Applied and Environmental Microbiology最新文献

{"title":"The cell surface-associated rhamnose-glucose polysaccharide represents the receptor of <i>Streptococcus thermophilus</i> bacteriophage P738.","authors":"Zoe Kampff, Irina Sadovskaya, Evgeny Vinogradov, Brian McDonnell, Douwe van Sinderen, Jennifer Mahony","doi":"10.1128/aem.01238-25","DOIUrl":"https://doi.org/10.1128/aem.01238-25","url":null,"abstract":"<p><p><i>Streptococcus thermophilus</i> is a key lactic acid bacterial species extensively used in dairy fermentations, where bacteriophage (phage) infections pose a significant threat to production efficiency. While the cell surface receptors for four of the five currently known streptococcal phage genera have previously been identified, the specific host-encoded receptor for the P738 phage group has not been elucidated to date. In this study, P738 bacteriophage-insensitive mutants of <i>S. thermophilus</i> UCCSt50 were isolated, and whole-genome sequencing revealed mutations in a glycosyltransferase-encoding gene within the <i>rgp</i> locus, responsible for the biosynthesis of the cell wall-associated <u>r</u>hamnose-<u>g</u>lucose <u>p</u>olysaccharide (RGP). Compositional and methylation analysis demonstrated that loss of a terminal rhamnose residue from the RGP side chain underpinned the observed resistance to P738 binding and infection. Fluorescent binding assays validated the biological functionality of the predicted receptor binding protein of P738, confirming the critical role of the RGP side chain in phage adsorption. These findings reveal a strict requirement for a complete tetrasaccharide side chain structure for P738 binding, contrasting with the less stringent requirements observed for the <i>Brussowvirus</i> SW13. This work offers valuable insights to guide the development of phage-robust starter cultures through knowledge-based strain selection and rotation strategies, thereby supporting more sustainable and reliable dairy fermentation processes.</p><p><strong>Importance: </strong><i>Streptococcus thermophilus</i> is one of the most extensively applied members of the lactic acid bacteria, being extensively used as a bacterial starter culture in the production of fermented foods, including cheeses and yogurt. Bacteriophage infections present a significant threat to industrial dairy fermentations, which can lead to substandard production processes and product quality. Understanding phage-host interactions, which commence with the recognition and binding of a given bacteriophage to a particular host-encoded, cell surface-associated receptor, is essential for developing strategies to minimize phage-related risks in dairy fermentations. This study identifies the specific cell surface polysaccharide structure produced by <i>Streptococcus thermophilus</i> as the receptor required for infection by phage P738, bridging a key knowledge gap in phage-host interactions in this important industrial bacterial species. By elucidating how phage P738 recognizes and binds to its host, this work offers valuable information to aid strain selection and the development of phage-robust starter cultures.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0123825"},"PeriodicalIF":3.7,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145038897","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":"CalR is an activator of biofilm formation in <i>Vibrio parahaemolyticus</i>.","authors":"Jingyang Chang, Yining Zhou, Miaomiao Zhang, Xue Li, Nan Zhang, Xi Luo, Bin Ni, Renfei Lu, Yiquan Zhang","doi":"10.1128/aem.00724-25","DOIUrl":"https://doi.org/10.1128/aem.00724-25","url":null,"abstract":"<p><p><i>Vibrio parahaemolyticus</i>, the leading cause of seafood-associated gastroenteritis, often exists in a biofilm state. Biofilm formation in this bacterium is regulated by a complex network of factors, including the second messenger c-di-GMP. CalR, a LysR-type transcriptional regulator, has been demonstrated to play a role in regulating the expression of virulence genes and swarming motility of <i>V. parahaemolyticus</i>. In this study, we demonstrate that CalR positively regulates biofilm formation by enhancing the production of exopolysaccharides (EPSs), extracellular proteins, extracellular DNA (eDNA), and c-di-GMP. RNA sequencing reveals that CalR regulates the transcription of 167 genes, including those potentially involved in c-di-GMP metabolism (e.g., <i>vpa0184</i>, <i>vpa0198</i>, and <i>vpa1429</i>) and biofilm-associated regulators (e.g., <i>scrP</i>). CalR directly suppresses the transcription of <i>scrP</i>, <i>vpa0184</i>, and <i>vpa0198</i> while activating <i>vpa1429</i> transcription in a direct manner. Additionally, CalR directly activates the transcription of <i>cpsA</i> but indirectly activates that of <i>scvE</i>, both of which are involved in EPS production. In summary, these findings elucidate the regulatory mechanisms by which CalR promotes biofilm formation in <i>V. parahaemolyticus</i> and highlight its role in modulating c-di-GMP homeostasis and biofilm matrix production. This work enhances our understanding of the regulatory network governing biofilm formation by <i>V. parahaemolyticus</i>.IMPORTANCEBiofilm formation is a critical survival strategy for <i>V. parahaemolyticus</i>, allowing it to persist in adverse environments. Understanding the regulatory mechanisms underlying biofilm formation is essential for developing strategies to control infections caused by this pathogen. This work demonstrates that CalR positively regulates the production of EPS, extracellular proteins, and eDNA, as well as biofilm formation by <i>V. parahaemolyticus</i>. CalR regulates the global gene expression in <i>V. parahaemolyticus</i>, including genes such as <i>scrP</i>, <i>vpa0184</i>, <i>vpa0198</i>, and <i>vpa1429</i>. ScrP negatively impacts <i>V. parahaemolyticus</i> biofilm formation, whereas <i>vpa0184</i>, <i>vpa0198</i>, and <i>vpa1429</i> contribute to c-di-GMP metabolism. CalR represses <i>scrP</i>, <i>vpa0184</i>, and <i>vpa0198</i> while activating <i>vpa1429</i> and also promotes the production of c-di-GMP. These findings indicate how CalR positively regulates biofilm formation by <i>V. parahaemolyticus</i>.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0072425"},"PeriodicalIF":3.7,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145032553","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":"Enhanced metagenomic surveillance for bovine respiratory disease pathogens and antimicrobial resistance by hybridization capture sequencing.","authors":"Jennifer N Russell, Daniël Kos, Elhem Yacoub, Ashton N Sies, Brian Warr, Murray Jelinski, Antonio Ruzzini, Andrew D S Cameron","doi":"10.1128/aem.00977-25","DOIUrl":"https://doi.org/10.1128/aem.00977-25","url":null,"abstract":"<p><p>Bovine respiratory disease (BRD) is the primary disease of cattle and is responsible for most of the antibiotic use in the beef industry, both for metaphylaxis and treatment. Infection prevention and targeted treatments would benefit from detecting and identifying bacterial pathogens and, ideally, assessing antibiotic sensitivity. Here, we report success refining targeted metagenomics by hybridization capture sequencing (CapSeq) to detect and genotype bacterial pathogens and genes for antibiotic resistance in BRD. We developed a novel multi-locus sequence typing (MLST) strategy to both enhance assay sensitivity and provide epidemiological data compatible with traditional typing assays. Phylogenetically informed panel design by ProbeTools coupled with hybridization capture enabled the sequencing of novel genotypes and elucidated coinfection by distinct strains of <i>Mycoplasmopsis bovis</i>. CapSeq was orders of magnitude more sensitive than classical metagenomics at a scale compatible with low-throughput DNA sequencing capacity in diagnostic laboratories. Iterative design and testing of longer typing loci confirmed improvements in locus detection through a strategy applicable to future target selection. CapSeq detected bacterial pathogens that evaded detection by traditional metagenomics, and it demonstrated greater range and sensitivity for antibiotic resistance gene detection.</p><p><strong>Importance: </strong>Shotgun metagenomic sequencing for infectious disease diagnostics and surveillance benefits from simultaneous detection of multiple pathogens in a sample. Adding a hybridization probe capture step to the metagenomics workflow enriches targeted loci to improve the sensitivity of pathogen detection without compromising the ability to detect pathogen variants. Our custom probe panel enables multi-locus sequence typing of bovine respiratory disease agents as well as capture of antibiotic resistance genes, which improves the sensitivity of metagenomic testing and provides genotyping data compatible with traditional assays. This study demonstrates the utility of new design principles for probe panels; it also demonstrates how targeted metagenomics provides important new insights into co-infections and is equally useful for surveillance of environmental reservoirs of disease agents.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0097725"},"PeriodicalIF":3.7,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145028739","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":"Primary production by the purple nonsulfur bacterium <i>Rhodopila globiformis</i> in an acidic, moderately sulfidic warm spring.","authors":"Kristopher M Fecteau, Katelyn M Weeks, R Vincent Debes, Tanner J Barnes, Kirtland J Robinson, Joshua J Nye, Melody R Lindsay, Eric S Boyd, Everett L Shock","doi":"10.1128/aem.01217-25","DOIUrl":"10.1128/aem.01217-25","url":null,"abstract":"<p><p>Populations of the acidophilic purple nonsulfur bacterium <i>Rhodopila globiformis</i> were identified in two geographically distinct thermal areas in Yellowstone National Park (Wyoming, USA), as confirmed by 16S rRNA gene sequencing and detection of characteristic methoxylated ketocarotenoids. Microcosm-based carbon uptake assays where oxygenic photosynthesis was excluded via addition of 3-(3,4-dichlorophenyl)-1,1-dimethylurea yielded a light-driven dissolved inorganic carbon (DIC) assimilation rate (7 ± 2 mg C g C^-1 h^-1) comparable to those of highly productive algal mats in acidic hot springs, suggesting that <i>R. globiformis</i> may be performing photoautotrophy at the time of the assay. Rates of acetate assimilation were more than two orders of magnitude lower than DIC assimilation and did not differ between light and dark treatments, indicating photoheterotrophic use of acetate was not occurring, though photoheterotrophic assimilation of other organic compounds cannot be excluded. The tepid (35°C) spring waters are acidic (pH = 3.7) with moderate dissolved hydrogen sulfide (0.2 mM) and abundant DIC (11 mM), an apparently rare set of conditions thought to arise from extremely shallow mixing of oxygenated meteoric water and volcanic gases. Though originally isolated and cultured photoheterotrophically, in nature, <i>R. globiformis</i> may grow photoautotrophically under the normal conditions of its habitat, utilizing a stable supply of DIC afforded by the injection of CO₂-rich volcanic gases. To our knowledge, these are the most acidic conditions under which light-driven DIC assimilation has been observed in the domain Bacteria.IMPORTANCEPurple nonsulfur bacteria are ecologically diverse and metabolically versatile anoxygenic phototrophs; however, only a few acid-tolerant species are known. We identified populations of the purple nonsulfur bacterium <i>Rhodopila globiformis</i> in warm, acidic springs with moderate (~0.2 mM) concentrations of dissolved hydrogen sulfide in two thermal areas of Yellowstone National Park (Wyoming, USA). Comprehensive geochemical analyses of the spring waters illustrate that they are formed by mixing of groundwater and CO₂-rich volcanic gases extremely close to the surface, relatively rare conditions that lead to characterization of <i>R. globiformis</i> as an endangered species. A high rate of light-driven assimilation of dissolved CO₂ that rivals rates for acidophilic algae was observed, indicating that <i>R. globiformis</i> is responsible for a significant amount of primary production and suggesting it may primarily grow photoautotrophically in nature. These observations constitute the first insights into the physiological ecology of the most acidophilic anaerobic anoxygenic phototroph presently known.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0121725"},"PeriodicalIF":3.7,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145028733","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 thermostable Cas9-based genome editing system for thermophilic acetogenic bacterium <i>Thermoanaerobacter kivui</i>.","authors":"Yilin Le, Xue Liu, Shidong Zhou, Pengju Wu, Mengqi Zhang, Jianzhong Sun, Jinfeng Ni, Huilei Wang","doi":"10.1128/aem.01170-25","DOIUrl":"https://doi.org/10.1128/aem.01170-25","url":null,"abstract":"<p><p><i>Thermoanaerobacter kivui</i> is a thermophilic acetogenic bacterium capable of thriving at elevated temperatures up to 66°C. It metabolizes carbohydrates such as glucose, mannose, and fructose and can also grow lithotrophically utilizing hydrogen (H₂) and carbon dioxide (CO₂) or carbon monoxide (CO), with acetate serving as its main product. A simple and efficient genome editing system for <i>T. kivui</i> would not only facilitate the understanding of the physiological function of enzymes involved in energy and carbon metabolism but also enable metabolic engineering. To address this issue, we developed a thermostable Cas9-based genome editing system for targeted gene knockout and gene integration into the <i>T. kivui</i> genome. Gene knockout assays were conducted on the <i>adh</i> gene, responsible for encoding alcohol dehydrogenase, and the <i>ldh</i> gene, encoding lactate dehydrogenase. Furthermore, the <i>adhE</i> gene from <i>Thermoanaerobacter ethanolicus</i>, which encodes a bifunctional aldehyde/alcohol dehydrogenase enzyme, was successfully integrated into the <i>T. kivui</i> genome. As a result, the engineered strain was able to produce ethanol. Following a liquid culturing period with kanamycin sulfate for about 72 hours, the efficiency of gene editing was enhanced, resulting in a ratio of mutants out of all colonies obtained of 90%. The results confirm the validity and efficiency of the thermostable Cas9-based genome editing system in <i>T. kivui</i> for gene editing.IMPORTANCEThermophilic acetogenic microorganisms represent an emerging metabolic engineering platform for the production of various biochemicals from hydrogen and carbon dioxide, or synthesis gas, under conditions of high-temperature fermentation. Gas fermentation has gained significant research interest due to its excellent thermodynamics, economic feasibility, and multisubstrate utilization. However, a major obstacle to the use of thermophilic acetogenic microorganisms as metabolic engineering platforms is the scarcity of genetic tools. This study demonstrates a proof of concept for a thermostable Cas9-based genome editing of the thermophilic acetogenic bacterium <i>T. kivui</i>. The system is an important expansion to the genetic toolbox of <i>T. kivui</i>, enabling a better understanding of key enzyme functions and the construction of cell factories for the biotechnological conversion of carbon dioxide and organic substrates into value-added products.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0117025"},"PeriodicalIF":3.7,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145013649","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":"Variable inhibition of different <i>Legionella</i> species by antagonistic bacteria.","authors":"Alessio Cavallaro, Silke Probst, Tobias Duft, Max Rieder, Oliver Abo El Fateh, Josch Stricker, Marco Gabrielli, Serina Robinson, Frederik Hammes","doi":"10.1128/aem.01164-25","DOIUrl":"https://doi.org/10.1128/aem.01164-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The genus &lt;i&gt;Legionella&lt;/i&gt; includes opportunistic pathogens inhabiting engineered aquatic ecosystems, where managing their presence and abundance is crucial for public health. In these environments, &lt;i&gt;Legionella&lt;/i&gt; interact positively or negatively with multiple members of the microbial communities. Here, we identified bacteria and compounds with &lt;i&gt;Legionella&lt;/i&gt;-antagonistic properties. We isolated 212 bacterial colonies from various water sources in Switzerland and screened them for their ability to inhibit one reference strain of &lt;i&gt;Legionella pneumophila&lt;/i&gt;. Ten selected antagonistic isolates were subsequently tested with spot-on-lawn assays for inhibition toward seven environmental and two clinical isolates of &lt;i&gt;Legionella&lt;/i&gt;, representing different species and strains. The antagonists produced highly variable inhibition patterns, highlighting distinct differences in susceptibility among &lt;i&gt;Legionella&lt;/i&gt; species and even strains. Only three isolates, all identified as &lt;i&gt;Pseudomonas lurida&lt;/i&gt;, inhibited all &lt;i&gt;Legionella&lt;/i&gt; species. We analyzed the genomes of the antagonistic bacteria and identified genes for several probable inhibitory compounds. We specifically found the gene cluster for the biosurfactant viscosin to be uniquely encoded by all three &lt;i&gt;P. lurida&lt;/i&gt; isolates. This compound was subsequently detected in the supernatant of co-cultures inoculated with &lt;i&gt;P. lurida&lt;/i&gt; and selected &lt;i&gt;Legionella&lt;/i&gt; strains. However, additional experiments with a viscosin-deficient mutant of &lt;i&gt;Pseudomonas fluorescens&lt;/i&gt; did not definitively demonstrate the importance of this compound for &lt;i&gt;Legionella&lt;/i&gt; inhibition. This study provides new insights on the ability of aquatic microorganisms to compete with &lt;i&gt;Legionella&lt;/i&gt; in controlled laboratory settings. It specifically highlights the diversity across and within &lt;i&gt;Legionella&lt;/i&gt; species in their resistance to external antagonistic stress and further supports the potential anti-&lt;i&gt;Legionella&lt;/i&gt; activity of some biosurfactants. These results can contribute to the understanding of how different &lt;i&gt;Legionella&lt;/i&gt; species inhabit separate niches in the environment and expand the discussion around alternative &lt;i&gt;Legionella&lt;/i&gt; mitigation strategies.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Understanding the nature of bacterial interactions allows us to have a broader overview of their lifestyle and their differences, while also paving the way toward new research and potential applications. This paper provides insights into the response of multiple pathogenic species of &lt;i&gt;Legionella&lt;/i&gt; to aquatic antagonistic bacteria, highlighting interesting intra-genus differences that are then discussed in light of potential ecological implications. Moreover, we identified new antagonistic bacteria toward &lt;i&gt;Legionella&lt;/i&gt; spp. and identified the biosurfactant viscosin as one of the likely compounds active against at least some &lt;i&gt;Legionella&lt;/i&gt; species. Together, these results suggest different","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0116425"},"PeriodicalIF":3.7,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145013670","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":"Removal and inactivation of human coronavirus surrogates from hard and soft surfaces using disinfectant wipes.","authors":"Runan Yan, Angela Fraser, Xiuping Jiang","doi":"10.1128/aem.01337-25","DOIUrl":"https://doi.org/10.1128/aem.01337-25","url":null,"abstract":"<p><p>Disinfectant wipes are widely used to reduce microbial contamination on surfaces, yet there is limited information on how viruses are physically removed or chemically inactivated during wiping. This study aimed to address this gap by comparing the contributions of physical removal and chemical inactivation to overall disinfection efficacy. Glass and vinyl coupons were contaminated with SARS-CoV-2 surrogates, bovine coronavirus (BCoV), or human coronavirus OC43, at an initial titer of 5-6 log TCID₅₀/surface with 5% soil load. After air drying, coupons were wiped using one of the following treatments: (i) pre-wetted blank polypropylene wipe, (ii) hydrogen peroxide (H₂O₂)-based disinfectant wipe, or (iii) quaternary ammonium compound (QAC)-based disinfectant wipe. Wiping was performed manually by hand or mechanically using a Gardco Gardner-scrub. The wiping process followed the U.S. Environmental Protection Agency protocol. After a 1 min exposure, residual disinfectant on both coupons and wipes was neutralized separately. Viruses were recovered by sonication for 30 s and quantified using the TCID₅₀ assay with HRT-18G cells. Using blank wipe, more virus was transferred to the wipe from glass (23%-59%) than vinyl (21%-30%), while less virus remained on glass (2%-5%) than vinyl (16%-24%). No significant difference in virus titers was observed between hand wiping and machine wiping, either on the surfaces or in the used wipes. Both disinfectant wipes reduced >3 log₁₀ TCID₅₀ of virus from surfaces, with virus remaining on used wipes below the limit of detection. These results suggest that disinfectant wipes can significantly and rapidly reduce coronavirus contamination and cross-contamination risk.IMPORTANCESurfaces contaminated with respiratory viruses, such as SARS-CoV-2, pose a potential risk for indirect transmission in public and healthcare settings. This study evaluated the effectiveness of disinfectant wipes in reducing two SARS-CoV-2 surrogates from different surface types within a 1 min contact time. Results showed that both hydrogen peroxide (H₂O₂)-based and quaternary ammonium compound (QAC)-based disinfectant wipes reduced infectious virus levels by more than 3 logs. Physical removal of viruses was more efficient on hard, nonporous surfaces (glass) compared to soft, non-porous surfaces (vinyl). No significant difference was observed between hand wiping and mechanical wiping, indicating that standard wiping procedures can be consistently effective regardless of method. Importantly, our findings highlight that disinfectant wipes function through both physical removal and chemical inactivation mechanisms. These data support evidence-based recommendations for surface disinfection practices to mitigate coronavirus contamination and reduce the risk of fomite-mediated viral transmission.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0133725"},"PeriodicalIF":3.7,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145013729","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":"Large- and small-scale population structure of <i>Xanthomonas oryzae</i> pv. <i>oryzicola</i>, a bacterial pathogen of rice.","authors":"Anne Sicard, Sara C D Carpenter, Amadou Diallo, Shivranjani Baruah, Cheick Tekete, Lazeni Konate, Ibrahim Keita, Hinda Doucoure, Phuong Duy Nguyen, Quyen Le Cao, Soungalo Sarra, Mamadou Dembele, Charlotte Tollenaere, Lucie Poulin, Hamidou Tall, Laurence Blondin, Valérie Verdier, Ralf Koebnik, Sylvain Zougrana, Harinjaka Raveloson, Lionel Gagnevin, Geoffrey Onaga, Sebastien Cunnac, Christian Vernière, Issa Wonni, Ousmane Koita, Boris Szurek, Adam Bogdanove, Mathilde Hutin","doi":"10.1128/aem.01121-25","DOIUrl":"https://doi.org/10.1128/aem.01121-25","url":null,"abstract":"<p><p><i>Xanthomonas oryzae</i> pv. <i>oryzicola</i> is a pathogen of rice responsible for bacterial leaf streak, a disease that can cause up to 32% yield loss. While it was first reported a century ago in Asia, its first report in Africa was in the 1980s. Since then, it has been discovered in several countries of both East and West Africa. In this study, we used a combination of genomics and genotyping tools to shed light on its global and local diversity and population structure with a focus on West Africa. Our findings group <i>X. oryzae</i> pv. <i>oryzicola</i> strains into three clades, an Asian, an East African-Asian, and a West African clade, and provide evidence of several introduction events from Asia being at the origin of outbreaks in East Africa and probably in West Africa. Our results further highlight the role of human activities in the local spread of this pathogen and the possible role of several wild rice species and weeds as reservoirs. Finally, our results globally support a clonal evolution of <i>X. oryzae</i> pv. <i>oryzicola</i>. However, coinfection of plants with distinct strains of <i>X. oryzae</i> pv. <i>oryzicola</i>, observed in Mali and Senegal, may facilitate some degree of genetic exchange.IMPORTANCEWest Africa has faced a rapid expansion of rice cultivation with importation of rice varieties mostly from Asia, and rice now constitutes 37% of the cereal consumed in the region. The bacterial pathogen <i>Xanthomonas oryzae</i> pv. <i>oryzicola</i> (<i>Xoc</i>) is causing bacterial leaf streak and threatening rice production in West Africa. Little is known about the pathogen's reservoirs and its modes and routes of dissemination. We used genome sequencing and tandem repeat sequences to describe large- and small-scale population structure and molecular epidemiology. Our results support the role of rice seed trade in the local and global spread of <i>Xoc</i>. This study further suggests different introduction events from Asia to both East and West Africa. We describe local natural dispersal events with some clonal diversification and the possible role of wild rice and weed species as reservoirs. Overall, our results indicate that weed management and the enforcement of phytosanitary measures on rice seeds could help control the spread of bacterial leaf streak.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0112125"},"PeriodicalIF":3.7,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145013654","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":"Arbuscular mycorrhizal fungi mitigated nitrogen leaching by enhancing soil nitrogen retention in <i>Camellia oleifera</i> Abel. soils.","authors":"Fei Wu, Ziran Ma, Tuanjie Che, Yuxuan Huang, Ting Li, Na Wu, Xian Zhang, Linping Zhang, Xuetai Zhu, Xiaoling Zheng, Guoxiu Zhu, Rui Zhang","doi":"10.1128/aem.01487-25","DOIUrl":"https://doi.org/10.1128/aem.01487-25","url":null,"abstract":"<p><p>Nitrogen leaching is a major pathway of nitrogen fertilizer loss. Although arbuscular mycorrhizal (AM) fungi are known to reduce nitrogen leaching by improving plant nitrogen uptake, the soil-based mechanisms remain unclear. A pot experiment was conducted using a randomized complete block design, with four nitrogen levels (0, 3.75, 7.5, and 15 mM) and two AM fungal inoculation treatments. The study evaluated plant nitrogen uptake, hyphal length density, glomalin-related soil protein (GRSP) content, soil aggregation, soil nitrogen content, and nitrogen leaching loss in <i>Camellia oleifera</i> soils. Results showed that both NH₄⁺-N and NO₃^--N in leachate increased with increasing nitrogen application. AM fungi reduced NH₄⁺-N (by 19.04% and 44.96%) and total nitrogen (TN, by 20.74% and 24.70%) in the leachate under high nitrogen conditions (7.5 and 15 mM). Under high nitrogen levels, AM fungi significantly increased soil easily extractable and total GRSP contents, NO₃^--N, TN, and the proportion of 0.05-1.00 mm aggregates, while reducing soil dissolved total nitrogen (DTN) content, and the proportion of 0.002-0.05 mm aggregates. Redundancy analysis (RDA) showed that hyphal length density, DTN, soil NH₄⁺-N, NO₃^--N, and aggregate distribution were strongly associated with nitrogen leaching. Partial least squares path modeling indicated that soil DTN explained 96% of the variation in nitrogen leaching; AM fungi likely reduce soil DTN through increased soil aggregation via GRSP secretion and direct nitrogen absorption by extraradical hyphae. These findings highlight that changes in soil structure play a key role in reducing nutrient loss mediated by AM fungi.IMPORTANCENitrogen fertilizers are essential for crop productivity, but low nitrogen use efficiency remains a major challenge in agriculture. Nitrogen leaching is a key contributor to nitrogen loss. Arbuscular mycorrhizal (AM) fungi are known to reduce fertilizer loss by enhancing nitrogen uptake in host plants. This study explored how AM fungi affect nitrogen leaching, plant nitrogen uptake, hyphal development, glomalin-related soil protein (GRSP) production, soil aggregation, and soil nitrogen content in <i>Camellia oleifera</i> soils. The results show that AM fungi can reduce nitrogen in soluble form and subsequently decrease nitrogen leaching, not only by facilitating nitrogen uptake via extraradical hyphae but also by altering soil structure-especially by promoting aggregate formation through the secretion of GRSP. The findings underscore that the functional significance of AM fungi should not be limited to their interactions with plant components, as their role in soil amelioration is equally important.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0148725"},"PeriodicalIF":3.7,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145013664","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":"Seasonal patterns of viromes in urban aquatic environments of Manitoba.","authors":"Jhannelle D Francis, Kadir Yanaç, Miguel I Uyaguari-Diaz","doi":"10.1128/aem.00408-24","DOIUrl":"https://doi.org/10.1128/aem.00408-24","url":null,"abstract":"<p><p>Although wastewater treatment plants harbor many pathogens, traditional methods that monitor the microbial quality of surface water and wastewater have not changed since the early 1900s and often disregard the presence of other types of significant waterborne pathogens such as viruses. We used metagenomics and quantitative PCR to assess the taxonomy, functional profiling, and seasonal patterns of DNA and RNA viruses, including the virome distribution in aquatic environments receiving wastewater discharges. Environmental water samples were collected at 11 locations in Winnipeg, Manitoba, along the Red and Assiniboine rivers during the Spring, Summer, and Fall 2021. Samples were filtered and underwent skimmed milk flocculation for viral concentration. The taxonomy of classified DNA was primarily bacteriophages such as <i>Autographiviridae</i>, <i>Kyanoviridae</i>, and <i>Peduoviridae,</i> which were abundant to a lesser extent. Phage-related functionalities such as portal proteins and bacteriophage T4 major head proteins accounted for approximately 20%-40% of aquatic samples across seasons, which may possibly correspond to the DNA phages that were previously identified. RNA viruses went unclassified in the study; however, similar to DNA viruses, many were found to be non-enveloped or \"naked viruses\" such as <i>Partiviridae, Picobirnaviridae, Tombusviridae,</i> and <i>Picornaviridae,</i> which accounted for 3%-30% of RNA viruses in the study locations across season. Interestingly, aquatic samples were revealed to maintain an abundance of RNA phage-related functionalities such as long tail fiber protein and putative tail proteins, which accounted for approximately 2%-5% of aquatic samples during the Fall of 2021.</p><p><strong>Importance: </strong>Municipal wastewater effluents discharged into the Red and Assiniboine rivers of Winnipeg, Manitoba, rely on traditional methods that monitor the microbial quality of effluents and receiving surface waters focus solely on the detection of coliforms, which are not necessarily good indicators of viruses or other pathogens. There is also a lack of current wastewater system effluent regulations at the federal and provincial level. Furthermore, previous literature has shown that when viral DNA and RNA sequences are blasted against current genomic databases, approximately 50% of the viral reads are classified as unknown. The significance of our research in characterizing the virome distribution in aquatic environments addresses a knowledge gap in the current effluent guidelines and a need for regulatory practices. In the long run, fecal indicator bacteria, combined with the detection of enteric viruses, may complement assessment of water quality in effluents discharged into rivers.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0040824"},"PeriodicalIF":3.7,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145013704","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}