Applied and Environmental Microbiology最新文献

{"title":"Heterotrophic inorganic carbon fixation varies with temperature and resource availability in marine and soil bacterial isolates.","authors":"Emma K Brown, Kadin Pulliam, Katelyn Weeks, Carolynn M Harris, William D Leavitt, Jaclyn K Saunders, Elizabeth Trembath-Reichert","doi":"10.1128/aem.00628-26","DOIUrl":"https://doi.org/10.1128/aem.00628-26","url":null,"abstract":"<p><p>Inorganic carbon use in cellular metabolism is ubiquitous in all living organisms. The assimilation of inorganic carbon into biomass via heterotrophic inorganic carbon fixation (HICF) is estimated to contribute significantly to global carbon fixation, yet the controls on this process in strictly heterotrophic microorganisms remain poorly understood. To identify potential drivers of HICF, we cultivated well-characterized heterotrophic Gammaproteobacteria (<i>Pseudomonas putida</i> and <i>Pseudoalteromonas carrageenovora</i>) at two temperatures (optimal vs colder) and resource treatments (high vs low organic carbon), all of which were amended with NaH¹³CO₃. We performed bulk and single-cell stable carbon isotope probing (SIP) analysis to detect and quantify HICF in each condition, and assessed other measures of metabolic state, including C/N ratio, natural abundance nitrogen isotope ratios, and cell size. We observed HICF in all treatments, with the percent of biomass originating from ¹³C-dissolved inorganic carbon (DIC) for <i>P. putida</i> (0.006% to 0.029%) and <i>P. carrageenovora</i> (0.18% to 1.1%) on the lower end of estimates for the contribution of anaplerotic fixation to heterotrophic biomass (1% to 8%). HICF was generally highest during exponential phase, at the optimal growth temperature, and under low carbon conditions, and these trends were also observed at the single-cell level. Overall, temperature and resource availability appear to influence HICF rates. These findings suggest that HICF may be more relevant under environmental conditions where DIC and nitrogen are not limiting, and the flux of digestible organic carbon is limited or intermittent. Environmental applications of ¹³C-DIC SIP in such systems may record heterotrophic contributions to community carbon fixation.IMPORTANCEHeterotrophic microorganisms are abundant across ecosystems and play a central role in environmental carbon cycling by storing, transforming, and decomposing organic matter. However, heterotrophs can also incorporate inorganic carbon into biomass, but this is rarely considered in models of the carbon cycle. Our experiments on heterotrophic bacteria from soil (<i>Pseudomonas putida</i>) and marine environments (<i>Pseudoalteromonas carrageenovora</i>) show that inorganic carbon uptake is impacted by both resource availability and temperature and may be undetectable without stable isotope probing. By integrating single-cell techniques, our study measures variation in inorganic carbon uptake among individual cells across growth phases and conditions. Our study highlights heterotrophic inorganic carbon fixation as a variable source of ¹³C-dissolved inorganic carbon incorporation into microbial biomass, underscoring the importance of considering this process in the design and interpretation of environmental stable isotope probing studies.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0062826"},"PeriodicalIF":4.2,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069301","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":"Prospective metagenomic sequencing of wastewater across the United States yields robust viral enrichment and concordance with digital PCR measurements.","authors":"Marlene K Wolfe, Devin North, Alexander L Jaffe, Alessandro Zulli, Dorothea Duong, Bridgette Shelden, Miriam Goldman, Miles Richardson, Peter Thana, Vikram Chan-Herur, Pouya Kheradpour, Amanda L Bidwell, Stephen P Hilton, Sheena Conforti, Abigail P Paulos, Alexandria B Boehm","doi":"10.1128/aem.01020-26","DOIUrl":"https://doi.org/10.1128/aem.01020-26","url":null,"abstract":"<p><p>Metagenomic sequencing is increasingly applied to wastewater to characterize the diversity, dynamics, and relative abundance of human and animal viruses. Among these sequencing approaches are those that enrich viral nucleic acids from the wastewater matrix, aiming to increase the viral read fraction for analysis. However, the feasibility of scaling targeted viral sequencing to diverse sewersheds across large geographic scales is currently unknown. In this study, we apply hybrid capture metagenomic sequencing to nearly 450 weekly wastewater samples collected during the respiratory virus season in the United States and evaluate sequencing performance for generating public health-relevant data. Analysis of data from 15 wastewater treatment plants demonstrates that our approach enabled efficient capture of pathogens of interest, achieving a median viral read fraction over 19%. Importantly, relative abundance estimates of common pathogens correlated with direct quantification of viral targets using reverse transcription digital droplet PCR. Together, our results demonstrate that hybrid capture sequencing of wastewater is a viable tool to monitor both common and rare pathogens across geographically diverse sewersheds.IMPORTANCEWastewater testing is commonly used to identify and quantify human pathogens at a community scale. However, the most commonly used approaches rely on targeted, PCR-based methods that are highly specific to a single virus. Metagenomic sequencing provides an opportunity to detect and quantify the relative abundance of a wide range of viruses that are important for human health from wastewater, and hybrid capture approaches work by first enriching samples for these extremely rare targets to increase sensitivity. We demonstrate that hybrid capture metagenomic sequencing successfully enriches wastewater samples from diverse locations across the United States and that data derived from sequences are associated with detections of 11 key viruses using standard RT-ddPCR methods. This work suggests that scaling hybrid capture metagenomics for viruses in wastewater is a feasible way to generate data critical for public health to support infectious disease outbreak response.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0102026"},"PeriodicalIF":4.2,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069379","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":"PhpR, as a unique transcriptional regulator, represses the expression of pyridoxal 5'-phosphate-binding protein YggS in <i>Alcaligenes</i>.","authors":"Qimiao Xu, Changchang Wang, Jiaxi Liu, Fuyu Song, De-Feng Li, Jiasong Li, Shang Dai, Xin Yan, Qing Hong, Jiandong Jiang, Shuang-Jiang Liu, Jian He, Jiguo Qiu","doi":"10.1128/aem.01399-26","DOIUrl":"https://doi.org/10.1128/aem.01399-26","url":null,"abstract":"<p><p>YggS (COG0325 family) was widely conserved across the three domains of life and had been implicated in pyridoxal 5'-phosphate (PLP) homeostasis. However, transcriptional regulators that directly controlled <i>yggS</i> had remained unknown. Here, using <i>Alcaligenes faecalis</i> JQ135, PhpR, a previously unrecognized MocR-family regulator, was identified as a transcriptional regulator that directly controlled <i>yggS</i>. Deletion of <i>yggS</i> in strain JQ135 impaired cell growth and caused intracellular PLP imbalance. PhpR (PLP homeostasis-related protein regulator, <i>phpR</i>) directly repressed <i>yggS</i> transcription by binding a conserved non-palindromic promoter motif in a PLP-dependent manner. Comparative genomic analyses further revealed that the adjacent <i>yggS-phpR</i> gene pair was divergently transcribed and highly conserved, but restricted to <i>Alcaligenes</i> species. Together, these findings established the first direct transcriptional regulatory mechanism for a YggS-family protein and revealed a PLP-responsive regulatory circuit linking cofactor homeostasis in bacteria.</p><p><strong>Importance: </strong>Pyridoxal 5'-phosphate (PLP), the main catalytically active form of vitamin B6, was an essential cofactor for many enzymes, particularly those involved in amino acid metabolism. PLP deficiency could impair the activity of PLP-dependent enzymes and disrupt cellular metabolism, whereas excessive accumulation of free PLP could also cause metabolic imbalance. YggS-family proteins were widely conserved PLP homeostasis factors, yet how their expression was regulated had remained largely unknown. Here, we identified PhpR as a previously uncharacterized MocR-family transcriptional regulator that directly repressed the expression of YggS in <i>Alcaligenes</i>, establishing a direct link between intracellular PLP availability and <i>yggS</i> expression. These findings revealed a previously unknown regulatory mechanism governing bacterial PLP homeostasis and provided new insight into how PLP-responsive transcriptional regulation coordinated cofactor balance with cellular metabolism.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0139926"},"PeriodicalIF":4.2,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069384","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":"Comparative evaluation of two high-throughput qPCR systems for environmental and clinical microbiology applications.","authors":"Hao Wang, Satoshi Ishii","doi":"10.1128/aem.01222-26","DOIUrl":"https://doi.org/10.1128/aem.01222-26","url":null,"abstract":"<p><p>High-throughput quantitative PCR (HT-qPCR) is useful for the simultaneous quantification of various genes, such as microbial source tracking (MST) markers, fecal indicator bacteria, pathogens, and antibiotic resistance genes (ARGs) for environmental and clinical studies. While multiple HT-qPCR platforms are commercially available, their performance has rarely been directly compared. In this study, we evaluated and compared two commonly used HT-qPCR platforms, the Takara Bio SmartChip and the Standard BioTools Biomark HD system, using TaqMan probe-based MST assays and intercalating dye-based ARG assays. Despite differences in sample preparation workflows and reaction volumes, the two platforms produced the same detection results for 94.3% of MST sample × assay combinations, and 87.4% of ARG sample × assay combinations. Because HT-qPCR reactions are performed at nanoliter volumes (6.7-100 nL), a specific target amplification (STA) step is often used to improve the detection of low-abundance targets. Comparison of samples before and after STA showed that STA substantially increased detection frequencies on the Biomark HD platform, but had little effect on the SmartChip platform. Although most assays showed strong agreement between pre- and post-STA measurements and between platforms, discrepancies were observed for a subset of assays. Conventional qPCR and digital PCR results indicated that assay-specific amplification efficiency and sample quality contributed to the observed differences. Overall, these results demonstrate that both HT-qPCR platforms can provide reliable quantitative measurements when properly validated. However, consumable costs, workflow complexity, and maintenance requirements differed between platforms. Therefore, platform selection should consider sample throughput, assay requirements, available resources, and study objectives.</p><p><strong>Importance: </strong>High-throughput qPCR is a powerful tool to detect and quantify various genes simultaneously. Numerous studies have used HT-qPCR for environmental and clinical microbiology applications; however, it is unclear whether different HT-qPCR platforms (e.g., Biomark and SmartChip) produce comparable results or not, as the HT-qPCR protocols are platform-specific. In particular, the use of pre-amplification reaction, also known as specific target amplification (STA), varies across studies. This study shows that both Biomark and SmartChip platforms provide similar quantitative data for most assays and that the STA reaction is useful to improve the detection of low-abundance targets without major biases. To accurately quantify on HT-qPCR platforms, assays should be carefully selected and validated. To guide current and future users, this study provides a general framework for assay selection in HT-qPCR.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0122226"},"PeriodicalIF":4.2,"publicationDate":"2026-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149036103","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 deeply divergent TcdB-like toxin in a cryptic clade C-III <i>Clostridioides</i> strain from a One Health genomic survey in Japan.","authors":"César Rodríguez","doi":"10.1128/aem.01139-26","DOIUrl":"https://doi.org/10.1128/aem.01139-26","url":null,"abstract":"<p><p>In a recent One Health genomic survey of community-associated <i>Clostridioides difficile</i> in Japan, S. Yoshizawa, K. Komori, K. Aoki, T. Sawa, et al. (Appl Environ Microbiol 92:e00397-26, 2026, https://doi.org/10.1128/aem.00397-26) deposited the genome of strain TUM20227, a human <i>tcdA</i>^-/<i>tcdB</i>⁺ isolate assigned to the novel sequence type ST919. Reanalysis of its publicly available genome shows that TUM20227 belongs to cryptic clade C-III and carries a chromosomally encoded, monotoxin PaLoc-like locus encoding a 2,367-amino acid TcdB-family protein. This TcdB-like protein shares less than 83% amino acid identity with all recognized TcdB subtypes (B1-B12) and forms a deeply divergent branch in both full-length and domain-resolved phylogenies, with heterogeneous nearest neighbors across domains and an atypical predicted receptor-binding profile. TcdB_TUM20227 should therefore be regarded as representative of a previously unrecognized, deeply divergent TcdB lineage.IMPORTANCE<i>Clostridioides difficile</i> is a leading cause of diarrhea, and its principal virulence factor, the toxin TcdB, is both a diagnostic target and a template for therapeutics. The recognized diversity of TcdB is captured in a scheme composed of 12 subtypes largely built from strains of the five <i>C. difficile</i> clades, whereas the <i>Clostridioides</i> cryptic clades and their toxins remain comparatively underexplored, even though they can encode divergent toxins with altered receptor use and antigenicity. Here, reanalysis of a single, previously unremarked genome from a One Health survey uncovers a deeply divergent and apparently complete and intact TcdB-family toxin gene whose product falls outside the established subtype framework. This finding shows that systematic data mining of animal, human, and environmental strains can unearth novel toxin genes and provide critical insight into the evolution, receptor specificity, and subtype boundaries of the toxin genes of this important human pathogen.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0113926"},"PeriodicalIF":4.2,"publicationDate":"2026-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149036062","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":"Uncovering potential autotrophs in coal seams: characterization, enrichment, and genome-resolved metabolisms of a subsurface coal seam microbiome.","authors":"Djuna Gulliver, Daniel E Ross, Samuel Flett","doi":"10.1128/aem.00624-26","DOIUrl":"https://doi.org/10.1128/aem.00624-26","url":null,"abstract":"<p><p>Biological transformation of inorganic carbon into organic compounds is an extremely important biosynthetic process, and many organisms catalyze this reaction autotrophically, using CO₂ as the sole carbon source. Natural autotrophic pathways are diverse, as are the organisms that employ them, driven in part by the varied ecological niches they inhabit. One understudied ecological niche, coal seams, contains autotrophic acetogens that catalyze an intermediate step in the conversion of coal to methane. Here, we characterize the geochemistry and microbiology of coal seam produced water (CSPW) from the Appalachian Basin and, through continued anaerobic enrichment on H₂:CO₂, show enhanced growth and acetate production. Specifically, the enriched CSPW microbiome was comprised of <i>Proteiniphilum, Proteiniclasticum, Gudongella, Acetobacterium, Propionicimonas,</i> and <i>Mesobacillus</i>. Genome-resolved metabolisms revealed six potential autotrophic pathways, including four natural pathways (the reductive pentose phosphate pathway, the reversed oxidative tricarboxylic acid cycle, the reductive acetyl-CoA pathway, and the reductive glycine pathway) and two proposed synthetic pathways (the serine-threonine cycle and the pyruvate formate-lyase threonine cycle), with many metagenome-assembled genomes encoding multiple pathways. Overall, these findings suggest a nuanced and adaptable carbon conversion strategy, shedding light on carbon reactions in coal seams, and the potential applications for biological production of valuable chemicals/fuels using mixed microbial communities.</p><p><strong>Importance: </strong>Coal seams harbor taxonomically diverse microorganisms, specifically acetogens and methanogens, suggesting an untapped potential for autotrophic carbon conversion. Here, we show that an enriched coal seam-produced water microbiome utilized CO₂ and/or NaHCO₃ for growth and produced acetate. Genome-resolved metabolisms revealed that most microorganisms encode multiple autotrophic pathways, with the reductive glycine pathway being the most prevalent. This work provides insight into potential microbial strategies for obtaining and transforming carbon in coal seams, and importantly, with proper engineering of operational parameters and reactor design, the enriched microbiome has the potential to be used as a biocatalyst for alternative carbon conversion technologies.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0062426"},"PeriodicalIF":4.2,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149036112","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":"Regulatory cascade of NdpR and NdpR2 in controlling nicotine degradation operons in <i>Sphingomonas melonis</i> TY.","authors":"Qi Tang, Ziliang He, Shihan Wang, Yiming Cheng, Haixia Wang, Weihong Zhong","doi":"10.1128/aem.01130-26","DOIUrl":"10.1128/aem.01130-26","url":null,"abstract":"<p><p>In <i>Sphingomonas melonis</i> TY, the TetR-family NdpR and AraC-family NdpR2 coregulate nicotine catabolism. Despite overlapping target promoters, their hierarchical relationship remained unclear. Here, we elucidate a multi-layered cascade regulatory network where NdpR directly binds to the <i>ndpR2</i> promoter and represses its transcription. Structural and mutational analyses elucidate the structure-function relationship of NdpR, featuring a wide HTH span that supports a strong steric barrier mechanism on core promoters. The intermediate 2,5-dihydroxypyridine (2,5-DHP) acts as an effector, preventing NdpR from binding the <i>ndpR2</i> promoter. Furthermore, molecular simulations demonstrate a direct NdpR-NdpR2 physical interaction. We propose a double-lock regulatory mechanism operating synergistically at the transcriptional and protein levels. This precise dynamic regulatory balance enables cells to sensitively perceive environmental signals via basal metabolism and rapidly activate target gene expression upon signal confirmation, thereby achieving a balance between energy economy and efficient substrate degradation. Based on this cascade, we constructed a multi-factor system in <i>Pseudomonas</i> sp. JY-Q exhibiting bidirectional, reversible responses to nicotine, 2,5-DHP, and IPTG (isopropyl β-D-1-thiogalactopyranoside). This study uncovers microbial adaptive strategies and provides programmable, tunable regulatory tools for synthetic biology.IMPORTANCEDuring microbial degradation of complex pollutants like nicotine, substrate uptake, transport, and catabolism are typically coregulated by multiple factors. Understanding how this complex regulatory network prevents metabolic energy waste, rapidly responds to substance changes, and thereby achieves temporal control over related gene expression is crucial for the development of metabolic control elements. This study reveals the cascade regulatory logic of two regulatory proteins within the same metabolic pathway and the regulatory balance during metabolism. Through structural and functional analyses of NdpR, we elucidated the molecular mechanisms underlying its target sequence recognition, binding of the effector 2,5-DHP, and interaction with NdpR2, thereby clarifying the dynamic regulatory process by which this system responds to environmental changes. Finally, we applied this system in a heterologous Pseudomonas host to develop a programmable multi-factor gene circuit. This study deepens our mechanistic understanding of microbial adaptive strategies and provides a dynamically tunable regulatory tool for synthetic biology and metabolic engineering.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0113026"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599538/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148711206","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":"Influence of polyvinyl chloride (PVC) microplastic morphology on bacterial survival during thermal and ultraviolet-C inactivation in aqueous systems.","authors":"Sungjun Hwang, Wenjing Lu, Xu Yang, Kang Huang","doi":"10.1128/aem.01025-26","DOIUrl":"10.1128/aem.01025-26","url":null,"abstract":"<p><p>Microplastics are increasingly detected in water and food-associated environments, yet how particle morphology influences microbial persistence during inactivation remains poorly understood. This study aims to develop polyvinyl chloride (PVC) microplastic particles with distinct morphologies and controlled size ranges, and to evaluate how particle morphology influences bacterial attachment and survival during thermal and ultraviolet-C (UVC) inactivation in aqueous systems. First, we developed a PVC microplastic model system with distinct morphologies and controlled size fractions. Original PVC particles were relatively smooth and rounded, whereas irregular particles were generated by compounding, pelletizing, and cryogenically grinding the same PVC material, followed by sieving into defined size ranges. Second, using this model system, we evaluated how PVC particle morphology affected bacterial attachment and survival during thermal and UVC inactivation in aqueous systems. <i>Escherichia coli</i> O157:H7 and <i>Listeria innocua</i> were used as model gram-negative and gram-positive bacteria. Confocal microscopy showed attachment of <i>E. coli</i> to both particle types, with stronger association on ground PVC particles. In the presence of PVC particles, thermal log reductions decreased to approximately 4.0-5.1 log CFUs/mL, compared with about 5.9 log CFU/mL in microplastic-free controls, while UVC log reductions decreased to about 3.9-4.6 log CFU/mL, compared with about 5.2-6.0 log CFU/mL in microplastic-free controls. Ground PVC provided greater protection during thermal treatment, whereas both particle types similarly reduced UVC inactivation. These findings show that PVC microplastics can interfere with microbial control processes and highlight particle morphology as an important factor influencing bacterial survival in aqueous environments.IMPORTANCEMicroplastics are increasingly present in water and food-related environments, but their effects on microbial control processes remain poorly understood. This study demonstrates that PVC microplastics can reduce the effectiveness of both thermal and UVC inactivation of foodborne pathogens in aqueous systems. By developing PVC particles with distinct and defined morphologies, we further demonstrate that particle shape and surface characteristics influence bacterial attachment and survival, particularly during thermal treatment. These findings provide new mechanistic insight into how microplastics may alter bacterial persistence under disinfection or food-processing conditions. This work highlights microplastic morphology as a previously underappreciated factor affecting microbial inactivation and establishes a useful PVC microplastic model system for future studies on microplastic-microbe interactions in environmental and food-associated settings.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0102526"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599510/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148838897","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":"Diversity of Antarctic sea ice and under-ice seawater RNA viruses.","authors":"Shujuan Sun, Kaiyang Zheng, Yue Su, Yantao Liang, Miaolan Wu, Hao Yu, Jianhua Sun, Wei Wang, Andrew Martin, Fraser Kennedy, Ken Ryan, Chen Gao, Andrew McMinn, Min Wang","doi":"10.1128/aem.01472-26","DOIUrl":"10.1128/aem.01472-26","url":null,"abstract":"<p><p>Sea ice is vital to polar ecosystems and serves as a natural laboratory for studying microbial adaptations in extreme environments. Nevertheless, the diversity and ecology of Antarctic marine RNA viruses have not been sufficiently explored. Here, 11 metatranscriptomes from Antarctic sea ice and ice-associated environments were analyzed to characterize RNA viral communities and their ecological differentiation between sea ice and seawater. Diverse RNA viral lineages were identified, of which <i>Cryppavirales</i> and <i>Picornavirales</i> were dominant. <i>Lenarviricota</i> was predominant in sea ice, highlighting the differential distribution between the two ecosystems. Evolutionary analyses showed lower Ka/Ks values in sea ice-associated RNA viruses, suggesting stronger purifying constraints and a more conserved evolutionary pattern compared with under-ice seawater. More than half of the viral operational taxonomic units (vOTUs) could be assigned to hosts, primarily fungi and algae, suggesting a potential role for viruses in fungal-algal symbiotic/parasitic systems. This study provides new insights into the diversity and distinctiveness of RNA viruses in Antarctic sea ice-seawater systems.</p><p><strong>Importance: </strong>Polar sea ice is a vital component of Antarctic ecosystems and plays an important role in climate regulation, yet the diversity and ecological roles of its viral communities remain largely unknown. This study documents the diversity and complexity of RNA viruses in Antarctic sea ice-seawater systems. The potential host lineages of RNA viruses in Antarctic sea ice were explored, shedding light on the cryptic RNA viral communities in these extreme environments. These findings provide important insights into the diversity and ecology of RNA viruses in these habitats, enhancing the understanding of polar viral ecology.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0147226"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599536/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148817169","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":"Sulfur source-driven global remodeling of gene expression in the fuel-biodesulfurizing <i>Rhodococcus qingshengii</i> IGTS8.","authors":"Ashraf El Nayal, Vartul Sangal, Abdelmalek Alioua, Aurélie Hirschler, Sandrine Koechler, Dimitri Heintz, Christine Carapito, Alain Van Dorsselaer, Wael Ismail","doi":"10.1128/aem.01549-26","DOIUrl":"https://doi.org/10.1128/aem.01549-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Recent proteomics and metabolomics studies have confirmed the significance of understanding the fuel biodesulfurization phenotype at a global scale beyond the desulfurization 4S pathway. To reveal the transcriptomic adaptations in the model strain &lt;i&gt;Rhodococcus qingshengii&lt;/i&gt; IGTS8 under biodesulfurization conditions, we conducted a time series comparative RNA-seq study using cultures of IGTS8 grown on either dibenzothiophene (DBT) or MgSO&lt;sub&gt;4&lt;/sub&gt; as the sulfur source. The RNA-seq data revealed many differentially expressed genes (DEGs) depending on the sulfur source and growth phase, and the strongest transcriptomic response was evident during the late-log phase. In total, 6,690 transcripts were detected in the DBT and MgSO&lt;sub&gt;4&lt;/sub&gt; cultures, representing 99.5% of the total protein-coding genes. A substantial fraction of the DEGs encodes ABC-type transporters and hypothetical proteins. In the DBT culture, 623 DEGs were upregulated, and 587 DEGs were downregulated. Generally, the DEGs covered key physiological processes, such as stress response, regulation of gene expression, uptake of nutrients, metabolism of lipids, amino acids, carbohydrates, proteins, nucleotides, cell division, and cell wall biosynthesis/degradation. While genes of carbohydrate metabolism were mostly downregulated in the DBT culture, those encoding amino acid and fatty acid degradation, as well as energy conservation, were upregulated. Moreover, genes encoding mobile genetic elements, C1 metabolism enzymes, carbonic anhydrase, and nitrile hydratase were upregulated under biodesulfurization conditions. In contrast, dihydrofolate reductase was strongly downregulated. The growth phase-dependent transcriptomic rearrangements under biodesulfurization conditions appear to prioritize cellular homeostasis and protection rather than proliferation.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Commercial application of fuel biodesulfurization requires exceptionally robust and catalytically active desulfurizing microbes that can tolerate and sustain activity under the harsh operational conditions in oil refineries. It is generally accepted that naturally occurring bacteria may not meet these industrial requirements. Therefore, synthetic biology and metabolic engineering hold promise. However, a thorough understanding of the physiology, metabolism, and stress response of fuel-desulfurizing bacteria, which is currently lacking, is key toward further developments in this field. Considering these knowledge gaps, our findings provide mechanistic insights into the transcriptional responses of the reference biodesulfurizing strain &lt;i&gt;Rhodococcus qingshengii&lt;/i&gt; IGTS8, which, when integrated together with our recently reported proteomics and metabolomics data, enable a multifaceted and deeper understanding of the biodesulfurization phenotype, facilitating rational design of more efficient recombinant biodesulfurizers. Hence, this study represents a step forward toward developing a commerci","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0154926"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149023451","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}