Applied and Environmental Microbiology最新文献

{"title":"The diatom <i>Thalassiosira gravida</i> under Arctic change: algal exudates and their microbial transformation under contrasting temperatures and photoperiods.","authors":"Frederik Bussmann, Jakob K Giesler, Sylke Wohlrab, Oliver J Lechtenfeld, Jan Kaesler, Tilmann Harder, Boris P Koch","doi":"10.1128/aem.01429-26","DOIUrl":"https://doi.org/10.1128/aem.01429-26","url":null,"abstract":"<p><p>Climate change threatens polar ecosystems through rising temperatures and changing light regimes. Phytoplankton release of dissolved organic carbon (DOC) is a major carbon-cycle component, yet it remains unclear how temperature, light, and associated bacteria jointly affect DOC and dissolved organic matter (DOM) composition. Here, we analyzed axenic and xenic cultures of the Arctic diatom <i>Thalassiosira gravida</i> at 9°C and 13.5°C under 16:8 h and 24:0 h light:dark cycles. Extracellular DOC was quantified, and molecular composition characterized by untargeted ultrahigh-resolution mass spectrometry in original culture filtrates. In axenic cultures, growth rates were 266% higher at 13.5°C 24:0 h, and cell-normalized DOC concentrations 52% lower compared to 9°C 16:8 h, suggesting a shift in carbon allocation. Xenic cultures contained 50-80% lower cell-normalized DOC concentrations than axenic cultures and converged at 11.7 ± 0.9 pmol DOC cell^-1. Despite similar DOC concentrations in xenic cultures, the 13.5°C 24:0 h treatment showed lower chemodiversity (-8%), H/C ratios (-7%), and higher oxidation (+24%) than 9°C 16:8 h, consistent with more strongly processed DOM. At 9°C, axenic 24:0 h cultures showed higher chemodiversity (+14%) and H/C ratios (+7%) compared to 16:8 h, indicating that prolonged photoperiods altered DOM composition toward signatures associated with greater putative bioavailability. Contrasting axenic-xenic patterns suggest that bacterial presence weakened the treatment-dependent DOM responses observed in axenic cultures. Overall, temperature and photoperiods altered algal DOC quantity and quality, and its microbial transformation, with implications for carbon cycling.IMPORTANCEThe Arctic Ocean is warming rapidly, and changing sea-ice conditions alter light availability. Phytoplankton release dissolved organic carbon (DOC), which can be transformed by associated bacteria, thus playing an essential role in the marine carbon cycle. Still, the fate of such DOC transformations remains difficult to predict in the scope of future climate change scenarios. Using axenic and xenic cultures of the Arctic diatom <i>Thalassiosira gravida</i> as a model, our findings emphasize that algal extracellular release and its microbial transformation must be evaluated not only in the framework of bulk DOC dynamics but also with respect to molecular diversity and composition. Therefore, physiological responses of Arctic phytoplankton to higher temperatures and prolonged photoperiods may affect algal carbon exudation as well as the diversity and composition of microbially processed DOM in a warming Arctic Ocean.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0142926"},"PeriodicalIF":4.2,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148890673","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":"A peptide that binds the Asian citrus psyllid gut reduces transmission of the citrus greening pathogen <i>Candidatus</i> Liberibacter asiaticus.","authors":"Miltan C Roy, Clebson S Tavares, Ruchir Mishra, Erik L Roldan, Lukasz L Stelinski, Kirsten S Pelz-Stelinski, Bryony C Bonning","doi":"10.1128/aem.00577-26","DOIUrl":"https://doi.org/10.1128/aem.00577-26","url":null,"abstract":"<p><p>Citrus greening disease, associated with the bacterium <i>Candidatus</i> Liberibacter asiaticus (<i>C</i>Las), has severely impacted citrus yields on a global scale. <i>C</i>Las is vectored by the Asian citrus psyllid, <i>Diaphorina citri</i> Kuwayama, in a circulative and propagative manner. Extensive application of chemical insecticides for suppression of psyllid populations has resulted in widespread resistance. Despite considerable effort and expenditure, citrus greening disease continues to impair citrus production. For transmission to occur, <i>C</i>Las must bind and infect the psyllid vector via the gut epithelium, but little is known of the specific molecular interactions involved. By screening a phage display library, we selected ten psyllid gut binding peptides, a subset of which have sequence similarity to <i>C</i>Las surface proteins. Peptide binding to the surface of the psyllid gut epithelium was confirmed by identification of gut proteins bound by specific peptides. We evaluated whether these peptides could interfere with the interaction between <i>C</i>Las and the gut epithelium of <i>D. citri</i>, thereby impeding pathogen transmission. Peptide DcNy2 significantly reduced <i>C</i>Las acquisition and inoculation by <i>D. citri</i> compared to control treatments. Nymphs fed specific peptides exhibited reduced <i>C</i>Las acquisition and infection of both the alimentary canal and salivary glands without negatively impacting psyllid fecundity, development, or survival. These results support peptide-mediated disruption of <i>C</i>Las transmission by <i>D. citri</i> as a potential component of integrated strategies to manage citrus greening disease.IMPORTANCECitrus greening disease, or huanglongbing, causes billions of dollars in losses and represents one of the greatest challenges facing global citrus production. Despite significant investment on multiple fronts, effective disease management strategies are lacking. This study shows for the first time that short peptides that bind to the surface of the gut of the Asian citrus psyllid vector interfere with <i>C</i>Las association with the gut. This critical first gut binding step is required for <i>C</i>Las to infect and propagate within the psyllid vector. The downstream consequence of this peptide-mediated interference is reduced acquisition and transmission of the citrus pathogen. This work provides the foundation for new transgenic or paratransgenic tools for use in the management of citrus greening disease.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0057726"},"PeriodicalIF":4.2,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148890667","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>Trichoderma reesei</i> Nsd3 transcription factor: pleiotropic roles in development, stress response, secondary metabolism, and cellulase production.","authors":"David Batista Maués, Lucas Matheus Soares Pereira, Andrei Stecca Steindorff, Amanda Cristina Campos Antoniêto, Rafael Silva-Rocha, Marcelo Damário Gomes, Zachary A Lewis, Roberto N Silva","doi":"10.1128/aem.00865-26","DOIUrl":"https://doi.org/10.1128/aem.00865-26","url":null,"abstract":"<p><p><i>Trichoderma reesei</i> is known for its ability to secrete high amounts of cellulases, enzymes of fundamental importance in generating products from lignocellulosic biomass. Diverse signaling pathways and transcription factors (TFs) control the cellulolytic repertoire in <i>T. reesei</i> to ensure correct adaptation to the environment. Here, we analyzed RNA-Seq data and identified a new potential regulator of cellulase production in <i>T. reesei</i>: a novel TF named Nsd3, a homolog of NsdC from <i>Aspergilli</i>. Deletion of <i>nsd3</i> reduced vegetative growth and conidiation on solid medium. Phenotypic characterization of the Δ<i>nsd3</i> strain showed that it is more sensitive to osmotic stress, but more resistant to cell wall and oxidative stresses. Our results showed that Nsd3 is a repressor of cellulase expression by directly regulating key genes in the cellulolytic pathway, an unreported role for this TF in fungi. Loss of <i>nsd3</i> leads to a faster and more robust induction of cellulolytic genes, and higher cellulase and hemicellulase activities. Transcriptional profiling by RNA-Seq, chromatin accessibility profiling by ATAC-Seq, and protein-DNA interaction assays showed that sugar transporters are important targets of Nsd3 during cellulase expression regulation. Combined with microscopy and gene expression analyses, the ATAC-Seq data also highlighted Nsd3 as a central regulator of cell wall remodeling and organization. Furthermore, the transcriptomics also showed that Nsd3 regulates genes involved in secondary metabolism. These results showed that Nsd3 regulates several physiological processes and provide novel insights into the regulatory system of cellulases in <i>T. reesei</i> that can be used in the design of high-performance strains for biorefinery.IMPORTANCE<i>Trichoderma reesei</i> is a key player in the production of hydrolytic enzymes for the degradation of lignocellulose biomass, and transcription factors are important targets for genetic engineering to construct cellulase-hyperproducing strains. Here, we identified the transcription factor Nsd3 and characterized its role as a regulator of cellulase production in <i>T. reesei</i>. We applied two powerful genomics methods (transcriptome sequencing and chromatin accessibility sequencing) to unravel the global role of Nsd3 and its regulatory mechanism. Nsd3 participates in various biological processes in <i>T. reesei</i>, including cell wall remodeling, calcium metabolism, and secondary metabolism, in addition to regulating the expression of sugar transporters. Protein-DNA interaction assays demonstrate that Nsd3 acts through important genes to regulate cellulase expression, including ace4, crt1, stp1, and cel1b. Our study provides mechanistic insights about how Nsd3 regulates diverse physiological processes in <i>T. reesei</i>. This work also applied ATAC-Seq for the first time to study chromatin accessibility in <i>T. reesei</i>.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0086526"},"PeriodicalIF":4.2,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148886196","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":"Phage vB_KpnM_NB cocktail synergizing with amikacin in inhibiting persister cells of <i>Klebsiella pneumoniae</i>.","authors":"Bingqing Xu, Mengye Ma, Yiping Wang, Xingyu Li, Jieting Pan, Yi Jin, Ruiqin He, Lijian Ding, Liming Jiang","doi":"10.1128/aem.01367-26","DOIUrl":"https://doi.org/10.1128/aem.01367-26","url":null,"abstract":"<p><p>The emergence of multidrug-resistant <i>Klebsiella pneumoniae</i> (KPN) and antibiotic-tolerant persister cells poses a significant challenge to existing anti-infection therapies. Given the urgent need for sustainable alternatives to antibiotics, phage cocktails are emerging as a promising alternative to control <i>K. pneumoniae</i> infections. We isolated three lytic phages vB_KpnM_NB (1-3) from Ningbo environmental samples, classified them into the Drexlerviridae family, and determined the biological characteristics of two representative phages. Genomic analysis confirmed that these phages are closely related and lack resistance and virulence genes, ensuring biosafety. Subsequently, a stable KPN persister model was established using amikacin, with a biphasic killing pattern observed during treatment. At a multiplicity of infection of 10, the phage cocktail eliminated 99.00% of persister cells, while individual phages were less effective. The phage cocktail also inhibited persister-derived biofilm formation, showing improved results when combined with amikacin. This combination significantly reduced capsule polysaccharide production in persisters, weakening the outer membrane barrier. These findings demonstrate that the phage cocktail-amikacin combination effectively targets planktonic cells, persister cells, and biofilms, providing a promising strategy against persisters and recurrent <i>K. pneumoniae</i> infections.</p><p><strong>Importance: </strong>This study fills the critical gap in understanding how phage cocktails synergize with amikacin against <i>K. pneumoniae</i> persister cells. By constructing a highly specific phage vB_KpnM_NB cocktail, establishing a stable persister model, and performing <i>in vitro</i> bactericidal and biofilm assays, we demonstrate that the cocktail effectively eliminates planktonic cells, persisters, and biofilms. We clarify the core synergistic mechanism: inhibiting capsular polysaccharide synthesis, improving phage adsorption, and disrupting the bacterial outer membrane barrier. These findings provide experimental evidence for the prevention and control of multidrug-resistant and carbapenem-resistant <i>K. pneumoniae</i> persister infections, establishing a safe and effective phage-antibiotic combination therapy. The results are crucial for addressing antibiotic tolerance and controlling chronic, recurrent infections. They hold significant theoretical and translational value for the treatment of refractory infections in clinical settings and offer new insights into the development of novel antimicrobial strategies.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0136726"},"PeriodicalIF":4.2,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148886233","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":"Transferable <i>optrA-</i>mediated linezolid resistance in enterococci from high-altitude river sediments of Gilgit-Baltistan, Pakistan.","authors":"Serena Simoni, Andrea Brenciani, Alessandra Di Gregorio, Francesca Romana Massacci, Lucilla Cucco, Maisoor Ahmed Nafees, Saif Ud Din, Nelofar Hanif, Stefania Gorbi, Francesco Regoli, Eleonora Giovanetti, Carla Vignaroli","doi":"10.1128/aem.01129-26","DOIUrl":"https://doi.org/10.1128/aem.01129-26","url":null,"abstract":"<p><p>Environmental dissemination of antimicrobial resistance is a growing global concern. This study investigated the occurrence, genetic context, and mobility of the oxazolidinone resistance genes in enterococci isolated from high-altitude river sediments in the Gilgit-Baltistan region of Pakistan. A total of 17 florfenicol-resistant enterococci were recovered from 3 of the 12 sampling sites analyzed. Four multidrug-resistant strains (two <i>Enterococcus faecium</i>, one <i>E. faecalis</i>, and one <i>E. hirae</i>) harboring the <i>optrA</i> gene were selected for whole-genome sequencing using Illumina and Nanopore platforms. Genomic analyses showed that <i>optrA</i> was plasmid-borne in all isolates and co-localized with additional resistance genes, including macrolide, phenicol, and tetracycline resistance determinants. The <i>optrA</i> genetic context was frequently associated with insertion sequences, suggesting their role in the mobilization of multidrug-resistance elements. Mini-translocatable units of the <i>optrA</i> genetic context were detected as circular forms in two of four strains, further supporting their mobility potential. Conjugation assays demonstrated successful horizontal transfer of the <i>optrA</i> gene mediating linezolid resistance, with transfer frequencies ranging from 2.03 × 10⁻⁶ to 6.36 × 10⁻⁴ transconjugants per recipient cell. <i>optrA</i>-carrying plasmids remained stable after serial passages without antibiotic pressure. Phylogenetic analysis showed that isolates belonged to distinct sequence types and clustered with strains of diverse geographic and ecological origins, suggesting dissemination of <i>optrA</i> across different genetic backgrounds rather than clonal expansion. The occurrence of linezolid-resistant enterococci in high-altitude river sediments suggests their widespread distribution and emphasizes the need for broader environmental surveillance programs to monitor clinically relevant resistances even in remote ecosystems.</p><p><strong>Importance: </strong>This study provides important insights into the environmental dissemination of antimicrobial resistance by demonstrating the occurrence and genetic diversity of clinically relevant resistance determinants in enterococci isolated from remote high-altitude river sediments. The findings emphasize that natural environments could serve as reservoirs and exchange hubs for antimicrobial resistance, even in ecosystems with limited direct anthropogenic impact. Therefore, integrated One Health surveillance strategies that include environmental compartments alongside human and animal populations are required to better monitor and mitigate the emergence of clinically significant resistant bacteria.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0112926"},"PeriodicalIF":4.2,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148878865","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":"Identification of beneficial bacterial strains for tomato growth promotion and biocontrol of bacterial canker caused by <i>Clavibacter michiganensis</i>.","authors":"Nasim Sedighian, Marie-Christine Groleau, Eric Déziel","doi":"10.1128/aem.01087-26","DOIUrl":"https://doi.org/10.1128/aem.01087-26","url":null,"abstract":"<p><p>Bacterial canker of tomato, caused by <i>Clavibacter michiganensis</i> (<i>Cm</i>), remains difficult to control due to lack of effective management options. In this study, a collection of over 500 bacterial isolates was screened <i>in vitro</i> for antagonistic activity against <i>Cm</i> and plant growth-promoting traits. Based on these results, 32 candidates were evaluated <i>in planta</i>, leading to the identification of three highly effective strains: <i>Pantoea agglomerans</i> SO16PY and two <i>Pseudomonas marginalis sensu lato</i> strains, IRDA16 and SO16PC, which consistently enhanced tomato vegetative growth. Notably, <i>P. agglomerans</i> SO16PY delayed disease onset in <i>Cm</i>-inoculated plants by up to 7 days and significantly reduced wilting severity, lowering the disease severity score from 85% to 45%. Strains IRDA16 and SO16PC also restricted disease development, reducing severity scores to 67.5% and 57.5%, respectively. Whole-genome sequencing and comparative genomics revealed that strains IRDA16 and SO16PC form a distinct, specialized plant-associated lineage within the <i>Pseudomonas marginalis</i> group, exhibiting average nucleotide identity ≈ 96% and digital DNA-DNA hybridization ≈ 69.5% values near species delineation thresholds. Genome mining identified diverse biosynthetic gene clusters encoding non-ribosomal peptide synthetases, the lipopeptide viscosin, and terpenes, which likely drive the biostimulant and antagonistic traits of this novel <i>Pseudomonas</i> lineage. Together, these findings characterize promising bacterial candidates with dual biostimulant and biocontrol capacities while uncovering a genomically distinct <i>Pseudomonas</i> lineage optimized for beneficial plant-microbe interactions in sustainable agriculture.IMPORTANCE<i>Clavibacter michiganensis</i> (<i>Cm</i>) is a major bacterial pathogen of tomato and poses a significant economic threat to global production. It is classified as an A2 quarantine pathogen by the European and Mediterranean Plant Protection Organization (EPPO). Current management strategies rely largely on chemical control, including copper-based compounds (e.g., Bordeaux mixture, copper oxychloride), mancozeb, and antibiotics like streptomycin. However, these approaches raise increasing concerns related to environmental contamination, phytotoxicity, and the development of resistant pathogen populations. As a sustainable alternative, plant growth-promoting bacteria have emerged as promising biocontrol agents. In this study, we identified bacterial strains exhibiting antagonistic activity against <i>Cm</i> both <i>in vitro</i> and <i>in planta</i>. Notably, these strains also enhanced tomato growth parameters, demonstrating their dual functionality. Given the environmental drawbacks associated with chemical inputs, the use of such beneficial microorganisms represents a promising strategy for advancing sustainable and eco-friendly tomato production systems.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0108726"},"PeriodicalIF":4.2,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148878999","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":"Seasonal dynamics of microbial communities and potential human pathogens in <i>Crassostrea hongkongensis</i> and ambient water in southern China.","authors":"Xiaoxia Liu, Xianyu Wang, Haipeng Zhu, Wenqi Chen, Xin Hong, Yi Wan, Jiaomei Huang, Chunsheng Liu","doi":"10.1128/aem.01056-26","DOIUrl":"https://doi.org/10.1128/aem.01056-26","url":null,"abstract":"<p><p>Oysters are a popular raw seafood worldwide, yet their contamination with human pathogens poses substantial public health risks. However, the seasonal dynamics of host-associated microbiota and the environmental drivers of pathogen accumulation in <i>Crassostrea hongkongensis</i> remain poorly understood. Here, we conducted 16S rRNA amplicon sequencing to profile the gill and intestinal microbiota of <i>C. hongkongensis</i>, sampled quarterly over a 1-year period in Beihai and Zhanjiang, southern China. A pronounced divergence in oyster-associated bacterial communities was observed between the two locations in December. Key bacterial families, such as Lachnospiraceae and Muribaculaceae, showed significant temporal fluctuations in abundance, suggesting their potential role in maintaining bacterial community stability within oysters. These microbial shifts were significantly correlated with environmental parameters such as chlorophyll <i>a</i> and pH. In parallel, we used plate counting to quantify five foodborne pathogens and total viable counts. Vibrios were more frequently detected in oyster tissues than in ambient seawater. Pathogen-associated amplicon sequence variants exhibited a strong response to variations in pH and chlorophyll <i>a</i>, whereas the abundance of culturable <i>Vibrio vulnificus</i> was significantly negatively correlated with temperature and nitrate. The integration of high-throughput sequencing and culture-based methods provides comprehensive insights into the dynamics of pathogenic bacteria within oysters under natural mariculture settings. This study offers valuable ecological insights into the interactions within the oyster-associated microbial ecosystem, contributing to a deeper understanding of its dynamics and implications for public health.</p><p><strong>Importance: </strong>Mariculture of <i>Crassostrea hongkongensis</i> serves as a critical interface between coastal ecology and public health, yet seasonal dynamics of its microbiome and core stabilizing taxa remain poorly understood in subtropical aquaculture. This study identified Acetobacteraceae, Lachnospiraceae, Prevotellaceae, and Muribaculaceae as key families associated with seasonal microbiome stability in <i>C. hongkongensis</i>, highlighting their potential contribution to community resilience. It further revealed that <i>Vibrio</i> species detection was negatively correlated with temperature. These findings advance our understanding of interactions between the oyster microbiome and the environment, and provide a theoretical basis for improving oyster health management and promoting sustainable aquaculture practices.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0105626"},"PeriodicalIF":4.2,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148878738","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":"From trees to graphs: rethinking phylogeny in microbiome prediction.","authors":"Qiao Yu, Defeng Bai, Yao Wang, Yong-Xin Liu","doi":"10.1128/aem.01432-26","DOIUrl":"https://doi.org/10.1128/aem.01432-26","url":null,"abstract":"<p><p>Microbiome prediction models overlook phylogeny or fail to preserve evolutionary structure. In a recent <i>Applied and Environmental Microbiology</i> article (B. Dong, B. Wang, J. Chen, X. Xu, and Z. Z. Xu, Appl Environ Microbiol 92:e00788-26, 2026, https://doi.org/10.1128/aem.00788-26), Dong et al. present PhyloGCNE, a graph-convolutional framework that addresses these limitations by preserving evolutionary topology and learning adaptive edge-aware signal propagation. This commentary evaluates whether and when phylogenetic information improves microbiome-based prediction and considers how biological relevance and transferability can be established across contexts.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0143226"},"PeriodicalIF":4.2,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148863536","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":"Spore-forming <i>Clostridia</i> as overlooked determinants of microbial risk in wastewater reuse systems.","authors":"Daniel N Miller, Lisa M Durso","doi":"10.1128/aem.01000-26","DOIUrl":"https://doi.org/10.1128/aem.01000-26","url":null,"abstract":"<p><p>Using treated municipal wastewater for crop irrigation is a key strategy to combat drought-induced water scarcity. However, current wastewater reclamation standards systematically underestimate risks from spore-forming pathogens. As highlighted in a recent minireview by A. Mrozinski, C. Le Maréchal, and E. Topp in <i>Applied and Environmental Microbiology</i> (92:e00173-26, 2026, https://doi.org/10.1128/aem.00173-26), <i>Clostridioides difficil</i>e and <i>Clostridium perfringens</i> survive conventional disinfection, persist indefinitely in agricultural soils, and harbor critical antibiotic resistance genes. To safeguard the food supply and protect public health, regulatory frameworks must shift from relying solely on standard vegetative bacterial indicators and include monitoring resilient, spore-forming pathogens.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0100026"},"PeriodicalIF":4.2,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148862798","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":"Genomic and physiological characterization of newly isolated nitrous oxide-reducing bacterium <i>Stutzerimonas frequens</i> strain E49 from landfill leachate-treating activated sludge.","authors":"Jameil Magomnang, Shohei Yasuda, Akihiko Terada","doi":"10.1128/aem.00743-26","DOIUrl":"https://doi.org/10.1128/aem.00743-26","url":null,"abstract":"<p><p>Nitrous oxide (N₂O) is a potent greenhouse gas and ozone-depleting substance, with a global warming potential 273 times greater than CO₂ over a 100-year horizon. Microbial reduction of N₂O to dinitrogen represents a key pathway for mitigating emissions under diverse environmental conditions. Here, we report the first comprehensive genomic and physiological characterization of <i>Stutzerimonas frequens</i> strain E49, a newly isolated N₂O-reducing bacterium obtained from activated sludge treating landfill leachate. Whole-genome sequencing revealed a 4.51-Mbp circular chromosome and a 35.3-kbp plasmid with high completeness. Functional annotation identified a complete denitrification gene set, including <i>nosZ</i>, as well as the <i>ectABCD</i>-ask gene cluster associated with ectoine biosynthesis, suggesting adaptation to osmotic stress. Strain E49, a uniform rod-shaped bacterium (1.5-2.5 μm), efficiently reduced N₂O under anaerobic conditions in the absence of an externally supplied organic carbon source, achieving a biomass-specific rate of 0.70 ± 0.02 µmol-N₂O/mg-biomass/h and a cell-specific rate of 7.93 ± 0.23 × 10^-10 µmol-N₂O/cell/h. Among the cultivation regimens tested, nitrate-free DSMZ 1180 medium supplemented with NH₄Cl yielded the highest activity, indicating medium-dependent regulation of N₂O respiration. Comparative analysis showed that strain E49 outperformed several reported N₂O-reducing isolates under carbon-limited conditions. These findings demonstrate the metabolic versatility of strain E49 and highlight its potential role as a biological sink for N₂O in low-nutrient environments.IMPORTANCENitrous oxide is a powerful greenhouse gas that contributes to climate change and ozone depletion. Microorganisms that convert nitrous oxide into nitrogen gas play an essential role in reducing these emissions. In this study, we investigated <i>Stutzerimonas frequens</i> strain E49, a bacterium isolated from wastewater treatment sludge. We found that this organism can efficiently reduce nitrous oxide even without an external supply of organic carbon, which is typically required by most bacteria. This suggests that the bacterium can rely on internal energy reserves to carry out this process. We also identified the genetic basis for its nitrous oxide reduction and its ability to adapt to environmental stress. These findings improve our understanding of how nitrous oxide-reducing bacteria function in nutrient-limited environments and may support the development of strategies to mitigate emissions in wastewater treatment and other engineered systems.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0074326"},"PeriodicalIF":4.2,"publicationDate":"2026-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148863531","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}