Environmental Microbiology Reports最新文献

{"title":"Complete Genome of an Alkali-Resistant Rhizobium anhuiense Symbiont of Pea Reveals Species-Specific Plasmid Fusion and Genomic Plasticity.","authors":"Jiashun Miao, Chi Zhang, Qifan Jiang, Zhangliang Yao, Kuirong Cao, Jie Chen, Hua Wang, Na Liu","doi":"10.1111/1758-2229.70366","DOIUrl":"10.1111/1758-2229.70366","url":null,"abstract":"<p><p>The rhizosphere microbiome is crucial for plant growth and stress resilience in sustainable horticulture. Here, we report the complete genome assembly and functional characterisation of Rhizobium anhuiense Xianghu001, a nitrogen-fixing symbiont isolated from pea (Pisum sativum) root nodules. A hybrid assembly strategy combining PacBio reads and Illumina reads yielded a 7.36 Mb high-quality assembly comprising one chromosome, one megaplasmid and four accessory plasmids, encoding 6899 protein-coding genes, of which 66.64% are located on the chromosome. Phylogenomics and synteny confirmed its placement within R. anhuiense. We detected a lineage-specific plasmid fusion forming the megaplasmid, while three accessory plasmids appear to be strain-specific and potentially acquired via horizontal gene transfer. Insertion sequence profiling suggests genome rearrangement shaping plasmid structure. To explore intraspecies diversity, we sequenced six additional local R. anhuiense isolates from pea. Despite their close geographic origin, genomic comparison revealed extensive divergence. Phenotypic assays demonstrated that Xianghu001 significantly promotes pea growth under nitrogen-deficient conditions, increasing chlorophyll content and nitrogen accumulation. It synthesises high levels of IAA (~184 mg/L), tolerates mild salinity (≤ 0.15% NaCl) and grows optimally at alkaline pH (8.0-10.0). Our findings provide a comprehensive genomic and functional framework for R. anhuiense Xianghu001 and underscore its potential as a biofertiliser.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 3","pages":"e70366"},"PeriodicalIF":3.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13240570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148012699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extension of Sous Vide Preservation of Wild Turkey (Meleagris gallopavo L.) Meat With Rosmarinus officinalis Essential Oil: A Study on Chemical Composition and Antibacterial Effectiveness Against Listeria monocytogenes and Other Population of Isolated Microbiota.","authors":"Miroslava Kačániová, Guiguo Zhang, Suzana Popovic, Alessandro Bianchi, Zhaojun Ban, Li Li, Natália Čmiková, Joel Horacio Elizondo-Luevano, Anis Ben Hsouna, Rania Ben Saad, Peter Haščík, Stefania Garzoli","doi":"10.1111/1758-2229.70299","DOIUrl":"10.1111/1758-2229.70299","url":null,"abstract":"<p><p>In our study, we focused on the chemical composition of Rosmarinus officinalis essential oil (ROEO), its antimicrobial effects. Drawing from existing research, we further investigated the antimicrobial properties of ROEO under in vivo conditions. Specifically, we examined its effects on sous vide meat from wild turkeys and its activity against Listeria monocytogenes. The dominant compound identified in ROEO was 1,8-cineole, which made up 48.5% of the oil. During our experiments, we assessed the total viable count, coliform numbers, and the presence of L. monocytogenes on sous vide wild turkey meat. Furthermore, we analysed the abundance of various bacterial species in each of the tested groups. Our findings suggest that the ROEO-treated groups exhibited a lower microbial load compared to the control groups or those treated solely with pathogenic microorganisms. Our microbial counts revealed that heat treatment had a noticeable effect on the microbial populations. ROEO demonstrated significant antimicrobial properties, as our results indicated its positive impact across all experimental groups. Additionally, mass spectrometry results highlighted differences in the microbiota composition following the application of ROEO and the inoculation of L. monocytogenes. The primary bacterial species isolated from the sous vide wild turkey meat were Citrobacter freundii and Pantoea agglomerans.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 3","pages":"e70299"},"PeriodicalIF":3.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13239209/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148051526","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Seasonal Analysis of Candida auris Detection Rates at 80 Wastewater Monitoring Sites in the United States, December 2023-November 2024.","authors":"Jorge Chavez, Alessandro Zulli, Dustin Duffy, Mariya Campbell, Meghan Lyman, Angela Coulliette-Salmond, D Joseph Sexton","doi":"10.1111/1758-2229.70376","DOIUrl":"10.1111/1758-2229.70376","url":null,"abstract":"<p><p>Candida auris is an emerging fungal pathogen known to cause outbreaks in healthcare settings that are difficult to control. Here, data from 80 wastewater treatment plants were collected between December 2023 and November 2024 to compare C. auris seasonal detection rates across the four meteorological seasons. The mean C. auris seasonal detection rate communicated as a percentage (((# of detections per site/# test days per site)/# total sites)*100) was highest in the summer (7%), followed by fall (4%), spring (4%) and winter (2%). A Kruskal-Wallis test identified a significant difference between the seasons (H = 43.6, p < 0.0001) and a Dunn's post hoc test with Bonferroni correction identified pairwise differences between summer and each of the other seasons (p < 0.05). Statistical significance and 95% confidence intervals (CI) were further assessed by a bootstrapping analysis that also identified a significant difference between summer and all other seasons (p < 0.01). Proportionally, 39 (48%) sites had their highest seasonal detection rate in summer, followed by 21 (27%) in fall, 15 (18%) in spring and five (7%) in winter. These results collectively document elevated C. auris seasonal detection rates in summer, providing new context to apply C. auris wastewater surveillance.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 3","pages":"e70376"},"PeriodicalIF":3.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13246258/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148203629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Third Generation Genome Sequencing of the Endobacterium Corynebacterium kroppenstedtii subsp. demodicis Reveals Details of Its Microbe-Host-Interaction With the Most Complex Human Commensal, Demodex folliculorum.","authors":"T Steegmüller, S Walch, S Gschwendtner, A Klingl, L E French, M Flaig, B M Clanner-Engelshofen","doi":"10.1111/1758-2229.70374","DOIUrl":"10.1111/1758-2229.70374","url":null,"abstract":"<p><p>Demodex mites inhabit the pilosebaceous unit despite harsh environmental conditions including UV radiation, variable salinity, and cosmetics. Their recently characterized endobacterium may contribute to this resilience. This study aimed to elucidate mechanisms of the microbe-host interaction that help mites withstand environmental stress. The genome of Corynebacterium kroppenstedtii subsp. demodicis was sequenced using PacBio technology and annotated via MicroScope. Metabolic and symbiotic traits were analyzed using KEGG and compared with the Demodex folliculorum secretome from published transcriptome data. The complete 2,456,075 bp genome contains 2034 coding sequences and exhibits reduced variable genes compared to other Corynebacterium species. Primary metabolism comprises an almost complete minimal gene set but lacks two tRNA synthetases and genes for phosphatidylethanolamine and NAD⁺ biosynthesis. Carbohydrate pathways are incomplete and fatty acid synthase I is absent. Secondary metabolism includes complete mevalonate and β-carotene biosynthetic pathways, while the methylerythritol phosphate pathway is missing. UV protection and oxidative stress tolerance are supported by β-carotene, ClpB, RecN, MsrA, KatA, SodA, and manganese transporter SitB. The secretome contains hydrolases likely aiding mite digestion. These findings provide genomic insights into mite-bacterium symbiosis and follicular adaptation. All functional inferences are based on genomic data and in silico predictions; experimental validation remains to be established.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 3","pages":"e70374"},"PeriodicalIF":3.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13244258/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148196740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolic Flux Analysis Reveals Entner-Doudoroff Pathway Dominance in Heterotrophic Deep-Sea Bacterial Isolates.","authors":"Yuxue Yang, Yue Wu, Keni Ma, Yue Li, Junwei Cao, Yuli Wei, Ruilian Yao, Weichao Wu","doi":"10.1111/1758-2229.70379","DOIUrl":"10.1111/1758-2229.70379","url":null,"abstract":"<p><p>Deep-sea microorganisms adapt to extreme conditions by diverse metabolic strategies, yet their intracellular carbon fluxes remain largely unexplored. Here, we investigated the central carbon metabolic fluxes of four bacterial strains isolated from Pacific Ocean sediments and deep waters, including Stutzerimonas marianensis PS1, Shewanella piezotolerans WP3, Georhizobium profundi WS11 and Parasedimentitalea marina W43. Using ¹³C metabolic flux analysis with multiple ¹³C-labelled glucose isotopologues, all strains preferentially degraded glucose via the Entner-Doudoroff pathway (EDP) with fluxes accounting for 66.7%-94.0% of total glycolytic flux, indicating that EDP is a conserved and dominant glycolytic route among deep-sea heterotrophs. S. piezotolerans WP3 uniquely exhibited substantial flux through both oxidative and non-oxidative branches of the pentose phosphate pathway, suggesting heightened precursor and redox demands. The strains also displayed diverse anaplerotic strategies, engaging either phosphoenolpyruvate or pyruvate carboxylation to replenish tricarboxylic acid cycle intermediates and enhance carbon utilisation efficiency. Oxidative stress assays further revealed a link between intracellular energy status and tolerance to hydrogen peroxide. Collectively, these findings provide comparative fluxomic evidence for central carbon metabolism in deep-sea bacteria and highlight metabolic traits that support survival in carbon-limited, high-pressure marine environments.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 3","pages":"e70379"},"PeriodicalIF":3.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13261371/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148222110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Polyphasic Characterization of Acetobacter indonesiensis UNPADCC 01-5 Isolated From a Traditional Fermented Food, Oncom Merah.","authors":"Yolani Syaputri, Erisa Zahra, Rianti Nur Azzahra, Annisa, Diffa Amanda Iswhara, Felice Olivia Lengkey, Syiffa Fauzia, Xiwu Jia, Asri Peni Wulandari, Ratu Safitri","doi":"10.1111/1758-2229.70346","DOIUrl":"10.1111/1758-2229.70346","url":null,"abstract":"<p><p>Acetobacter indonesiensis UNPADCC 01-5 is a recently discovered acetic acid bacterium isolated from fermented food, oncom merah. With its current lack of polyphasic approach in classification, this study aims to provide the first morphological, physiological, biochemical and molecular analyses. These analyses are achieved by morphological and physiological characterization, Kirby-Bauer antibiotic susceptibility, biochemical profiling, gas chromatography-mass spectrometry and whole-genome sequencing (WGS). The results found that A. indonesiensis UNPADCC 01-5, a non-motile cell, is a gram-negative, short rod-shaped cell that formed cream-white colonies with 0.3-1.3 in diameter. It exhibited environmental resilience, including acid-tolerant, halotolerant and thermotolerant. Against antibiotics, it showed resistance towards chloramphenicol. Biochemical tests revealed its ability to ferment glucose, rhamnose, melibiose and arabinose, as well as to produce bioactive metabolites such as acetoin and acetic acid. WGS identified potential gene expressions associated with acetic acid production, stress tolerance, nitrogen fixation, hydrocarbon degradation and heavy-metal resistance. WGS analysis revealed no detectable genes associated with human virulence factors or pathogenic secretion systems. The results suggested that A. indonesiensis UNPADCC 01-5 from oncom merah possessed adaptive traits which, with future assessments and industrial-scale tests, hold potential as a functional/adjunct culture for acidic fermentations and a biofunctional agent.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 3","pages":"e70346"},"PeriodicalIF":3.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13238706/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148160905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional Diversity and Community Composition of Soil Fungi Associated With Canopy Dieback in Araucaria araucana Forests of Contrasting Edaphic Conditions.","authors":"Valeria Arriagada, Adrian Garrido, Francisca Madariaga, Rodrigo Hasbun, Eugenio Sanfuentes","doi":"10.1111/1758-2229.70361","DOIUrl":"10.1111/1758-2229.70361","url":null,"abstract":"<p><strong>Background: </strong>Soil fungal communities play vital roles in forest ecosystem functioning, yet their relationship with tree health remains insufficiently characterized in many endangered species.</p><p><strong>Aims: </strong>This study, investigated the composition and functional structure of soil fungi associated with symptomatic and asymptomatic individuals of Araucaria araucana in the Nahuelbuta Coastal Range, Chile.</p><p><strong>Materials and methods: </strong>Using high-throughput ITS1 sequencing and trait-based annotation, we compared fungal assemblages across two forest sectors with contrasting edaphic conditions.</p><p><strong>Results: </strong>Marked differences in taxonomic and functional composition were observed between sites, with more even and functionally diverse communities in less restrictive soils. Within this site, where both tree health conditions co-occur, no significant differences in alpha or beta diversity were detected; nevertheless, species-level and functional guild analyses revealed shifts in composition. A shared core microbiome included taxa putatively identified as endophytes, including Cladophialophora minutissima, Fraxinicola europaea, Linnemannia hyalina, saprotrophs (Solicoccozyma terricola, Helicodendron conglomeratum, Pseudogymnoascus roseus) and a plant pathogen (Penicillium excelsum). Symptomatic trees harboured unique stress-tolerant taxa, including cold-adapted saprotrophs and ericoid mycorrhizal fungi, while asymptomatic trees supported lignocellulose decomposers, mutualists and early-successional symbionts.</p><p><strong>Discussion: </strong>The observed fungal shifts suggest that canopy dieback is associated with a functional reorganization of the rhizosphere microbiome rather than a simple loss of diversity.</p><p><strong>Conclusion: </strong>These findings provide new insights into the fungal ecology of A. araucana forest and contribute to understanding how soil microbiomes respond to forest decline under contrasting edaphic conditions.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 3","pages":"e70361"},"PeriodicalIF":3.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13290381/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148306282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Virulence Associated Morphology of Different Strains of Melissococcus plutonius, a Brood Pathogen of Honey Bees.","authors":"Oleg Lewkowski, Gerd Hause, Silvio Erler","doi":"10.1111/1758-2229.70369","DOIUrl":"10.1111/1758-2229.70369","url":null,"abstract":"<p><p>The causative agent of European foulbrood, Melissococcus plutonius, kills young larvae of honey bees. Although, several clonal complexes have been studied, the specific role of bacterial phenotype regarding bacterial morphology and other physiological parameters are less well understood. Insights from prominent bacterial pathogens (e.g., Enterococcus faecalis) have revealed that features like chain formation and separation play a critical role in the infection process and the course of bacterial diseases. Here, we explored the diversity in cell morphology and growth behaviour of three M. plutonius strains employing electron microscopy of larvae faeces and cultured bacteria, light microscopy on cultured bacteria and expression analysis of glycan-binding protein candidate genes. We found cell morphological differences of strains from the digestive tract of infected larvae and potentially associated expressional differences of several candidate genes. A growth assay in culture medium resulted in distinct chain length profiles of tested strains. An experimental transfer of supernatant from the highly virulent (49.3) to a less virulent strain (119) consistently led to cell separation suggesting a regulatory compound released from the highly virulent strain. Our results illustrate the mechanism of cell separation and the formation of individual cocci and short chains, potentially shedding light on the underlying mechanisms.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 3","pages":"e70369"},"PeriodicalIF":3.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13239739/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148147687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spiroplasma Are Protective Heritable Symbionts With Low Physiological Impact in the Drosophilid Fly Zaprionus kolodkinae.","authors":"Nuha Alamer, Stefanos Siozios, Chris Corbin, Emily A Hornett, Jordan E Jones, Gregory D D Hurst","doi":"10.1111/1758-2229.70365","DOIUrl":"10.1111/1758-2229.70365","url":null,"abstract":"<p><p>Spiroplasma bacteria are widespread associates of insects, with Drosophila serving as a key model for understanding maternally inherited symbioses. Most research has focused on the poulsonii-citri clade of Spiroplasma, leaving other lineages comparatively understudied. Here, we characterise the symbiosis between the drosophilid Zaprionus kolodkinae and its ixodetis group Spiroplasma (sZko). We assembled a complete genome for sZko, which encodes multiple candidate symbiosis factors, including ankyrin repeat domain proteins and diverse ribosome-inactivating protein (RIP) toxins typically linked to protective interactions. Notably, the genome also harbours a gene with a predicted ricin B lectin-binding domain, a candidate for establishing microbe-insect interactions at the eukaryotic cell surface. Phenotypic assays confirmed maternal inheritance of sZko with no evidence of reproductive parasitic phenotypes. Infected flies were protected against attack by the generalist parasitoid wasp Leptopilina heterotoma. There was no detectable impact of sZko on its host's starvation tolerance, suggesting minimal physiological cost to the host, and this low impact was mirrored for the protective symbiont sHy1 in D. hydei but contrasted with previous results for D. melanogaster. We conclude the Z. kolodkinae-Spiroplasma association is primarily defensive, and genomic analysis raises the possibility that protection involves a novel coupling between lectin-binding domains and RIPs.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 3","pages":"e70365"},"PeriodicalIF":3.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13240588/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148040372","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to 'Isolation and Identification of Pathogenic Bacteria Present in Commercially Important Fish, Shellfish, Water, and Soil Samples of Kaptai Lake, Bangladesh'.","authors":"","doi":"10.1111/1758-2229.70367","DOIUrl":"10.1111/1758-2229.70367","url":null,"abstract":"","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 3","pages":"e70367"},"PeriodicalIF":3.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13239436/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148136270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}