in the soil and reduce greenhouse gas emissions. However, bacterial anaerobic DNRA has certain drawbacks, such as the requirement for strictly anaerobic conditions, complex management, and high cost. A new actinomycete strain EM-F5 was isolated and identified as <i>Streptomyces hydrogenans</i>. Strain EM-F5 showed broad environmental adaptability (pH 6.20-9.20, 0.10-0.50 × 10⁸ CFU/mL of inoculum size, 3.30-7.25 mg/L of dissolved oxygen, and 18℃-38℃). Using starch as the carbon source, the strain EM-F5 achieved 98.04% nitrate reduction and 54.89% ammonium production efficiency via aerobic DNRA, whereas only 37.35% of nitrate was converted under anaerobic conditions. Electron transport system activity (ETSA), adenosine triphosphate (ATP), and nicotinamide adenine dinucleotide (NADH/NAD⁺) reached up to 0.11 μgO₂g^-1min^-1, 29.73 μmol/g, and 5.24, respectively, confirming the high efficiency of aerobic DNRA. The specific activity of nitrate reductase (NR) and nitrite reductase (NIR) was detected as 0.323 and 0.018 U/mg protein, respectively, confirming its key catalytic function in the DNRA pathway. Nitrogen balance (nitrogen loss of 25.46%) experiments further confirmed the aerobic DNRA pathway of strain EM-F5 was NO₃^--N→NO₂^--N→NH₄⁺-N. These findings expand the current understanding of DNRA in actinomycetes and provide a promising microbial resource for nitrogen recycling in soil.</p><p><strong>Importance: </strong>Strain EM-F5 effectively performed dissimilatory nitrate reduction to ammonium (DNRA) with starch as the carbon source under aerobic conditions. Nitrate reduction was as high as 98.04%, and the ammonium production efficiency accounted for 54.89% of the total converted nitrate nitrogen. The aerobic DNRA pathway of strain EM-F5 was NO₃^--N→NO₂^--N→NH₄⁺-N. Meanwhile, it converted 37.35% of nitrate in anaerobic environments. So far, there have been few studies that have demonstrated that actinomycetes can efficiently perform DNRA under aerobic conditions and also convert nitrate under anaerobic conditions. This provides a superior microbial source for treating highly nitrate-contaminated soil.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0103926"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599545/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148817115","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 and physiological characterization of newly isolated nitrous oxide-reducing bacterium <i>Stutzerimonas frequens</i> strain E49 from landfill leachate-treating activated sludge.","authors":"Jameil Magomnang, Shohei Yasuda, Akihiko Terada","doi":"10.1128/aem.00743-26","DOIUrl":"10.1128/aem.00743-26","url":null,"abstract":"<p><p>Nitrous oxide (N₂O) is a potent greenhouse gas and ozone-depleting substance, with a global warming potential 273 times greater than CO₂ over a 100-year horizon. Microbial reduction of N₂O to dinitrogen represents a key pathway for mitigating emissions under diverse environmental conditions. Here, we report the first comprehensive genomic and physiological characterization of <i>Stutzerimonas frequens</i> strain E49, a newly isolated N₂O-reducing bacterium obtained from activated sludge treating landfill leachate. Whole-genome sequencing revealed a 4.51-Mbp circular chromosome and a 35.3-kbp plasmid with high completeness. Functional annotation identified a complete denitrification gene set, including <i>nosZ</i>, as well as the <i>ectABCD</i>-ask gene cluster associated with ectoine biosynthesis, suggesting adaptation to osmotic stress. Strain E49, a uniform rod-shaped bacterium (1.5-2.5 μm), efficiently reduced N₂O under anaerobic conditions in the absence of an externally supplied organic carbon source, achieving a biomass-specific rate of 0.70 ± 0.02 µmol-N₂O/mg-biomass/h and a cell-specific rate of 7.93 ± 0.23 × 10^-10 µmol-N₂O/cell/h. Among the cultivation regimens tested, nitrate-free DSMZ 1180 medium supplemented with NH₄Cl yielded the highest activity, indicating medium-dependent regulation of N₂O respiration. Comparative analysis showed that strain E49 outperformed several reported N₂O-reducing isolates under carbon-limited conditions. These findings demonstrate the metabolic versatility of strain E49 and highlight its potential role as a biological sink for N₂O in low-nutrient environments.IMPORTANCENitrous oxide is a powerful greenhouse gas that contributes to climate change and ozone depletion. Microorganisms that convert nitrous oxide into nitrogen gas play an essential role in reducing these emissions. In this study, we investigated <i>Stutzerimonas frequens</i> strain E49, a bacterium isolated from wastewater treatment sludge. We found that this organism can efficiently reduce nitrous oxide even without an external supply of organic carbon, which is typically required by most bacteria. This suggests that the bacterium can rely on internal energy reserves to carry out this process. We also identified the genetic basis for its nitrous oxide reduction and its ability to adapt to environmental stress. These findings improve our understanding of how nitrous oxide-reducing bacteria function in nutrient-limited environments and may support the development of strategies to mitigate emissions in wastewater treatment and other engineered systems.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0074326"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599507/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148863531","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 beneficial bacterial strains for tomato growth promotion and biocontrol of bacterial canker caused by <i>Clavibacter michiganensis</i>.","authors":"Nasim Sedighian, Marie-Christine Groleau, Eric Déziel","doi":"10.1128/aem.01087-26","DOIUrl":"10.1128/aem.01087-26","url":null,"abstract":"<p><p>Bacterial canker of tomato, caused by <i>Clavibacter michiganensis</i> (<i>Cm</i>), remains difficult to control due to lack of effective management options. In this study, a collection of over 500 bacterial isolates was screened <i>in vitro</i> for antagonistic activity against <i>Cm</i> and plant growth-promoting traits. Based on these results, 32 candidates were evaluated <i>in planta</i>, leading to the identification of three highly effective strains: <i>Pantoea agglomerans</i> SO16PY and two <i>Pseudomonas marginalis sensu lato</i> strains, IRDA16 and SO16PC, which consistently enhanced tomato vegetative growth. Notably, <i>P. agglomerans</i> SO16PY delayed disease onset in <i>Cm</i>-inoculated plants by up to 7 days and significantly reduced wilting severity, lowering the disease severity score from 85% to 45%. Strains IRDA16 and SO16PC also restricted disease development, reducing severity scores to 67.5% and 57.5%, respectively. Whole-genome sequencing and comparative genomics revealed that strains IRDA16 and SO16PC form a distinct, specialized plant-associated lineage within the <i>Pseudomonas marginalis</i> group, exhibiting average nucleotide identity ≈ 96% and digital DNA-DNA hybridization ≈ 69.5% values near species delineation thresholds. Genome mining identified diverse biosynthetic gene clusters encoding non-ribosomal peptide synthetases, the lipopeptide viscosin, and terpenes, which likely drive the biostimulant and antagonistic traits of this novel <i>Pseudomonas</i> lineage. Together, these findings characterize promising bacterial candidates with dual biostimulant and biocontrol capacities while uncovering a genomically distinct <i>Pseudomonas</i> lineage optimized for beneficial plant-microbe interactions in sustainable agriculture.IMPORTANCE<i>Clavibacter michiganensis</i> (<i>Cm</i>) is a major bacterial pathogen of tomato and poses a significant economic threat to global production. It is classified as an A2 quarantine pathogen by the European and Mediterranean Plant Protection Organization (EPPO). Current management strategies rely largely on chemical control, including copper-based compounds (e.g., Bordeaux mixture, copper oxychloride), mancozeb, and antibiotics like streptomycin. However, these approaches raise increasing concerns related to environmental contamination, phytotoxicity, and the development of resistant pathogen populations. As a sustainable alternative, plant growth-promoting bacteria have emerged as promising biocontrol agents. In this study, we identified bacterial strains exhibiting antagonistic activity against <i>Cm</i> both <i>in vitro</i> and <i>in planta</i>. Notably, these strains also enhanced tomato growth parameters, demonstrating their dual functionality. Given the environmental drawbacks associated with chemical inputs, the use of such beneficial microorganisms represents a promising strategy for advancing sustainable and eco-friendly tomato production systems.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0108726"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148878999","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}