Applied and Environmental Microbiology最新文献

{"title":"Longitudinal and cross-sectional sampling and whole genome sequencing of <i>Campylobacter</i> in a chicken abattoir reveal highly dynamic population structure.","authors":"Shanwei Tong, Kaidi Wang, Shenmiao Li, Michael Trimble, Yunxuan Chen, Lixue Liu, Jun Duan, Eduardo Taboada, Xiaonan Lu, William Hsiao","doi":"10.1128/aem.02369-24","DOIUrl":"https://doi.org/10.1128/aem.02369-24","url":null,"abstract":"<p><p><i>Campylobacter</i> is a leading cause of human gastroenteritis worldwide and is commonly identified in poultry products. Current knowledge of its dissemination patterns in poultry production largely relies on the less sensitive traditional genotyping methods. In this study, whole-genome sequencing was applied to 324 <i>Campylobacter</i> isolates sampled from a chicken abattoir in the Greater Vancouver area throughout 2020. Core genome multi-locus sequence typing analysis revealed a highly diverse and dynamic <i>Campylobacter</i> population containing 27 distinct lineages. A wide range of plasmids was characterized, and a high prevalence of antibiotic resistance was observed among these isolates. Distinct subpopulations were identified in 10 lineages, suggesting that some <i>Campylobacter</i> populations may have diversified within the local agricultural environment. Some lineages were frequently reintroduced to the abattoir, suggesting the potential presence of hidden <i>Campylobacter</i> reservoirs upstream of slaughter. Comparisons between biological and environmental samples suggest a high probability of between-batch cross-contamination. Locally sourced public <i>Campylobacter</i> isolates showed strong genomic correlations with the lineages identified in this study. Notably, lineages 1629a and 1629b were identified to have persisted within the local poultry production ecosystem for several years, explaining their recurrent detection. In conclusion, this study enhances our understanding of <i>Campylobacter</i> population dynamics in the chicken abattoir environment, providing insights for controlling this foodborne pathogen in poultry production systems.IMPORTANCEUsing whole-genome sequencing, this study revealed a highly diverse and dynamic <i>Campylobacter</i> population within the chicken abattoir. The high prevalence of antibiotic resistance marked the critical need for surveillance in this region. The findings highlighted the likely existence of a hidden common source of <i>Campylobacter</i> upstream in the poultry production chain, which significantly contributes to the repeated introduction of the same lineages into the abattoir. Given the frequent reintroductions, the current understanding of <i>Campylobacter</i> persistence in the abattoir environment (up to 21 days) may require revision. Additionally, batch-to-batch dissemination of <i>Campylobacter</i> strains during processing is highly possible. A robust geographic association was also observed between the <i>Campylobacter</i> population in the abattoir and the local community. In sum, this study provides insights into the dynamics of <i>Campylobacter</i> contamination in the poultry production chain, offering guidance for improving prevention and control strategies.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0236924"},"PeriodicalIF":3.9,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143974460","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":"<i>Escherichia coli</i> resistant to the highest priority critically important fluoroquinolone or 3rd and 4th generation cephalosporin antibiotics persist in pigsties.","authors":"Nicola M Pfeifer, Michael Weber, Elisabeth Wiegand, Stefanie A Barth, Christian Berens, Christian Menge","doi":"10.1128/aem.01386-24","DOIUrl":"https://doi.org/10.1128/aem.01386-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Antimicrobial resistance threatens human and animal health, with antimicrobial usage being a key driver of selection, transmission, and spread of resistant bacteria. Livestock represents a potential reservoir for human transmission, leading authorities to restrict veterinary usage of fluoroquinolones and certain cephalosporins. However, growing evidence indicates that the corresponding resistance determinants can be retained even in the drugs' absence. To obtain data on the magnitude and dynamics of this phenomenon in pig farming, we quantitatively and qualitatively assessed fluoroquinolone- and cephalosporin-resistant &lt;i&gt;Escherichia coli&lt;/i&gt; in Thuringian pigsties practicing a closed management system to minimize the impact of externally introduced strains. Pooled fecal samples from consecutive fattening runs at one conventional and two organic farms and from 25 piglet groups from another conventional farm were collected over 16 months and screened for &lt;i&gt;E. coli&lt;/i&gt; on plates containing enrofloxacin, ceftiofur, or cefquinome. Resistant bacteria were isolated on all farms; their counts varied strongly but were generally higher in piglets and declined with increasing animal age. Phylogenetic comparison of 393 isolates was performed via multiple-locus variable number tandem repeat analysis (MLVA) to follow strain dynamics and persistence. The isolates displayed large phylogenetic heterogeneity, featuring 52 different MLVA patterns. Still, conserved MLVA patterns indicated long-term persistence of specific strains in each farm's environment. This suggests that resistant strains appear well-adapted to the particular farm and its management practices, implying that, beyond restricting usage, further measures, including, e.g., consideration of the type of resistance as well as its persistence and transmission dynamics, will be indispensable to reduce the antimicrobial resistance load in pork production.IMPORTANCEAntimicrobial resistance (AMR) represents a global threat to human and animal health, with animals considered a reservoir for transmission of AMR to humans. Because antimicrobial usage is a driver for resistance, one approach to decrease the AMR burden is to reduce its usage. However, this can, but does not necessarily, lead to lower AMR prevalence. German and EU legislation restrict the use of fluoroquinolones and certain cephalosporins, substance classes designated as highest priority critically important antimicrobials for human medicine, in animal husbandry. Longitudinal sampling of organic and conventional farms in Thuringia for resistance to these antibiotic classes revealed that certain resistant &lt;i&gt;Escherichia coli&lt;/i&gt; strains can persist in the farm environment over extended time periods. These strains displayed farm specificity, indicating adaptation to the particular farm and its management practices, so that their elimination might be difficult, requiring either procedures acting generally against Enterobacterales or targeted","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0138624"},"PeriodicalIF":3.9,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143956958","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":"Metabolic engineering of <i>Escherichia coli</i> for high-yield dopamine production via optimized fermentation strategies.","authors":"Xu Li, Yanghao Liu, Ling Ma, Wenjing Jiang, Tangen Shi, Lanxiao Li, Changgeng Li, Zhichao Chen, Xiaoguang Fan, Qingyang Xu","doi":"10.1128/aem.00159-25","DOIUrl":"https://doi.org/10.1128/aem.00159-25","url":null,"abstract":"<p><p>Dopamine (DA) is a high-value metabolic product; however, its biosynthesis has multiple limitations due to metabolic regulation and fermentation strategies. This study aimed to construct a high-yield dopamine-producing <i>Escherichia coli</i> strain devoid of plasmids and defects using <i>E. coli</i> W3110 as the chassis strain. We constitutively expressed the <i>DmDdC</i> gene from <i>Drosophila melanogaster</i> in <i>E. coli</i>, which was combined with the <i>hpaBC</i> gene from <i>E. coli</i> BL21 (DE3), successfully constructed a dopamine biosynthesis module, and achieved preliminary dopamine synthesis in <i>E. coli</i>. By optimizing the promoters of the key enzyme genes, we achieved a coordinated balance between the generation and utilization of intermediate metabolites. Subsequently, we used metabolic engineering strategies, such as increasing the carbon flux through the dopamine synthesis pathway, elevating the gene copy number of key enzymes, and constructing an FADH₂-NADH supply module to create a high-yield strain, DA-29. In this study, a two-stage pH fermentation strategy was developed to enhance fermentation. The first stage ensures the normal growth of the strain, whereas the second stage reduces dopamine degradation by maintaining a low pH. Finally, using a combined Fe²⁺ and ascorbic acid feeding strategy, we obtained 22.58 g/L of dopamine in a 5 L bioreactor, demonstrating that the constructed strain DA-29 possesses high dopamine production capacity, providing strong support for the industrial-scale dopamine production.</p><p><strong>Importance: </strong>In this study, we developed a plasmid-free, defect-free <i>Escherichia coli</i> strain with high dopamine production. We further optimized the fermentation process for this strain by applying the dual-stage pH fermentation strategy developed in this research, combined with an Fe²⁺-ascorbic acid co-feeding strategy. This approach significantly increased dopamine yield and addressed the issue of dopamine oxidation during fermentation. The yield reached 22.58 g/L, marking the highest known yield to date and laying a solid foundation for future scale-up production. This research explores the metabolic pathway of dopamine and the efficient fermentation methods for its production, providing a novel fermentation strategy. It offers new insights into microbial production of aromatic amino acid derivatives, advancing research in this field.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0015925"},"PeriodicalIF":3.9,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143967261","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":"Deciphering the ammonia transformation mechanism of a novel marine multi-stress-tolerant yeast, <i>Pichia kudriavzevii</i> HJ2, as revealed by integrated omics analysis.","authors":"Kunmei Huang, Huashan Bai, Can Meng, Muhammad Kashif, Zhiling Wei, Zaihang Tang, Shu He, Shanguang Wu, Sheng He, Chengjian Jiang","doi":"10.1128/aem.02211-24","DOIUrl":"https://doi.org/10.1128/aem.02211-24","url":null,"abstract":"<p><p>Ammonia nitrogen posed a significant threat to aquatic animals in aquaculture environments, and the substantial potential of microorganisms in removing ammonia nitrogen had garnered considerable attention. This study identified a marine yeast, <i>Pichia kudriavzevii</i> HJ2, which effectively removed ammonia nitrogen. By combining transcriptomics and metabolomics, the ammonia nitrogen transformation mechanism of HJ2 was elucidated. HJ2 achieved 100% ammonia nitrogen removal efficiency within 1 day of fermentation at 35°C with 300 mg/L ammonia nitrogen and 73.56% removal efficiency within 36 h with 600 mg/L ammonia nitrogen. Transcriptomics revealed that exposure to 600 mg/L ammonia nitrogen resulted in 541 up-regulated genes and 567 down-regulated genes in the HJ2 strain. Differentially expressed genes (DEGs) were primarily involved in the tricarboxylic acid (TCA) cycle and amino acid metabolism. Metabolomics revealed that HJ2 facilitated the production of 383 up-regulated metabolites and suppressed 137 down-regulated metabolites when exposed to 600 mg/L ammonia nitrogen. Integrating transcriptomics and metabolomics analyses showed that HJ2 removed ammonia nitrogen by sensing its presence in the extracellular environment, activating the TCA cycle, enhancing amino acid metabolism and nucleotide metabolism, and promoting its robust growth and reproduction. Amino acid metabolism played an important role in the ammonia transformation mechanism of HJ2. The result was confirmed by the increased activity of glutamate dehydrogenase (GDH) and aspartate aminotransferase (GOT). Up-regulated nitrogen metabolites such as L-glutamate, L-aspartic acid, spermidine, and trigonelline were produced. The results of enzyme activity tests, construction of overexpressing strains, and adding exogenous amino acid experiments demonstrated that HJ2 could utilize GDH and GOT ammonia assimilation pathways.<b>IMPORTANCE</b>Ammonia nitrogen removal ability was a universal characteristic among the ammonia-oxidizing bacteria or archaea. Recently, yeast strains from the genus <i>Pichia</i> were found to have ammonia nitrogen removal ability. However, the mechanism of ammonia nitrogen removal in <i>Pichia</i> had not been reported. In the study, the ammonia nitrogen removal efficiency of <i>Pichia kudriavzevii</i> HJ2 was identified, and the mechanisms by which HJ2 transformed ammonia nitrogen into non-toxic organic nitrogen were elucidated, offering potential solutions to pollution challenges in aquaculture and helping minimize resource waste. The study offered new insights into the transformation mechanism of microbial ammonia nitrogen removal and its environmentally friendly application.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0221124"},"PeriodicalIF":3.9,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143960619","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 tale of two vineyards: parsing site-specific differences in bacterial and fungal communities of wine grapes from proximal vineyards and their changes during processing in a single winery.","authors":"Reid G Griggs, Lena Flörl, Michael Swadener, Rodrigo Hernández-Velázquez, David A Mills, Nicholas A Bokulich","doi":"10.1128/aem.00526-25","DOIUrl":"https://doi.org/10.1128/aem.00526-25","url":null,"abstract":"<p><p>Wine is a microbial product, naturally transformed through fermentation by a consortium of fungi and bacteria that originate from the vineyard and the cellar, in addition to any microorganisms that are intentionally inoculated. Previous work has shown that grapevine-associated microbiota follow distinct biogeographic patterns, associated with climate and soil properties, and that even neighboring vineyards can harbor distinct microbial communities, but it is unclear whether these differences persist when controlling for variations in farming practices, cultivar, and climate and whether site-specific microbial profiles change during processing in the winery. Here, we investigated the bacterial and fungal microbiota of fruits pre- and post-harvest from two neighboring vineyards planted to a single variety, geographically close to one another, and farmed the same way and then processed in a single winery. These communities underwent subtle changes during processing, yet retained distinct site-specific signatures, indicating the partial contribution of the winery environment to the microbiota of grape must and juice pre-fermentation. We also profiled the microbiota of key microbial sources in the winery environment, including fruit flies (<i>Drosophila</i> spp.) and processing equipment, demonstrating that the microbiota at these sites reflect contact with the plant material, harbor communities distinct from the fruit, and appear to partially contribute to the fermentation assemblage, especially via the contribution of fermentative yeasts that are rare or missing in the vineyard environment. These results bolster previous reports of site-specific microbial signatures in winegrowing and make a first estimation of the changes to the grape-associated microbiome during early processing.IMPORTANCENative wine fermentations are driven by microbes carried over from the vineyard or introduced in the winery. In this study, we tracked the microbiome dynamics of wine fermentations from two Chardonnay vineyards planted in close proximity in order to examine the relative contribution of vineyard- and winery-resident microbiota on microbial succession during wine fermentation. By tracking microbial changes from the vineyard to winery, we show that the winery environment, including processing equipment and fruit flies, contributes to the fermentation microbiome but does not override vineyard-specific microbial differences. These findings support the concept of microbial terroir and highlight the importance of vineyard microbiomes in shaping wine fermentation. This work advances our understanding of how microbial diversity influences wine production and provides insights into the ecological dynamics of fermentation. By identifying key microbial sources and their contributions, this study lays the groundwork for future research on microbiomes in viticulture and winemaking.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0052625"},"PeriodicalIF":3.9,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143960155","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":"Exploring sub-species variation in food microbiomes: a roadmap to reveal hidden diversity and functional potential.","authors":"Lena Flörl, Annina Meyer, Nicholas A Bokulich","doi":"10.1128/aem.00524-25","DOIUrl":"https://doi.org/10.1128/aem.00524-25","url":null,"abstract":"<p><p>Within-species diversity of microorganisms in food systems significantly shapes community function. While next-generation sequencing (NGS) methods have advanced our understanding of microbiomes at the community level, it is essential to recognize the importance of within-species variation for understanding and predicting the functional activities of these communities. This review highlights the substantial variation observed among microbial species in food systems and its implications for their functionality. We discuss a selection of key species in fermented foods and food systems, highlighting examples of strain-level variation and its influence on quality and safety. We present a comprehensive roadmap of methodologies aimed at uncovering this often overlooked underlying diversity. Technologies like long-read marker-gene or shotgun metagenome sequencing offer enhanced resolution of microbial communities and insights into the functional potential of individual strains and should be integrated with techniques such as metabolomics, metatranscriptomics, and metaproteomics to link strain-level microbial community structure to functional activities. Furthermore, the interactions between viruses and microbes that contribute to strain diversity and community stability are also critical to consider. This article highlights existing research and emphasizes the importance of incorporating within-species diversity in microbial community studies to harness their full potential, advance fundamental science, and foster innovation.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0052425"},"PeriodicalIF":3.9,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143953027","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":"Standardizing a microbiome pipeline for body fluid identification from complex crime scene stains.","authors":"Meghna Swayambhu, Mario Gysi, Cordula Haas, Larissa Schuh, Larissa Walser, Fardin Javanmard, Tamara Flury, Sarah Ahannach, Sarah Lebeer, Eirik Hanssen, Lars Snipen, Nicholas A Bokulich, Rolf Kümmerli, Natasha Arora","doi":"10.1128/aem.01871-24","DOIUrl":"https://doi.org/10.1128/aem.01871-24","url":null,"abstract":"<p><p>Recent advances in next-generation sequencing have opened up new possibilities for applying the human microbiome in various fields, including forensics. Researchers have capitalized on the site-specific microbial communities found in different parts of the body to identify body fluids from biological evidence. Despite promising results, microbiome-based methods have not been integrated into forensic practice due to the lack of standardized protocols and systematic testing of methods on forensically relevant samples. Our study addresses critical decisions in establishing these protocols, focusing on bioinformatics choices and the use of machine learning to present microbiome results in case reports for forensically relevant and challenging samples. In our study, we propose using operational taxonomic units (OTUs) for read data processing and generating heterogeneous training data sets for training a random forest classifier. We incorporated six forensically relevant classes: saliva, semen, skin from hand, penile skin, urine, and vaginal/menstrual fluid, and our classifier achieved a high weighted average F1 score of 0.89. Systematic testing on mock forensic samples, including mixed-source samples and underwear, revealed reliable detection of at least one component of the mixture and the identification of vaginal fluid from underwear substrates. Additionally, when investigating the sexually shared microbiome (sexome) of heterosexual couples, our classifier could potentially infer the nature of sexual activity. We therefore highlight the value of the sexome for assessing the nature of sexual activities in forensic investigations while delineating areas that warrant further research.IMPORTANCEMicrobiome-based analyses combined with machine learning offer potential avenues for use in forensic science and other applied fields, yet standardized protocols remain lacking. Moreover, machine learning classifiers have shown promise for predicting body sites in forensics, but they have not been systematically evaluated on complex mixed-source samples. Our study addresses key decisions for establishing standardized protocols and, to our knowledge, is the first to report classification results from uncontrolled mixed-source samples, including sexome (sexually shared microbiome) samples. In our study, we explore both the strengths and limitations of classifying the mixed-source samples while also providing options for tackling the limitations.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0187124"},"PeriodicalIF":3.9,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143972865","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":"Distinctive physiology of polyphosphate-accumulating <i>Beggiatoa</i> suggests an important role in benthic phosphorus cycling.","authors":"Nadezhda Iakovchuk, Jenny Fabian, Olaf Dellwig, Christiane Hassenrück, Heide N Schulz-Vogt","doi":"10.1128/aem.02330-24","DOIUrl":"https://doi.org/10.1128/aem.02330-24","url":null,"abstract":"<p><p>Filamentous sulfide-oxidizing <i>Beggiatoa</i> spp., which occasionally form extensive white microbial mats, are widespread in marine coastal environments and can achieve significant biomass because of their large size. Their ability to store phosphates in the polymerized form of polyphosphates makes them potential key players in altering the phosphorus (P) cycle at the sediment-water interface. This study examined phosphate uptake and polyphosphate formation in a P-starved culture of <i>Beggiatoa</i> sp. 35Flor strain. Remarkably, even after sustained P starvation over five generations, the mat establishment rate of the examined culture was 46%, demonstrating considerable plasticity in response to different levels of phosphate availability. Under these P-depleted conditions, at least 17% of filaments still contained polyphosphates, highlighting their critical role in their metabolism. Upon reintroduction of phosphate to starved cultures, an extremely rapid phosphate uptake was observed within the first 10 min, with rates reaching up to 12.4 mmol phosphate g^-1 protein h^-1, which is significantly higher than values previously reported in the literature for similar-sized organisms. The high phosphate uptake capacity of <i>Beggiatoa</i> spp., estimated at 0.6-6 mmol m^-2 d^-1 for typical densities of filaments in coastal sediments, suggests that under certain environmental conditions, these bacteria could act as a P sink and thus play an important role in benthic P cycling.</p><p><strong>Importance: </strong>Sulfide-oxidizing bacteria of the genus <i>Beggiatoa</i> occur ubiquitously in marine coastal sediments and have a large potential to influence phosphate fluxes at the sediment-water interface, owing to their ability to accumulate polyphosphate and their large size. However, the extent to which these bacteria can contribute to phosphorus (P) sequestration or release remains poorly assessed. The importance of this study lies in demonstrating the remarkable flexibility in the adaptation of the strain <i>Beggiatoa</i> sp. 35Flor to varying P availability, including prolonged P starvation and its capacity to rapidly uptake and store available phosphate in the form of polyphosphate. When considered on a global scale, these physiological traits could form the basis for <i>Beggiatoa</i>'s role in moderating P fluxes.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0233024"},"PeriodicalIF":3.9,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959410","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":"Advancing transcriptomic profiling of airborne bacteria.","authors":"Emily Antoinette Kraus, Bharath Prithiviraj, Mark Hernandez","doi":"10.1128/aem.00148-25","DOIUrl":"https://doi.org/10.1128/aem.00148-25","url":null,"abstract":"<p><p>Aerobiology research focusing on bioaerosol particle dynamics has catalogued the identity, distribution, and abundance of airborne microbes in a broad variety of indoor environments and, more recently, indoor disinfection methods for medically relevant microbes. Given their importance in environmental health and our constant exposure to airborne microbes in our daily lives, surprisingly little is known about the activity of live bioaerosols and their metabolic responses to aerosolization and suspension stress. In this context, microbial messenger RNA (mRNA) is a powerful information source of near-real-time organismal responses that cannot be attained through genomic, proteomic, or metabolomic studies. This review discusses current knowledge from transcriptomic studies describing airborne bacterial cellular activity in response to a myriad of environmental stresses imparted rapidly upon aerosolization and continued suspension as a microscopic bioaerosol. In the context of transcriptome profiling, potential artifacts associated with aerosolization/collection of bioaerosols are discussed from the perspective of preserving mRNA and maintaining its fidelity as it exists in airborne microbes. Recommendations for advancing live bioaerosol metabolic profiling through gene expression studies are presented to mitigate inherent artifacts and challenges with modern bioaerosol experiments. These recommendations include the use of larger experimental chambers, temperature control during aerosolization processes, and liquid capture bioaerosol sampling into a nucleic acid preservative to improve the fidelity of collected RNA and better capture the transcriptional activity of airborne microorganisms. Eventually, improvements in profiling bioaerosol activity can contribute toward answering fundamental questions on the aerobiome such as: is the atmosphere a temporary highway or a habitat for microorganisms?</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0014825"},"PeriodicalIF":3.9,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143954199","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":"Correlation of <i>in vitro</i> biofilm formation capacity with persistence of antibiotic-resistant <i>Escherichia coli</i> on gnotobiotic lamb's lettuce.","authors":"Rudolf O Schlechter, Elisabet Marti, Mitja N P Remus-Emsermann, David Drissner, Maria-Theresia Gekenidis","doi":"10.1128/aem.00299-25","DOIUrl":"https://doi.org/10.1128/aem.00299-25","url":null,"abstract":"<p><p>Bacterial contamination of fresh produce is a growing concern for food safety, as apart from human pathogens, antibiotic-resistant bacteria (ARB) can persist on fresh leafy produce. A prominent persistence trait in bacteria is biofilm formation, as it provides increased tolerance to stressful conditions. We screened a comprehensive collection of 174 antibiotic-susceptible and -resistant <i>Escherichia coli</i> originating from fresh leafy produce and its production environment. We tested the ability of these strains to produce biofilms, ranging from none or weak to extreme biofilm-forming bacteria. Next, we tested the ability of selected antibiotic-resistant isolates to colonize gnotobiotic lamb's lettuce (<i>Valerianella locusta</i>) plants. We hypothesized that a higher <i>in vitro</i> biofilm formation capacity correlates with increased colonization of gnotobiotic plant leaves. Despite a marked difference in the ability to form <i>in vitro</i> biofilms for a number of <i>E. coli</i> strains, <i>in vitro</i> biofilm formation was not associated with increased survival on gnotobiotic <i>V. locusta</i> leaf surfaces. However, all tested strains persisted for at least 21 days, highlighting potential food safety risks through unwanted ingestion of resistant bacteria. Population densities of biofilm-forming <i>E. coli</i> exhibited a complex pattern, with subpopulations more successful in colonizing gnotobiotic <i>V. locusta</i> leaves. These findings emphasize the complex behavior of ARB on leaf surfaces and their implications for human safety.IMPORTANCEEach raw food contains a collection of microorganisms, including bacteria. This is of special importance for fresh produce such as leafy salads or herbs, as these foods are usually consumed raw or after minimal processing, whereby higher loads of living bacteria are ingested than with a food that is heated before consumption. A common bacterial lifestyle involves living in large groups embedded in secreted protective substances. Such bacterial assemblies, so-called biofilms, confer high persistence and resistance of bacteria to external harsh conditions. In our research, we investigated whether stronger <i>in vitro</i> biofilm formation by antibiotic-resistant <i>Escherichia coli</i> correlates with better survival on lamb's lettuce leaves. Although no clear correlation was observed between biofilm formation capacity and population density on the salad, all tested isolates could survive for at least 3 weeks with no significant decline over time, highlighting a potential food safety risk independently of <i>in vitro</i> biofilm formation.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0029925"},"PeriodicalIF":3.9,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143962907","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}