Applied and Environmental Microbiology最新文献

{"title":"<i>sll1019</i> and <i>slr1259</i> encoding glyoxalase II improve tolerance of <i>Synechocystis</i> sp. PCC 6803 to methylglyoxal- and ethanol- induced oxidative stress by glyoxalase pathway.","authors":"Kai Ji, Yihang Zhang, Tianyuan Zhang, Daixi Li, Yuan Yuan, Li Wang, Qiaoyun Huang, Wenli Chen","doi":"10.1128/aem.00564-24","DOIUrl":"10.1128/aem.00564-24","url":null,"abstract":"<p><p>The glyoxalase pathway is the primary detoxification mechanism for methylglyoxal (MG), a ubiquitous toxic metabolite that disrupts redox homeostasis. In the glyoxalase pathway, glyoxalase II (GlyII) can completely detoxify MG. Increasing the activity of the glyoxalase system can enhance the resistance of plants or organisms to abiotic stress, but the relevant mechanism remains largely unknown. In this study, we investigated the physiological functions of GlyII genes (<i>sll1019</i> and <i>slr1259</i>) in <i>Synechocystis</i> sp. PCC 6803 under MG or ethanol stress based on transcriptome and metabolome data. High-performance liquid chromatography (HPLC) results showed that proteins Sll1019 and Slr1259 had GlyII activity. Under stress conditions, <i>sll1019</i> and <i>slr1259</i> protected the strain against oxidative stress by enhancing the activity of the glyoxalase pathway and raising the contents of antioxidants such as glutathione and superoxide dismutase. In the photosynthetic system, <i>sll1019</i> and <i>slr1259</i> indirectly affected the light energy absorption by strains, synthesis of photosynthetic pigments, and activities of photosystem I and photosystem II, which was crucial for the growth of the strain under stress conditions. In addition, <i>sll1019</i> and <i>slr1259</i> enhanced the tolerance of strain to oxidative stress by indirectly regulating metabolic networks, including ensuring energy acquisition, NADH and NADPH production, and phosphate and nitrate transport. This study reveals the mechanism by which <i>sll1019</i> and <i>slr1259</i> improve oxidative stress tolerance of strains by glyoxalase pathway. Our findings provide theoretical basis for breeding, seedling, and field production of abiotic stress tolerance-enhanced variety.IMPORTANCEThe glyoxalase system is present in most organisms, and it is the primary pathway for eliminating the toxic metabolite methylglyoxal. Increasing the activity of the glyoxalase system can enhance plant resistance to environmental stress, but the relevant mechanism is poorly understood. This study revealed the physiological functions of glyoxalase II genes <i>sll1019</i> and <i>slr1259</i> in <i>Synechocystis</i> sp. PCC 6803 under abiotic stress conditions and their regulatory effects on oxidative stress tolerance of strains. Under stress conditions, <i>sll1019</i> and <i>slr1259</i> enhanced the activity of the glyoxalase pathway and the antioxidant system, maintained photosynthesis, ensured energy acquisition, NADH and NADPH production, and phosphate and nitrate transport, thereby protecting the strain against oxidative stress. This study lays a foundation for further deciphering the mechanism by which the glyoxalase system enhances the tolerance of cells to abiotic stress, providing important information for breeding, seedling, and selection of plants with strong stress resistance.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0056424"},"PeriodicalIF":3.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11577758/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142456515","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":"Pangenome analysis of <i>Paenibacillus polymyxa</i> strains reveals the existence of multiple and functionally distinct <i>Paenibacillus</i> species.","authors":"Federica Maggi, Anna Maria Giuliodori, Anna Brandi, Lucia Cimarelli, Roberto Alcántara, Stefano Pallotti, Consuelo Amantini, Dezemona Petrelli, Attilio Fabbretti, Roberto Spurio, Valerio Napolioni","doi":"10.1128/aem.01740-24","DOIUrl":"10.1128/aem.01740-24","url":null,"abstract":"<p><p><i>Paenibacillus polymyxa</i>, a Gram-positive bacterium commonly found in soil and plant roots, plays an important role in the environment due to its nitrogen-fixing ability and is renowned for producing antibiotics like polymyxin. In this study, we present a robust framework for investigating the evolutionary and taxonomic connections of strains belonging to <i>P. polymyxa</i> available at the National Center for Biotechnology Information, as well as five new additional strains isolated at the University of Camerino (Italy), through pangenome analysis. These strains can produce secondary metabolites active against <i>Staphylococcus aureus</i> and <i>Klebsiella pneumoniae</i>. Employing techniques such as digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) estimation, OrthoFinder, and ribosomal multilocus sequence typing, we consistently divided these <i>P. polymyxa</i> strains into four clusters, which differ significantly in terms of ANI and dDDH percentages, both considered as reference indices for separating bacterial species. Moreover, the strains of Cluster 2 were re-classified as belonging to the <i>Paenibacillus ottowii</i> species. By comparing the pangenomes, we identified the core genes of each cluster and analyzed them to recognize distinctive features in terms of biosynthetic/metabolic potential. The comparison of pangenomes also allowed us to pinpoint differences between clusters in terms of genetic variability and the percentage of the genome dedicated to core and accessory genes. In conclusion, the data obtained from our analyses of strains belonging to the <i>P. polymyxa</i> species converge toward a necessary reclassification, which will require a fundamental contribution from microbiologists in the near future.</p><p><strong>Importance: </strong>The development of sequencing technologies has led to an exponential increase in microbial sequencing data. Accurately identifying bacterial species remains a challenge because of extensive intra-species variability, the need for multiple identification methods, and the rapid rate of taxonomic changes. A substantial contribution to elucidating the relationships among related bacterial strains comes from comparing their genomic sequences. This comparison also allows for the identification of the \"pangenome,\" which is the set of genes shared by all individuals of a species, as well as the set of genes that are unique to subpopulations. Here, we applied this approach to <i>Paenibacillus polymyxa</i>, a species studied for its potential as a biofertilizer and biocontrol agent and known as an antibiotic producer. Our work highlights the need for a more efficient classification of this bacterial species and provides a better delineation of strains with different properties.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0174024"},"PeriodicalIF":3.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11577871/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142543208","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":"Targeted discovery of polyketides with antioxidant activity through integrated omics and cocultivation strategies.","authors":"Cancan Wang, Chenjie Wang, Yanjun Liu, Yujie Yue, Xingyue Lu, Hong Wang, Youmin Ying, Jianwei Chen","doi":"10.1128/aem.01603-24","DOIUrl":"10.1128/aem.01603-24","url":null,"abstract":"<p><p>Fungi generate a diverse array of bioactive compounds with significant pharmaceutical applications. However, the chemical diversity of natural products in fungi remains largely unexplored. Here, we present a paradigm for specifically discovering diverse and bioactive compounds from fungi by integrating genome mining with building block molecular network and coculture analysis. Through pangenome and sequence similarity network analysis, we identified a rare type I polyketide enzyme from <i>Penicillium</i> sp. ZJUT-34. Subsequent building block molecular network and coculture strategy led to the identification and isolation of a pair of novel polyketides, (±)-peniphenone E [(±)-<b>1</b>], three known polyketides (<b>2-4</b>), and three precursor compounds (<b>5-7</b>) from a combined culture of <i>Penicillium</i> sp. ZJUT-34 and <i>Penicillium</i> sp. ZJUT23. Their structures were established through extensive spectroscopic analysis, including NMR and HRESIMS. Chiral HPLC separation of compound <b>1</b> yielded a pair of enantiomers (+)-<b>1</b> and (-)-<b>1</b>, with their absolute configurations determined using calculated ECD methods. Compound (±)-<b>1</b> is notable for its unprecedented structure, featuring a unique 2-methyl-hexenyl-3-one moiety fused with a polyketide clavatol core. We proposed a hypothetical biosynthetic pathway for (±)-<b>1</b>. Furthermore, compounds <b>2</b>, <b>5</b>, and <b>6</b> exhibited strong antioxidant activity, whereas (-)-<b>1</b>, (+)-<b>1</b>, <b>3</b>, and four exhibited moderate antioxidant activity compared to the positive control, ascorbic acid. Our research demonstrates a pioneering strategy for uncovering novel polyketides by merging genome mining, metabolomics, and cocultivation methods. This approach addresses the challenge of discovering natural compounds produced by rare biosynthetic enzymes that are often silent under conventional conditions due to gene regulation.IMPORTANCEPolyketides, particularly those with complex structures, are crucial in drug development and synthesis. This study introduces a novel approach to discover new polyketides by integrating genomics, metabolomics, and cocultivation strategies. By combining genome mining, building block molecular networks, and coculturing techniques, we identified and isolated a unique polyketide, (±)-peniphenone E, along with three known polyketides and three precursor compounds from <i>Penicillium</i> sp. ZJUT-34 and <i>Penicillium</i> sp. ZJUT23. This approach highlights the potential of using combined strategies to explore fungal chemical diversity and discover novel bioactive compounds. The successful identification of (±)-peniphenone E, with its distinctive structure, demonstrates the effectiveness of this integrated method in enhancing natural product discovery and underscores the value of innovative approaches in natural product research.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0160324"},"PeriodicalIF":3.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11577776/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142493389","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":"Asymptomatic bacteriuria screening for developing countries using a modified water quality test kit.","authors":"Jolie A Stocki, Rachel C Fleck, Ivy B Nguyen, Ryan Walde, Harry L T Mobley, Allyson E Shea","doi":"10.1128/aem.01567-24","DOIUrl":"10.1128/aem.01567-24","url":null,"abstract":"<p><p>Between 2% and 15% of pregnant women unknowingly experience asymptomatic bacteriuria (ASB), defined as ≥10⁵ CFU per milliliter of urine in the absence of symptoms. ASB increases the risk of adverse pregnancy outcomes including pyelonephritis, preterm labor, and low-birth weight infants. While pregnant women in the United States are routinely screened for ASB, those in developing countries with limited resources and funding lack an accurate mechanism for ASB screening. Aquagenx water quality test kits detect <i>Escherichia coli</i>, the most common causative agent of ASB, and total coliform bacteria in drinking water via colorimetric and fluorescent indicators. We found that the Aquagenx system is compatible with human urine and then proceeded to develop an ASB screening protocol using disposable inoculating loops. Our protocol diagnosed artificial ASB^- samples (10⁴ CFU/mL <i>E. coli</i>) with a false positive (FP) rate of 33% (<i>n</i> = 18) and ASB⁺ (10⁵ CFU/mL <i>E. coli</i>) with a false negative (FN) rate of 5.6% (<i>n</i> = 18). Clinical sample testing with our protocol revealed a FP rate of 0% in ASB^- samples (<i>n</i> = 28) and a FN rate of 0% in ASB⁺ samples caused by coliforms (<i>n</i> = 13). Aquagenx did not detect ASB in nine clinical samples with non-coliform etiological agents due to the limitations of the technology. However, with very high accuracy for detection of <i>E. coli</i> and other causative agents that collectively account for 90.1% of ASB cases, these kits could be used as a diagnostic ASB screening tool in developing countries in which there is currently no alternative to urine culture.IMPORTANCEAsymptomatic bacteriuria (ASB) affects 2%-15% of pregnant women and can result in adverse maternal and fetal outcomes if left undetected and untreated. In the United States and other developed nations, pregnant women are regularly screened for ASB via urine culture. However, in low-resource countries where bacterial culture is not available, dipstick testing is used. Although accurate in cases of symptomatic bacteriuria, dipstick detection is ineffective for detecting ASB. Here, we made use of an existing water quality field test for ASB urine screening, which would be readily deployable in low-resource settings. We optimized a dilution protocol for sampling patient urine within the detection limits of the Aquagenx kit technology. Overall, we were able to detect ASB samples with Gram-negative pathogens that collectively account for 90% of all ASB cases. Utilization of this repurposed technology for proactive medical screening may help prevent adverse pregnancy and birth outcomes due to ASB.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0156724"},"PeriodicalIF":3.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11577777/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142543187","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":"Multisite community-scale monitoring of respiratory and enteric viruses in the effluent of a nursing home and in the inlet of the local wastewater treatment plant.","authors":"Catherine Manoha, Anne-Laure Dequiedt, Lucie Thery, Marina Marotel, Floriane Pez, Bruno Vouillon, Eric Gueneau, Alexis de Rougemont","doi":"10.1128/aem.01158-24","DOIUrl":"10.1128/aem.01158-24","url":null,"abstract":"<p><p>The aim of this study was to evaluate whether community-level monitoring of respiratory and enteric viruses in wastewater can provide a comprehensive picture of local virus circulation. Wastewater samples were collected weekly at the wastewater treatment plant (WWTP) inlet and at the outlet of a nearby nursing home (NH) in Burgundy, France, during the winter period of 2022/2023. We searched for the pepper mild mottle virus as an indicator of fecal content as well as for the main respiratory viruses [severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza, and respiratory syncytial virus] and enteric viruses (rotavirus, sapovirus, norovirus, astrovirus, and adenovirus). Samples were analyzed using real-time reverse transcription PCR-based methods. SARS-CoV-2 was the most frequently detected respiratory virus, with 66.7% of positive samples from the WWTP and 28.6% from the NH. Peaks of SARS-CoV-2 were consistent with the chronological incidence of infections recorded in the sentinel surveillance and the nearby hospital databases. The number of positive samples was lower in the NH than in WWTP for the three respiratory viruses. Enteric viruses were frequently detected, most often sapovirus and norovirus genogroup II, accounting both for 77.8% of positive samples in the WWTP and 57.1% and 37%, respectively, in the NH. The large circulation of sapovirus was unexpected in particular in the NH. Combined wastewater surveillance using simple optimized methods can be a valuable tool for monitoring viral circulation and may serve as a suitable early warning system for identifying both local outbreaks and the onset of epidemics. These results encourage the application of wastewater-based surveillance (WBS) to SARS-CoV2, norovirus, and sapovirus.IMPORTANCEWBS provides valuable information on the spread of epidemic viruses in the environment using appropriate and sensitive detection methods. By monitoring the circulation of viruses using reverse transcription PCR methods in wastewater from the inlet of a wastewater treatment plant and the outlet of a nearby retirement home (connected to the same collective sewer network), we aimed to demonstrate that implementing combined WBS at key community sites allows effective detection of the occurrence of respiratory (influenza, respiratory syncytial virus, and SARS-CoV-2) and enteric (norovirus, rotavirus, and sapovirus) virus infections within a given population. This analysis on a localized scale provided new information on the viral circulation in the two different sites. Implementing WBS to monitor the circulation or the emergence of infectious diseases is an important means of alerting the authorities and improving public health management. WBS could participate actively to the health of humans, animals, and the environment.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0115824"},"PeriodicalIF":3.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11577779/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142456531","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":"Solubilization of K and P nutrients from coal gangue by <i>Bacillus velezensis</i>.","authors":"Zhigang Wang, Mingwu Liu, Xiangrong Liu, Yuan Bao, Yaya Wang","doi":"10.1128/aem.01538-24","DOIUrl":"10.1128/aem.01538-24","url":null,"abstract":"<p><p>Accumulation of coal gangue (CG) poses significant risks to both human health and ecological systems, underscoring the urgent need for sustainable methods to utilize this abundant waste material effectively. In this study, we successfully screened and isolated the <i>Bacillus velezensis</i> bacterial strain to enhance the solubilization of potassium (K) and phosphorus (P) nutrients from CG. The study employed XRD, FTIR, SEM, and HPLC techniques to investigate the underlying mechanisms of CG solubilization. Various parameters such as CG particle size, incubation time, initial inoculation ratio, concentration of CG, pH, and temperature were optimized to maximize solubilization efficiency. The <i>Bacillus velezensis</i> bacterium can dissolve minerals of CG by adhering to its surface and secreting various kinds of organic acids, particularly succinic acid. Pot experiments further demonstrated that <i>Bacillus velezensis</i>, in conjunction with CG, promotes alfalfa growth. These combined findings suggest that <i>Bacillus velezensis</i> and coal gangue hold promising potential as mineral soil conditioners, effectively enhancing plant growth. This approach presents a viable alternative for the environmentally responsible utilization of CG, addressing both ecological concerns and agricultural sustainability.</p><p><strong>Importance: </strong>Coal gangue piles not only occupy significant amounts of arable land but also cause serious environmental pollution. Therefore, finding sustainable methods for the clean utilization of CG is imperative. Although previous studies have shown that bacteria can promote the solubilization of available phosphorus and available potassium from CG, their impact on promoting plant growth remains understudied. To our knowledge, this study is the first to demonstrate the potential of Bacillus velezensis in enhancing the effectiveness of CG as a mineral fertilizer to support alfalfa growth. The evidence presented in this study provides an ecological strategy for the utilization of CG.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0153824"},"PeriodicalIF":3.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11577778/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142456532","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":"Insights into the regulatory mechanisms and application prospects of the transcription factor Cra.","authors":"Ying Huang, Kai-Zhi Jia, Wei Zhao, Li-Wen Zhu","doi":"10.1128/aem.01228-24","DOIUrl":"10.1128/aem.01228-24","url":null,"abstract":"<p><p>Cra (catabolite repressor/activator) is a global transcription factor (TF) that plays a pleiotropic role in controlling the transcription of several genes involved in carbon utilization and energy metabolism. Multiple studies have investigated the regulatory mechanism of Cra and its rational use for metabolic regulation, but due to the complexity of its regulation, there remain challenges in the efficient use of Cra. Here, the structure, mechanism of action, and regulatory function of Cra in carbon and nitrogen flow are reviewed. In addition, this paper highlights the application of Cra in metabolic engineering, including the promotion of metabolite biosynthesis, the regulation of stress tolerance and virulence, the use of a Cra-based biosensor, and its coupling with other transcription factors. Finally, the prospects of Cra-related regulatory strategies are discussed. This review provides guidance for the rational design and construction of Cra-based metabolic regulation systems.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0122824"},"PeriodicalIF":3.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11577769/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567932","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":"Articles of Significant Interest in This Issue.","authors":"","doi":"10.1128/aem.02224-24","DOIUrl":"https://doi.org/10.1128/aem.02224-24","url":null,"abstract":"","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":"90 11","pages":"e0222424"},"PeriodicalIF":3.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142674995","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":"Screening and functional characterization of isocitrate lyase AceA in the biofilm formation of <i>Vibrio alginolyticus</i>.","authors":"Weibo Shi, Ya Li, Weiwei Zhang","doi":"10.1128/aem.00697-24","DOIUrl":"10.1128/aem.00697-24","url":null,"abstract":"<p><p>Biofilm is a well-known sessile lifestyle for bacterial pathogens, but a little is known about the mechanism on biofilm formation in <i>Vibrio alginolyticus</i>. In this study, we screened <i>V. alginolyticus</i> strains with strong biofilm formation ability from coastal seawater. The antibiotic resistance of the biofilm cells (BFs) was higher than that of the planktonic cells (PTs). To study the genes and pathways involved in biofilm formation, we performed transcriptome analysis of the BFs and PTs of <i>V. alginolyticus</i> R9. A total of 685 differentially expressed genes (DEGs) were upregulated, and 517 DEGs were downregulated in the BFs. The upregulated DEGs were significantly enriched in several pathways including glyoxylate and dicarboxylate metabolism, while the downregulated genes were significantly enriched in the flagellar assembly pathways. The key gene involved in glyoxylate shunt, <i>aceA</i>, was cloned, and Δ<i>aceA</i> mutant was constructed to determine the function of AceA in carbon source utilization, biofilm formation, and virulence. Real-time reverse transcription PCR showed that the expression of <i>aceA</i> was higher at the mature stage but lower at the disperse stage of biofilm formation, and the expression of the flagellar related genes was upregulated in Δ<i>aceA</i>. This is the first study to illustrate the global gene expression profile during the biofilm formation of <i>V. alginolyticus</i>, and isocitrate lyase AceA, the key enzyme involved in glyoxylate shunt, was shown to maintain biofilms accompanied by downregulation of flagellation but promoted dispersal of BFs at the late stage.IMPORTANCEBiofilms pose serious public problems, not only protecting the cells in it from environmental hazard but also affecting the composition and abundance of bacteria, algae, fungi, and protozoa. The important opportunistic pathogen <i>Vibrio alginolyticus</i> is extremely ubiquitously present in seawater, and it also exhibited a strong ability to form biofilm; thus, investigation on the biofilm formation of <i>V. alginolyticus</i> at molecular level is fundamental for the deeper exploration of the environmental concerns arose by biofilm. In this study, transcriptome analysis of biofilm cells (BFs) and planktonic cells (PTs) from <i>V. alginolyticus</i> was performed and AceA was screened to play an important role in biofilm formation. AceA was shown to maintain biofilms accompanied by downregulation of flagellation but promoted dispersal of BFs at the disperse stage. This method was helpful to further understand the ability and mechanism of <i>V. alginolyticus</i> biofilm formation and provide clues for prevention of <i>V. alginolyticus</i> infection.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0069724"},"PeriodicalIF":3.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11577800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387433","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":"Fire-associated microbial shifts in soils of western conifer forests with Armillaria root disease.","authors":"Ada J Fitz Axen, Mee-Sook Kim, Ned B Klopfenstein, Sara Ashiglar, John W Hanna, Patrick Bennett, Jane E Stewart","doi":"10.1128/aem.01312-24","DOIUrl":"10.1128/aem.01312-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Fires in coniferous forests throughout the northern United States alter ecosystem processes and ecological communities, including the diversity and composition of microbial communities living in the soil. In addition to its influence on ecosystem processes and functions, the soil microbiome can interact with soilborne pathogens to facilitate or suppress plant disease development. Altering the microbiome composition to promote taxa that inhibit pathogenic activity has been suggested as a management strategy for forest diseases, including Armillaria root disease caused by &lt;i&gt;Armillaria solidipes&lt;/i&gt;, which causes growth loss and mortality of conifers. These forest ecosystems are experiencing increased wildfire burn severity that could influence &lt;i&gt;A. solidipes&lt;/i&gt; activity and interactions of the soil microbiome with Armillaria root disease. In this research, we examine changes to the soil microbiome following three levels of burn severity in a coniferous forest in northern Idaho, United States, where Armillaria root disease is prevalent. We further determine how these changes correspond to the soil microbiomes associated with the pathogen &lt;i&gt;A. solidipes,&lt;/i&gt; and a putatively beneficial species, &lt;i&gt;A. altimontana&lt;/i&gt;. At 15-months post-fire, we found significant differences in richness and diversity between bacterial communities associated with unburned and burned areas, yet no significant changes to these metrics were found in fungal communities following fire. However, both bacterial and fungal communities showed compositional changes associated with burn severity, including microbial taxa with altered relative abundance. Further, significant differences in the relative abundance of certain microbial taxa in communities associated with the three burn severity levels overlapped with taxa associated with various &lt;i&gt;Armillaria&lt;/i&gt; spp. Following severe burn, we observed a decreased relative abundance of beneficial ectomycorrhizal fungi associated with the microbial communities of &lt;i&gt;A. altimontana,&lt;/i&gt; which may contribute to the antagonistic activity of this soil microbial community. Additionally, &lt;i&gt;A. solidipes&lt;/i&gt; and associated microbial taxa were found to dominate following high-severity burns, suggesting that severe fires provide suitable environmental conditions for these species. Overall, our results suggest that shifts in the soil microbiome and an associated increase in the activity of &lt;i&gt;A. solidipes&lt;/i&gt; following high-severity burns in similar conifer forests may result in priority areas for monitoring and proactive management of Armillaria root disease.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;With its influence on ecosystem processes and functions, the soil microbiome can interact with soilborne pathogens to facilitate or suppress plant disease development. These forest ecosystems are experiencing increased wildfire frequency and burn severity that could influence the fungal root pathogen, &lt;i&gt;Armillaria solidipes&lt;/i&gt;, and interaction","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0131224"},"PeriodicalIF":3.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11577770/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567931","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}