Applied and Environmental Microbiology最新文献

{"title":"Seasonal dynamics and nutrient controls of biogenic silica in Baltic Sea surface microplankton and picoplankton communities.","authors":"Yelena Churakova, Anabella Aguilera, Evangelia Charalampous, Daniel J Conley, Daniel Lundin, Jarone Pinhassi, Hanna Farnelid","doi":"10.1128/aem.00676-25","DOIUrl":"https://doi.org/10.1128/aem.00676-25","url":null,"abstract":"<p><p>In recent years, new contributors to the marine silica cycle have emerged, including pico-sized phytoplankton (<2-3 µm in size) such as <i>Synechococcus</i> and picoeukaryotes. Their contribution and relevance to silica cycling are still under investigation. Field studies reporting the biogenic silica (bSi) standing stock in the pico-sized fraction are limited to silica-poor oligotrophic environments, and the mechanism of bSi accumulation in picoplankton remains unknown. We investigated the variability of bSi standing stocks in two size fractions (picoplankton, 0.22-3 µm and microplankton, >3 µm) in the dissolved silica-replete Baltic Sea via biweekly time series samplings spanning 2 years. Time series data showed that the large changes in bSi standing stock in the Baltic Proper were primarily related to microplankton biomass and community composition. Meanwhile, picoplankton were, at times, surprisingly high contributors to total bSi year-round (up to 21.6%). Simultaneously, we performed microcosm incubation experiments with natural phytoplankton communities in each season to examine how nutrient additions affected bSi concentrations. In these experiments, increases in microplankton bSi were directly correlated to increases in diatom biomass, highlighting their influential role in the Baltic Sea silica cycle. Meanwhile, phosphorus additions triggered an increase in picoplankton bSi accumulation in all experiments. This uncovers a potential control of bSi accumulation in picoplankton, which can help identify the cellular mechanisms behind this process and uncover their role in silica cycling. The results link phytoplankton community composition and silica cycling, which is important for understanding the consequences of organism shifts due to climate change.IMPORTANCEThe marine carbon and silica cycles are tightly intertwined and largely controlled by diatoms. Nevertheless, recent studies, mostly in oligotrophic waters, have proposed new contributors to the marine silica cycle: picoplankton. Here, we report the first study of seasonal dynamics of biogenic silica (bSi) standing stock in microplankton and picoplankton in the silica-replete Baltic Sea. Microplankton bSi dynamics were correlated with changes in composition and biomass. Picoplankton were consistent contributors to bSi, and for the first time in diverse natural communities, we found a direct correlation between phosphorus and bSi accumulation. The results are important for understanding how climate change-predicted phytoplankton composition shifts will affect carbon and silica cycling and provide a direction for future research on nutrient controls of silica accumulation in picoplankton.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0067625"},"PeriodicalIF":3.9,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143963494","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":"Cinnamaldehyde effectively disrupts <i>Desulfovibrio vulgaris</i> biofilms: potential implication to mitigate microbiologically influenced corrosion.","authors":"Arianna Scardino, Gianmarco Mangiaterra, Barbara Citterio, Sarah Hijazi, Caterina Ciacci, Mauro Fehervari, Emanuela Frangipani","doi":"10.1128/aem.02200-24","DOIUrl":"https://doi.org/10.1128/aem.02200-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Microbiologically influenced corrosion poses significant challenges to various industries, as metal surfaces degrade due to the formation of microbial biofilms. Sulfate-reducing bacteria (SRB) are key contributors to this process in anoxic environments (e.g., oil and gas pipelines), mainly by producing highly corrosive hydrogen sulfide. Current prevention methods involving biocides often have drawbacks such as high toxicity and disposal costs, calling for novel environmentally friendly alternatives. Essential oils with their antimicrobial properties and biodegradability may represent promising candidates against microbial corrosion. In this study, cinnamaldehyde was selected both for its antimicrobial activity and its well-documented role as a corrosion inhibitor; then, its antibiofilm activity was investigated against &lt;i&gt;Desulfovibrio vulgaris&lt;/i&gt;, in comparison with the well-known reference biocide glutaraldehyde. Both compounds were bactericidal against &lt;i&gt;D. vulgaris&lt;/i&gt; at 12.5 µg/mL. &lt;i&gt;D. vulgaris&lt;/i&gt; biofilms were developed and monitored by confocal microscopy, and then 72-h-old biofilms were exposed to serial cinnamaldehyde and glutaraldehyde concentrations (12.5-100 µg/mL) for a further 48 h, to evaluate their disruptive effects. Both compounds caused a significant disruption of pre-formed biofilms, at 50 µg/mL. The reduction compared to the untreated controls was ca. 90% vs 85% for biomass, 60% vs 45% for average thickness, and 85% vs 80% for surface area, respectively. Interestingly, cinnamaldehyde applied to a &lt;i&gt;D. vulgaris&lt;/i&gt; biofilm grown on representative metal coupons completely inhibited the recovery of viable adherent cells. These data, altogether, highlight the potential of cinnamaldehyde as an effective alternative for controlling and mitigating microbiologically influenced corrosion, with comparable efficacy to glutaraldehyde.IMPORTANCEThe increasing environmental and health concerns associated with the use of conventional biocides to manage and control microbiologically influenced corrosion highlight the need for eco-friendly alternatives. Sulfate-reducing bacteria (SRB) represent the main players in this process, by adhering and proliferating as biofilms on metal infrastructures, producing metabolites that accelerate corrosion. Essential oils have long been regarded as potent antimicrobials endowed with low toxicity; however, there is limited knowledge about their potential use against anaerobic bacteria responsible for corrosion. This study focuses on the antimicrobial activity of cinnamaldehyde and shows its efficacy in eradicating biofilm-grown &lt;i&gt;D. vulgaris&lt;/i&gt;, a model species to study SRB energy metabolism. Notably, cinnamaldehyde is also a well-known corrosion inhibitor, which makes it an appealing candidate for industrial applications, particularly where SRB-induced corrosion is prevalent. Altogether, our results pave the way for the future development of green sustainable strategies involving the use of c","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0220024"},"PeriodicalIF":3.9,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143966685","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":"Arsenic biosorption mediated by arsenic-binding proteins QueF and QueE in <i>Lysinibacillus</i> sp. OR-15.","authors":"Qing Xu, Weishi Tian, Hongliang Liu, Gejiao Wang, Kaixiang Shi","doi":"10.1128/aem.00441-25","DOIUrl":"https://doi.org/10.1128/aem.00441-25","url":null,"abstract":"<p><p>Microorganisms play a crucial role in arsenic transformation, with associated genes highly conserved within the <i>ars</i> operon. Although microorganisms can absorb arsenic, no specific genes responsible for intracellular sequestration have been found within this operon. This suggests that genes outside the <i>ars</i> operon may also contribute to bacterial arsenic resistance. Here, we identified an arsenic-resistant <i>Lysinibacillus</i> sp. OR-15 that exhibits consistent biosorption capacity for arsenic. Our findings indicate that the expression of heavy metal-related genes <i>queF</i> and <i>queE</i>, which are not located in the <i>ars</i> operon, is also induced by arsenite [As(III)]. When <i>queF</i> or <i>queE</i> is expressed in the arsenic-sensitive bacterium AW3110, it enhances both the resistance to As(III) and the biosorption capacity. Purified QueF and QueE demonstrate binding abilities for both As(III) and arsenate [As(V)]. Site-directed mutagenesis studies reveal that the conserved cysteine residue at position 101 in QueF and position 37 in QueE are critical for As(III) and As(V) binding. The transcriptional regulation mechanism involves the arsenic-responsive protein ArsR, which binds to the promoter region of the <i>que</i> operon and regulates its expression. This study elucidates the molecular mechanisms underlying QueF/QueE-mediated arsenic biosorption in <i>Lysinibacillus</i> sp. OR-15.IMPORTANCEArsenic is a ubiquitous metalloid pollutant in the environment, and its bioavailable concentration significantly influences its toxicity. Microorganisms play a crucial role in the geochemical cycling of arsenic, with certain species capable of reducing its bioavailability through biosorption. Consequently, elucidating the mechanisms of bacterial biosorption of As(III) is essential. This study identifies arsenic-binding proteins, QueF and QueE, which are regulated by ArsR in <i>Lysinibacillus</i> sp. OR-15. These proteins can directly bind intracellular As(III), facilitating its biological fixation and mitigating the toxic effects of As(III) to cells. This discovery provides valuable insights into the microbial mechanisms of microbial arsenic biosorption.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0044125"},"PeriodicalIF":3.9,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143963204","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":"Mer overexpression in <i>Methanosarcina acetivorans</i> affects growth and methanogenesis during substrate adaptation.","authors":"Darla Brennan, Dillon Lieber, Mary Walter, Morgan Price, Nicole R Buan","doi":"10.1128/aem.00675-25","DOIUrl":"https://doi.org/10.1128/aem.00675-25","url":null,"abstract":"<p><p>Evidence suggests that multienzyme complexes are involved in biological methane production (methanogenesis), although the composition of the Wolfe Cycle methanogenesis complexes may vary between diverse methanoarchaeal taxa. Methylenetetrahydromethanopterin reductase (Mer) is the first committed step in C1 oxidation to CO₂ during methylotrophic methanogenesis. However, Mer is downregulated when cells use acetate as a substrate. We hypothesized that Mer overexpression during methylotrophic methanogenesis would be beneficial, while overexpression during acetoclastic methanogenesis would be detrimental for energy conservation. To test this hypothesis, we overexpressed Mer and characterized strain physiology on methanol, acetate, and when switching substrates. We found that Mer overexpression results in faster growth on methanol, with less C fixation into biomass, and no effect on methanogenesis. Growth on acetate was not affected by Mer overexpression, but switching between substrates was affected. The native Mer overexpressing strain was slower to adjust from methanol to acetate and vice-versa. These data suggest that tight regulation of Mer expression is necessary to regulate C flux through methylotrophic versus acetoclastic methanogenesis pathways in <i>Methanosarcina</i>.IMPORTANCEMethanoarchaea thrive near the \"thermodynamic limit of life\" and have likely evolved efficient mechanisms to control flux of substrates to conserve energy. Methylenetetrahydromethanopterin reductase (Mer) is a highly conserved, key enzyme in the Wood-Ljungdahl and Wolfe Cycle methanogenesis pathways. Our study sheds light on how Mer enzyme stoichiometry affects methanogenesis and suggests avenues for engineering the organism to promote renewable fuel or bioproduct synthesis.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0067525"},"PeriodicalIF":3.9,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143966455","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":"CrAssphage distribution analysis in an Amazonian river based on metagenomic sequencing data and georeferencing.","authors":"David Tavares Martins, Oscar Victor Cardenas Alegria, Carlos Willian Dias Dantas, Edian Franklin Franco De Los Santos, Paulo Rógenes Monteiro Pontes, Rosane Barbosa Lopes Cavalcante, Rommel Thiago Jucá Ramos","doi":"10.1128/aem.01470-24","DOIUrl":"https://doi.org/10.1128/aem.01470-24","url":null,"abstract":"<p><p>Viruses are the most abundant biological entities in all ecosystems of the world. Their ubiquity makes them suitable candidates for indicating fecal contamination in rivers. Recently, a group of Bacteroidetes bacteriophages named CrAssphages, which are highly abundant, sensitive, and specific to human feces, were studied as potential viral biomarkers for human fecal pollution in water bodies. In this study, we evaluated the presence, diversity, and abundance of viruses with a focus on crAssphages via metagenomic analysis in an Amazonian river and conducted correlation analyses on the basis of physicochemical and georeferencing data. Several significant differences in viral alpha diversity indexes were observed among the sample points, suggesting an accumulation of viral organisms in the river mouth, whereas beta diversity analysis revealed a significant divergence between replicates of the most downstream point (IT4) when compared to the rest of the samples, possibly due to increased human impact at this point. In terms of the presence of crAssphage, the analysis identified 61 crAssphage contigs distributed along the Itacaiúnas River. Moreover, our analysis revealed significant correlations between 19 crAssphage contigs and human population density, substantiating the use of these viruses as possible markers for human fecal pollution in the Itacaiúnas River. This study is the first to assess the presence of crAssphages in an Amazonian river, with results suggesting the potential use of these viruses as markers for human fecal pollution in the Amazon.</p><p><strong>Importance: </strong>The Amazon biome is one of the most diverse ecosystems in the world and contains the most vast river network; however, the continuous advance of urban centers toward aquatic bodies exacerbates the discharge of pollutants into these water bodies. Fecal contamination contributes significantly to water pollution, and the application of an improved fecal indicator is essential for evaluating water quality. In this study, we evaluated the presence, diversity, and abundance of crAssphages in an Amazonian river and performed correlation analysis on the basis of physicochemical and georeferencing data to test whether crAssphages are viable fecal pollution markers. Our analysis revealed both the presence of crAssphages and their correlation with physicochemical data and showed significant correlations between the relative abundance of crAssphages and human density. These results suggest the potential use of these viruses as markers for water quality assessment in Amazonian rivers.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0147024"},"PeriodicalIF":3.9,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959808","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":"Elucidation of novel turnagainolides and their biosynthetic gene cluster in <i>Bacillus subtilis</i>.","authors":"Peng Li, Shuang Han, Min Wang, Xuejiao Zhang, Shuai Zhi, Meiling Jin, Jouni Jokela, Shan He, Liwei Liu","doi":"10.1128/aem.02574-24","DOIUrl":"https://doi.org/10.1128/aem.02574-24","url":null,"abstract":"<p><p>Turnagainolides represent a unique class of cyclic depsipeptides characterized by the presence of a rare (<i>E</i>)-3-hydroxy-5-phenylpent-4-enoic acid (Hppa) residue, exhibiting diverse bioactivities. While previous studies have identified turnagainolides and their congeners from various microorganisms, including <i>Microascus</i>, <i>Bacillus</i>, <i>Arthrobacter</i>, and <i>Streptomyces</i>, their biosynthetic gene cluster and pathways remained elusive. Here, we uncovered four novel compounds, turnagainolide congeners D-G (<b>3-6</b>), and two known compounds, turnagainolides A-B (<b>1, 2</b>), from <i>Bacillus subtilis</i> LP. Their chemical structures were elucidated through a combination analysis of LC-MS analysis, NMR spectroscopy, and the Mosher derivatization technique. To investigate their biosynthetic gene cluster, comprehensive genome sequencing, phylogenetic analysis, and anti-SMASH-based prediction were conducted, and gene knockout experiments confirmed the correlation between the <i>tur</i>-BGC and the biosynthesis of these compounds. The alignment of protein sequences encoded by <i>tur</i>-BGC against public protein databases revealed homologous proteins exclusively in <i>Bacillus</i> species. These findings not only expand the chemical diversity of cyclic peptides in <i>Bacillus</i> but also provide critical insights into the biosynthetic pathway of turnagainolides and their evolutionary lineage.</p><p><strong>Importance: </strong>Microbial natural products represent an invaluable resource in drug discovery, providing a vast reservoir of structurally and functionally diverse compounds with promising therapeutic potential. A comprehensive understanding of natural product biosynthesis not only deepens our knowledge of their chemical complexity but also drives advancements in chemical synthesis and metabolic engineering, paving the way for the generation of novel bioactive compounds. In this study, we report that a marine axenic culture of <i>B. subtilis</i> LP synthesizes six turnagainolides (<b>1-6</b>), which exhibit both biofilm-inhibitory and cytotoxic activities. These findings expand our understanding of the structure-activity relationships of turnagainolides and offer new insights into their potential biological roles. Moreover, the identification of biosynthetic gene clusters and the proposed biosynthetic pathway provide a valuable framework for elucidating turnagainolide biosynthesis, laying the groundwork for future efforts to optimize their production and explore their applications in drug development.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0257424"},"PeriodicalIF":3.9,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143967297","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>Bacillus haimaensis</i> sp. nov.: a novel cold seep-adapted bacterium with unique biosynthetic potential.","authors":"Yuanyuan Wang, Luyi Yang, Wenbo Wu, Zhengqi Feng, Jian He, Changjun Guo, Jianguo He","doi":"10.1128/aem.02456-24","DOIUrl":"https://doi.org/10.1128/aem.02456-24","url":null,"abstract":"<p><p>Deep-sea cold seeps harbor unique microbial communities that play crucial roles in biogeochemical cycles and possess potential biotechnological applications. Herein, we report the isolation, characterization, and genomic analysis of a novel <i>Bacillus</i> species, <i>Bacillus haimaensis</i> sp. nov. (type strain CSS-39^T, CCTCC M20241382), obtained from sediments collected at a depth of 1,350 m in the Haima cold seep, South China Sea. Phylogenomic analysis, revealing an average nucleotide identity of 87.78% and a digital DNA-DNA hybridization value of 34.0% with its closest relative <i>B. tianshenii</i> DSM 25879^T, confirms the taxonomic novelty of the genus <i>Bacillus</i>. The complete 4.54 Mb genome of <i>B. haimaensis</i> reveals adaptations to the cold seep environment, including enhanced nutrient acquisition capabilities and stress response mechanisms. Comparative genomic analysis identifies 27 unique gene clusters related to spore germination and sulfate assimilation, suggesting specialized metabolic strategies for this extreme habitat. Furthermore, six biosynthetic gene clusters, including a novel lassopeptide cluster, indicate a potential for secondary metabolite production. Phenotypic characterization demonstrates the strain's ability to utilize diverse carbon sources and tolerate a wide range of environmental conditions. Our findings provide insights into microbial adaptations to deep-sea cold seeps and highlight the potential of <i>B. haimaensis</i> for biotechnological applications in bioremediation and natural product discovery. This study expands our understanding of microbial diversity in extreme marine environments and offers a new model bacterium for investigating bacterial adaptations to deep-sea ecosystems.IMPORTANCEThe discovery of <i>Bacillus haimaensis</i> sp. nov. in the Haima cold seep of the South China Sea represents a significant advancement in our understanding of microbial adaptations to extreme marine environments. This novel species exhibits remarkable metabolic versatility and unique genomic features, providing insights into bacterial survival strategies in nutrient-variable, high-pressure deep-sea ecosystems. Comprehensive genomic analysis reveals distinctive biosynthetic gene clusters, suggesting untapped potential for discovering novel natural product. Furthermore, <i>B. haimaensis</i> exhibits promising capabilities for aromatic compound degradation, indicating potential applications in marine bioremediation. This work not only expands our knowledge of microbial diversity in understudied deep-sea habitats but also highlights the biotechnological promise of extremophiles. The adaptive mechanisms elucidated in <i>B. haimaensis</i>, particularly those related to sporulation and sulfate assimilation, contribute to our broader understanding of microbial ecology in cold seeps and may inform future research on climate change impacts on deep-sea ecosystems.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0245624"},"PeriodicalIF":3.9,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143966505","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":"Effects of soluble electron shuttles on microbial iron reduction and methanogenesis.","authors":"Bhim Sen Thapa, Theodore M Flynn, Zena D Jensvold, Kenneth M Kemner, Margaret F Sladek, Edward J O'Loughlin, Christopher W Marshall","doi":"10.1128/aem.02222-24","DOIUrl":"https://doi.org/10.1128/aem.02222-24","url":null,"abstract":"<p><p>In many aquatic and terrestrial ecosystems, iron (Fe) reduction by microorganisms is a key part of biogeochemical cycling and energy flux. The presence of redox-active electron shuttles in the environment potentially enables a phylogenetically diverse group of microbes to use insoluble iron as a terminal electron acceptor. We investigated the impact that different electron shuttles had on respiration, microbial physiology, and microbial ecology. We tested eight different electron shuttles, seven quinones and riboflavin, with redox potentials between 0.217 and -0.340 V. Fe(III) reduction coupled with acetate oxidation was observed with all shuttles. Once Fe(III) reduction began to plateau, a rapid increase in acetate consumption was observed and coincided with the onset of methane production, except in the incubations with the shuttle 9,10-anthraquinone-2-carboxylic acid (AQC). The rates of iron reduction, acetate consumption, methanogenesis, and the microbial communities varied significantly across the different shuttles independent of redox potential. In general, shuttles appeared to reduce the overall diversity of the community compared to no shuttle controls, but certain shuttles were exceptions to this trend. Geobacteraceae were the predominant taxonomic family in all enrichments except in the presence of AQC or 1,2-dihydroxyanthraquinone (AQZ), but each shuttle enriched a unique community significantly different from the no shuttle control conditions. This suggests that the presence of different redox-active electron shuttles can have a large influence on the microbial ecology and total carbon flux in the environment.IMPORTANCEIron is the fourth most abundant element in the Earth's crust, and the reduction of iron by microbes is an important component of global biogeochemical cycles. A phylogenetically diverse group of microbes is capable of conserving energy with oxidized iron as a terminal electron acceptor, but the environmental conditions favoring certain taxonomic clades in iron-reducing environments are unclear. One complicating factor often overlooked in small-scale enrichments is the influence of soluble, redox-active electron shuttles on the rate and microbial ecology of iron reduction. We tested the effects of eight different electron shuttles on microbial physiology and ecology in iron-reducing enrichments derived from a local wetland. Each electron shuttle varied the microbial activity and enriched for a microbial community distinct from the no shuttle control condition. Therefore, in complex subsurface environments with many redox-active compounds present, we propose electron shuttles as a reason for the coexistence of multiple clades of iron-reducing bacteria.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0222224"},"PeriodicalIF":3.9,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143957629","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":"Population and pan-genomic analyses of <i>Staphylococcus pseudintermedius</i> identify geographic distinctions in accessory gene content and novel loci associated with AMR.","authors":"Jordan D Zehr, Qi Sun, Kristina Ceres, Amy Merrill, Gregory H Tyson, Olgica Ceric, Jake Guag, Sarah Pauley, Holly C McQueary, Kelly Sams, Guillaume Reboul, Patrick K Mitchell, Renee Anderson, Rebecca Franklin-Guild, Cassandra Guarino, Brittany D Cronk, Claire R Burbick, Rebecca Wolking, Laura Peak, Yan Zhang, Rebeccah McDowall, Aparna Krishnamurthy, Durda Slavic, Prabhjot Kaur Sekhon, David Needle, Robert Gibson, Casey Cazer, Jennifer Rodriguez, Beth Harris, Michael J Stanhope, Laura B Goodman","doi":"10.1128/aem.00010-25","DOIUrl":"https://doi.org/10.1128/aem.00010-25","url":null,"abstract":"<p><p><i>Staphylococcus pseudintermedius</i> is a common representative of the normal skin microbiota of dogs and cats but is also a causative agent of a variety of infections. Although primarily a canine/feline bacterium, recent studies suggest an expanded host range including humans. This paper details population genomic analyses of the largest yet assembled and sequenced collection of <i>S. pseudintermedius</i> isolates from across the USA and Canada and assesses these isolates within a larger global population genetic context. We then employ a pan-genome-wide association study analysis of over 1,700 <i>S</i>. <i>pseudintermedius</i> isolates from sick dogs and cats, covering the period 2017-2020, correlating loci at a genome-wide level, with <i>in vitro</i> susceptibility data for 23 different antibiotics. We find no evidence from either core genome phylogenies or accessory genome content for separate lineages colonizing cats or dogs. Some core genome geographic clustering was evident on a global scale, and accessory gene content was noticeably different between various regions, some of which could be linked to known antimicrobial resistance (AMR) loci for certain classes of antibiotics (e.g., aminoglycosides). Analysis of genes correlated with AMR was divided into different categories, depending on whether they were known resistance mechanisms, on a plasmid, or a putatively novel resistance mechanism on the chromosome. We discuss several novel chromosomal candidates for follow-up laboratory experimentation, including, for example, a bacteriocin (subtilosin), for which the same protein from <i>Bacillus subtilis</i> has been shown to be active against <i>Staphylococcus aureus</i> infections, and for which the operon, present in closely related <i>Staphylococcus</i> species, is absent in <i>S. aureus</i>.IMPORTANCE<i>Staphylococcus pseudintermedius</i> is an important causative agent of a variety of canine and feline infections, with recent studies suggesting an expanded host range, including humans. This paper presents global population genomic data and analysis of the largest set yet sequenced for this organism, covering the USA and Canada as well as more globally. It also presents analysis of <i>in vitro</i> antibiotic susceptibility testing results for the North American (NA) isolates, as well as genetic analysis for the global set. We conduct a pan-genome-wide association study analysis of over 1,700 S. <i>pseudintermedius</i> isolates from sick dogs and cats from NA to correlate loci at a genome-wide level with the <i>in vitro</i> susceptibility data for 23 different antibiotics. We discuss several chromosomal loci arising from this analysis for follow-up laboratory experimentation. This study should provide insight regarding the development of novel molecular treatments for an organism of both veterinary and, increasingly, human medical concern.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0001025"},"PeriodicalIF":3.9,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143967301","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>Glutamicibacter</i> sp. ZY1 antagonizes pathogenic <i>Vibrio parahaemolyticus</i> via iron competition.","authors":"Zhili Shi, Ya Li, Weibo Shi, Zhixin Mu, Qingxi Han, Weiwei Zhang","doi":"10.1128/aem.00009-25","DOIUrl":"https://doi.org/10.1128/aem.00009-25","url":null,"abstract":"<p><p>Probiotics are prior agents for treating bacterial infection with advantages of inhibiting pathogenic bacteria and improving immune responses of hosts, thus increasing the survival rate of cultured animals. In this study, one <i>Vibrio parahaemolyticus</i> YDE17 pathogenic to shrimp and its antagonist <i>Glutamicibacter</i> sp. ZY1 were screened, and ZY1 showed stable inhibitory effects on diverse <i>Vibrio</i> spp., especially <i>V. parahaemolyticus</i>. ZY1 secreted inhibitory substances into supernatant, and the activity of inhibitory substances did not change after being treated under different temperatures, proteinase K, and pH (6-10), which indicated that the inhibitory substances might be small molecules, which led us to trace the siderophore production. The siderophore production of YDE17 co-incubated with the cell-free supernatant of ZY1 was greater than that of YDE17 alone, which indicated that the cell-free supernatant of ZY1 created iron-limiting conditions for YDE17. This finding was confirmed by iron supplementation assays, in which the inhibitory activity of the cell-free supernatant of ZY1 on YDE17 as well as the siderophore production of YDE17 decreased in the presence of FeCl₃. The effect of iron on inhibition was further confirmed by <i>in vivo</i> infection. The relative percent survival of ZY1 to shrimp challenged by YDE17 was 83.3%, but the survival rates of shrimp challenged with YDE17/ZY1/FeCl₃ were similar to that of YDE17, both of which were significantly lower than the 70% survival rate of shrimps simultaneously challenged by ZY1/YDE17. Our study offers a new probiotic resource to control vibriosis, which works through iron competition with the opportunistic pathogens of <i>Vibrio</i> spp.IMPORTANCEBacteria belonging to <i>Vibrio</i> spp., especially <i>Vibrio parahaemolyticus</i>, are important opportunistic pathogens infecting a wide range of hosts including fish, shrimp, shellfish, and crab. Antibiotics are effective but show the disadvantages of antibiotic generation, microecology destruction, and biological toxicology; thus, new treatments of <i>Vibrio</i> infection are urgently recommended. In our present study, <i>Glutamicibacter</i> sp. ZY1, belonging to the phylum Actinomycetes, was selected and showed high inhibitory activity to inhibit <i>V. parahaemolyticus</i> pathogenic to shrimp. <i>Glutamicibacter</i> sp. ZY1 antagonized <i>V. parahaemolyticus</i> YDE17 through producing siderophore to compete for iron, based on the results of both <i>in vitro</i> and in <i>vivo</i> experiments under different iron levels. This study offers a new strategy to control <i>Vibrio</i> infection in aquaculture.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0000925"},"PeriodicalIF":3.9,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143962053","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}