Applied and Environmental Microbiology最新文献

{"title":"Integrated metagenomic-metabolomic insights into plant-microbe interactions mediated by <i>Bacillus</i> volatile compounds.","authors":"Haiqian Yang, Wei Liu, Jiwei Niu, Biao Geng, Pengfei Qiu, Hongshun Li, Junping Bao, Xin Pu, Yong Li, Xiaojing Jia, Yingxiang Sun, Yejun Han","doi":"10.1128/aem.02523-25","DOIUrl":"10.1128/aem.02523-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Modulation of plant-microbe interactions with signaling molecules offers a promising strategy to promote plant growth and stress adaptation. However, identifying effective signaling molecules and elucidating the mechanisms for regulating the rhizosphere microbiome remain major challenges. In this study, the roles and mechanisms of &lt;i&gt;Bacillus&lt;/i&gt; volatile compounds as potential signaling molecules in plant-microbe interactions were investigated. First, the genome and metabolism of a novel &lt;i&gt;Bacillus subtilis&lt;/i&gt; strain capable of producing acetoin and 2,3-butanediol were studied, and the titers of the two compounds were increased to 86.76 g/L by sequential metabolic engineering. Subsequently, the effects of volatile compounds on the growth of vegetables (&lt;i&gt;Brassica rapa&lt;/i&gt; and &lt;i&gt;Solanum lycopersicum&lt;/i&gt; var.) were studied. Plant growth, nutrient (nitrogen, phosphorus, and potassium) utilization efficiency, and salt stress resistance were improved significantly. Compared with water as a control, significant changes in the abundance of 109 microbial genera of &lt;i&gt;B. rapa&lt;/i&gt;'s rhizosphere microbiome were identified with volatile compound application. Notably increased microbes included nitrogen-fixing, phosphate- and potassium-solubilizing, stress-resistant, plant growth-promoting, and auxin-secreting microbes. Additionally, genes involved in nitrogen, phosphorus, and potassium utilization in the rhizosphere microbiome were significantly increased, and corresponding metabolism was found. Finally, metabolomic analyses of &lt;i&gt;S. lycopersicum&lt;/i&gt; var.'s roots and leaves revealed 67 significantly upregulated compounds with the application of volatile compounds. These compounds were primarily involved in stress resistance, oxidative stress alleviation, free radical scavenging, and auxin-related plant growth promotion. This work demonstrates that &lt;i&gt;Bacillus&lt;/i&gt; volatile compounds regulate rhizosphere microbiome and plant-microbe interactions and enhance plant nutrient utilization efficiency, stress tolerance, and growth.IMPORTANCEPlant productivity and stress resilience are strongly influenced by interactions between plants and the rhizosphere microbiome, yet practical strategies to rationally modulate native soil microbial communities remain limited. This study demonstrates that &lt;i&gt;Bacillus&lt;/i&gt; volatile compounds, specifically acetoin and 2,3-butanediol, function as effective signaling molecules that coordinate plant-microbe interactions in the rhizosphere. By integrating plant physiology, metagenomics, and metabolomics, we show that these volatile compounds not only enhance plant growth and nutrient use efficiency but also reprogram rhizosphere microbial communities toward functions that benefit nitrogen, phosphorus, and potassium acquisition and stress adaptation. Notably, volatile application improved plant salt tolerance, highlighting their strong ecological and physiological impact. This work provides mechanistic evidence that &lt;i&gt;Bacillus&lt;","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0252325"},"PeriodicalIF":3.7,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101463/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147571797","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":"Automated air-flow cytometry enables real-time monitoring of <i>Plasmopara viticola</i> sporangia in vineyards.","authors":"Amanda Malvessi Cattani, Yanick Zeder, Elias Graf, Andreas Schwendimann, Roberta Coronelli, Tara Smit-Sadki, Jean-Philippe Burdet, Esteban Alfonso, Augustine Jaccard, Erny Niederberger, Markus Rienth","doi":"10.1128/aem.02152-25","DOIUrl":"10.1128/aem.02152-25","url":null,"abstract":"<p><p>Fungal diseases such as downy mildew (<i>Plasmopara viticola</i>) can severely affect grapevine yield and quality, making precise fungicide applications critical. Decision Support Systems (DSS) in precision viticulture guide treatment timing, but most rely primarily on weather data and overlook biological indicators, such as real-time spore dynamics. To address this, we evaluated an automatic air-flow cytometer (SwisensPoleno Jupiter) for real-time detection and quantification of <i>P. viticola</i> sporangia. The instrument integrates holographic imaging, fluorescence spectroscopy, and AI-based classification. Laboratory data sets (>5,000 events) from naturally and artificially infected leaves enabled the development of classifiers based on Random Forest models. Field validation in Swiss vineyards combined Hirst-type spore traps (microscopy and qPCR DNA quantification) with SwisensPoleno measurements. Correlations between manual and automatic sporangium quantification emerged during a 2023 pilot (60 days) and strengthened over the 2024 season (140 days). Correlations were weak early in the season, during leaf development and the onset of flowering, but improved as vine phenology progressed and disease pressure increased, reaching up to <i>r</i> = 0.94 with microscopy counting and <i>r</i> = 0.83 with DNA quantification. Additionally, airborne sporangium concentrations were influenced by daily air temperature and the SwisensPoleno instrument inlet height. Visual assessments in 2024 confirmed severe downy mildew, affecting nearly all unprotected leaves, and <i>P. viticola</i> DNA concentrations were strongly correlated with symptom severity (<i>r</i> = 0.82). With further refinement, these first models for real-time and automatic identification of <i>P. viticola</i> sporangia have the potential to provide reliable spore-monitoring data for DSS integration, supporting precision viticulture worldwide.</p><p><strong>Importance: </strong>The automatic, real-time classification of <i>Plasmopara viticola</i> spores presented in this study offers a significant advancement in disease risk forecasting. By integrating airborne spore detection, this approach reduces the likelihood of false-positive recommendations, applying fungicides when weather conditions are favorable, but disease risk is low and false negatives, when spores are present, but treatments are not advised. Consequently, this strategy can decrease treatment frequency and overall fungicide use, promoting more sustainable and precise disease management in vineyards.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0215225"},"PeriodicalIF":3.7,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147571801","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":"From genome to lifestyle: adaptive strategies of <i>Pseudomonas</i> sp. AU10 and its Antarctic lineage.","authors":"César X García-Laviña, Pablo Smircich, Susana Castro-Sowinski","doi":"10.1128/aem.02470-25","DOIUrl":"10.1128/aem.02470-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Antarctica harbors diverse &lt;i&gt;Pseudomonas&lt;/i&gt; lineages, yet their evolutionary histories and ecological strategies remain poorly understood. Growing genomic resources now enable comparative analyses that link genome information to lifestyles. Here, we report the complete genome of &lt;i&gt;Pseudomonas&lt;/i&gt; sp. AU10, an Antarctic freshwater isolate, and use it as a model to investigate polar adaptation through phylogenomics, pangenomics, metabolic reconstruction, and phenotypic assays. Incorporating the 40 most closely related genomes from public databases, we identified that all 11 strains from permanently cold environments clustered into two well-defined monophyletic clades with contrasting biogeographic patterns: a geographically restricted \"Antarctic clade,\" to which AU10 belongs, and a \"cold clade\" distributed worldwide from the Himalayas to the Arctic and Antarctica. The two lineages lacked a shared conserved gene set for adaptation to permanently frozen habitats; instead, clade-specific genomic signatures suggested independent adaptive strategies. The Antarctic clade resolved into two species, both sharing distinctive features related to ionic/osmotic homeostasis, respiratory flexibility, and virulence factors, including insecticidal toxins. Within this clade, AU10's species showed expanded virulence factors and iron acquisition systems. Genomic evidence pointed to a potential pathogenic lifestyle involving freshwater arthropods, supported by AU10's metabolism oriented toward protein, lipid, and chitin hydrolysis and the overrepresentation of transport systems for amino and organic acids. Intraspecific variability involved the replacement of O-antigen gene clusters and a mobilome comprising a natural plasmid and several prophages carrying UV-resistance and outer-envelope modification genes. Overall, these findings place AU10 within a long-evolving Antarctic lineage with distinct adaptations, offering insights into bacterial evolution in extreme environments.IMPORTANCEAntarctica is one of the most extreme environments on Earth, yet it sustains diverse microbial life. How these microorganisms adapt to permanent cold conditions and the lifestyles they adopt remain difficult to elucidate. The growing wealth of genomic data offers opportunities to reconstruct these evolutionary histories. Still, in versatile genera such as &lt;i&gt;Pseudomonas&lt;/i&gt;, extracting consistent biological meaning from comparative genomics remains challenging. Here, we focused on a restricted set of genomes closely related to the Antarctic strain &lt;i&gt;Pseudomonas&lt;/i&gt; sp. AU10 and integrated genomic analyses with phenotypic assays and metabolic reconstruction. This strategy uncovered two cold-adapted lineages with contrasting biogeographic patterns, highlighted lineage-specific genomic features associated with adaptation to the extreme Antarctic environment, and provided insights into their ecological strategies. Ultimately, this approach underscores the value of linking genomic, ","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0247025"},"PeriodicalIF":3.7,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147503108","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":"Exometabolome variation in the fungal pathogen of humans <i>Candida albicans</i> reveals specificities at the genetic clade and strain levels.","authors":"Leovigildo Rey Alaban, Andrei Bunescu, Joséphine Abi-Ghanem, Frédéric Bequet, Julien Lebrat, Pawel Tulinski, Daria Kosmala, Marie-Elisabeth Bougnoux, Christophe d'Enfert, Vincent Thomas","doi":"10.1128/aem.01512-25","DOIUrl":"10.1128/aem.01512-25","url":null,"abstract":"<p><p><i>Candida albicans</i> is a fungal pathobiont that thrives in different host niches and successfully confronts the host immune defenses. The success of <i>C. albicans</i> as a pathogen relies on a highly plastic metabolism, with examples of variations across isolates; however, detailed characterization of how <i>C. albicans</i> genetic diversity impacts the content of the metabolome is still missing. Here, we have implemented an NMR (nuclear magnetic resonance)-based high-throughput workflow to probe exometabolome variation in <i>in vitro</i> cultures of 96 clinical isolates spread across several genetic clusters (clades) that structure the <i>C. albicans</i> population. Our workflow allowed for batch analysis, with robust replication (six or more replicates) of the culture supernatants from these isolates. Results of this analysis highlighted the extent of metabolic divergence between clades (clade-specific variation) and within clades (isolate-specific variation). In particular, Clade 13 isolates (corresponding to the <i>Candida africana</i> isolates) showed metabolic specificities relative to isolates in other clades, notably non-consumption of trehalose and weak utilization of choline. Isolate-specific variation was mainly driven by metabolites involved in central carbon metabolism.IMPORTANCEThis study provides one of the most extensive analyses of <i>Candida albicans</i> exometabolome- comprising 96 isolates across all major genetic clades. By developing an NMR (nuclear magnetic resonance)-based, high-throughput workflow for the analysis of supernatants of <i>in vitro</i> cultured <i>C. albicans</i>, we demonstrated the extent of metabolic differences both between clades (clade-specific variation) and among isolates within each clade (isolate-specific variation). Isolates from Clade 13, which corresponds to <i>Candida africana</i>, exhibited distinct metabolic profiles compared to isolates from other clades, particularly in their inability to utilize trehalose and their reduced capacity to use choline. Variation among individual isolates was largely attributable to differences in metabolites associated with central carbon metabolism.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0151225"},"PeriodicalIF":3.7,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101467/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147472374","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":"Viruses in marine sediments: a review of their effect on biogeochemistry and microbial interactions.","authors":"Jacob R A Williams, Jennifer F Biddle","doi":"10.1128/aem.00275-25","DOIUrl":"10.1128/aem.00275-25","url":null,"abstract":"<p><p>Viruses are known to impact the flow of carbon through the environment, while also impacting the microbial community around them. While this has been reexamined in recent years in the marine water column, viral impacts on marine sediments, the microbes, and carbon contained within are due for a reassessment. This review synthesizes findings from studies on marine sediment microbial communities to examine the extent of viral contribution to biogeochemical cycling, through ecological impacts as well as through cell lysis. Viruses have been shown to increase metabolic activity within the sediment microbial community as well as increase biodiversity, improving the range and ability of microbial communities to degrade organic matter. Viruses have also been found to have more direct effects on sedimentary geochemistry, with viral-mediated cell lysis allowing for the release of organic matter into the sediment while also being able to act as reservoirs for biologically relevant chemicals such as dissolved organic phosphorus. Viruses have been shown to impact the biogeochemistry of buried marine sediment, with less attention being paid to freshwater sediments and surficial marsh sediments. The interest in viral activities in sediments can help us to understand the drivers of biotic contributions to diagenesis.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0027525"},"PeriodicalIF":3.7,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147353473","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":"Genetic modification of <i>Clostridium kluyveri</i> for heterologous <i>n</i>-butanol and <i>n</i>-hexanol production.","authors":"Caroline Schlaiß, Saskia T Baur, James W Marsh, Kurt Gemeinhardt, Largus T Angenent","doi":"10.1128/aem.00058-26","DOIUrl":"10.1128/aem.00058-26","url":null,"abstract":"<p><p>The mesophilic microbe <i>Clostridium kluyveri</i> serves as the most commonly used model microbe to elucidate the physiology and biochemistry of ethanol-based chain elongation via reverse β-oxidation. In this pathway, ethanol and acetate are converted into short- and medium-chain carboxylates. However, to date, no genetic system has been published in a peer-reviewed publication. Here, we report the development of versatile genetic tools for <i>C. kluyveri</i>, utilizing the pMTL <i>Clostridia</i> shuttle vector system and thiamphenicol as a selective marker. We identified the native restriction-modification system of <i>C. kluyveri</i> as a critical barrier to DNA transfer and overcame it by identifying and characterizing the crucial methyltransferase. To mimic the native DNA methylation pattern of <i>C. kluyveri</i>, we performed <i>in-vivo</i> methylation of the shuttle vector plasmid by expressing the methyltransferase in <i>Escherichia coli</i>, followed by DNA transfer via conjugation. After validating the genetic system, we demonstrated heterologous expression of different combinations of both NADH- and NADPH-dependent alcohol dehydrogenases from <i>Clostridium acetobutylicum</i>. The expression of these genes was controlled by the P<i>_thl</i> promoter, which is commonly used in <i>Clostridia</i>, and the P<i>_adhE2</i> promoter, leading to <i>n</i>-butanol and <i>n</i>-hexanol production of the mutant strains. This genetic system for <i>C. kluyveri</i> will not only enable further research on the metabolism of this microbe but also enable more profound insights into ethanol-based chain elongation in general.</p><p><strong>Importance: </strong>Medium-chain carboxylates are required in various everyday products, including cosmetics, pharmaceuticals, and fragrances, and show a natural antimicrobial property. Furthermore, they represent food additives and serve as chemical building blocks for several other compounds. Traditionally, these carboxylates are produced from fossil resources, contributing to increased greenhouse gas emissions. Alternatively, they are derived from animal- or plant-based fat (e.g., coconut oil), which competes with agricultural land that is needed for food production. However, microbial chain elongation, which is a biotechnological approach relying on microbes, such as <i>Clostridium kluyveri</i>, is sustainable and a promising alternative to the conventional production of medium-chain carboxylates. Notably, it enables the use of industrial waste streams (e.g., off-gases and carbohydrate-rich industrial waste) as substrates, making the process more environmentally friendly. By applying our genetic system for <i>C. kluyveri</i>, a better understanding of microbial chain elongation can be achieved and potentially even enable an extension of its product portfolio.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0005826"},"PeriodicalIF":3.7,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101501/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147442174","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":"Intra-strain and inter-strain heterogeneity shape phage-host interactions and phenotypic adaptation in <i>Pseudomonas aeruginosa</i>.","authors":"Bingrui Sui, Xiaoyu Li, Lili Wang, Yongping Xu, Yumin Hou, Muhammad Saleem Iqbal Khan, Na Li, Demeng Tan","doi":"10.1128/aem.00050-26","DOIUrl":"10.1128/aem.00050-26","url":null,"abstract":"<p><p>The efficacy of phage therapy relies on a precise understanding of phage-host interactions, particularly how phages recognize bacterial surface receptors and how these interactions shape host adaptation. In <i>Pseudomonas aeruginosa</i>, the O-antigen of lipopolysaccharide (LPS) is a common but incompletely characterized determinant of phage susceptibility. Here, we used an O-antigen-specific lytic podophage, phipa9, to prove receptor plasticity in <i>P. aeruginosa</i> strain ZS-PA-11. Phage-resistant mutants arose through either a point mutation in <i>gtaB</i> (phipa9-G), encoding UTP-glucose-1-phosphate uridylyltransferase, or a large chromosomal deletion (411 kb) (phipa9-B) encompassing <i>gtaB</i>. Functional analyses revealed that <i>gtaB</i> is essential for O-antigen synthesis, phage adsorption, and infection. Disruption of <i>gtaB</i> altered the LPS profile, reduced motility, and promoted biofilm formation. Both resistant mutants (phipa9-G and phipa9-B) exhibited attenuated virulence in <i>Galleria mellonella</i>, with the 411 kb deletion mutant showing a more pronounced reduction, underscoring the contribution of O-antigen and deleted loci to bacterial virulence. Comparative assays with another O-antigen-specific phage, phipa10, revealed distinct host ranges and inhibition profiles, highlighting receptor-dependent diversity and possible roles of intracellular defenses. Together, these findings demonstrate that natural variation in O-antigen biosynthetic pathways governs phage susceptibility and bacterial physiology. By uncovering <i>gtaB</i>-mediated intra-strain heterogeneity that restricts phage infection while reshaping host phenotypes, this work underscores the dual role of surface receptors in mediating phage-host dynamics and provides mechanistic insight for the rational design of therapeutic phages targeting <i>P. aeruginosa</i>.IMPORTANCEEffective phage therapy against multidrug-resistant <i>Pseudomonas aeruginosa</i> requires understanding how surface receptors govern susceptibility and resistance. We show that <i>gtaB</i>-mediated loss of the O-antigen blocks phage adsorption, alters bacterial physiology, and promotes population heterogeneity through pleiotropic phenotypic alterations. These multifaceted consequences reveal that phage resistance is not binary but instead reprograms bacterial adaptation and virulence. Comparison of two O-antigen-dependent phages with distinct host specificities further demonstrates that natural receptor variation critically shapes infection outcomes. Thus, receptor-based resistance represents both a barrier and an opportunity: while it limits phage efficacy, it can also attenuate virulence and expose new vulnerabilities. Recognizing these trade-offs is essential for designing phage therapies that both eradicate pathogens and harness the evolutionary costs of resistance.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0005026"},"PeriodicalIF":3.7,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101515/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147343539","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":"Secreted factors of <i>Staphylococcus aureus</i> promote co-invasion with <i>Candida albicans</i> by inducing hypha formation and invasion.","authors":"Raymond Pasman, Bastiaan P Krom, Jianbo Zhang, Stanley Brul, Sebastian A J Zaat","doi":"10.1128/aem.01961-25","DOIUrl":"10.1128/aem.01961-25","url":null,"abstract":"<p><p>Interkingdom interactions between <i>Candida albicans</i> and <i>Staphylococcus aureus</i> promote lethal dissemination of the bacterium. During this process, <i>C. albicans</i> hypha invasion aids <i>S. aureus</i> dissemination through Als1p/Als3p-facilitated co-invasion. The effects of <i>S. aureus</i> on <i>C. albicans</i> hypha formation and invasion are, however, unknown. In this study, we used both liquid mDMEM-DMP as well as a previously constructed semi-solid adaptation of the medium (mDMEM-DMPA) to study the effects of <i>C. albicans/S. aureus</i> co-culturing on hypha formation and invasion. Semi-solid-based co-culturing significantly increased colony size and generally increased hypha invasion. Liquid growth-based time-lapse microscopy showed that <i>S. aureus</i> significantly promoted both <i>C. albicans</i> hypha length and elongation rate. Further semi-solid-based growth results revealed that >3 kDa-secreted <i>S. aureus</i> factors were accountable for the increase in <i>C. albicans</i> hypha growth. A newly constructed <i>in vitro</i> assay confirmed the co-invasion of <i>S. aureus</i> during co-culturing and showed that deletion of <i>C. albicans</i> Als1p/Als3p abolished the co-invasion of <i>S. aureus</i> during co-culturing. In conclusion, our study shows that <i>S. aureus</i> affects <i>C. albicans</i> virulence by actively stimulating <i>C. albicans</i> hypha extension through the production of, presently unknown, secreted factors and sequentially using hypha proteins Als1p and Als3p to co-invade. Therefore, <i>S. aureus</i> can stimulate <i>C. albicans</i> epithelial invasion even prior to attaching to its hyphae, providing the foundation for subsequent co-invasion.IMPORTANCEEpithelial barriers normally protect against invasion and systemic infection by <i>S. aureus</i>, but frequently, such infections occur without a port of entry. One route of <i>S. aureus</i> epithelial traversal is through co-invasion with the highly invasive <i>Candida albicans</i>. Understanding this interaction in detail is of high importance in view of the prevention of these infections. Our study shows how the <i>S. aureus</i> and C. <i>albicans</i> interaction results in mutual benefit. <i>S. aureus</i> appeared to affect <i>C. albicans</i> virulence by actively stimulating <i>C. albicans</i> hypha extension through the production of, presently unknown, secreted factors and sequentially using hypha proteins Als1p and Als3p to bind to the hyphae and co-invade. These insights are important from a microbial ecological perspective and offer important potential targets for interfering with the interaction and reducing the virulence of these opportunistic pathogens.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0196125"},"PeriodicalIF":3.7,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101462/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147580090","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":"Whole-genomic and transcriptomic analyses elucidate <i>p</i>-cresol and styrene degradation metabolism in <i>Rhodococcus opacus</i> 1CP.","authors":"Selvapravin Kumaran, Thomas Heine, Janosch A D Gröning, Michael Schlömann, Andreas Albersmeier, Tobias Busche, Jörn Kalinowski, Christian Rückert-Reed, Lena Schaffert, Dirk Tischler","doi":"10.1128/aem.00045-26","DOIUrl":"10.1128/aem.00045-26","url":null,"abstract":"<p><p>The genus <i>Rhodococcus</i> comprises numerous strains recognized for degradation of pollutants and production of secondary metabolites, including biosurfactants, lignin breakdown, and utilization of volatile organic compounds. Often, gene redundancies and the evolution of alternative pathways are attributed to such characteristics. <i>Rhodococcus opacus</i> 1CP, initially isolated as a chlorophenol-degrading strain, was found to be a model organism comprising several such features. In this study, we analyzed the genome and transcriptome and provided evidence that the strain 1CP uses three different pathways of <i>ortho-</i>, <i>meta-</i>, and side-chain attack for the degradation of aromatic compounds. The wild-type strain and the single and double knock-out mutants of phenol hydroxylases were able to attack substituted phenols via the classical <i>ortho</i>-route. In contrast, the triple knock-out mutant expressed <i>meta</i>-pathway genes to act on <i>p</i>-cresol, indicating that this pathway serves as a reserve in strain 1CP. Growth of 1CP on phenol, <i>p</i>-cresol, and styrene induces several gene clusters that are associated with lignin metabolization. Catechol, protocatechuate, and phenylacetic acid are major key intermediates that are funneled into central metabolic pathways, which enable strain 1CP to degrade acetophenone, benzoate, phenol, 2-phenylethanol, and styrene. Strain 1CP possesses an alternative, modified <i>ortho</i>-cleavage pathway that allows it to degrade 2-chlorophenol. Interestingly, in almost all cases, redundant genes were identified; however, only in a few cases, such as phenol hydroxylases, were they found to be active and simultaneously involved in metabolic activities. The transcriptomic and kinetic data showed that the redundant styrene oxide isomerase is upregulated and involved in styrene degradation.IMPORTANCE<i>Rhodococcus opacus</i> 1CP is a model organism for various biotechnological applications due to its capabilities to metabolize a vast range of aromatic and xenobiotic compounds. Although strain 1CP has been used for decades in bioremediation, the complete metabolic pathways underlying degradation have never been elucidated. In this study, the ability of the strain to bypass phenol hydroxylase deletions and degrade substituted phenols is described using genomics, transcriptomics, and gene knock-out analyses. Despite its metabolic versatility, strain 1CP has been reported only for the <i>ortho</i>-cleavage pathway. No enzymatic or metabolic evidence has supported the presence of a <i>meta</i>-cleavage pathway to degrade aromatic compounds. Genes associated with such <i>meta</i>-pathways have been identified, but are not clustered with known degradation operons. In this study, we demonstrate that a triple knock-out mutant can utilize a <i>meta</i>-cleavage pathway for the degradation of substituted phenols.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0004526"},"PeriodicalIF":3.7,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101518/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147525720","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":"Insect herbivory reshapes rhizosphere bacterial and fungal networks in a stage-specific manner.","authors":"Márcia Leite-Mondin, Priscila A Auler, Rafael L Oliveira, Felipe M R Barros, Fernando D Andreote, Marcio C Silva-Filho","doi":"10.1128/aem.00071-26","DOIUrl":"https://doi.org/10.1128/aem.00071-26","url":null,"abstract":"<p><p>Plants interact with diverse above- and belowground biota, with defense phenotypes shaped by these multiorganismal networks, particularly in the rhizosphere. We tested how insect herbivory reorganizes rhizosphere microbiomes across plant phenology and how it differs from mechanical damage. In <i>Arabidopsis thaliana</i> exposed to feeding by the generalist caterpillar <i>Spodoptera frugiperda</i> at pre-flowering, flowering, and post-flowering stages, we profiled rhizosphere communities and compared them to mechanically wounded plants. Bacterial alpha diversity was driven largely by phenology, whereas fungal alpha diversity was more sensitive to injury type. PCA revealed clear, treatment-specific separations within each stage, indicating compositional remodeling beyond diversity shifts. Herbivory increased <i>Streptomyces</i>, <i>Sphingomonas</i>, and <i>Acinetobacter</i>, while mechanical injury produced distinct, stage-dependent bacterial signatures, including <i>Dyella</i> and <i>Pseudolabrys</i>. Fungal responses were stage contingent: fermentative yeasts before flowering and saprotrophic or opportunistic genera after flowering. Co-occurrence networks under both injuries exhibited more positive correlations, with herbivory enhancing bacteria-fungi connectivity. Functional inference showed strong, stage-dependent restructuring: symbiotroph and endophyte guilds clustered at flowering, and post-flowering communities were enriched for hydrogenotrophy, nitrogen fixation, and pathogen/pathotroph functions. Herbivory further elevated inferred chemotrophy, fermentation, and nitrate reduction, whereas mechanical injury reduced chemotrophy, saprotroph abundance, and nitrate-reducing functions. Together, these results indicate that insect herbivory is a biologically distinct disturbance that reorganizes rhizosphere communities and interaction networks in a phenology-dependent manner, underscoring aboveground-belowground linkages with implications for crop resistance and productivity.</p><p><strong>Importance: </strong>Plants rely on soil-dwelling microbes around their roots to grow and defend themselves. Yet we know little about how insects reshape root‑zone communities as plants develop, or whether this differs from simple wounding. We studied <i>Arabidopsis thaliana</i> fed on by the generalist caterpillar <i>Spodoptera frugiperda</i> before, during, and after flowering and compared these plants to those with mechanical damage. We found that insect feeding, not just injury, acts as a distinct disturbance that reorganizes the root‑zone microbial community in stage‑specific ways. It altered which microbes were present and how they interacted, strengthening links between bacteria and fungi and shifting likely nutrient and defense functions. These results reveal strong connections between aboveground attack and belowground life, with practical implications for breeding and managing crops for resilience and productivity.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0007126"},"PeriodicalIF":3.7,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147760219","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}