Applied and Environmental Microbiology最新文献

{"title":"An antibiotic-free antimicrobial combination of bacteriocins and a peptidoglycan hydrolase: <i>in vitro</i> and <i>in vivo</i> assessment of its efficacy.","authors":"Christian Kranjec, Thomas F Oftedal, Kirill V Ovchinnikov, Vinícius da Silva Duarte, Simen Hermansen, Magdalena Kaus-Drobek, Izabela Sabała, Davide Porcellato, Harald Carlsen, Morten Kjos","doi":"10.1128/aem.02433-24","DOIUrl":"https://doi.org/10.1128/aem.02433-24","url":null,"abstract":"<p><p>Mastitis is an inflammatory disease of the mammary gland usually caused by bacterial pathogens that gain physical access to the glandular epithelium through the teat canal. In bovines, common mastitis-causing agents are environmental or pathogenic bacterial species, including staphylococci, streptococci, enterococci, and gram-negative bacteria such as <i>Escherichia coli</i>. Current therapeutic strategies for bovine mastitis typically involve the administration of antibiotic formulations into the infected udder, which can result in increased selection for antibiotic resistance and the accumulation of antibiotic residues in milk. In this study, we sought to develop an antibiotic-free antimicrobial formulation for the treatment of bovine mastitis based on bacterial antimicrobial peptides (bacteriocins) and proteins (peptidoglycan hydrolases). Using a combination of <i>in vitro</i> assays with a range of bacteriocins, we show that the combination of the thiopeptide micrococcin P1 (MP1) and the lantibiotic nisin A (NisA) is a robust antimicrobial formulation that effectively inhibits the growth of bovine mastitis-derived bacteria, both in planktonic and biofilm-associated growth modes. The addition of AuresinePlus (Aur, a staphylococcus-specific peptidoglycan hydrolase) further increased the antimicrobial potency against <i>S. aureus</i>. Furthermore, using two mouse models, a skin infection model and a mastitis model, we show that the combination MP1-NisA-Aur effectively inhibits methicillin-resistant <i>S. aureus in vivo</i>. We discuss the potential and challenges of using antibiotic-free antimicrobial combinations in the treatment of bacterial infections.IMPORTANCEThe spread of antibiotic resistance is a major global concern. This is reflected in the One Health concept, which is based on the premise that the spread of antibiotic resistance can only be addressed through coordinated efforts to promote \"healthy people, healthy environments, and healthy animals.\" It is therefore of great importance to reduce the use of medically important antibiotics in agriculture, where treatment of bovine mastitis is one of the major drivers of antibiotics use. In this work, we investigate the use of antimicrobial peptides and proteins as an alternative treatment for bovine mastitis pathogens.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0243324"},"PeriodicalIF":3.9,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473849","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":"Prolonged light exposure time enhances the photosynthetic investment in osmotrophic <i>Ochromonas</i>.","authors":"Xiaoqing Xu, Xiaoyu Cheng, Zhihao Shao, Zhou Yang, Lu Zhang","doi":"10.1128/aem.01032-25","DOIUrl":"https://doi.org/10.1128/aem.01032-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The photoperiod, as a critical external environmental signal, triggers a cascade of signaling responses in organisms that significantly affect photosynthetic efficiency and photomorphogenesis in autotrophs, while also influencing behavioral patterns and activity rhythms of heterotrophs. Despite its importance, the mechanisms by which mixotrophs respond to photoperiod changes remain largely unexplored. It is crucial for understanding metabolic plasticity how mixotrophs respond to light availability and make optimal decisions during diurnal transitions by regulating their autotrophic and osmotrophic pathways. Therefore, this study focused on &lt;i&gt;Ochromonas gloeopara&lt;/i&gt;, a eukaryotic protist capable of both photoautotrophic and osmotrophic growth, aiming to explore the metabolic strategies of mixotrophs in response to changes in photoperiod. The results showed the following. (i) Under autotrophic conditions, the optimal photoperiod for photosynthetic efficiency in &lt;i&gt;Ochromonas&lt;/i&gt; was approximately 12 h of light exposure, while prolonged light exposure beyond this duration reduced photosynthetic investment and efficiency, accompanied by an increase in heat dissipation to prevent photodamage. (ii) Under osmotrophic conditions, &lt;i&gt;O. gloeopara&lt;/i&gt; adapted to prolonged light exposure by reducing. The reliance on external organic carbon sources and enhancing photosynthetic capacity, thereby shifting towards a more autotrophic metabolic mode. This study systematically elucidates the nutritional strategies of mixotrophic &lt;i&gt;O. gloeopara&lt;/i&gt; in response to photoperiod changes at the levels of population dynamics, photosynthetic physiology, and carbon acquisition pathways, deepening our understanding of the response to photoperiodic changes in mixotrophs. These findings provide important theoretical insights for understanding the functional roles of mixotrophs in ecosystems and for accurately predicting changes in global carbon cycles.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Mixotrophs possess flexible metabolism modes and multiple ecological roles, making them sensitive to environmental changes. Due to their widespread distribution and unique nutritional strategy, they serve as key functional groups in marine and freshwater ecosystems, with significant roles in global biogeochemical cycles. Photoperiod, a critical environmental cue, regulates circadian rhythms and may influence the metabolic strategies of mixotrophs. Therefore, this study focused on how the mixotrophic microorganisms &lt;i&gt;Ochromonas gloeopara&lt;/i&gt; adjusted autotrophic and osmotrophic pathways in response to photoperiodic changes. These findings highlight the metabolic flexibility of mixotrophic organisms in response to photoperiodic changes, providing new insight on how mixotrophs regulate the flow of materials and reshape the food web structures. This research offers valuable and innovative perspectives for understanding the functional roles of mixotrophic microorganisms in ecosystems, wit","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0103225"},"PeriodicalIF":3.9,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473794","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":"Phenotypic analysis of various <i>Clostridioides difficile</i> ribotypes reveals consistency among core processes.","authors":"Merilyn A Beebe, Daniel Paredes-Sabja, Larry K Kociolek, César Rodríguez, Joseph A Sorg","doi":"10.1128/aem.00964-25","DOIUrl":"10.1128/aem.00964-25","url":null,"abstract":"<p><p><i>Clostridioides difficile</i> infections (CDI) cause almost 300,000 hospitalizations per year, of which ~15%-30% are the result of recurring infections. The prevalence and persistence of CDI in hospital settings have resulted in an extensive collection of <i>C. difficile</i> clinical isolates and their classification, typically by ribotype. While much of the current literature focuses on one or two prominent epidemic ribotypes (e.g., RT027), recent years have seen several other ribotypes dominate the clinical landscape (e.g., RT106 and RT078). Some ribotypes are associated with severe disease and/or increased recurrence rates, but why certain ribotypes are more prominent or harmful than others remains unknown. Because <i>C. difficile</i> has a large, open pan-genome, this observed relationship between ribotype and clinical outcome could be a result of the genetic diversity of <i>C. difficile</i>. Thus, we hypothesize that the core biological processes of <i>C. difficile</i> are conserved across ribotypes/clades. We tested this hypothesis by observing the growth kinetics, sporulation, germination, production of toxin A and toxin B, bile acid sensitivity, bile salt hydrolase activity, and surface motility of 15 strains belonging to various ribotypes spanning each known <i>C. difficile</i> clade. In viewing these phenotypes across each strain, we see that core phenotypes (growth, germination, sporulation, and resistance to bile salt toxicity) are remarkably consistent across clades/ribotypes. This suggests that variations observed in the clinical setting may be due to unidentified factors in the accessory genome or due to unknown host factors.IMPORTANCE<i>Clostridioides difficile</i> infections impact thousands of individuals every year, many of whom experience recurring infections. Clinical studies have reported an unexplained correlation between some clades/ribotypes of <i>C. difficile</i> and disease severity/recurrence. Here, we demonstrate that <i>C. difficile</i> strains across major clades/ribotypes are consistent in their core phenotypes. This suggests that such phenotypes are not responsible for variations in disease severity/recurrence and are ideal targets for the development of therapeutics meant to treat <i>C. difficile</i>-related infections.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0096425"},"PeriodicalIF":3.9,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473793","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":"Distinct microbiome profiles on vaginally inserted polypropylene midurethral mesh slings compared to vaginal, urinary, and skin microbiomes.","authors":"Nazish Abbas, Thomas Willmott, Paul M Campbell, Gurdeep Singh, Maya Basu, Fiona Reid, Andrew J McBain","doi":"10.1128/aem.02463-24","DOIUrl":"https://doi.org/10.1128/aem.02463-24","url":null,"abstract":"<p><p>Midurethral slings are widely used in the treatment of stress urinary incontinence in women. However, little is known about the microbiomes that develop on these implants, their relationship to the urinary and vaginal microbiomes, or their potential role in mesh-related complications. In this study, we characterized the microbiomes of explanted midurethral slings and examined associations with clinical complications. Seventy-four women provided a total of 397 samples, including explanted mesh, urine, and swabs from the vagina and groin or suprapubic skin. Participants were categorized into clinical groups: chronic pain, vaginal mesh exposure, lower urinary tract perforation, or recurrent incontinence (control group). Samples underwent 16S rRNA gene sequencing. The mesh microbiome was dominated by Firmicutes, Proteobacteria, and Actinobacteria, with <i>Enterococcus</i> particularly abundant. Microbial diversity was significantly higher in mesh samples compared to vaginal and skin swabs, but not urine. The mesh microbiome was compositionally distinct from the urinary, vaginal, and skin microbiomes, potentially reflecting vaginal microbiome alterations due to urinary incontinence at the time of implantation. Differences in microbial diversity in mesh and skin samples among women with pain suggest a possible microbial contribution to mesh complications. These findings demonstrate the presence of distinct, site-specific microbial communities on explanted midurethral slings, with potential implications for understanding mesh-related complications.IMPORTANCEStress urinary incontinence commonly affects women, and effective treatment is essential. Midurethral mesh slings have provided effective relief; however, long-term complications such as chronic pain, vaginal mesh exposure, and lower urinary tract perforation have emerged. The pathophysiology of these complications is not well understood but is thought to involve a heightened inflammatory response to mesh implants. The local microbiome may contribute to this inflammation. We have shown that the mesh samples harbored a distinct microbiome and that differences in microbial composition may be associated with mesh complications. Understanding the role of specific bacteria in modulating host responses may offer new insights into the pathogenesis of mesh complications and inform future clinical approaches.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0246324"},"PeriodicalIF":3.9,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473851","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":"Wastewater monitoring allows the detection of uncommon and highly pathogenic enterovirus types.","authors":"Lucia Mangeri, Annalisa Scarazzato, Francesco Righi, Elisa Galuppini, Giulia Magagna, Michela Tilola, Virginia Filipello, Enrico Pavoni, Vito Tranquillo, Maria Antonia De Francesco, Marina Nadia Losio, Barbara Bertasi","doi":"10.1128/aem.00534-25","DOIUrl":"https://doi.org/10.1128/aem.00534-25","url":null,"abstract":"<p><p>The genus <i>Enterovirus</i> (EV) includes small ubiquitous viruses with a single-stranded positive-RNA genome. Most EV infections are asymptomatic, but pathogenic EVs are responsible for a wide range of diseases and occasionally epidemics. The aim of the work was to monitor the distribution of EVs present in wastewater collected during the 2 year study period (2022-2023). Three hundred ninety-nine samples were received from three wastewater treatment plants of the Brescia, Cremona, and Bergamo provinces, Lombardy, Italy. One-step real-time reverse transcription-PCR screening showed positivity in 107 samples. Of these, 67 were successfully genotyped: 8 by Sanger sequencing only, 7 by next-generation sequencing metabarcoding only, and 52 by both methods. The most detected species was <i>Enterovirus B</i>, followed by <i>Enterovirus A</i>, <i>Enterovirus C,</i> and <i>Enterovirus D</i>. As many as 26 different types of non-polio EVs were identified, of which the most frequently detected were two <i>Enterovirus B</i>: echovirus 11 (E11) and coxsackievirus B5 (CVB5). Among <i>Enterovirus A</i>, the predominant types were CVA16 and CVA6. As for <i>Enterovirus C</i>, the types with the highest frequency were CVA13 and EV-C99; in addition, CVA24, which has been associated with outbreaks of acute hemorrhagic conjunctivitis, was found in two samples from Verziano (Brescia) and one from Bergamo. The <i>Enterovirus D</i> species was represented only by type EV-D68, which has recently been related to outbreaks in Europe and the United States. This study reveals a wide EV presence in urban wastewater in the considered area.IMPORTANCEWastewater-based epidemiology uses urban wastewater as a source of dynamic observation for monitoring the circulation of pathogens. A major strength of this surveillance approach is its ability to detect both symptomatic and asymptomatic infections. Through molecular characterization, it was possible to identify uncommon EVs that may lead to serious complications. Furthermore, next-generation sequencing metabarcoding allowed the identification of multiple EV types within a single sample. Wastewater monitoring could therefore be further leveraged as a complementary tool to support the monitoring of severe non-polio EV-related diseases.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0053425"},"PeriodicalIF":3.9,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473795","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":"Acid-resistant <i>Bacillus velezensis</i> effectively controls pathogenic <i>Colletotrichum capsici</i> and improves plant health through metabolic interactions.","authors":"Yuxiang Peng, Chi Zhou, Fangying Qiu, Di Peng, Xinyu Wang, Xin Li","doi":"10.1128/aem.00340-25","DOIUrl":"https://doi.org/10.1128/aem.00340-25","url":null,"abstract":"<p><p><i>Colletotrichum capsici</i> is the etiological agent of Capsicum anthracnose. <i>Bacillus velezensis</i> has traditionally been recognized as an effective biocontrol agent; however, its efficacy decreases due to soil acidification. In this study, we domesticated <i>Bacillus velezensis</i> XY40-1 along an acid resistance gradient, resulting in a strain capable of growth at pH 4, and might adapt to acidic environments by regulating genes related to spore formation. Notably, the domesticated <i>Bacillus velezensis</i> XY40-1 exhibits significant antagonistic activity against <i>Colletotrichum capsici</i> in acidic dual cultures and effectively reduces the disease index in <i>Capsicum</i>. The domesticated strain employs a direct antifungal strategy under acidic conditions, with the production of amylocyclicin, regulated by <i>acnA</i>, potentially serving as a primary mechanism through which <i>Bacillus velezensis</i> combats <i>Colletotrichum capsici</i>. Conversely, under neutral conditions, domesticated <i>Bacillus velezensis</i> focuses on bolstering its defense mechanisms by increasing the expression of <i>katA</i>, <i>ahpF</i>, and <i>ahpC</i> genes to detoxify peroxides. In addition, a dual RNA-Seq analysis comprehensively investigated the acid tolerance mechanisms and defensive responses of <i>B. velezensis</i> and the pathogenic mechanisms of <i>C. capsici</i>, providing a foundation for the practical application of <i>B. velezensis</i> as a biocontrol agent. These findings offer important insights into the impact of soil acidification on plant disease suppression and contribute to the development of sustainable agricultural practices.</p><p><strong>Importance: </strong>Recently, the increasing issue of soil acidification has worsened anthracnose disease in Capsicum, caused by <i>Colletotrichum capsici</i>. Our study demonstrated that <i>Bacillus velezensis</i> can effectively inhibit the growth of <i>Colletotrichum capsici</i>. However, the molecular mechanisms underlying the interaction between <i>Bacillus velezensis</i> and <i>Colletotrichum capsici</i> remain largely unexplored. Here, we developed an interaction system between <i>Bacillus velezensis</i> and <i>Colletotrichum capsici</i> to explore their dynamic relationship. By employing dual RNA-Seq methods, we were able to comprehensively investigate the acid tolerance mechanisms and defense responses of <i>Bacillus velezensis</i>, alongside the pathogenic mechanisms of <i>Colletotrichum capsici</i>. This establishes the groundwork for utilizing <i>Bacillus velezensis</i> as an effective biocontrol agent in agriculture.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0034025"},"PeriodicalIF":3.9,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473848","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":"Cryptic cycling by electroactive bacterioplankton in Trout Bog Lake.","authors":"Charles N Olmsted, Mark Gahler, Eric Roden, Ben Peterson, James Lazarcik, Patricia Q Tran, Maureen Berg, Donald A Bryant, Danielle Goudeau, Rex R Malmstrom, Mohan Qin, Katherine D McMahon","doi":"10.1128/aem.01789-24","DOIUrl":"10.1128/aem.01789-24","url":null,"abstract":"<p><p>The potential for extracellular electron transfer (EET) is a prevailing genomic feature of humic lake bacterioplankton. However, there has been little evidence for the substantial ecological contribution predicted by genetics. We hypothesized that anoxygenic phototrophic electrotrophs and accompanying heterotrophic electrogens cycle dissolved organic matter (DOM) between oxidized and reduced states. We predicted that such bacterioplankton would exhibit diel-scale oscillations due to the light dependency of photosynthesis. Using Trout Bog Lake in Wisconsin, USA, as our model ecosystem, we profiled the water column with depth-discrete metagenomic, physiochemical, and electrochemical analyses. We observed variation in oxidation reduction potential (ORP) in response to sunlight, initiating at depths populated by anoxygenic phototrophs with EET genes. We developed an automated buoy to measure electric current flow between many pairs of electrodes simultaneously, observing correlation in electron consumption to sunlight. Our results, combined with published metatranscriptomic analysis, indicate the occurrence of electron cycling between phototrophic oxidation (electrotrophic metabolism) by <i>Chlorobium</i> and anaerobic respiration (electrogenic metabolism) by <i>Geothrix</i>, involving DOM. We also repeatedly observed gradual seasonal increases in hypolimnion ORP throughout summer. These diel and seasonal patterns imply that electroactive DOM mediates the ecology of electroactive bacteria in lakes, controlling humic lake methane emissions.IMPORTANCEWe investigated the physical, chemical, and redox characteristics of a bog lake and electrodes hung therein to test the hypothesis that dissolved organic matter is being cycled between oxidized and reduced states by electroactive bacterioplankton powered by phototrophy. To do so, we performed field-based analyses on multiple timescales using both established and novel instrumentation. We paired these analyses with recently developed bioinformatics pipelines for metagenomics data to investigate genes that enable electroactive metabolism and accompanying metabolisms. Our results are consistent with our hypothesis and yet upend some of our other expectations. Our findings have implications for understanding greenhouse gas emissions from lakes, including electroactivity as an integral part of lake metabolism throughout more of the anoxic parts of lakes and for a longer portion of the summer than expected. Our results also give a sense of what electroactivity occurs at given depths and provide a strong basis for future studies.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0178924"},"PeriodicalIF":3.9,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144332347","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":"Landscape-scale endophytic community analyses in replicated grapevine stands reveal that dieback disease is unlikely to be caused by specific fungal communities.","authors":"Vinciane Monod, Valérie Hofstetter, Olivier Viret, Vivian Zufferey, Katia Gindro, Daniel Croll","doi":"10.1128/aem.00782-25","DOIUrl":"10.1128/aem.00782-25","url":null,"abstract":"<p><p>Tree diebacks are complex and multifactorial diseases with suspected biotic and abiotic components. Microbiome effects on plant health are challenging to assess due to the complexity of fungal and bacterial communities. Grapevine wood dieback is the main threat to sustainable production worldwide, and no causality with microbial species has been established despite long-standing claims of fungal drivers. Here, we aimed to test the hypothesis that grapevine esca disease progression has reproducible drivers in the fungal species community. For this, we analyzed a set of 21 vineyards planted simultaneously with a single susceptible cultivar to provide unprecedented replication at the landscape scale. We sampled a total of 496 plants at the graft union across vineyards in 2 different years to perform deep amplicon sequencing analyses of the fungal communities inhabiting grapevine trunks. The communities were highly diverse with a total of 4,129 amplified sequence variants assigned to 697 distinct species. We detected trunk fungal community shifts over years of sampling, vineyards and climatic conditions, as well as disease status. However, we detect no specific fungal species driving symptom development across vineyards, contrary to long-standing expectations. The high degree of environmental standardization in the decade-long experimental plots and the well-powered replication provide the clearest evidence yet that grapevine wood dieback is most likely caused by environmental factors rather than specific pathogens. Furthermore, our study shows how landscape-scale replicated field surveys allow for powerful hypothesis testing for complex dieback disease drivers and prioritize future research directions.IMPORTANCETree diebacks are complex diseases suspected to be caused by both biological and environmental drivers. Grapevine wood dieback is a major threat to vineyards worldwide, but no specific microbial species have been experimentally implicated, despite claims that fungi are causing the symptoms. Here, we tested whether the progression of grapevine esca disease is driven by specific fungal species. We analyzed 21 long-established vineyards planted at the same time with the same susceptible grape variety to ensure consistent conditions. Over the years, we observed changes in the fungal communities inhabiting the trunk depending on the vineyard, climate, and disease status. However, contrary to expectations, we did not detect any specific fungal species that consistently could cause symptoms across the vineyards. The high level of environmental control and replication in our study provides strong evidence that grapevine wood dieback is more likely caused by environmental factors rather than specific pathogens.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0078225"},"PeriodicalIF":3.9,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144332362","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":"Efficacy of three chemical disinfectants and steam against <i>Clostridioides difficile</i> endospores on nylon carpet with two different backing systems.","authors":"Jinge Huang, Angela Fraser, Xiuping Jiang","doi":"10.1128/aem.00861-25","DOIUrl":"10.1128/aem.00861-25","url":null,"abstract":"<p><p>Carpet could serve as a potential vehicle for transmitting <i>Clostridioides difficile</i> endospores, a leading cause of healthcare-associated infections. To develop carpet disinfection practices, a validated recovery method and standard efficacy testing method are necessary. The recovery method was optimized to detect <i>C. difficil</i>e endospores on carpet by using different concentrations of Tween-80 and varying stomaching times. Adding 0.2% Tween-80 followed by stomaching for 3 min and sonication increased the recovery rate of <i>C. difficile</i> endospores to >60%. The efficacy of three disinfectants (two hydrogen peroxide-based products, A and B, and one chlorine-based product, C) and steam was tested against <i>C. difficile</i> endospores on two types of nylon carpet (with water-permeable backing and waterproof backing). The results showed that product B was the most effective among the chemical disinfectants, achieving a 5.8 and 4.9 log₁₀ CFU reduction of <i>C. difficile</i> endospores in 30 min on carpets with water-permeable and waterproof backings, respectively. A steam treatment of 120 s resulted in 4.9 and >6.0 log₁₀ CFU reduction on water-permeable and waterproof backings, respectively. On water-permeable backing, 30 s steam treatment followed by application of H₂O₂-based products A and B resulted in a 4.4 and >6.1 log₁₀ CFU reduction of <i>C. difficile</i> endospores, respectively. Overall, a 120 s steam treatment was more effective than any of the three disinfectants tested. Disinfectant efficacy varied by carpet backing type, underscoring the need for guidance in carpet selection for healthcare safety.</p><p><strong>Importance: </strong><i>Clostridioides difficile</i>, a spore-forming anaerobic bacterium and a leading cause of healthcare-associated infections, can be transmitted from the floor to other surfaces via air movement. Therefore, disinfection of all floors after cleaning, regardless of type, might be necessary to prevent recurrent <i>C. difficile</i> infections among patients. To develop carpet disinfection practices, a validated recovery method and standard efficacy testing method are necessary. In this study, we first optimized the spore recovery method from carpets. Next, our study demonstrated that carpet backing affected the efficacy of chemical disinfectants and steam against <i>C. difficile</i> endospores. Steam was particularly effective on carpets with waterproof backing, while only product B showed strong efficacy on carpets with water-permeable backing. When steam was combined with a chemical disinfectant, the efficacy of both H₂O₂-based products against <i>C. difficile</i> endospores was enhanced. These findings can inform the development of carpet disinfection practices.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0086125"},"PeriodicalIF":3.9,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144332348","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":"Vip3C proteins from <i>Paenibacillus</i> spp. for controlling lepidopteran crop pests.","authors":"Todd Ciche, William Moar, Aqeel Ahmad, David Bowen, Catherine Chay, Arlene Howe, Uma Kesanapalli, Jennifer Lutke, Gregory Bean, Jason Milligan, Michael Pleau, Yong Yin, Waseem Akbar, Marty Heppler, Cara Griffith, Kimberly Morrell, Katherine Dunkmann, Heather Anderson, Jeffrey Ahrens, Pacifica Sommers, E Sethe Burgie, Fred Zinnel, Meiying Zheng, James Fitzpatrick, Michael Rau, Timothy Rydel, Tommi White, David Kerns, James Roberts","doi":"10.1128/aem.00253-25","DOIUrl":"10.1128/aem.00253-25","url":null,"abstract":"<p><p>New proteins are needed to control insects not controlled with <i>Bacillus thuringiensis</i> (Bt) crops, and those evolving resistance to Bt crops. These proteins are increasingly being reported from non-Bt organisms to control Bt-resistant insects. However, these proteins mostly control the corn rootworm, <i>Diabrotica</i> spp. (Coleoptera), whereas most Bt-resistant insects are lepidopteran. We hypothesized that diversifying our search for proteins into non-Bt organisms, such as those related to <i>Paenibacillus popilliae,</i> used to control Japanese beetle <i>Popillia japonica</i>, could yield proteins with new insecticidal activities against Lepidoptera. Here, we identified Vip3Cb1 and Vip3Cc1 with broad lepidopteran activity, the first Vip3 proteins discovered from strains in the <i>P. popilliae-</i>containing clade. Vip3Cb1 protected plants against cotton bollworm, <i>Helicoverpa zea</i> and tobacco budworm<i>, Chloridea virescens</i> and <i>H. zea,</i> fall armyworm, <i>Spodoptera frugiperda</i>, and Southwestern corn borer, <i>Diatraea grandiosella</i>, in cotton and maize, respectively, like commercial Vip3Aa. Distinct from Vip3Aa, Vip3Cb1 also protected maize against European corn borer, <i>Ostrinia nubilalis</i>, the primary maize pest in the United States, with recent reports of resistance to Bt proteins. Consistent with previous reports, insects resistant to Vip3Aa were cross-resistant to Vip3Cb1. Cryo-electron microscopy demonstrated that Vip3Cb1 formed a pore-shaped tetramer upon proteolytic activation, in agreement with the pore-forming mechanism of action of Vip3Aa. Thus, diversifying the search beyond Bt has led to the discovery of the first Vip3 proteins from <i>Paenibacillus</i> spp. with different activity spectra from Vip3Aa, providing additional tools to control pests, including those currently resistant to Bt Cry proteins.IMPORTANCENew insecticidal proteins are needed for controlling insect pests that can devastate crop yield if left uncontrolled. Diversifying our search for new insecticidal proteins in <i>Paenibacillus</i> spp. resulted in the discovery of Vip3Cb1 and Vip3Cc1 insecticidal proteins active against lepidopteran crop pests. Structure and cross-resistance studies indicate overlap in the mechanism of action between Vip3Cb1 and commercial Vip3Aa. However, new activities, such as controlling European corn borer, make these proteins important new tools in the insect control toolbox.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0025325"},"PeriodicalIF":3.9,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144332363","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}