Applied and Environmental Microbiology最新文献

{"title":"SmsB-SmsC machinery in <i>Thermococcus kodakarensis</i> functions as an archaeal scaffold mediating Fe-S cluster assembly.","authors":"Jian-Qiang Jin, Takaaki Sato, Haruyuki Atomi","doi":"10.1128/aem.01438-25","DOIUrl":"10.1128/aem.01438-25","url":null,"abstract":"<p><p>The SUF system is one of the multiprotein machineries responsible for iron-sulfur (Fe-S) cluster biogenesis. In bacterial and eukaryotic SUF systems, SufB, SufC, and SufD form a SufBC₂D complex as the scaffold for Fe-S cluster assembly. SMS (SUF-like minimal system), composed only of SufB and SufC homologs (SmsB and SmsC) without a SufD component, has recently been established, and representatives from methanogenic archaea have been experimentally verified to function in Fe-S cluster biogenesis. SMS has been proposed to be an ancestor of the SUF system. The hyperthermophilic archaeon <i>Thermococcus kodakarensis</i> harbors candidate proteins for SmsB and SmsC (<i>Tk</i>-SmsB and <i>Tk</i>-SmsC) encoded by TK0730 and TK0731 genes, respectively. As <i>Tk</i>-SmsB is phylogenetically positioned in a clade distinct from the previously characterized SmsB proteins from methanogens, here, we examined whether <i>Tk</i>-SmsB and <i>Tk</i>-SmsC can also function in Fe-S cluster generation and transfer. <i>Tk</i>-SmsB and <i>Tk</i>-SmsC formed a heterotetrameric SmsB₂C₂ complex. <i>Tk</i>-SmsC displayed ATPase activity, and its catalytic efficiency (<i>k</i>_cat/<i>K</i>_m) increased up to 10-fold upon complex formation with <i>Tk</i>-SmsB. The <i>Tk</i>-SmsB₂C₂ complex could generate Fe-S clusters in the presence of ferric and sulfide ions. The holo-<i>Tk</i>-SmsB₂C₂ complex could transfer the Fe-S clusters to the apo-form of the Fe-S cluster-dependent lipoyl synthase LipS from <i>T. kodakarensis</i>, resulting in a LipS with sulfur insertion activity for lipoyl group biosynthesis. In the presence of cysteine desulfurase and ATP, the apo-<i>Tk</i>-SmsB₂C₂ complex could also generate Fe-S clusters utilizing cysteine as a sulfur donor and activate LipS.IMPORTANCEA representative of an SmsB protein from <i>T. kodakarensis</i> (<i>Tk</i>-SmsB) that lies in a clade phylogenetically distinct from those of previously verified SmsB proteins has been examined. The results demonstrate that <i>Tk</i>-SmsB, along with <i>Tk</i>-SmsC, functions as a scaffold for Fe-S cluster synthesis in <i>T. kodakarensis</i>, adding further support to the proposition that SMS represents the primitive form of the SUF systems widely present in bacteria and eukaryotes.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0143825"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442378/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144871074","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":"Evaluation of respiratory virus transmissibility and resilience from fomites: the case of 11 SARS-CoV-2 clinical isolates.","authors":"Sofia Sisti, Elena Criscuolo, Benedetta Giuliani, Mattia Cavallaro, Michela Sampaolo, Matteo Castelli, Roberto Burioni, Massimo Locatelli, Nicola Clementi","doi":"10.1128/aem.00774-25","DOIUrl":"10.1128/aem.00774-25","url":null,"abstract":"<p><p>The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a global pandemic, significantly impacting social and economic aspects of society. While belonging to the <i>Coronaviridae</i> family, SARS-CoV-2 exhibited unique characteristics that facilitated its widespread transmission and pathogenicity. This study aimed to investigate the molecular characterization and infection kinetics of emerging SARS-CoV-2 variants, focusing on four key virological aspects: viral entry mechanisms, replication dynamics, immune evasion strategies, and surface persistence. We isolated 11 SARS-CoV-2 variants from clinical samples and conducted <i>in vitro</i> studies using Calu-3 cell lines and pseudovirus systems to explore viral entry. Whole-genome sequencing identified mutations linked to increased replication and enhanced immune evasion, particularly through the inhibition of interferon responses. Additionally, persistence studies on common environmental surfaces (copper, aluminum, and plastic) revealed that certain variants, such as G446S, contributed to increased viral stability, suggesting potential for indirect transmission beyond direct person-to-person contact. Furthermore, we evaluated the effectiveness of \"green\" disinfectants, including tea tree oil and quercetin-based compounds, which demonstrated viral load reductions of over 95% within minutes, outperforming conventional alcohol- and UV-based disinfection methods. Notably, two influenza virus isolates belonging to highly divergent subtypes are sanitized as well while showing different persistence surface profiles compared to SARS-CoV-2. These findings highlight the evolutionary strategies employed by SARS-CoV-2 to ensure transmission, its ability to adapt under selective pressure, and the importance of ongoing surveillance of emerging variants. Moreover, the efficacy of environmentally sustainable disinfectants presents a promising strategy for reducing viral transmission in both clinical and community settings.IMPORTANCEIn this study, we evaluated the molecular profile of 11 SARS-CoV-2 variants, focusing on four key virological aspects: viral entry mechanisms, replication dynamics, immune evasion strategies, and surface persistence. Through whole-genome sequencing, we identified mutations linked to enhanced replication and immune evasion, notably through the suppression of interferon responses. Additionally, persistence studies on common environmental surfaces (copper, aluminum, and plastic) demonstrated that certain mutations, such as G446S, exhibited increased stability, suggesting a potential role for indirect transmission. This study underscores the need for continuous monitoring and the potential of eco-friendly disinfection approaches in controlling the spread of SARS-CoV-2 and possibly of other respiratory viruses.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0077425"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442357/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144939788","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":"Root exudates protect rhizosphere <i>Pseudomonas</i> from water stress.","authors":"Ankita Bhattacharyya, Clint D Pablo, Olga V Mavrodi, Alex S Flynt, David M Weller, Linda S Thomashow, Dmitri V Mavrodi","doi":"10.1128/aem.00768-25","DOIUrl":"10.1128/aem.00768-25","url":null,"abstract":"<p><p>Arid and semi-arid regions, which account for over 40% of global land area, are affected by fluctuations in temperatures and rainfall. In these environments, plants recruit beneficial rhizosphere microorganisms to mitigate stress and enhance survival. This study investigates the molecular mechanisms by which <i>Pseudomonas synxantha</i> 2-79, a rhizobacterium associated with wheat grown in arid regions, adapts to water stress through its interaction with root exudates. We found that water-stressed wheat root exudates contain elevated levels of choline and glycine betaine, which serve as osmoprotectants for 2-79. Exposure to these exudates upregulated genes involved in the uptake and catabolism of these quaternary ammonium compounds (QACs), enhancing the bacterium's ability to cope with osmotic stress. Mutants lacking QAC transporters displayed reduced growth under osmotic stress, highlighting the importance of these pathways in rhizosphere competence. Furthermore, the study revealed that 2-79 also produces biofilms containing protective exopolysaccharides, such as alginate and Psl, which aid in stress resilience. Overall, our findings provide insights into how root exudates shape bacterial adaptation to the water-stressed rhizosphere and highlight the role of QAC metabolism and biofilm formation in microbial survival and plant-microbe interactions under drought conditions.IMPORTANCEThis study advances our understanding of plant-microbe interactions in water-stressed environments by revealing how rhizobacteria adapt to osmotic stress through metabolic responses to plant-derived exudates. The utilization of compatible solutes such as choline and glycine betaine, which are abundant in water-stressed plants, contributes strongly to microbial survival and colonization of the dryland rhizosphere. By uncovering the molecular mechanisms underlying this adaptation, including the upregulation of QAC transporters and biofilm formation, the study highlights the potential to leverage beneficial microbes in sustainable agricultural practices. Understanding these interactions offers valuable insights for improving drought resilience in crops and developing microbiome-based strategies to enhance plant productivity in water-limited conditions.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0076825"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442406/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144783313","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":"Time-resolved monitoring of yeast responses to lipopolysaccharide exposure by cell-released volatile organic compounds.","authors":"Huaying Liu, Maosheng Yao","doi":"10.1128/aem.00785-25","DOIUrl":"10.1128/aem.00785-25","url":null,"abstract":"<p><p>Volatile organic compound (VOC) profiles function as dynamic fingerprints of physiological states and disease progression. Here, the eukaryotic organism <i>Saccharomyces cerevisiae</i> was used to investigate the emission characteristics of VOCs induced by lipopolysaccharide (LPS). Using multi-omics techniques and physiology methods, yeast cells were observed to undergo both stress and adaptation phases upon exposure, as characterized by changes in acetic acid-D and higher alcohols/aldehydes. The oxidative phosphorylation process in yeast was inhibited during the stress response, leading to an oxidative stress accompanied by growth inhibition and cell wall remodeling. The adaptive stage of cells reprogrammed metabolism to consume excess metabolic substrates generated during the stress stage, thus resulting in the production of secondary metabolites such as higher alcohols/aldehydes as biomarkers. Acetic acid detected could, in contrast, serve as an early biomarker for the oxidative stress of yeast. Using flow cytometry together with FITC labeling, LPS was further shown to bind to cells, leading to internalization and membrane damage compared to controls. This study provides time-resolved mechanistic insights into VOCs as non-invasive biomarkers. These findings suggest that dynamic VOC profiles from cells hold promise as a \"surveillance camera\" for monitoring cellular health.IMPORTANCEThe analysis of metabolically derived volatile organic compounds (VOCs) provides an approach for tracking cellular stress dynamics. We demonstrate that the VOC profile released by <i>S. cerevisiae</i> cells dynamically evolved with time during lipopolysaccharide (LPS)-induced stress, coordinated with transcriptomic and proteomic reprogramming. Through multiple omics techniques and physiology, yeast cells were observed to undergo both stress and adaptation phases, as characterized by changes in acetic acid-D and higher alcohols/aldehydes. These findings establish VOCs as real-time, non-invasive indicators of time-resolved stress responses, highlighting their potential as surveillance tools to detect early cellular perturbations caused by external threats.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0078525"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144788104","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":"Coculture fermentation processes in wheat sourdough simulation media with <i>Companilactobacillus crustorum</i> LMG 23699 and <i>Wickerhamomyces anomalus</i> IMDO 010110 reflect their competitiveness and desirable traits for sourdough and sourdough bread production.","authors":"Inés Pradal, Jasper Kaesemans, Thomas Gettemans, Víctor González-Alonso, Luc De Vuyst","doi":"10.1128/aem.01325-25","DOIUrl":"10.1128/aem.01325-25","url":null,"abstract":"<p><p>Mixed-strain starter cultures can be used to steer sourdough production and yield sourdoughs containing different volatile organic compounds (VOCs), such as esters with fruity notes. The present study aimed to characterize the fermentation dynamics, including ester production capacity, and investigate the involvement of the latter during potential interactions between a novel lactic acid bacteria (LAB)-yeast consortium composed of <i>Companilactobacillus crustorum</i> LMG 23699 and <i>Wickerhamomyces anomalus</i> IMDO 010110. Therefore, mono- and co-culture fermentation processes were carried out in a wheat sourdough simulation medium (WSSM) and a modified WSSM that contained ester precursor molecules (mWSSM). The coculture fermentation (CF) processes carried out in WSSM resulted in a faster pH drop and a higher lactic acid production compared with the monoculture ones, which could be of interest in view of the competitive advantage of the LAB-yeast consortium toward background microorganisms. Moreover, these CF processes resulted in higher carbon dioxide production and different VOC profiles, which could be of interest for the production of sourdough breads with desirable specific volumes and flavorful crumbs. Fermentation processes carried out in mWSSM confirmed ethyl lactate biosynthesis by <i>Coml. crustorum</i> LMG 23699 and showed a change in the ester profile of the yeast strain. However, the CF processes carried out in this medium showed the vulnerability of the yeast strain toward acidic stress. To conclude, the laboratory fermentation processes of the present study showed the ester production and competitiveness of <i>Coml. crustorum</i> LMG 23699 and <i>W. anomalus</i> IMDO 010110 as a mixed-strain starter culture for the production of novel sourdoughs and sourdough bread.IMPORTANCEStrains of specific species of yeasts and lactic acid bacteria (LAB) often form a stable consortium during sourdough production. Hence, the intentional use of mixed-strain starter cultures composed of such strains can steer sourdough production to obtain, for instance, sourdoughs containing esters with fruity notes. The present study valorized a novel LAB-yeast consortium composed of <i>Companilactobacillus crustorum</i> LMG 23699 and <i>Wickerhamomyces anomalus</i> IMDO 010110 for the production of such sourdoughs. The application of coculture fermentation processes in wheat sourdough simulation media showed their ester biosynthesis potential and competitiveness. These data will allow the valorization of mixed-strain starter cultures composed of the strains examined.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0132525"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442410/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144820412","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":"Adaptively evolved <i>Methylorubrum extorquens</i> with enhanced formate tolerance and its application in 3-hydroxypropionic acid production.","authors":"Xuhua Mo, Yan Zhao, Lin Zhu, Changtai Zhang, Zhe Liu, Zengxin Ma, Kai Bao, Song Yang","doi":"10.1128/aem.02560-24","DOIUrl":"10.1128/aem.02560-24","url":null,"abstract":"<p><p><i>Methylorubrum extorquens</i> AM1, a native formate-utilizing bacterium, has exhibited limited capacity to tolerate formate. In this study, we employed an adaptive laboratory evolution (ALE) strategy to develop an evolved strain FT3 derived from <i>M. extorquens</i> AM1, with enhanced formate tolerance. When cultivated with a mixture of carbon sources containing 90 mM formate and 30 mM methanol, the FT3 strain exhibited 5.3 times higher optical density (OD₆₀₀) compared to the parental strain. FT3 strain was shown to efficiently utilize both methanol and formate in experiments using ¹³C-labeled carbon sources. Furthermore, the mechanism underlying the enhanced formate tolerance in FT3 strain was investigated through a combination of DNA re-sequencing, transcriptome analysis, and ALE-inspired gene manipulation experiments. The FT3 strain was identified as a hypermutant, and its enhanced formate tolerance was attributed to increased formate transport, an improved methanol oxidation pathway, and enhanced formate oxidation and assimilation pathways. In addition, gene overexpression experiments indicated the involvement of genes <i>META1_0287*</i>, <i>META1_3027</i>, <i>META1_3028</i>, <i>META1_3029</i>, <i>META1_1261</i>, <i>META1_1418</i>, and <i>META1_2965</i> in formate tolerance. Notably, the addition of formate resulted in a significant improvement in the generation of NADH and NADPH in the FT3 strain. Moreover, using the FT3 strain as a chassis, an improved 3-hydroxypropionic acid (3-HP) production of 2.47 g/L through fed-batch fermentation was achieved. This study provides an important foundation for further engineering of the evolved <i>M. extorquens</i> strain as an efficient platform for the co-utilization of methanol and formate in the production of reduced chemicals.</p><p><strong>Importance: </strong>In the present study, we successfully obtained an evolved strain FT3 derived from M. extorquens AM1 with high formate tolerance using the ALE strategy. The FT3 strain was identified as a hypermutant, with its enhanced formate tolerance attributed to increased formate transport, an improved methanol oxidation pathway, and enhanced formate oxidation and assimilation pathways. Through transcriptome analysis and ALE-inspired gene manipulation experiments, we identified several genes that contribute to the FT3 strain's tolerance to formate. The enhanced levels of reducing equivalents and the increased tolerance to 3-HP make FT3 a suitable chassis for 3-HP production, achieving an improved yield of 2.47 g/L through fed-batch fermentation. This study provides an important foundation for further engineering of the evolved <i>M. extorquens</i> strain as an efficient platform for the co-utilization of methanol and formate in the production of reduced chemicals.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0256024"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12445348/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833790","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":"Directed assembly of biofilm communities for marine biofouling prevention.","authors":"Cristina I Amador, Naireen Fatima, Amanda Sofie Sejer Jakobsen, Lorrie Macario, Phillip Pichon, Nick Aldred, Mette Burmølle","doi":"10.1128/aem.01392-25","DOIUrl":"10.1128/aem.01392-25","url":null,"abstract":"<p><p>Bio-based solutions depend on the application of living organisms to combat current challenges, including marine biofouling, which is characterized by the adhesion and growth of organisms on surfaces at sea. Such solutions traditionally involve single bacterial strains with specific, desirable activities or properties, thereby omitting the advantages conferred by the community context. We propose a novel approach, whereby desirable emergent properties of multispecies communities can be selected, such as those producing a thick and robust biofilm that is impenetrable to settling larvae. Here, bacterial biofilms from natural and artificial marine surfaces were studied, focusing on their adhesion, cohesion, stability, and antifouling properties both as single isolates and in multispecies communities. Using bottom-up assembly, we identified multispecies biofilm communities that exhibited greater tolerance to temperature variations compared to the component species. Additionally, some isolates, alone or as multispecies biofilms, prevented the settlement of barnacle larvae in short-term laboratory biofouling experiments. Broadly, our findings highlight the complexity of bacterial interactions within biofilms, revealing competition with occasional cooperation. More specifically, we present the possibility of a novel approach to biofouling control, whereby communities of marine isolates produce biofilms with the physical properties of a protective coating and, thus, move the industry a step toward environmentally friendly, regenerative antifouling coatings.IMPORTANCEMarine biofouling poses a significant challenge to maritime industries, resulting in lower efficiency, higher maintenance costs, environmental impact and structural damage. Marine antifouling coatings are the first line of defense against biofouling and their biocidal mechanism of action has remained largely unchanged for decades. Although the concept of \"living coatings\" has been mooted previously, we take a novel approach. By exploiting useful emergent properties from multispecies communities, we propose that the resulting biofilms will be more environmentally stable than single-species biofilms, allow departure from a focus on active protection via toxic metabolites, and will eventually enable the development of biological coatings with desirable physical properties. By highlighting the competitive and cooperative dynamics within biofilms, the research identifies microbial communities that reduce barnacle larval settlement while tolerating environmental stressors like temperature variation. These findings are a first step towards eco-friendly, biofilm-based antifouling strategies that are both self-regenerating and environmentally compatible.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0139225"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442356/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144939823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of a novel <i>ipp</i> gene cluster responsible for 2-isopropylphenol degradation in strain <i>Rhodococcus</i> sp. D-6.","authors":"Qian Zhu, Kangning Wei, Kaihua Pan, Gang Hu, Weihao Zhu, Yanni Huang, Changchang Wang, Qian Li, Mingliang Zhang, Jiguo Qiu, Qing Hong","doi":"10.1128/aem.00995-25","DOIUrl":"10.1128/aem.00995-25","url":null,"abstract":"<p><p>Isoprocarb (IPC), a widely used carbamate insecticide, causes environmental contamination and poses risks to humans and ecosystems. <i>Rhodococcus</i> sp. D-6, capable of utilizing IPC as the sole growth substrate, was isolated by our lab. Strain D-6 initiates IPC degradation through ester bond hydrolysis by the hydrolase IpcH, yielding 2-isopropylphenol (IPP). In this study, the catabolic pathway of IPP in strain D-6 was elucidated, and the <i>ipp</i> gene cluster responsible for its degradation was predicted by transcriptomic analysis. Key genes, including a novel two-component IPP monooxygenase gene <i>ippA1A2</i> and a 2-isopropylhydroquinone dioxygenase gene <i>ippB</i>, are responsible for the successive conversion of IPP, resulting in the ring cleavage of IPP. IppA1, a group D flavin-dependent monooxygenase, along with its reductase component IppA2, hydroxylates IPP to 2-isopropylhydroquinone using reduced nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FAD) as cofactors. The optimal molar ratio of IppA1 to IppA2 was 3:1. The apparent <i>K</i>_m and <i>k</i>_cat values of IppA1 for IPP were 60.52 ± 1.27 µM and 70.07 ± 0.85 s^-1, respectively. IppB, an extradiol dioxygenase, catalyzes 2-isopropylhydroquinone ring cleavage to generate 2-isopropyl-4-hydroxymuconic semialdehyde. The apparent <i>K</i>_m and <i>k</i>_cat values of IppB for 2-isopropylhydroquinone were 29.07 ± 1.54 μM and 147.65 ± 1.92 s^-1, respectively. This study provides critical insights into the molecular mechanisms of IPP degradation, contributing to a comprehensive understanding of IPC degradation.IMPORTANCECarbamate insecticides kill pests by inhibiting the activity of acetylcholinesterase (AChE) and have been widely used in agriculture. Compared to the studies on the degradation mechanisms of carbofuran and carbaryl, little is known about IPC degradation. An IPC-degrading strain <i>Rhodococcus</i> sp. D-6 was isolated by our lab, and the hydrolase gene <i>ipcH</i> responsible for hydrolyzing IPC to IPP has been identified previously. This study further elucidates the IPP degradation pathway in strain D-6 and identifies the novel two-component IPP monooxygenase IppA1A2 and 2-isopropylhydroquinone dioxygenase IppB, which are respectively responsible for IPP hydroxylation and its subsequent ring cleavage. These findings enhance our understanding of the microbial degradation mechanism of IPC.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0099525"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442392/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144854275","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":"Machine learning in understanding environmental variability of vibriosis in coastal waters.","authors":"Bailey M Magers, Kyle D Brumfield, Sunil Kumar, Rita R Colwell, Antarpreet S Jutla","doi":"10.1128/aem.00716-25","DOIUrl":"10.1128/aem.00716-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Vibrio spp.&lt;/i&gt; comprise ecologically significant bacteria that thrive in warm, moderately saline water, and their incidence and proliferation are strongly influenced by environmental factors. In recent years, &lt;i&gt;Vibrio spp&lt;/i&gt;. infections have been reported more frequently and over a greater geographical area along the US eastern seaboard. This study provides an analysis of &lt;i&gt;Vibrio spp&lt;/i&gt;. infections, notably caused by &lt;i&gt;Vibrio alginolyticus&lt;/i&gt;, &lt;i&gt;Vibrio cholerae&lt;/i&gt; non-O1/non-O139, &lt;i&gt;Vibrio fluvialis&lt;/i&gt;, &lt;i&gt;Vibrio mimicus&lt;/i&gt;, &lt;i&gt;V. parahaemolyticus&lt;/i&gt;, and &lt;i&gt;V. vulnificus&lt;/i&gt;, extracted from the Centers for Disease Control and Prevention's Cholera and Other &lt;i&gt;Vibrio&lt;/i&gt; Illness Surveillance system, located within 200 km of the eastern US coast, to analyze latitudinal distribution trends between 1990 and 2019. For each &lt;i&gt;Vibrio spp&lt;/i&gt;., case incidence (presence/absence) was modeled, including environmental data and employing extreme gradient boosting machine learning algorithms (XGBoost). Environmental parameters associated with the incidence of vibriosis were clustered using k-means clustering. The northern limit of total cases of vibriosis was found to have increased &lt;i&gt;ca&lt;/i&gt;. 40 km/year, with &lt;i&gt;V. alginolyticus&lt;/i&gt; (&lt;i&gt;ca&lt;/i&gt;. 70 km/year), &lt;i&gt;V. fluvialis&lt;/i&gt; (&lt;i&gt;ca&lt;/i&gt;. 60 km/year), and &lt;i&gt;Vibrio parahaemolyticus&lt;/i&gt; (&lt;i&gt;ca&lt;/i&gt;. 60 km/year) showing the greatest latitudinal shifts. These changes were found to be linked to environmental parameters that enhance the proliferation of &lt;i&gt;Vibrio spp&lt;/i&gt;. The average accuracy of the XGBoost models was 60.9%-71.0%, with temperature and salinity being the most significant predictors. Relationships among other environmental parameters were complex and nonlinear, but phytoplankton and precipitation served to differentiate the models. Clustering using k-means yielded results that supported temperature, salinity, and phytoplankton as important environmental parameters. Research in progress will aid in developing global predictive risk models for &lt;i&gt;Vibrio spp&lt;/i&gt;. infections.IMPORTANCE&lt;i&gt;Vibrio spp&lt;/i&gt;. are ecologically significant bacteria, and their incidence and proliferation are strongly influenced by environmental factors. In recent years, &lt;i&gt;Vibrio spp&lt;/i&gt;. infections have been reported more frequently and over a greater geographical area along the US eastern seaboard. This study provides an analysis of latitudinal distribution trends of &lt;i&gt;Vibrio spp&lt;/i&gt;. infections, notably caused by &lt;i&gt;Vibrio alginolyticus&lt;/i&gt;, &lt;i&gt;Vibrio cholerae&lt;/i&gt; non-O1/non-O139, &lt;i&gt;Vibrio fluvialis&lt;/i&gt;, &lt;i&gt;Vibrio mimicus&lt;/i&gt;, &lt;i&gt;Vibrio parahaemolyticus&lt;/i&gt;, and &lt;i&gt;V. vulnificus&lt;/i&gt;, within 200 km of the eastern US coast. The northern limit of total cases of vibriosis was found to have increased &lt;i&gt;ca&lt;/i&gt;. 40 km/year. These changes were found to be linked to environmental parameters that enhance the proliferation of &lt;i&gt;Vibrio spp&lt;/i&gt;. Temperature and salinity were the most significant predictors of v","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0071625"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442386/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144854276","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":"Correction for Wang et al., \"Effects of <i>Vibrio parahaemolyticus</i> on physiology and metabolism of <i>Thalassiosira weissflogii</i> in the co-culture system\".","authors":"Jiahui Wang, Mengzhen Cheng, Xin Wang, Guangyuan Wang, Delin Duan, Zhanru Shao","doi":"10.1128/aem.01394-25","DOIUrl":"10.1128/aem.01394-25","url":null,"abstract":"","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0139425"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442343/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144871066","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}