Applied and Environmental Microbiology最新文献

{"title":"Genomic evolution of <i>Salmonella</i> Dublin in cattle and humans in the United States.","authors":"Sophia M Kenney, Nkuchia M M'ikanatha, Erika Ganda","doi":"10.1128/aem.00689-25","DOIUrl":"10.1128/aem.00689-25","url":null,"abstract":"<p><p>Increasingly, antimicrobial-resistant (AMR) <i>Salmonella</i> Dublin is a threat to human and animal health, therefore requiring a One Health approach to comprehensively understand pathogen evolution. Moreover, <i>S</i>. Dublin dissemination throughout the United States and the food supply chain is a concern for food safety and security. Here, we leveraged multi-agency biosurveillance data and genomic sequencing of <i>S</i>. Dublin strains to provide a robust analysis of its evolution across human, animal, and environmental reservoirs. This study advances our understanding of AMR <i>S</i>. Dublin, elucidates factors driving AMR emergence, and informs interventions to protect public health. In total, 2,150 strains collected between 2002 and 2023 throughout the United States from clinical bovine (<i>N</i> = 581), clinical human (<i>N</i> = 664), and environmental (<i>N</i> = 905) sources were identified. After uniform quality control, raw reads were assembled <i>de novo</i> followed by genome annotation and characterization of plasmids, antimicrobial resistance genes, and virulence factors. Strain relatedness was evaluated using a core genome maximum-likelihood phylogeny and pairwise core genome single-nucleotide polymorphism (SNP) differences. We identified the highest prevalence of drug-specific antimicrobial resistance genes and multidrug resistance plasmid, IncA/C2 (<i>P</i> < 0.001), in bovine clinical strains, which also had the greatest genetic diversity. Despite source-dependent differences in antimicrobial resistance gene frequency and types, 72% of <i>S</i>. Dublin strains in our study differed with at least one other strain by 20 or fewer SNPs. This high degree of genomic similarity highlights the potential for cross-transmission between humans, animals, and the environment and underscores the importance of considering strain source when assessing and monitoring antimicrobial resistance.IMPORTANCE<i>Salmonella</i> Dublin is a zoonotic, sometimes foodborne, pathogen that causes severe illness in cattle and humans. Our study takes a One Health approach to understanding genetic differences in strains within and between different reservoirs in the United States. We identified differences in antimicrobial resistance potential and genome content between clinical bovine, clinical human, and environmental strains. Nonetheless, the U.S. population of <i>S</i>. Dublin is highly related and diverges minimally over time and geography. These findings highlight the importance of the One Health framework when combating zoonotic antimicrobial-resistant pathogens like <i>Salmonella</i> Dublin.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0068925"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442401/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144871070","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":"Characterization of an isobutylene epoxide hydrolase (IbcK) from the isobutylene-catabolizing bacterium <i>Mycolicibacterium</i> sp. ELW1.","authors":"Nicholas W Faulkner, John B Joyce, Christy Smith, Paul Swartz, Robert B Rose, Eric S Miller, Michael R Hyman","doi":"10.1128/aem.00393-25","DOIUrl":"10.1128/aem.00393-25","url":null,"abstract":"<p><p>Isobutylene (IB) is produced on a large scale by the petrochemical industry and is metabolized by the aerobic alkene-metabolizing bacterium <i>Mycolicibacterium</i> sp. ELW1. The initial metabolite of IB catabolism by this bacterium is proposed to be 2-methyl-1,2-epoxypropane (isobutylene oxide [IBO]). The epoxide is then thought to be rapidly converted into 2-methyl-1,2-propanediol (MPD) by an epoxide hydrolase. A gene (<i>ibcK</i>) encoding a hydrolase is in a putative IB catabolism gene cluster on a ~222-kbp megaplasmid. This gene was cloned, heterologously expressed, and purified by Ni-NTA affinity chromatography. The purified protein rapidly and stoichiometrically hydrolyzed IBO to MPD with a specific activity of 29 µmoles min^-1 mg protein^-1. Additional epoxides were also hydrolyzed by IbcK, including 1,2-epoxypropane, 1,2-epoxybutane, 1,2-epoxypentane, epichlorohydrin, and cyclohexane oxide, albeit at lower rates than IBO. IbcK also slowly hydrolyzed both <i>cis</i>- and <i>trans</i>-2,3-epoxybutane, which are the only other epoxides other than IBO known to support the growth of <i>Mycolicibacterium</i> sp. ELW1. Furthermore, IbcK also appears to be enantioselective towards chiral <i>trans</i> 2,3-epoxybutane. The crystal structure of IbcK was determined at 2.29 Å resolution, revealing a two-domain structure with an α/β hydrolase fold topology at its core. IbcK has high similarity to the epoxide hydrolase EchA from <i>Agrobacterium radiobacter</i> AD1, including the key active site residues Asp 117, Asp 256, and His 284. IbcK was observed to be in monomer-dimer equilibrium, which we propose occurs through interactions between the \"cap\" domains.IMPORTANCEThe initial metabolites generated during catabolism of volatile alkenes by aerobic alkene-oxidizing bacteria are consistently epoxides. These bacteria employ several different mechanisms to protect DNA, lipids, and proteins from damage by these reactive metabolites. The most common mechanisms are conjugation with coenzyme M or glutathione. In contrast, the role for hydrolases in the bacterial metabolism of volatile alkenes and their epoxides has not been frequently observed. The enzymatic, functional, and structural characterization of an epoxide hydrolase (IbcK) from the IB-utilizing bacterium <i>Mycolicibacterium</i> sp. ELW1 described here advances our understanding of these enzymes and suggests their potential application as an enantioselective catalyst. This study advances our understanding of how microorganisms utilize aliphatic alkenes, such as carbon and energy sources, including the role of epoxide hydrolases in these catabolic pathways.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0039325"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442371/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144939869","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":"Establishing microbial communities to promote the growth of <i>Pleurotus ostreatus</i> through a top-down approach is hindered by the dominance of antagonistic interactions.","authors":"Marie Bonduelle, Frédérique Desrochers-Noiseux, Audrey-Anne Durand, Simon Barnabé, Philippe Constant","doi":"10.1128/aem.00898-25","DOIUrl":"10.1128/aem.00898-25","url":null,"abstract":"<p><p>Few attempts have been made to examine the diversity and functions that characterize microbial communities compatible with and beneficial to the biotechnologically relevant mushroom <i>Pleurotus ostreatus</i>. The quest for complementarity is complicated by the variable nature of beneficial traits, impairing the rational assembly of synthetic communities to improve bioprocesses. This study investigated whether the compatibility between <i>P. ostreatus</i> and microbial enrichments is lessened in conditions favoring saprophyte metabolism and is enhanced when a combination of recalcitrant and labile carbon is integrated in the enrichment. The microbial diversity of enrichment cultures and substrates colonized by <i>P. ostreatus</i> was analyzed through PCR amplicon sequencing, and the proliferation of <i>P. ostreatus</i> was assessed by quantitative image analysis. In general, co-inoculation of lignocellulosic substrate with microbial enrichment reduced the growth of <i>P. ostreatus</i>. The saprophytic enrichment conditions were more conducive to the development of antagonistic communities inhibiting <i>P. ostreatus</i> growth than enrichment cultures integrating labile carbon substrates. Both microbial community analyses and <i>in vitro</i> assays led to the identification of a single phylotype affiliated with <i>Brevundimonas</i> spp., which displayed neutral interaction with <i>P. ostreatus</i>. Recalcitrant and labile carbon degradation functions were not primary factors driving beneficial microbial communities for <i>P. ostreatus</i>. Additional functions beyond carbon metabolism are likely to promote beneficial interactions. Directed enrichment cultures, integrating the mushroom in the earliest stage of the procedure, are expected to promote more beneficial interactions than top-down approaches.IMPORTANCELignocellulosic biomass upcycling biotechnologies integrating solid-state fermentation by fungi are aligned with sustainable development perspectives. While the recalcitrance of this biomass imposes a challenge for the implementation of these bioprocesses converting the lignocellulosic feedstock into bioenergy and bioproducts, pretreatment of lignocellulose biomass with fungi is efficient and generates fewer by-products than chemical approaches. Optimization and stabilization of this bioprocess by integrating microbial consortia has received little attention. The significance of our research is to bridge that knowledge gap by examining how interactions between the biotechnologically relevant basidiomycete <i>Pleurotus ostreatus</i> and microbial communities influence fungal growth in lignocellulosic substrate. Directed enrichment cultures integrating <i>Pleurotus ostreatus</i> as a selective agent are expected to trigger more beneficial interactions promoting mushroom growth than our top-down approaches, due to a dominance of antagonistic mushroom-bacteria interactions.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0089825"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442370/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144939835","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":"Serotonergic and immunomodulatory properties of the psychobiotic candidate <i>Bacteroides finegoldii</i> UO.H1052 and its extracellular vesicles.","authors":"Basit Yousuf, Galal Ali Esmail, Nazila Nazemof, Nour Elhouda Bouhlel, Zoran Minic, Riadh Hammami","doi":"10.1128/aem.00891-25","DOIUrl":"10.1128/aem.00891-25","url":null,"abstract":"<p><p><i>Bacteroides finegoldii</i> UO.H1052, a human gut commensal, was evaluated for its potential psychobiotic and immunomodulatory properties. Whole-genome analysis confirmed the absence of virulence factors, plasmids, and antibiotic-resistance genes. Metabolomic profiling of cell-free supernatants (CFSs) and extracellular vesicle (EV) postbiotics revealed a high- and medium-dependent production of neuroactive metabolites, including γ-aminobutyric acid, tryptophan, tyrosine, and tyramine, as well as physiologically relevant levels of short-chain fatty acids, such as acetate, propionate, and butyrate. Functionally, CFS enhanced epithelial barrier integrity by increasing transepithelial electrical resistance and mitigating LPS-induced disruption in Caco2/HT29 monolayers without cytotoxic effects. Both CFS and EVs exhibited immunomodulatory properties, characterized by elevated <i>Il-10</i>/<i>Tnf-α</i> ratios under basal conditions and significant suppression of <i>Tnf-α</i> expression in LPS-stimulated RAW 264.7 macrophages. Notably, CFS and EVs increased tryptophan hydroxylase 1 (<i>Tph1</i>) gene expression in enterochromaffin RIN14B cells by 6.6- and 3.2-fold, respectively, suggesting enhanced serotonergic activity. These findings highlight <i>B. finegoldii</i> UO.H1052 as a promising next-generation psychobiotic candidate with neuroactive, barrier-protective, and immunoregulatory properties, supporting its potential for gut-brain axis modulation.</p><p><strong>Importance: </strong>Emerging evidence supports the critical role of the gut microbiota in modulating host neurophysiology and immune function via the gut-brain axis. Here, we present a comprehensive characterization of <i>Bacteroides finegoldii</i> UO.H1052, a human gut commensal that exhibits promising psychobiotic attributes, including the production of neuroactive compounds and extracellular vesicles (EVs) with immunoregulatory and serotonin-inducing properties. The strain exhibits a favorable safety profile, with no detected virulence factors or transmissible antibiotic resistance. Importantly, cell-free supernatants and EVs enhanced epithelial barrier integrity, modulated pro- and anti-inflammatory cytokine responses, and significantly upregulated the expression of <i>Tph1</i>, a key enzyme in serotonin biosynthesis. These findings underscore the potential of <i>B. finegoldii</i> UO.H1052 as a next-generation psychobiotic candidate and highlight EVs as effective postbiotic mediators of host-microbe communication. This study advances the understanding of <i>Bacteroides</i>-derived psychobiotics and provides a foundation for their development in modulating gut-brain and immune pathways relevant to neuroinflammatory and gastrointestinal disorders.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0089125"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442397/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144939848","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":"Commensal acidification of specific gut regions produces a protective priority effect against enteropathogenic bacterial infection.","authors":"Jane L Yang, Haolong Zhu, Puru Sadh, Kevin Aumiller, Zehra T Guvener, William B Ludington","doi":"10.1128/aem.00707-25","DOIUrl":"10.1128/aem.00707-25","url":null,"abstract":"<p><p>The commensal microbiome has been shown to protect against newly introduced enteric pathogens in multiple host species, a phenomenon known as a priority effect. Multiple mechanisms can contribute to this protective priority effect, including antimicrobial compounds, nutrient competition, and pH changes. In <i>Drosophila melanogaster</i>, <i>Lactiplantibacillus plantarum</i> has been shown to protect against enteric pathogens. However, the strains of <i>L. plantarum</i> studied were derived from laboratory flies or non-fly environments and have been found to be unstable colonizers of the fly gut that mainly reside on the food. To study the priority effect using a naturally occurring microbial relationship, we isolated a wild fly-derived strain of <i>L. plantarum</i> that stably colonizes the fly gut in conjunction with a common enteric pathogen, <i>Serratia marcescens</i>. Flies stably associated with the <i>L. plantarum</i> strain were more resilient to oral <i>Serratia marcescens</i> infection as seen by longer life span and lower <i>S. marcescens</i> load in the gut. Through <i>in vitro</i> experiments, we found that <i>L. plantarum</i> inhibits <i>S. marcescens</i> growth due to acidification. We used gut imaging with pH indicator dyes to show that <i>L. plantarum</i> reduces the gut pH to levels that restrict <i>S. marcescens</i> growth <i>in vivo</i>. In flies colonized with <i>L. plantarum</i> prior to <i>S. marcescens</i> infection, <i>L. plantarum</i> and <i>S. marcescens</i> are spatially segregated in the gut, and <i>S. marcescens</i> is less abundant where <i>L. plantarum</i> heavily colonizes, indicating that acidification of specific gut regions is a mechanism of a protective priority effect.IMPORTANCEThe gut microbiomes of animals harbor an incredible diversity of bacteria, some of which can protect their hosts from invasion by enteric pathogens. Understanding the mechanisms behind this protection is essential for developing precision probiotics to support human and animal health. This study used <i>Drosophila melanogaster</i> as a model system due to its low cost, experimentally tractable gut microbiome, and overlap with bacterial species found in mammals. While resident microbes can protect hosts through various means, including toxin production and immune stimulation, we found that acidification was sufficient to limit a pathogen that normally reduces life span. Remarkably, specific gut regions are acidified either by host mechanisms or by the resident bacterium, <i>Lactiplantibacillus plantarum</i>, highlighting joint microbial and host control of gut chemistry. These findings are broadly relevant to microbiology and gut health, providing insight into how hosts may manage pathogens through their symbiotic microbiota.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0070725"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442404/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833791","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":"Long term tillage regime alters bacterial assimilation of xylose and cellulose.","authors":"Marie Schaedel, Chantal Koechli, Daniel H Buckley","doi":"10.1128/aem.00933-25","DOIUrl":"10.1128/aem.00933-25","url":null,"abstract":"<p><p>Microbial growth dynamics determine carbon fate in soil by transforming carbon inputs into microbial products available for stabilization on soil surfaces. Management practices such as tillage disturb microbial communities and promote C loss, but the degree to which tillage alters bacterial metabolism of soil C remains poorly described. We conducted a multi-substrate DNA stable isotope probing experiment using soil from a long-term field experiment with a 42-year legacy of either no-till or annual moldboard plowing. We predicted that this land use history would alter C assimilation dynamics due to differences in bacterial growth responses. We incubated soil from each tillage regime with ¹³C-xylose and ¹³C-cellulose, substrates that differ in bioavailability and which favor different bacterial life history strategies in soil. We identified 730 ¹³C-labeled bacterial taxa and tracked their abundance in bulk soil over a 30 day period. Carbon addition to soil rapidly altered bacterial community structure and function. ¹³C-labeling dynamics differed substantially between tilled and no-till soils with respect to both xylose and cellulose. Bacterial xylose metabolism in tilled soils exhibited substantial lag relative to no-till soils, and this lag corresponded with lower mineralization rates for xylose. In addition, bacterial cellulose metabolism was mediated primarily by specialist taxa in no-till soils, while dual incorporators dominated tilled soils. Differences in carbon assimilation corresponded to lower cellulose mineralization rates and cumulative cellulose mineralization in tilled soils. We show that soil management practices shape the path of carbon through bacterial communities by altering dynamic growth responses associated with bacterial life history strategies.IMPORTANCEWe applied DNA stable isotope probing in a microcosm experiment to understand the role of soil management (till vs no-till) in shaping bacterial carbon cycling. Our hypothesis was that a legacy of disturbance through tillage would exert a selective influence on bacterial growth dynamics, thereby altering bacterial processing of added carbon substrates. We found that lagged growth in tilled soil resulted in delayed bacterial assimilation of xylose and a streamlined, single carbon \"channel\" characterized by the co-metabolism of xylose and cellulose. In no-till soil, temporally distinct bacterial assimilation of xylose and cellulose by separate carbon \"channels\" was associated with higher carbon mineralization rates and total mineralization relative to tilled soil. Our findings indicate that soil management practices altered the growth dynamics of active carbon cycling bacteria. Lagged growth associated with a history of disturbance resulted in reduced carbon mineralization.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0093325"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442353/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144788044","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":"Development of loop-mediated isothermal amplification (LAMP) assays for the detection of diarrheagenic <i>E. coli</i> in wastewater.","authors":"Meret Zimmermann, Markus Schuppler, Timothy R Julian, Seju Kang","doi":"10.1128/aem.00880-25","DOIUrl":"10.1128/aem.00880-25","url":null,"abstract":"<p><p>Diarrheagenic <i>E. coli</i> is responsible for a substantial portion of foodborne diseases globally. The use of standard diagnostic tools for the detection of diarrheagenic <i>E. coli</i> often hampers the establishment of robust surveillance when no expensive laboratory equipment, such as thermocyclers, is present. Loop-mediated isothermal amplification (LAMP) has shown potential to enable the resource-efficient detection of pathogens. In this study, LAMP assays with two detection modes, fluorescence-based molecular beacon (MB) and nucleic acid lateral flow (NALF), were developed for the detection of the diarrheagenic <i>E. coli</i> strains Shiga toxin-producing <i>E. coli</i> (STEC), enteropathogenic <i>E. coli</i> (EPEC), and enterohemorrhagic <i>E. coli</i> (EHEC). Duplex LAMP assays for the virulence genes <i>eae</i> and <i>stx2</i> of STEC, EPEC, and EHEC were developed and validated against wastewater from an on-site containment as a model environmental medium for wastewater-based surveillance in non-sewered areas. The developed LAMP assays showed moderate specificity toward <i>eae</i> and <i>stx2</i>, enabling crude differentiation among STEC, EPEC, and EHEC. We assessed the sensitivity of the LAMP assays and estimated a Limit of Detection (LoD) of 10²-10³ gene copies per reaction and found moderate quantitative capability for the MB-based method. The development of LAMP assays for the specific detection of STEC, EPEC, and EHEC with two distinct detection modes provides various options for their surveillance in settings without access to thermocyclers.IMPORTANCEFoodborne diarrheagenic <i>E. coli</i> poses a public health threat, while the variability in transmissible agents hampers outbreak investigation. The lack of lab equipment, such as thermocyclers, in some laboratory settings obstructs the establishment of robust diagnostic tools. This study addresses the need for reliable diagnostic tools for thermocycler-independent application. Validation against wastewater from an on-site containment demonstrates detection of the targets in an environmental matrix that could provide representative epidemiological insights.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0088025"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144815598","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":"PrtA-mediated flagellar turnover is essential for robust biofilm development in <i>Serratia marcescens</i>.","authors":"Marisel R Tuttobene, Roberto E Bruna, María Victoria Molino, Eleonora García Véscovi","doi":"10.1128/aem.01261-25","DOIUrl":"10.1128/aem.01261-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Biofilm formation is crucial for bacterial persistence, requiring precise regulatory mechanisms to transition from motility to sessility. Here, we uncover the role of the metalloprotease PrtA in &lt;i&gt;Serratia marcescens&lt;/i&gt; biofilm development and its interaction with flagellar components. Loss of PrtA leads to reduced biofilm biomass, thickness, and viable cell counts, as shown through high-resolution confocal microscopy. The biofilm-deficient phenotype is rescued by wild-type PrtA expression but not by a proteolytically inactive PrtA&lt;sub&gt;E177A&lt;/sub&gt; mutant, underscoring the essential role of PrtA's enzymatic activity. Exogenous addition of purified PrtA restores biofilm formation, confirming its enzymatic necessity. Proteomic profiling identified flagellar proteins as primary PrtA targets, with an overrepresentation of flagellar components in &lt;i&gt;prtA&lt;/i&gt; mutant biofilms. In addition, PrtA selectively degrades depolymerized flagellar filaments, facilitating biofilm progression by removing excess flagellar material. Transcriptional analysis reveals an inverse expression pattern of flagellar master regulator (&lt;i&gt;flhDC&lt;/i&gt;) and &lt;i&gt;prtA&lt;/i&gt; during biofilm establishment, suggesting a coordinated regulatory axis that suppresses flagellar function while promoting biofilm development. Confocal microscopy at the liquid-air interface shows increased flagellar content in &lt;i&gt;prtA&lt;/i&gt; mutant biofilms, supporting PrtA's role in matrix organization and biofilm integrity. Collectively, these findings establish PrtA as a crucial mediator of flagellar turnover and extracellular proteolysis, linking motility suppression to robust biofilm formation. This work not only advances our understanding of biofilm regulation in &lt;i&gt;S. marcescens&lt;/i&gt; but also identifies PrtA as a potential target for novel biofilm control strategies.IMPORTANCEBiofilms are central to the persistence and pathogenicity of &lt;i&gt;Serratia marcescens&lt;/i&gt;, particularly in clinical settings where they contribute to chronic infections and antimicrobial resistance. This study identifies the metalloprotease PrtA as a critical regulator of biofilm development, acting through the selective degradation of flagellar components to mediate the transition from motility to sessility. By demonstrating that PrtA's proteolytic activity is essential for proper biofilm architecture and viability, and that it directly targets excess flagellar material, we provide mechanistic insight into how biofilm maturation is coordinated with motility suppression. The discovery of an inverse regulatory relationship between &lt;i&gt;prtA&lt;/i&gt; and the flagellar master regulator &lt;i&gt;flhDC&lt;/i&gt; further supports the existence of a finely tuned system controlling biofilm establishment. Together, these findings enhance our understanding of biofilm regulation in &lt;i&gt;Serratia marcescens&lt;/i&gt;, an opportunistic human pathogen increasingly associated with antibiotic resistance, and highlight PrtA as a promising target for novel anti-biofilm strategies","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0126125"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442352/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144939857","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 bradyrhizobial T3SS systems and their roles in symbiosis with peanut (<i>Arachis hypogaea</i>) and <i>Vigna</i> species (<i>V. radiata</i> and <i>V. mungo</i>).","authors":"Tarnee Phimphong, Shun Hashimoto, Pongpan Songwattana, Jenjira Wongdee, Teerana Greetatorn, Kamonluck Teamtisong, Pakpoom Boonchuen, Sachiko Masuda, Arisa Shibata, Ken Shirasu, Phoutthasone Sibounnavong, Panlada Tittabutr, Nantakorn Boonkerd, Shusei Sato, Djamel Gully, Eric Giraud, Pongdet Piromyou, Neung Teaumroong","doi":"10.1128/aem.00600-25","DOIUrl":"10.1128/aem.00600-25","url":null,"abstract":"<p><p>Symbiosis between <i>Bradyrhizobium</i> strains isolated from Lao People's Democratic Republic (Lao PDR) and intercropped legumes (<i>Arachis hypogaea</i>, <i>Vigna radiata</i>, and <i>V. mungo</i>) was regulated by the type III secretion system (T3SS), which delivers effector proteins (T3Es) into host plant cells to modulate nodulation. To explore this mechanism, we sequenced and analyzed seven <i>Bradyrhizobium</i> genomes, identifying putative T3Es across five T3SS groups (G.1-G.5), which were classified based on the sequence of <i>rhcN</i>, a conserved ATPase gene essential for T3SS function. Phylogenetic analysis of <i>rhcN</i> more closely reflected the evolutionary relationships of nodulation genes than those based on 16S rRNA or whole-genome comparisons, underscoring its symbiotic relevance. Functional assays using <i>rhcN</i> mutants revealed group-specific effects on nodulation; G.1 strains showed neutral effects on <i>A. hypogaea</i>, negative effects on <i>V. radiata</i>, and positive effects on <i>V. mungo</i>. G.2 strains consistently promoted nodulation across all hosts and lacked effectors related to SUMO (small ubiquitin-like modifier) pathways, which have been implicated in host defense regulation. G.3 strains reduced nodulation in <i>A. hypogaea</i> but enhanced it in <i>Vigna</i> species. G.4 strains suppressed nodulation in <i>A. hypogaea</i>, and G.5 strains inhibited nodulation across all tested legumes. These findings highlight the diversity in T3SS organization, effector composition, and symbiotic responses among native <i>Bradyrhizobium</i> strains. The identification of known and uncharacterized effectors suggests roles in host compatibility and specificity. These strains, along with their effector profiles, provide a foundation for future functional studies to better understand T3SS-mediated interactions and support the development of targeted inoculants for legume hosts.IMPORTANCEThis study advances our understanding of legume-<i>Bradyrhizobium</i> symbiosis by examining the genetic organization and evolutionary patterns of T3SS genes. Our findings revealed that T3SS gene evolution does not always align with phylogenies based on 16S rRNA or whole-genome sequences, suggesting that horizontal gene transfer and functional adaptation may shape diversification. The observed variation in T3SS architecture and effector profiles among the five distinct <i>Bradyrhizobium</i> groups was correlated with host-specific nodulation outcomes in <i>A. hypogaea</i>, <i>V. radiata</i>, and <i>V. mungo</i>. We also identified novel candidate genes influencing symbiotic signaling and compatibility. These insights into the diversity and function of T3SS components contribute to a broader understanding of host-microbe communication and may support the development of more targeted and efficient rhizobial inoculants for sustainable legume cultivation and improved biological nitrogen fixation.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0060025"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442349/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144798027","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":"Recent origin of iron oxidation in extant microbial groups and low clade fidelity of iron metabolisms.","authors":"Erik Tamre, Gregory Fournier","doi":"10.1128/aem.01662-24","DOIUrl":"10.1128/aem.01662-24","url":null,"abstract":"<p><p>Reduced iron was abundant in Earth's surface environments before their oxygenation, so iron oxidation could have been a common metabolism on the early Earth. Consequently, modern microbial iron oxidation is sometimes seen as a holdover from an earlier biosphere, but the continuity of involved lineages or the metabolic process itself has not been verified. Modern neutrophilic iron oxidizers use cytochrome-porin Cyc2 as the initial electron acceptor in iron oxidation. With the protein as a proxy for the metabolism, we performed a phylogenetic analysis of Cyc2 to understand the evolutionary history of this microbial iron oxidation pathway. In addition to known iron oxidizers, we identified Cyc2 orthologs in gammaproteobacterial endosymbionts of lucinid bivalves. These bivalves have a robust fossil record and rely on seagrass meadows that only appear in the Cretaceous, providing a valuable time calibration in the evolutionary history of Cyc2. Our molecular clock analysis shows that extant sampled Cyc2 diversity has surprisingly recent common ancestry, and iron oxidation metabolisms in Gallionellaceae, Zetaproteobacteria, and photoferrotrophic Chlorobi likely originated in the Neoproterozoic or the Phanerozoic via multiple transfer events. The groups responsible for microbial iron oxidation have thus changed over Earth history, possibly reflecting the instability of niches with sufficient reduced iron. We note that frequent transfer and changing taxonomic distribution may be a general pattern for traits which are selected sporadically across space and time. Based on iron metabolism and other processes, we explore this concept of a trait's \"clade fidelity\" (or lack thereof) and establish its evolutionary importance.IMPORTANCEBacteria can oxidize iron to produce energy. As there was plenty of reduced iron available on the early Earth and there is only a little today, it was sometimes thought that bacteria that oxidize iron today are a small remnant of a larger group that used to do it. We studied the evolutionary history of the iron oxidation pathway that modern bacteria use, and we found that they developed that pathway relatively recently: whatever did it in the past is no longer around today. It would probably be hard for any group of organisms to keep doing iron oxidation over billions of years since iron availability is so variable: they are likely to go extinct or lose this ability at some point. We suggest this as a general trend in evolution that traits which are only sporadically useful are commonly lost-and then re-invented or re-distributed-or the trait will go extinct.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0166224"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442345/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144820417","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}