Applied and Environmental Microbiology最新文献

{"title":"Inoculum growth impacts <i>Salmonella</i> and Shiga-toxin producing <i>Escherichia coli</i> resilience on wheat grain.","authors":"Yawei Lin, Carolyn Peterson, Bradley P Marks, Teresa M Bergholz","doi":"10.1128/aem.00177-25","DOIUrl":"10.1128/aem.00177-25","url":null,"abstract":"<p><p>Previous studies have shown that using a surface growth method for preparing inoculum impacted pathogen population stability and inactivation kinetics. Here, we quantified the desiccation survival and responses to tempering treatment of <i>Salmonella</i> and Shiga-toxin producing <i>Escherichia coli</i> (STEC) on wheat grain when grown using five different methods: broth, lawn-aerobic, lawn-anaerobic, lawn-acid-adapted, and lawn-low inoculum. Three strains of <i>Salmonella</i> and STEC each were individually inoculated onto wheat grain, conditioned to 0.45 <i>a</i>_w and stored up to 24 weeks. Pathogen survival curves on grain were different when inoculated with a lawn-grown culture compared to broth-grown. Acid adaptation of STEC led to increased (<i>P</i> < 0.001) tolerance to desiccation, while no change in <i>Salmonella</i> desiccation tolerance was observed. While most survival curves were better described by the log-linear model, survival of pathogens from broth-grown inoculum was better characterized by the Weibull model. Five-strain cocktails of each species were inoculated onto wheat, stored for 1, 2, 7, 28, and 84 days, followed by tempering for 18 h with three chemical interventions: water (control), 800 ppm chlorine, 5% lactic acid (LA) + 26.6% NaCl and 5% sodium bisulfate (SBS). These treatments led to different (<i>P</i> < 0.001) average reductions of 0.52, 1.04, 1.43, and 1.96 log CFU/g, respectively. The length of storage and inoculum growth method affected (<i>P</i> < 0.001) pathogen survival during tempering. In general, pathogens inoculated on grain survived better during tempering when inoculum was prepared by acid-adapted ≥ lawn-aerobic ≥ low inoculum > lawn-anaerobic = broth.IMPORTANCEOutbreaks linked to wheat flour increased interest in evaluating pathogen survival kinetics. With minimal information on how foodborne pathogens contaminate wheat grain, the \"worst-case scenario\" should be identified to characterize pathogen survival kinetics on grain and be used to assess the effectiveness of food safety interventions. Using an antimicrobial solution during wheat tempering, an existing unit operation where grain is exposed to water prior to milling into flour can be a cost-effective way to mitigate the risk of foodborne pathogens. The lack of consistent inoculum preparation methods makes it difficult to compare results across studies evaluating tempering treatments. We assessed five different inoculum growth methods to quantify pathogen survival during desiccation and long-term storage and pathogen inactivation efficacy of several existing tempering solutions. In addition, these data provide insights on statistically important parameters to consider for low-moisture food challenge study experimental design, such as inoculum growth, inoculation level, and pathogen adaptation.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0017725"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016515/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750789","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":"A call for healing and unity.","authors":"Patrick D Schloss","doi":"10.1128/aem.00448-25","DOIUrl":"10.1128/aem.00448-25","url":null,"abstract":"","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0044825"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016490/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514440","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":"Zooplankton protect viruses from sunlight disinfection.","authors":"J A Wang, O Aryal, L N Brownstein, H Shwwa, A L Rickard, A E Stephens, M Lanzarini-Lopes, N S Ismail","doi":"10.1128/aem.02540-24","DOIUrl":"10.1128/aem.02540-24","url":null,"abstract":"<p><p>Sunlight disinfection is an important inactivation process for enteric viruses in water. Understanding how dark biotic processes, such as zooplankton filter feeding, impact sunlight disinfection for viruses has important implications for public health. This research quantifies the uptake of MS2, a model for enteric viruses, by the filter feeder <i>Branchionus plicatilis</i> (rotifer) and the effects of such uptake on subsequent sunlight inactivation of MS2. Experiments co-incubating MS2 with rotifers showed 2.6 log viral removal over 120 hours. Viable virus was recovered from rotifer bodies after co-incubation, indicating incomplete viral inactivation via ingestion. When live rotifers were co-incubated with MS2 and the system was treated with sunlight, experimental treatments with rotifers showed that the virus was protected with 2-3 log viral inactivation compared to 4.5 log inactivation for sunlight controls without rotifers. Dead rotifers placed in the system did not show the same magnitude of protection effects, indicating that active filter feeding of rotifers is associated with protection from sunlight. Data from this study show that zooplankton may serve as a vector for viruses and reduce the efficiency of sunlight inactivation.IMPORTANCEEnteric viral contamination in water is a leading global cause of waterborne disease outbreaks. Sunlight inactivation is an important disinfection mechanism in natural waters, but accurately modeling inactivation is challenging due to the complex nature of aquatic systems. Zooplankton play a critical role in natural systems and are known to inactivate bacteria, but their interaction with viruses is not well understood. Our research examines the impact of a model zooplankton species on the sunlight disinfection of viruses. The results from this study address knowledge gaps in the importance of dark processes such as zooplankton filter feeding and their impact on viral fate.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0254024"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016492/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750792","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":"A dynamic protein interactome drives energy conservation and electron flux in <i>Thermococcus kodakarensis</i>.","authors":"Sere A Williams, Danielle M Riley, Teagan P Rockwood, David A Crosby, Katherine D Call, Jared J LeCuyer, Thomas J Santangelo","doi":"10.1128/aem.00293-25","DOIUrl":"10.1128/aem.00293-25","url":null,"abstract":"<p><p>Life is supported by energy gains fueled by catabolism of a wide range of substrates, each reliant on the selective partitioning of electrons through redox (<u>red</u>uction and <u>ox</u>idation) reactions. Electron flux through tunable and regulated protein interactions provides dynamic routes for energy conservation, but how electron flux is regulated <i>in vivo</i>, particularly for archaeal metabolisms that support rapid growth at the thermodynamic limits of life, is poorly understood. Identification of <i>bona fide in vivo</i> protein assemblies and how such assemblies dictate the totality of electron flux is critical to our understanding of the regulation imposed on metabolism, energy production, and energy conservation. Here, 25 key proteins in central metabolic redox pathways in the model, genetically accessible, hyperthermophilic archaeon <i>Thermococcus kodakarensis</i>, were purified to reveal an extensive, dynamic, and tightly interconnected network of protein interactions that responds to environmental cues (such as the availability of various reductive sinks) to direct electron flux to maximize energetic gains. Interactions connecting disparate functions suggest many catabolic and anabolic activities occur in spatial proximity <i>in vivo</i>, and while protein complexes have been historically defined under optimal conditions, many of these complexes appear to maintain alternative partnerships in changing conditions. The totality of the results obtained redefines our understanding of <i>in vivo</i> assemblies driving ancient metabolic strategies supporting the growth of modern Archaea.IMPORTANCEGiven the potential for rational genetic manipulations of biofuel- and biotech-promising archaea to yield transformative results for major markets, it is a priority to define how the metabolisms of such species are controlled, at least in part, by <i>in vivo</i> protein assemblies, and from such, define routes of energy flux that can be most efficiently altered toward biofuel or biotechnological gains. Proteinaceous electron carriers (PECs, such as ferredoxins) offer the potential for specific protein-protein interactions to coordinate selective reductive flow. Employing the model, genetically accessible, hyperthermophilic archaeon, <i>Thermococcus kodakarensis</i>, we establish the metabolic protein interactome of 25 key redox proteins, revealing that each redox active protein has a dynamic partnership profile, suggesting catabolic and anabolic activities may occur in concert and in temporal and spatial proximity <i>in vivo</i>. These results reveal critical importance in evaluating the newly identified partnerships and their role and utility in providing regulated redox flux in <i>T. kodakarensis</i>.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0029325"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016516/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143770952","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":"Microbial magnetite oxidation via MtoAB porin-multiheme cytochrome complex in <i>Sideroxydans lithotrophicus</i> ES-1.","authors":"Jessica L Keffer, Nanqing Zhou, Danielle D Rushworth, Yanbao Yu, Clara S Chan","doi":"10.1128/aem.01865-24","DOIUrl":"10.1128/aem.01865-24","url":null,"abstract":"<p><p>Most of Earth's iron is mineral-bound, but it is unclear how and to what extent iron-oxidizing microbes can use solid minerals as electron donors. A prime candidate for studying mineral-oxidizing growth and pathways is <i>Sideroxydans lithotrophicus</i> ES-1, a robust, facultative iron oxidizer with multiple possible iron oxidation mechanisms. These include Cyc2 and Mto pathways plus other multiheme cytochromes and cupredoxins, and so we posit that the mechanisms may correspond to different Fe(II) sources. Here, <i>S. lithotrophicus</i> ES-1 was grown on dissolved Fe(II)-citrate and magnetite. <i>S. lithotrophicus</i> ES-1 oxidized all dissolved Fe²⁺ released from magnetite and continued to build biomass when only solid Fe(II) remained, suggesting it can utilize magnetite as a solid electron donor. Quantitative proteomic analyses of <i>S. lithotrophicus</i> ES-1 grown on these substrates revealed global proteome remodeling in response to electron donor and growth state and uncovered potential proteins and metabolic pathways involved in the oxidation of solid magnetite. While the Cyc2 iron oxidases were highly expressed on both dissolved and solid substrates, MtoA was only detected during growth on solid magnetite, suggesting this protein helps catalyze oxidation of solid minerals in <i>S. lithotrophicus</i> ES-1. A set of cupredoxin domain-containing proteins were also specifically expressed during solid iron oxidation. This work demonstrated that the iron oxidizer <i>S. lithotrophicus</i> ES-1 utilized additional extracellular electron transfer pathways when growing on solid mineral electron donors compared to dissolved Fe(II).</p><p><strong>Importance: </strong>Mineral-bound iron could be a vast source of energy to iron-oxidizing bacteria, but there is limited physiological evidence of this metabolism, and it has been unknown whether the mechanisms of solid and dissolved Fe(II) oxidation are distinct. In iron-reducing bacteria, multiheme cytochromes can facilitate iron mineral reduction, and here, we link a multiheme cytochrome-based pathway to mineral oxidation, expanding the known functionality of multiheme cytochromes. Given the growing recognition of microbial oxidation of minerals and cathodes, increasing our understanding of these mechanisms will allow us to recognize and trace the activities of mineral-oxidizing microbes. This work shows how solid iron minerals can promote microbial growth, which, if widespread, could be a major agent of geologic weathering and mineral-fueled nutrient cycling in sediments, aquifers, and rock-hosted environments.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0186524"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016527/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143555578","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":"Overexpression of sulfide:quinone reductase (SQR) in <i>Acidithiobacillus ferrooxidans</i> enhances sulfur, pyrite, and pyrrhotite oxidation.","authors":"Heejung Jung, Yuta Inaba, Scott Banta","doi":"10.1128/aem.00170-25","DOIUrl":"10.1128/aem.00170-25","url":null,"abstract":"<p><p>Hydrogen sulfide is produced during the dissolution of some sulfidic minerals and during the microbial metabolism of reduced sulfur compounds. The sulfide:quinone reductase (SQR) enzyme is able to oxidize H₂S, and the bioleaching cells <i>Acidithiobacillus ferrooxidans</i> have two SQR genes, only one of which has been characterized. We cloned and overexpressed the two SQR genes in <i>A. ferrooxidans</i> and show that they both have SQR activity. Both AFE_0267 and AFE_1792 are active under anaerobic conditions, but only AFE_1792 is active under aerobic conditions. The effect of the SQR overexpression and the expression of related genes on sulfur metabolism was investigated. The overexpression of SQR improved cell growth and sulfur oxidation, suggesting enhanced SQR activity led to a reduction in H₂S toxicity as well as providing additional energy through H₂S oxidation. Additionally, the impact on the oxidation of pyrite and pyrrhotite was investigated. The rate of oxidation of pyrite by the engineered cells was enhanced, and, furthermore, the rate of pyrrhotite oxidation was more than doubled.IMPORTANCEH₂S is a toxic sulfur intermediate, and the SQR enzyme has evolved to oxidize H₂S in <i>A. ferrooxidans</i>. In addition to detoxification, H₂S oxidation provides energy, and overexpression of SQR enhanced aerobic and anaerobic growth on sulfur. The SQR overexpression also enhanced pyrite and pyrrhotite oxidation, which may facilitate the pyrometallurgical processing of a number of critical materials including copper, nickel, and the platinum group metals.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0017025"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016491/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699464","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":"Identity and timing of protist inoculation affect plant performance largely irrespective of changes in the rhizosphere microbial community.","authors":"Nathalie Amacker, Zhilei Gao, Alexandre L C Jousset, Stefan Geisen, George A Kowalchuk","doi":"10.1128/aem.00240-25","DOIUrl":"10.1128/aem.00240-25","url":null,"abstract":"<p><p>Bacterivorous soil protists can have positive impacts on plant performance, making them attractive targets for novel strategies to improve crop production. However, we generally lack the knowledge required to make informed choices regarding the protist species to be used or the optimal conditions for such amendments. Here, we examined how identity, diversity, and timing of inoculation of well-described protists impacted plant development and rhizosphere microbiome assembly. We first studied the impact of individual inoculation of six well-characterized protists on lettuce growth, with <i>Cercomonas</i> sp. S24D2 emerging as the strain with the largest impact on plant growth. In a second step, we created a three-protist species mixture inoculant by adding two protist species (<i>Acanthamoeba</i> sp. C13D2 and a heterolobosean isolate S18D10), based on differences in their feeding patterns. We then inoculated <i>Cercomonas</i> sp. either individually or in the protist mixture to lettuce plants 1 week before, simultaneously with, or 1 week after seedling transfer. We monitored plant growth and nutrient content, as well as impacts on the resident soil and rhizosphere microbiome composition. We found that early protist inoculation provided the greatest increase in aboveground biomass compared to the non-inoculated control. Single- and mixed-species inoculations had similar impacts on plant development and only minor impacts on prokaryotic community composition. While early inoculation seems to be the most promising timing for eliciting the positive effects of protist amendments, further, more systematic studies will be necessary to determine the conditions and ecological interactions that yield consistent and predictable improvements in plant performance.</p><p><strong>Importance: </strong>The application of microorganisms, including bacterivorous soil protists, has been increasingly suggested as a sustainable agricultural approach. While positive impacts of the presence of predatory protists have been generally reported, the effects of the selected species and amendment conditions are largely unknown. Here, we examined how identity, diversity, and timing of inoculation of well-described protists impacted plant development and rhizosphere microbiome assembly. One species emerged as the one having the strongest impact in our specific system. This result highlights the importance of species selection for optimal outcome, but also suggests a huge potential in the barely investigated protist diversity for targeted application. Furthermore, the application of the inoculants before plant transfer showed the strongest effects on plants, providing some useful and new insights on the optimal time for such amendments.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0024025"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016509/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750788","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":"Product formulation and rubbing time impact the inactivation of enveloped and non-enveloped virus surrogates by foam-based hand sanitizers.","authors":"Francis Torko, Kristen E Gibson","doi":"10.1128/aem.02474-24","DOIUrl":"10.1128/aem.02474-24","url":null,"abstract":"<p><p>Effective hand hygiene, such as hand washing and hand sanitizer use, is crucial in reducing infectious disease transmission via the hands. The efficacy of hand washing has been well-documented; however, relatively less is known regarding foam-based hand sanitizer efficacy, which is considered an effective alternative to washing hands with soap and water. Hand sanitizers are recommended by both the United States Centers for Disease Control and Prevention and the World Health Organization when the hands are not visibly dirty or greasy. This study examined the efficacy of five commercially available foam hand sanitizers-four alcohol-based and one non-alcohol-based-against enveloped and non-enveloped viruses using bacteriophage phi6 (Φ6) and bacteriophage MS2 as surrogates, respectively. A cocktail of MS2 and Φ6 (8 log PFU/mL) was inoculated on the hands and exposed to 3 or 6 mL of hand sanitizer product followed by rubbing the palmar surface of the hands together for 10 s or until dry. The results showed significant log reduction among the virus surrogates (<i>P</i> ≤ 0.05), with Φ6 consistently showing higher susceptibility across all factors compared with MS2 with log reductions of 2.83 ± 1.98 and 0.50 ± 0.53 log reduction, respectively. Although dosing volume did not significantly impact log reduction (<i>P</i> = 0.31), rubbing time significantly affected bacteriophage inactivation (<i>P</i> ≤ 0.05). Higher log reduction was observed when hands were rubbed until dry (2.69 ± 2.06), compared with the typical 10 s rubbing time (0.65 ± 0.75). This study revealed that the efficacy of commercially available foam hand sanitizers depends on rubbing time and overall product formulation, rather than exclusively on active ingredient concentration.IMPORTANCEHuman hands are a key factor in the transmission of viral diseases, and proper hand hygiene is regarded as the gold standard against the spread of such diseases. This study examined the effectiveness of a hand hygiene technique, that is, the application of foam-based hand sanitizers, against the inactivation of enveloped and non-enveloped virus surrogates on the hands. Factors such as virus type, rubbing time, volume of product used, and product formulation can significantly influence the efficacy of hand sanitizers. To assess these effects, we tested different rubbing times and product volumes across alcohol- and non-alcohol-based, foam hand sanitizer formulations, each with varying active ingredient concentrations and inactive ingredients. The study was performed on the palmar surface of human hands to realistically simulate real-world conditions, providing valuable evidence to inform future hand sanitizer practices aimed at maximizing the reduction of infectious viral pathogens on the hands.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0247424"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016521/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699467","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":"<i>Salmonella enterica</i> serovar Braenderup shows clade-specific source associations and a high proportion of molecular epidemiological clustering.","authors":"Harleen K Chaggar, Lauren K Hudson, Kelly Orejuela, Linda Thomas, Maya Spann, Katie N Garman, John R Dunn, Thomas G Denes","doi":"10.1128/aem.02594-24","DOIUrl":"10.1128/aem.02594-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Salmonella enterica&lt;/i&gt; serovar Braenderup (&lt;i&gt;S. enterica&lt;/i&gt; ser. Braenderup) is an important clinical serovar in the United States. This serovar was reported by the CDC in 2017 as the fifth most common &lt;i&gt;Salmonella enterica&lt;/i&gt; serovar associated with outbreaks in the United States, which have been linked to both fresh produce and food animal products. The goals of this study were to compare the relatedness of human clinical isolates from southeastern USA (Tennessee (&lt;i&gt;n&lt;/i&gt; = 106), Kentucky (&lt;i&gt;n&lt;/i&gt; = 48), Virginia (&lt;i&gt;n&lt;/i&gt; = 252), South Carolina (&lt;i&gt;n&lt;/i&gt; = 109), Georgia (&lt;i&gt;n&lt;/i&gt; = 159), Alabama (&lt;i&gt;n&lt;/i&gt; = 8), Arkansas (&lt;i&gt;n&lt;/i&gt; = 26), and Louisiana (&lt;i&gt;n&lt;/i&gt; = 91)) and global clinical (&lt;i&gt;n&lt;/i&gt; = 5,153) and nonclinical (&lt;i&gt;n&lt;/i&gt; = 1,053) isolates obtained from the NCBI. Additionally, we also examined the population structure of &lt;i&gt;S. enterica&lt;/i&gt; ser. Braenderup strains (&lt;i&gt;n&lt;/i&gt; = 3,131) on EnteroBase and found that all the strains of this serovar are associated with a single cgMLST eBurst group (ceBG 185), confirming that this serovar is monophyletic. We divided the &lt;i&gt;S. enterica&lt;/i&gt; ser. Braenderup population into two clades (Clade I and Clade II) and one clade group (Clade Group III). The composition of distinct environmental isolates in the clades differed: Clade I was significantly associated with produce (90.7%; &lt;i&gt;P&lt;/i&gt; &lt; 0.0001) and water, soil, and sediment (76.9%; &lt;i&gt;P&lt;/i&gt; &lt; 0.0001), and Clade II was significantly associated with poultry environments (62.8%; &lt;i&gt;P&lt;/i&gt; &lt; 0.0001). The clade-specific gene associations (e.g., Clade I-associated competence proteins and cytochrome_c_asm protein and Clade II-associated heme-exporter protein and dimethyl sulfoxide [DMSO] reductase-encoding genes) provide potential insights into possible mechanisms driving environmental adaptation and host-pathogen interaction. Phylogenetic analyses identified 218 molecular epidemiological clusters in the current study, which represented a greater proportion of potentially outbreak-related isolates than previously estimated.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;This study provides insights into the genomic diversity of &lt;i&gt;S. enterica&lt;/i&gt; ser. Braenderup by revealing distinct clade-specific source attribution patterns and showing that a greater proportion of isolates were associated with epidemiological clusters based on the genomic relatedness than previously estimated. Specifically, we analyzed the diversity of human clinical isolates from southeastern USA and compared them with the global clinical and nonclinical isolates. Our analysis showed different clades of &lt;i&gt;S. enterica&lt;/i&gt; ser. Braenderup linked to different environments, providing insights on the potential source of human sporadic infection and outbreaks. These findings can enhance public health surveillance and response strategies targeting &lt;i&gt;S. enterica&lt;/i&gt; serovar Braenderup by expanding our understanding of potential transmission pathways and the genomic diversity of clinical ","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0259424"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016519/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143673190","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":"Deletion of <i>Re</i>-citrate synthase allows for analysis of contributions of tricarboxylic acid cycle directionality to the growth of <i>Heliomicrobium modesticaldum</i>.","authors":"Alexandria M Layton, Christopher McCauley, Kevin E Redding","doi":"10.1128/aem.01772-24","DOIUrl":"10.1128/aem.01772-24","url":null,"abstract":"<p><p><i>Heliomicrobium modesticaldum,</i> a phototrophic member of the phylum Firmicutes and family Clostridiales, possesses most of the enzymes specific to the reductive tricarboxylic acid (rTCA) cycle, except for the key enzyme, ATP-citrate lyase. It is thought to utilize a split TCA cycle when growing on pyruvate as a carbon source, in which the oxidative TCA (oTCA) direction generates most of the 2-ketoglutarate, but some can be produced in the reductive direction. Although a typical <i>Si</i>-citrate synthase gene is not found in the genome, it was suggested that gene HM1_2993, annotated as homocitrate synthase, actually encodes <i>Re</i>-citrate synthase, which would function as the initial enzyme of the oTCA cycle. We deleted this gene to test this hypothesis and, if true, see what effect severing access to the oTCA cycle would have on this organism. The endogenous CRISPR-Cas system was used to replace the open reading frame with a selectable marker. The deletion mutants could grow on pyruvate but were unable to grow phototrophically on acetate + CO₂ as carbon source. Growth on acetate could be rescued by the addition of different electron sources (formate or ascorbate), suggesting that the oTCA cycle is used to oxidize acetate to generate electrons required to drive the carboxylation of acetyl-CoA. The deletion mutants were capable of growing in acetate minimal media without additional organic supplements beyond formate, demonstrating that the rTCA cycle can be employed to support sufficient 2-ketoglutarate production in this organism, unlike citrate synthase mutants in several chemoheterotrophic organisms utilizing the oTCA cycle.</p><p><strong>Importance: </strong>Heliobacteria are a unique group of phototrophic bacteria that are obligate anaerobes and possess a rudimentary system to use light as a source of energy. They do not make oxygen or fix carbon dioxide. Here, we explore their fundamental carbon metabolism to understand the role and operation of the central TCA cycle. This work shows both the role and operation of this cycle under different growth modes and explains how these organisms can obtain electrons to drive their biosynthetic metabolism. This foundational knowledge will be crucial in the future when attempts are made to use this organism as a platform for oxygen-sensitive synthesis of compounds in an anaerobe that can use light as its energy source.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0177224"},"PeriodicalIF":3.9,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143565839","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}