Applied and Environmental Microbiology最新文献

{"title":"Revisiting the dihaloelimination potential of <i>Dehalococcoides</i> revealed by genomic and proteomic analyses.","authors":"Xiaocui Li, Hongming Cai, Hongyan Wang, Jiubin Chen, Tong Zhang, Haiwei Wei, Lian Yu, Zongming Xiu, Jun Yan, Yi Yang","doi":"10.1128/aem.00209-26","DOIUrl":"https://doi.org/10.1128/aem.00209-26","url":null,"abstract":"<p><p><i>Dehalococcoides</i> (<i>Dhc</i>) has recently gained significant attention in microbial reductive dehalogenation due to its specialized ability to metabolize various halocarbons. While previous reports have documented <i>Dhc</i>-mediated dihaloelimination of 1,2-dichloroethane (1,2-DCA), 1,2-dichloropropane (1,2-DCP), and 1,2-dibromoethane, this study reveals an expansion of <i>Dhc</i>'s dihaloelimination substrate range. We successfully established PJ_DCA and PJ_TCA enrichment cultures from petroleum-contaminated soil, exhibiting dihaloelimination activity toward 1,1,2-trichloroethane (1,1,2-TCA), 1,2,3-trichloropropane (1,2,3-TCP), and 1,1,2,2-tetrachloroethane (1,1,2,2-TeCA)-substrates previously only known to be transformed by other organohalide-respiring bacteria (OHRB). Amplicon sequencing revealed the predominance of <i>Dhc</i> as the primary OHRB within the PJ_DCA and PJ_TCA cultures, leading to the identification of two novel <i>Dhc</i> populations, designated as strains PJ_DCA and PJ_TCA, respectively. These strains showed robust growth yields of 4.1 ± 0.4 × 10⁷ and 7.6 ± 0.4 × 10⁷ cells per μmol Cl^- released when using 1,2-DCA and 1,1,2-TCA as electron acceptors, respectively. Genomic analysis revealed a reductive dehalogenase (RDase) homologous to the characterized DcpA, an enzyme known for dihaloelimination activity. Proteomic studies confirmed the expression of this DcpA-like RDase during dihaloelimination of 1,2-DCA, 1,1,2-TCA, and 1,2-DCP. This work identifies <i>Dhc</i> strains that retain dihaloelimination activity toward classical substrates while expanding this capability to 1,1,2-TCA, 1,2,3-TCP, and 1,1,2,2-TeCA. The discovery of these versatile <i>Dhc</i> strains enhances our understanding of microbial dehalogenation potential across diverse geological settings and improves prospects for bioremediation of halogenated alkane contaminants.</p><p><strong>Importance: </strong>This study identifies <i>Dehalococcoides</i> strains capable of dihaloeliminating diverse chlorinated alkanes (1,1,2-TCA, 1,2,3-TCP, 1,1,2,2-TeCA), expanding their bioremediation potential. These compounds are persistent groundwater contaminants with high toxicity. The discovery of <i>Dhc</i> populations (PJ_DCA/PJ_TCA) with robust growth yields (10⁷ cells/μmol Cl^-) and broad substrate range offers new solutions for detoxifying complex halogenated pollutant mixtures. The identification and proteomic confirmation of DcpA-like RDases (DheA) provide the genetic and functional basis for this expanded dihaloelimination capacity. These findings advance strategies for <i>in situ</i> remediation of industrial sites contaminated with C₂-C₃ halocarbons, reducing ecological and human health risks.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0020926"},"PeriodicalIF":3.7,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147832717","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":"Polyacrylamide hydrogel-immobilized <i>Escherichia coli</i> cell lysate for efficient removal and reduction in transformability of extracellular antibiotic resistance genes in water.","authors":"Hua Li, Fangjuan Li, Yajie Shi, Xinxin Wang, Xiaomeng Wang, Guanyu Zheng, Lixiang Zhou, Barth F Smets","doi":"10.1128/aem.00253-26","DOIUrl":"https://doi.org/10.1128/aem.00253-26","url":null,"abstract":"<p><p>The dissemination of extracellular antibiotic resistance genes (eARGs) through horizontal gene transfer poses a serious threat to global water safety. While <i>Escherichia coli</i> MG1655 is known to employ intracellular nucleases to defend against foreign DNA, the potential of its cell lysate to enzymatically degrade plasmid-borne eARGs and disrupt their environmental propagation remains unexplored. This study demonstrated that <i>E. coli</i> MG1655 cell lysate can degrade the plasmid-borne <i>amp^R</i> gene by 99.9% within 48 h, and the maximum first-order degradation rate constant measured by long amplicon qPCR was 0.20 h^-1 at the selected dosage state. This degradation eliminated the ability of the plasmid pUC19 for transformation, reducing it to below detectable levels (<10^-6 transformants/recipients). The DNase I, produced by the chromosomal <i>endA</i> gene, was identified as the likely nuclease driving eARG cleavage. Environmental conditions critically modulated degradation efficiency: humic acid (50 mg/L) decreased the rate by 41.3%, while divalent cations (e.g., Mg²⁺) increased the rate by 1.65-fold. To transmit laboratory findings into real-world application, a polyacrylamide hydrogel-immobilized lysate (PAM-cell lysate) was engineered, which outperformed free lysate in treating plasmid-spiked real wastewater, sustaining 99.9% of <i>amp^R</i> removal across three treatment cycles. This research demonstrated that PAM-cell lysate, without genetic modification, can be a cost-effective and scalable solution for attenuating the spread of eARGs in water, advancing the development of complementary enzymatic strategies for sustainable water remediation.IMPORTANCEThe mitigation of extracellular antibiotic resistance genes (eARGs) is an urgent priority for controlling the spread of antibiotic resistance via natural transformation. Developing environmentally benign strategies to effectively degrade plasmid-borne eARGs and prevent their transformation is therefore essential. However, few studies have explored the potential of bacterial cell lysates retaining native nuclease activity for eARG removal. In this work, we demonstrate that a candidate <i>Escherichia coli</i> cell lysate can rapidly degrade the plasmid pUC19 carrying the <i>amp^R</i> gene, with DNase I identified as the primary degradative enzyme. Furthermore, we show that immobilized <i>E. coli</i> cell lysate can concurrently adsorb and enzymatically degrade eARGs, effectively suppressing horizontal gene transfer via transformation. These findings highlight a novel, cost-effective, and scalable biocatalytic strategy for controlling the dissemination of eARGs in water treatment and environmental systems.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0025326"},"PeriodicalIF":3.7,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147832687","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 nutritional link to antimicrobial resistance: iron scarcity promotes plasmid co-selection in <i>Escherichia coli</i>.","authors":"Minhyeok Cha, SeonWoo Kim, Jo Ann S Van Kessel, Bradd J Haley","doi":"10.1128/aem.01952-25","DOIUrl":"https://doi.org/10.1128/aem.01952-25","url":null,"abstract":"<p><p>Multidrug-resistant (MDR) <i>Escherichia coli</i> represents a larger fraction of the <i>E. coli</i> population in preweaned dairy calf feces compared to older postweaned calves and adult cows. Previous work demonstrated that the MDR genotype is strongly associated with iron-acquisition genes (<i>iucABCD-iutA</i> and <i>sitABCD</i>), which are primarily carried on IncFIB plasmids that frequently co-encode these systems with antimicrobial-resistance genes in bovine <i>E. coli</i>. We hypothesized that iron limitation in the preweaned calf gut favors <i>E. coli</i> carrying these iron-acquisition systems, thereby indirectly selecting for antimicrobial resistance. To test this, we quantified growth by isothermal microcalorimetry in bovine cecal medium and used RT-qPCR to measure expression of iron-acquisition genes under iron-replete and iron-limited conditions. Under iron-replete conditions, plasmid carriage imposed a negligible fitness cost. Under iron limitation, IncFIB-positive strains generated up to 3.5-fold more cumulative heat and sustained metabolic activity 6-10 h longer than their plasmid-negative counterparts. This advantage corresponded to strong siderophore gene upregulation, with <i>iucA</i> expression increased by up to 38.4-fold. Multivariate analysis further distinguished plasmid-bearing from plasmid-free groups under iron stress. The results of this study demonstrate that plasmid maintenance costs are negligible in rich medium, and they are fully offset by the significant growth advantage conferred by iron-acquisition systems in iron-limited growth conditions. These findings suggest that gut iron availability contributes to the maintenance of antimicrobial resistance in young calves and highlight nutrition-based strategies as potential interventions to reduce antimicrobial resistance in these animals.IMPORTANCEThe preweaned calf gut is an iron-poor environment that favors <i>Escherichia coli</i> carrying IncFIB plasmids encoding both siderophore systems and antimicrobial resistance genes. Our findings show that these plasmids convert a potential liability, the cost of extra DNA, into a fitness advantage under iron limitation. This nutritional-genetic interaction explains why multidrug-resistant strains persist in young calves and suggests that dietary iron management could help reduce antimicrobial resistance in livestock, with implications for food safety and public health.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0195225"},"PeriodicalIF":3.7,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147832659","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":"Aromatic lactic acid production by <i>Bifidobacterium longum</i> subsp. <i>infantis</i> is determined by cell density, substrate availability, and pH <i>in vitro</i>.","authors":"Thilde Garbøl Plenge, Mikael Pedersen, Martin Frederik Laursen","doi":"10.1128/aem.02511-25","DOIUrl":"https://doi.org/10.1128/aem.02511-25","url":null,"abstract":"<p><p><i>Bifidobacterium longum</i> subsp. <i>infantis (B. infantis</i>) is an important colonizer of the infant gut. This species is known to produce a variety of health-beneficial metabolites, including aromatic lactic acids (ALAs), supporting early-life immune development. However, the regulation of ALA production in <i>B. infantis</i> remains poorly understood. In this study, we investigated how environmental factors, such as substrate availability and pH, affect <i>B. infantis</i> DSM20088 growth and ALA production <i>in vitro</i>. Bacterial batch cultivations supplemented with different amino acid concentrations revealed a linear relationship between indole-3-lactic acid (ILA), 4-hydroxyphenyllactic acid (OH-PLA), and phenyllactic acid (PLA) production, and exogenous concentrations of tryptophan, tyrosine, and phenylalanine, respectively. Furthermore, chemostat cultivations at physiologically relevant pH levels (4.5, 5.5, and 6.5) showed that an acidic pH slowed growth and shifted ALA production by <i>B. infantis</i>. Overall, ALA concentrations correlated strongly with bacterial abundance across and within pH levels, showing that cell density is a major determinant of ALA production. After considering the growth-limiting effects of lower environmental pH, it had a limited impact on the total production of ALAs, but the relative production of PLA was stepwise enhanced at more acidic pH at the expense of ILA, independent of cell density. In conclusion, this study shows that cell density, substrate availability, and environmental pH determine aromatic lactic acid production by <i>B. infantis</i>.IMPORTANCE<i>Bifidobacterium longum</i> subsp. <i>infantis</i> can be an abundant bacterial species in the infant gut microbiota, where it supports immune development, e.g., through the production of aromatic lactic acids. In this study, we cultured <i>Bifidobacterium longum</i> subsp. <i>infantis</i> at different concentrations of aromatic amino acids and pH levels to investigate the effect of these environmental factors on aromatic lactic acid production. We show that there is a linear relationship between aromatic lactic acid production and the exogenous aromatic amino acid concentration, that the production strongly follows cell density, and that pH regulates the preference toward producing different aromatic lactic acids. This knowledge may help inform strategies to enhance or direct beneficial aromatic lactic acid (ALA) production in the infant gut.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0251125"},"PeriodicalIF":3.7,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147832706","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":"Comparative genomic analysis of <i>Sinorhizobium meliloti</i> LPU88: plasmid diversity and conjugative mechanisms.","authors":"Constanza Rey, Andrés M Toscani, Juliet F Nilsson, Lucas G Castellani, Ramiro E Rocco Welsh, Abril Luchetti, Tobias Busche, Jörn Kalinowski, Gonzalo Torres Tejerizo, Mariano Pistorio","doi":"10.1128/aem.01996-25","DOIUrl":"https://doi.org/10.1128/aem.01996-25","url":null,"abstract":"<p><p>In this study, we present a comprehensive genomic and comparative analysis of <i>Sinorhizobium meliloti</i> strain LPU88, highlighting the structure, function, and evolutionary dynamics of its plasmids. The complete genome sequencing revealed five replicons: a chromosome, two megaplasmids (pSymA-like pSmeLPU88c and pSymB-like pSmeLPU88d), and two accessory plasmids (pSmeLPU88a and pSmeLPU88b). Furthermore, the genome of LPU88 harbored a rich repertoire of mobile genetic elements, diverse replication modules, and unique gene clusters, reflecting its dynamic architecture. Strain LPU88 contained diverse conjugation systems distributed across its plasmids. Comparative analyses with other <i>S. meliloti</i> and <i>Sinorhizobium medicae</i> strains demonstrated the heterogeneous distribution of conjugative and regulatory elements, indicating variable evolutionary pressures among these plasmids. Besides, the mobilization of the pSymA-like plasmid pSmeLPU88c was mediated by a mating pair formation system encoded on the accessory plasmid pSmeLPU88a, reflecting the intricate mechanisms and evolutionary dynamics of horizontal gene transfer mediated by plasmids in <i>Sinorhizobium</i>. By integrating genomic sequencing, functional annotation, and comparative approaches, this work establishes LPU88 as a valuable model strain for understanding plasmid diversity, horizontal gene transfer, and symbiotic efficiency in rhizobia.</p><p><strong>Importance: </strong>Rhizobia are soil bacteria that establish symbiotic associations with legumes, converting atmospheric nitrogen into ammonia through biological nitrogen fixation, while the host provides nutrients. Among them, <i>Sinorhizobium meliloti</i> is one of the best-studied species. In this work, we compared the complete genomes of <i>S. meliloti</i> strains, including the laboratory model strain LPU88, with a particular focus on pSymA plasmids. Previous studies proposed that the pSymA plasmid could have been acquired through horizontal gene transfer. Analysis of their conjugation machinery revealed that all pSymA plasmids harbor a type II conjugation system, although in many cases the regulatory circuit required for activation was absent. In LPU88, we identified and characterized multiple conjugation systems, offering new insights into horizontal gene transfer in <i>S. meliloti</i>. Understanding these processes is essential for clarifying rhizobial evolutionary dynamics, improving the stability and efficiency of symbiotic interactions, and promoting their use as bioinoculants in sustainable agriculture.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0199625"},"PeriodicalIF":3.7,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147832666","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 freeze-thaw drives arsenic metabolism dynamics in sediments of a cold-region lake: microbial gene and community responses.","authors":"Wenjing Shi, Haoran Xu, Weiping Li, Jin Xu, Yan Qin, Long Bai","doi":"10.1128/aem.00485-26","DOIUrl":"https://doi.org/10.1128/aem.00485-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Seasonal freeze-thaw process critically regulates arsenic (As)-metabolizing microorganisms (AMMs) in lake sediments through redox-nutrient dynamics. However, the current understanding of microbially mediated As transformation and mobilization processes under freeze-thaw dynamics remains poorly constrained. This study systematically investigated the successional patterns and driving mechanisms of As-metabolizing functional genes and microbial community structures of AMMs in lake sediments during the freeze-thaw process. This study focused on Lake Wuliangsuhai-a typical mid-high latitude lake in northern China-and employed an integrated framework of co-occurrence networks, Mantel tests, and correlation heatmaps. The results revealed that freeze-thaw processes drive significant AMMs restructuring, altering taxonomic composition and functional gene expression while controlling As environmental fate through regulating microbial metabolic functions, altering redox regimes, and restructuring community interaction networks. Co-occurrence network revealed stage-specific restructuring of microbial interactions during freeze-thaw process: robust mutualism established foundational networks during the pre-freezing stage; simplified modularity reflected functional differentiation during the ice-covered period; post-thaw modularity increased during structural reorganization; and synergistic complexity characterized adaptive strategies during the open-water period. Integrated results from Mantel tests and correlation heatmaps identified total nitrogen (TN), total phosphorus (TP), Fe(II), As(III), and As(V) as key succession drivers, with stage-dependent influences on AMMs. This work elucidates fundamental regulatory mechanisms through which seasonal freeze-thaw processes govern As-metabolizing gene dynamics and microbial ecological functions in lake sediments. It further highlights how microbially driven As transformations exacerbate sedimentary contamination risks under climate change, providing critical theoretical foundations for regional water management and pollution mitigation strategies.IMPORTANCESeasonal freeze-thaw processes in cold lakes dramatically control arsenic pollution risks, but how microbes drive this process remains a critical knowledge gap. This study reveals how winter ice cover and spring thaw create \"hot moments\" for toxic arsenic release by activating specialized sediment microbes, necessitating stage-specific water quality management. Crucially, nutrient loading (total nitrogen/total phosphorus) exacerbates arsenic (As) transformations by stimulating functional gene expression and microbial interactions. As climate change shortens ice seasons, these contamination pulses may become more frequent and severe. By identifying key microbial indicators and high-risk transition periods, our findings empower lake managers to predict arsenic hazards. This science is vital for safeguarding freshwater ecosystems and human health across ice-af","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0048526"},"PeriodicalIF":3.7,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147832736","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":"Enhanced bacterial cellulose production from spent coffee grounds: a dual-strategy synergy via mannose metabolism and pellicle inoculation.","authors":"Fan Yang, Ahmed K Saleh, Lin Chen, Zhangjun Cao, Xingping Zhou, Feng F Hong","doi":"10.1128/aem.02439-25","DOIUrl":"https://doi.org/10.1128/aem.02439-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Mannose constitutes a principal component in numerous biomass hemicelluloses; however, its utilization by the cellulose-producing bacterium &lt;i&gt;Komagataeibacter xylinus&lt;/i&gt; is inefficient. Consequently, during biorefinery and the transformation of biomass rich in mannose for the production of the high-value biological product, bacterial cellulose (BC), the biomass components cannot be fully utilized, leading to resource wastage. Moreover, inappropriate discharge of the fermentation effluent may also result in environmental pollution. This study addressed the underutilization of mannose in spent coffee grounds (SCGs) by introducing a fusion vector expressing mannokinase and phosphomannose isomerase into &lt;i&gt;K. xylinus&lt;/i&gt; ATCC 23770, thereby enhancing mannose utilization in this strain model. SCG was pretreated with concentrated sulfuric acid to disrupt crystalline structures, followed by enzymatic hydrolysis to extract saccharides. When culturing in SCG hydrolysate, BC pellicle-derived inoculum achieved 1.2-fold higher BC yield than broth inoculum, attributed to BC matrix protection. The engineered strain &lt;i&gt;K. xylinus&lt;/i&gt; CGMCC 31806 demonstrated superior mannose assimilation, yielding 1.5-fold more BC than wild type in simulated SCG medium. In authentic SCG medium without extra nitrogen addition, BC production reached 3.80 g/L, a 1.2- to 2.5-fold increase. The obtained BC exhibited enhanced mechanical properties with 40-84% higher tensile strength and 20-75% increased Young's modulus. This study validates a dual strategy combining agro-waste valorization and targeted strain modification, establishing a collaborative optimization framework linking biomass feedstocks, microbial engineering, and bioprocessing for cost-effective BC production. Future research would utilize existing commercial high-yield strains to replicate the expression strategy of this fusion protein, in order to achieve truly efficient industrial production.IMPORTANCEThe inefficient utilization of mannose, a major hemicellulose component prevalent in biomass by &lt;i&gt;Komagataeibacter xylinus&lt;/i&gt; represents a significant bottleneck in the sustainable, cost-effective bioproduction of bacterial cellulose (BC). This underutilization would lead to wasted resources and potential environmental pollution from fermentation effluents. The study directly addresses this critical challenge by pioneering a synergistic \"Feedstock-Strain-Process\" integration strategy in advancing BC industrialization. We demonstrate the significant impact of engineering &lt;i&gt;K. xylinus&lt;/i&gt; for enhanced mannose assimilation coupled with optimized biorefinery of agro-industrial waste, taking mannose-rich spent coffee grounds, as the representative raw material. This integrated approach not only valorizes abundant agricultural waste streams significantly boosting BC yields under nutrient-limited conditions but also generates BC with superior mechanical properties. The study establishes an actionable blueprint for ","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0243925"},"PeriodicalIF":3.7,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147832685","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":"Variations in cow milk and teat skin microbiota across the lactation cycle with intramammary cephalosporin use at dry-off.","authors":"Wannes Van Beeck, Mateus L P Lemos, Ashley M Niesen, Peter Finnegan, Taylor M Shih, Anhha Ho, Heidi A Rossow, Maria L Marco","doi":"10.1128/aem.02312-25","DOIUrl":"https://doi.org/10.1128/aem.02312-25","url":null,"abstract":"<p><p>Cephalosporins and other broad-spectrum antibiotics are frequently administered prophylactically into the udder when dairy cows end their lactation cycle, termed dry-off, to reduce mastitis risk. However, the use of antibiotics on cows that do not have signs of infection may result in the selection of antibiotic-resistant microorganisms and negatively alter the udder microbiome. In this study, the effects of intramammary cephalosporin therapy with Cephapirin (CB) or Ceftiofur (CH) on milk and teat skin microbiota were examined for three dairies in California. Intramammary injections were given to healthy cows with high somatic cell counts (>200,000 cells/mL), indicative of infection. Samples were collected at dry-off (before treatment), 7 days later, and 55-75 days in milk (DIM) in the next lactation cycle. Dairy (milk: <i>R</i>² = 6.22, skin: <i>R</i>² = 7.56) and day of sampling (milk: <i>R</i>² = 4.74 and skin: <i>R</i>² = 3.77) had the highest impact on the milk and skin microbiota. CB or CH use was associated with a small but significant impact on milk microbiota beta-diversity (Bray-Curtis, <i>P</i> =0.003, <i>R</i>² = 1.4%), but no effect was observed on the skin. At one dairy (Dairy 3), milk from cows receiving CB and CH had reduced proportions of <i>Staphylococcaceae</i> at 55-75 DIM compared to untreated cows. Overall, antibiotic use did not result in large significant (beneficial or harmful) changes in bacterial diversity in milk or on the teat skin; instead, the microbiota differences were mainly influenced by the time and location of sampling.IMPORTANCEThe use of antibiotics in agriculture is under increasing scrutiny due to the rising spread of antimicrobial-resistant bacteria. Our study showed that common preventative antibiotic intramammary treatment of cows with cephalosporins at the end of their lactation (dry-off) had minimal effects on the milk and teat skin microbiota of asymptomatic cows with high somatic cell counts.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0231225"},"PeriodicalIF":3.7,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147832697","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":"Intrinsic temporal structure and lagged environmental effects shape the dynamics of airborne microscopic eukaryotes.","authors":"So-Yeon Jeong, Chi Won Lee, Tae Gwan Kim","doi":"10.1128/aem.00286-26","DOIUrl":"https://doi.org/10.1128/aem.00286-26","url":null,"abstract":"<p><p>Airborne microscopic eukaryotes play important ecological roles, yet their temporal dynamics often appear stochastic and difficult to predict using concurrent meteorological variables. We conducted a high-resolution, 3-year survey of airborne fungi, protists, and metazoa in a temperate urban environment using quantitative PCR and amplicon sequencing. Seasonality varied markedly among groups: fungi and metazoa exhibited distinct annual cycles (peaking in late summer and winter, respectively), while protists displayed stochastic fluctuations. Taxonomically, fungi were dominated by soil- and plant-associated taxa (e.g., <i>Cladosporium</i>), protists by aquatic and terrestrial taxa (e.g., <i>Phytophthora</i>), and metazoa by DNA from mammals and insects. Static (i.e., contemporaneous, non-time lagged) analyses based on correlation and multiple linear regression identified concurrent environmental associations but explained only a limited proportion of the variance (28%, 6%, and 14% for fungi, protists, and metazoa, respectively). In contrast, incorporating time-lagged effects using Granger causality and autoregressive integrated moving average with exogenous variables (ARIMAX) substantially improved explanatory power, accounting for up to 47% of the variance for fungi and ~29% for protists and metazoa. These improvements primarily reflected intrinsic temporal dependence, indicating that antecedent biological states and prior environmental conditions contributed to eukaryotic abundances. Our results suggest that relying solely on concurrent meteorology is insufficient, whereas integrating temporal dependence and lagged environmental effects provides a robust framework for predicting airborne eukaryotic dynamics.IMPORTANCEAirborne microscopic eukaryotes influence ecosystems, agriculture, and human health, yet their temporal behavior in the atmosphere remains poorly understood and difficult to predict. Using a 3-year, high-resolution survey, this study shows that different airborne eukaryotic groups follow fundamentally different temporal rules. Airborne fungi, dominated by plant- and soil-associated taxa such as <i>Cladosporium</i>, and animal-derived metazoan material exhibit clear and contrasting seasonal cycles, whereas protists, including the plant pathogen <i>Phytophthora</i>, fluctuate irregularly. Importantly, models based only on current weather conditions explain little of this variability. By incorporating biological memory and delayed environmental effects, time-series models substantially improve predictability across all groups. These findings demonstrate that airborne eukaryotes respond not only to present conditions but also to prior environmental states, providing a more realistic framework for forecasting bioaerosols relevant to ecosystem connectivity, plant disease spread, and air-quality risk assessment.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0028626"},"PeriodicalIF":3.7,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147832652","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 characterization of avian pathogenic <i>Escherichia coli</i> and its potential as a marker organism for antimicrobial resistance.","authors":"Pankaj Prakash Gaonkar, Reed Golden, Alinne L R Santana-Pereira, Alyssa Lambert, Courtney Higgins, Yagya Adhikari, Matthew Bailey, Kenneth Macklin, Laura Huber","doi":"10.1128/aem.02244-25","DOIUrl":"https://doi.org/10.1128/aem.02244-25","url":null,"abstract":"<p><p>Avian pathogenic <i>Escherichia coli</i> (APEC) poses a threat to poultry and public health due to its ability to cause avian disease, potentially contribute to foodborne illness, and carry antimicrobial resistance genes (ARGs). Given its ubiquitous nature and capacity to persist in diverse environments, APEC has potential as a marker organism for tracking antimicrobial resistance (AMR) in poultry production systems and surrounding environments. This study investigated the prevalence, genotypic diversity, AMR profile, and potential transmission of APEC across different production stages in commercial, vertically integrated broiler operations. APEC isolates were recovered from environmental samples across the production chain, including pullet, breeder, and broiler farms as well as processing plants. <i>E. coli</i> isolates were classified as APEC if carrying three or more out of five virulence genes. Whole genome sequencing was conducted on 42 APECs. We determined their serotypes, phylogroups, sequence types (ST), and AMR profiles and constructed a single-nucleotide polymorphism (SNP)-based phylogenetic tree. High-risk APEC strains were detected, with ST131 recovered at the post-chill stage, raising food safety concerns. All isolates shared a core resistome, while several ARGs were differently distributed across sample types. SNP analysis revealed genetically closely related APEC strains inside the poultry house and the adjacent outside environment, and critically, between broiler litter and carcass rinses collected at the processing plant that processed the same flock. We demonstrate APEC carrying clinically relevant ARGs spread within farm environment and along the production chain, supporting its utility for AMR surveillance.IMPORTANCEAvian pathogenic <i>Escherichia coli</i> (APEC) is a threat to poultry production and public health due to its ability to cause avian disease, economic losses, potential foodborne implications, and ability to carry antimicrobial resistance genes (ARGs) relevant to human health. In this study, we proposed APEC as a potential marker organism of antimicrobial resistance (AMR) due to its capacity to persist in diverse environments. Our findings show that APEC, across the vertically integrated poultry production chain, harbored clinically important ARGs and exhibited resistance to antimicrobials of human health importance. We also identified evidence of APEC transmission within the farm environment and into the processing plant, with the potential to reach consumers. By examining multiple stages of production and diverse environmental samples, our study provides a more comprehensive understanding of APEC ecology, its resistome, and dissemination. These insights highlight APEC's utility as a marker organism for AMR surveillance in poultry production.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0224425"},"PeriodicalIF":3.7,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147810000","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}