Applied and Environmental Microbiology最新文献

{"title":"Compartment-specific microbial communities highlight the ecological roles of fungi in a subtropical seagrass ecosystem.","authors":"Xiao Wang, Jiawei Chen, Sangwook Lee, Zhicheng Ju, Anirban Akhand, Hongbin Liu","doi":"10.1128/aem.00606-25","DOIUrl":"https://doi.org/10.1128/aem.00606-25","url":null,"abstract":"<p><p>Plant-associated compartments provide habitats for various microbes. Seagrasses are the only submerged marine angiosperms. However, the simultaneous investigation of fungi and prokaryotes inhabiting different seagrass-associated compartments is limited, and much remains to be learned about the functional roles of seagrass fungi. We examined the diversity, composition, and networks of fungal and prokaryotic communities in multiple compartments associated with the seagrass <i>Halophila ovalis</i> to shed light on the significance of fungi in the seagrass ecosystem. Seagrass compartments primarily differentiated the microbial communities. Notably, the root and rhizome tissues of visually healthy <i>H. ovalis</i> exhibited a very narrow, single-species dominated and enriched fungal spectrum, leading us to hypothesize the possible establishment of a symbiotic relationship between the Lulworthiaceae mycobiont, <i>Halophilomyces hongkongensis</i>, and the seagrass host. In addition, the Vibrionaceae family, represented by the genus <i>Vibrio</i>, emerged as the most abundant prokaryotic taxon enriched in the roots/rhizomes, showing exclusive positive correlations with <i>H. hongkongensis</i> within the tissues, implying a cross-kingdom reciprocal interaction between these taxa in the endosphere of <i>H. ovalis</i>. Fungal-prokaryotic interdomain network analysis identified <i>H. hongkongensis</i> as a keystone taxon, essential for coordinating microbial interactions in <i>H. ovalis</i>-associated compartments, while robustness analysis of interdomain networks suggested fungi plays a more crucial role in sustaining the network structures of <i>H. ovalis</i> inner tissues compared to surrounding compartments. These findings provide valuable insights into the seagrass-fungi relationship and emphasize the importance of fungi in the seagrass ecosystem.IMPORTANCEAlthough plant-associated microbes are key determinants of plant health, fitness, and stress resilience, microbial communities associated with seagrasses remain poorly understood compared to those in land plants, particularly concerning the diversity and ecological roles of their fungal associates. Our work provides a comprehensive assessment of fungal and prokaryotic communities across multiple above- and below-ground compartments associated with <i>Halophila ovalis</i>, the most widespread seagrass species in Hong Kong, through a year-round sampling. Our findings reveal compartment-specific patterns in diversity, network topology, and stability of microbial communities, highlighting the critical roles of fungi in seagrass-associated microbial networks and advancing our understanding of plant-fungal interactions in the marine environment.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0060625"},"PeriodicalIF":3.9,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537835","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":"Salinity-driven shifts in estuarine viral community composition and diversity near the Shenzhen coast.","authors":"Sarfraz Hussain, Xiaomeng Wang, Cong Pan, Songze Chen, Jiajia Xie, Nazia Mahtab, Shengwei Hou, Shuangfei Li","doi":"10.1128/aem.00407-25","DOIUrl":"https://doi.org/10.1128/aem.00407-25","url":null,"abstract":"<p><p>Estuarine viral communities play a key role in microbial dynamics and ecosystem functioning. However, how viruses adapt to the highly dynamic estuarine environments remains largely underexplored. This study uses viromic sequencing to investigate the DNA viruses in estuarine water samples adjacent to the Shenzhen coast. Samples were divided into two major groups based on variations in quantified water parameters, corresponding to low-salinity and high-salinity waters. A total of 16,497 viral operational taxonomic units (vOTUs) were recovered, of which 85.59% were identified as novel viruses. β-diversity of viral communities supported the partition of samples based on salinity, and viral α-diversity differed significantly between low and high salinity. Taxonomically, Caudoviricetes dominated across all sites, with Myoviridae and Podoviridae more abundant in low salinity sites and Siphoviridae and Baculoviridae more abundant in high salinity sites. Gammaproteobacteria and Bacteroidota were the dominant host taxa, with distinct shifts in host abundance across the salinity gradient. Functional analysis revealed the abundant auxiliary metabolic genes involved in lipid, nucleotide, cofactor, and polysaccharide metabolisms. In particular, the alginate-degrading polysaccharide lyase family 6 was particularly abundant at high salinity sites. These results suggested that environmental factors, particularly salinity, shape the genomic diversity of estuarine viruses, which may further impact the biogeochemical processes in estuarine ecosystems.IMPORTANCEEstuaries are highly dynamic ecosystems with strong environmental fluctuations, particularly in salinity and nutrients. This study highlights how environmental factors shape viral diversity and function by examining viral populations across the salinity gradient, providing new insights into viral dynamics in these ecosystems. We identified novel viruses and viral-encoded auxiliary metabolic genes in estuarine samples, including the discovery of a previously unreported viral alginate lyase gene that was abundant at high salinity sites, which sheds light on the ecological role of viruses in nutrient cycling and ecosystem partition. In addition, the study provides valuable information on distinct viral populations and virus-host interactions across the salinity gradient, which are essential for predicting ecosystem responses to salinity changes. These findings provide important implications for a broader understanding of microbial and viral ecology in estuarine ecosystems.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0040725"},"PeriodicalIF":3.9,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537837","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":"Hospital wastewater surveillance for SARS-CoV-2 identifies intra-hospital dynamics of viral transmission and evolution.","authors":"Medini K Annavajhala, Anne L Kelley, Lingsheng Wen, Maya Tagliavia, Sofia Z Moscovitz, Heekuk Park, Simian Huang, Jason E Zucker, Anne-Catrin Uhlemann","doi":"10.1128/aem.00501-25","DOIUrl":"https://doi.org/10.1128/aem.00501-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Wastewater testing has emerged as an effective, widely used tool for population-level severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surveillance. Such efforts have been implemented primarily at wastewater treatment plants, providing data for large resident populations but hindering the ability to implement targeted interventions or follow-ups. Conversely, building-level wastewater data exhibit increased variability due to rapid daily population dynamics but allow for targeted follow-up or mitigation efforts. Here, we implemented a three-site wastewater sampling strategy on our university-affiliated medical campus from May 2021 to March 2024, comprised of two distinct hospital quadrants and a building primarily consisting of research laboratories and classrooms. We first addressed several limitations in implementing hospital-level wastewater surveillance by optimizing sampling frequency and laboratory techniques. We subsequently improved our ability to model SARS-CoV-2 case counts using wastewater data by performing sensitivity analyses on viral shedding assumptions and testing the utility of internal normalization factors for population size. Our unique infrastructure allowed us to detect intra-hospital dynamics of SARS-CoV-2 prevalence and diversity and confirmed that direct sequencing of wastewater was able to capture corresponding clinical viral diversity. In contrast, research building wastewater sampling showed that for most non-residential settings, despite low overall viral loads, a threshold approach can still be used to identify peaks in cases or transmission among the general population. Our study expands on current wastewater surveillance practices by examining the utility of, and best practices for, upstream and particularly hospital settings, enabling the use of non-municipal, medium-scale wastewater testing to inform efforts for reducing the burden of coronavirus disease 2019 (COVID-19).IMPORTANCESince the onset of the coronavirus disease 2019 (COVID-19) pandemic, wastewater surveillance has been increasingly implemented to track the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Most wastewater testing across the United States occurs at municipal wastewater treatment plants. Yet, this testing method could also be beneficial at non-municipal and non-residential sites, including hospitals, where wastewater data for SARS-CoV-2 signals and viral diversity could directly impact hospital practices to control its spread. We analyzed both hospital and non-residential research building wastewater over a 3-year period to establish optimized methods for collecting and interpreting wastewater data at sites upstream of treatment plants. We found that even within a single hospital building, wastewater testing in different locations showed distinct signatures over time, which corresponded with data from patients hospitalized in those locations. This study provides a framework for the use of wastewater","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0050125"},"PeriodicalIF":3.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537836","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":"Mechanistic study on the susceptibility of <i>Staphylococcus aureus</i> to common antimicrobial preservatives mediated by wall teichoic acids.","authors":"Xia Wu, Jiayi Wang, Ji Li, Zheng Su, Jian Zha","doi":"10.1128/aem.01023-25","DOIUrl":"https://doi.org/10.1128/aem.01023-25","url":null,"abstract":"<p><p><i>Staphylococcus aureus</i> is a common food-borne pathogen that easily develops resistance to antibiotics and antimicrobial peptides partly because of wall teichoic acids (WTAs), the peptidoglycan-anchored polymers important for cell physiology. In the food industry, there is an increasing prevalence of <i>S. aureus</i> despite the widespread use of antimicrobial preservatives, and it remains elusive how WTAs affect the susceptibility of <i>S. aureus</i> to these preservatives. In this study, we first identified that the presence of WTAs altered <i>S. aureus</i> sensitivity to tea polyphenol, sodium dehydroacetate, and ε-polylysine after screening 14 frequently used antimicrobial food preservatives. Then, via a series of genetic and biochemical analyses combined with molecular dynamics simulation, we revealed three WTA-related mechanisms adopted by <i>S. aureus</i> for self-protection against sodium dehydroacetate and ε-polylysine: (i) charge repulsion mediated by D-alanylation to reduce preservative packing around the cell; (ii) hydrogen bonding and hydrophobic interactions involving WTA backbone and glycosylation to maintain the preservatives in the WTA layer and to reduce their passage across the cell membrane; (iii) steric hindrance to reduce cell wall permeability and minimize the contact of these antimicrobials with the cell membrane. In comparison, the latter two mechanisms were involved in cell interaction with tea polyphenol. This work highlights the complex roles played by WTAs in cell response to antimicrobial preservatives and provides guidance to further study on <i>S. aureus</i> tolerance to food preservatives and better control over food safety.</p><p><strong>Importance: </strong><i>Staphylococcus aureus</i> is a disease-causing bacterium frequently detected in raw and packaged food that can be strongly insensitive to many bacteria-inhibiting or bacteria-killing agents. With the widespread use of antimicrobial food preservatives during food processing and packaging, there is a potential risk that these preservatives may force <i>S. aureus</i> to become less sensitive. Given that <i>S. aureus</i> tolerates many antimicrobial agents using mechanisms related to wall teichoic acids (WTAs), the negatively charged polymers that are anchored in the cell wall of this bacterium, it is necessary to evaluate whether <i>S. aureus</i> presents WTA-dependent sensitivity to antimicrobial food preservatives and how WTAs affect <i>S. aureus</i> interaction with these preservatives. Our study answered these questions for tea polyphenol, sodium dehydroacetate, and ε-polylysine and revealed three WTA-related mechanisms including charge repulsion, surface trapping, and decline in cell wall permeability. This work emphasizes the need for further control over food safety.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0102325"},"PeriodicalIF":3.9,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144526201","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":"Contrasting patterns in diversity and community assembly of bacterioplankton and three size fractions of protists in the South China Sea.","authors":"Xinyi Zheng, Xin Guo, Xiaoqing Lin, Lingfeng Huang","doi":"10.1128/aem.00436-25","DOIUrl":"https://doi.org/10.1128/aem.00436-25","url":null,"abstract":"<p><p>The microbial food web plays a critical role in marine ecosystems, composed of various cell sizes of microbial organisms. Here, high-throughput sequencing of the 16S and 18S rRNA genes was conducted to detect the community structure and distribution patterns of bacterioplankton (0.2 µm-2 µm) and three size fractions of protist communities, i.e., pico-protist (0.2 µm-2 µm), nano-protist (2 µm-20 µm), and micro-protist (20 µm-200 µm), in the euphotic zone of the South China Sea. The trophic mode compositions of protist communities varied significantly across three size fractions, characterized by a substantial prevalence of parasitic pico-protists (40% amplicon sequence variants) and a greater predominance of mixotrophic taxa within nano- and micro-protist communities. Furthermore, we detected stronger vertical stratification of bacterial and pico-protist communities, corresponding to the wider niche breadth of smaller cells and reliance on passive dispersal. Additionally, both bacterial and protist community assemblies were dominated by stochastic processes. The relative contribution of homogeneous selection in nano-protist community assembly was greater compared to other size fractions, probably related to high relative abundance of mixotrophs. In summary, our results suggest that both cell size and trophic mode affect marine microbial community assembly, and that neither the \"size-plasticity\" hypothesis nor the \"size-dispersal\" hypothesis fully matched microbial communities. Our analyses are important for a better understanding of the assemblage processes of marine epipelagic microbial communities and how they will respond to global change.IMPORTANCECell size is a key feature that influences microbial biology at both the cellular and community levels. Poorly understood is the extent to which diverse ecological factors influence the assembly of microbial communities of various sizes. Two important hypotheses addressing the mechanisms of biome assembly are \"size-plasticity\" and \"size-dispersal.\" Here, we investigated epipelagic microbial communities to reveal differences in the ecological functions of various microbial sizes, to explore the association of ecological processes with niche and cell size, and to expand the current understanding of marine microbial community assemblages and their possible responses to future global change.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0043625"},"PeriodicalIF":3.9,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144493691","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":"Evaluation of the efficient propagation of <i>Rhizophagus intraradices</i> and its inoculation effects on rice.","authors":"Feng Shi, Xinghao Wang, Xue He, Tianle Xu, Mingguo Jiang, Wei Chang, Fuqiang Song","doi":"10.1128/aem.00558-25","DOIUrl":"https://doi.org/10.1128/aem.00558-25","url":null,"abstract":"<p><p>Arbuscular mycorrhizal fungi (AMF) are a key group of fungi closely associated with agricultural production within soil microbial communities. However, large-scale propagation of AMF inoculum faces various challenges, limiting our ability to obtain and utilize these inocula on a broad scale. To address this, we designed a monolayer mesh cultivation system employing a hydroponic approach for propagating arbuscular mycorrhizal fungi, specifically <i>Rhizophagus intraradices</i>. We conducted a comparative analysis of quality and inoculation efficiency between the water culture inoculum (w-Ri) and traditional soil-based inoculum (s-Ri). Our findings revealed the following. (i) The propagation cycle of w-Ri inoculum is 35 days and only 23% of the 150-day cycle required for s-Ri inoculum. (ii) The spore density, viability, and purity of w-Ri inoculum are 5.25 times, 1.09 times, and 1.26 times higher, respectively, than those of s-Ri inoculum. (iii) The w-Ri inoculants demonstrate effects on enhancing rice biomass, root morphology, and photosynthesis that are consistent with those of the s-Ri inoculants, while requiring only 10% of the application rate of the s-Ri inoculants. These results provide crucial theoretical references for establishing a pure and efficient arbuscular mycorrhizal fungus propagation system and its promotion and application.IMPORTANCEThe development of a monolayer mesh hydroponic cultivation system for propagating <i>Rhizophagus intraradices</i> offers a significant advancement in overcoming the challenges of large-scale AMF inoculum production, which is critical for enhancing agricultural sustainability. The comparative analysis of water culture-based (w-Ri) and traditional soil-based (s-Ri) inoculum demonstrates the superior efficiency of the w-Ri system in terms of propagation speed, spore density, and inoculum quality, highlighting its potential for large-scale application in farming practices. The findings that w-Ri inoculants are equally effective in promoting plant growth while requiring only a fraction of the application rate of s-Ri inoculants underscore the potential for reducing both cost and environmental impact in agricultural inoculation practices.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0055825"},"PeriodicalIF":3.9,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473852","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":"Cross-feeding and co-degradation within a bacterial consortium dominated by challenging-to-culture <i>Leucobacter</i> sp. HA-1 enhances sulfonamide degradation.","authors":"Guoqiang Zhao, Houyu Yu, Juanjuan Wang, Bo Jiang, Fangya Zhong, Rui Zhang, Tianzhi Jiang, Mo Yang, Hui Wang, Xing Huang","doi":"10.1128/aem.00590-25","DOIUrl":"https://doi.org/10.1128/aem.00590-25","url":null,"abstract":"<p><p>The use of sulfonamides (SAs) leads to residual environmental pollution. Bacteria play a crucial role in the degradation of SAs, and microbial consortium offers advantages over single bacterium. However, the complexity of the degradation processes and interaction mechanisms within such consortia remains a mystery. Here, a consortium named ACJ, comprising <i>Leucobacter</i> sp. HA-1, <i>Bacillus</i> sp. HC-1, and <i>Gordonia</i> sp. HAEJ-1, isolated from activated sludge in the wastewater treatment facilities of pharmaceutical plants, was identified as capable of degrading various SAs. Here, a pure culture of <i>Leucobacter</i> sp. HA-1, which plays a key role in SAs degradation, was obtained with the auxotrophic requirements (ARs) provided by strains HC-1 and HAEJ-1. Strain HA-1 initiated the breakdown of SAs molecules, releasing heterocyclic structure products and trihydroxybenzene (HHQ), which were further degraded and used for growth by strain HAEJ-1. Genomic, transcriptomic, and metabolomic analyses indicated that genes related to nucleotide repair, ABC transporters, quorum sensing, the TCA cycle, and the cell cycle in strain HA-1 were upregulated during co-culture compared to cultures without the other two strains, which indicated that certain factors of strains HC-1 and HAEJ-1 activated the growth of strain HA-1. These results demonstrate a bidirectional ecological relationship of cross-feeding and co-degradation among the consortium members. Overall, this study provides new insights into the mechanisms of microbial interaction and co-degradation in sulfonamides-contaminated environments.IMPORTANCESulfonamides (SAs) are widely used antibiotics that have significantly harmed the ecological environment, emerging as a new environmental pollutant. Currently, limited research exists on the mechanisms of microbial consortium interaction and co-degradation of environmental pollutants. Addressing challenges in environmental pollutant degradation, this study isolated a bacterial consortium, ACJ, dominated by the challenging-to-culture <i>Leucobacter</i> sp. HA-1 from a sewage treatment plant and unveiled their interaction and co-degradation mechanisms during SAs degradation. Toxicological experiments demonstrated that the degradation of SAs by consortium ACJ substantially reduced environmental damage. These findings offer new insights into the collaborative mechanisms of the consortium of environmental pollutant-degrading microbial consortia and provide valuable microbial resources for the remediation of antibiotic-contaminated environments.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0059025"},"PeriodicalIF":3.9,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473850","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":"An antibiotic-free antimicrobial combination of bacteriocins and a peptidoglycan hydrolase: <i>in vitro</i> and <i>in vivo</i> assessment of its efficacy.","authors":"Christian Kranjec, Thomas F Oftedal, Kirill V Ovchinnikov, Vinícius da Silva Duarte, Simen Hermansen, Magdalena Kaus-Drobek, Izabela Sabała, Davide Porcellato, Harald Carlsen, Morten Kjos","doi":"10.1128/aem.02433-24","DOIUrl":"https://doi.org/10.1128/aem.02433-24","url":null,"abstract":"<p><p>Mastitis is an inflammatory disease of the mammary gland usually caused by bacterial pathogens that gain physical access to the glandular epithelium through the teat canal. In bovines, common mastitis-causing agents are environmental or pathogenic bacterial species, including staphylococci, streptococci, enterococci, and gram-negative bacteria such as <i>Escherichia coli</i>. Current therapeutic strategies for bovine mastitis typically involve the administration of antibiotic formulations into the infected udder, which can result in increased selection for antibiotic resistance and the accumulation of antibiotic residues in milk. In this study, we sought to develop an antibiotic-free antimicrobial formulation for the treatment of bovine mastitis based on bacterial antimicrobial peptides (bacteriocins) and proteins (peptidoglycan hydrolases). Using a combination of <i>in vitro</i> assays with a range of bacteriocins, we show that the combination of the thiopeptide micrococcin P1 (MP1) and the lantibiotic nisin A (NisA) is a robust antimicrobial formulation that effectively inhibits the growth of bovine mastitis-derived bacteria, both in planktonic and biofilm-associated growth modes. The addition of AuresinePlus (Aur, a staphylococcus-specific peptidoglycan hydrolase) further increased the antimicrobial potency against <i>S. aureus</i>. Furthermore, using two mouse models, a skin infection model and a mastitis model, we show that the combination MP1-NisA-Aur effectively inhibits methicillin-resistant <i>S. aureus in vivo</i>. We discuss the potential and challenges of using antibiotic-free antimicrobial combinations in the treatment of bacterial infections.IMPORTANCEThe spread of antibiotic resistance is a major global concern. This is reflected in the One Health concept, which is based on the premise that the spread of antibiotic resistance can only be addressed through coordinated efforts to promote \"healthy people, healthy environments, and healthy animals.\" It is therefore of great importance to reduce the use of medically important antibiotics in agriculture, where treatment of bovine mastitis is one of the major drivers of antibiotics use. In this work, we investigate the use of antimicrobial peptides and proteins as an alternative treatment for bovine mastitis pathogens.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0243324"},"PeriodicalIF":3.9,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473849","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":"Prolonged light exposure time enhances the photosynthetic investment in osmotrophic <i>Ochromonas</i>.","authors":"Xiaoqing Xu, Xiaoyu Cheng, Zhihao Shao, Zhou Yang, Lu Zhang","doi":"10.1128/aem.01032-25","DOIUrl":"https://doi.org/10.1128/aem.01032-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The photoperiod, as a critical external environmental signal, triggers a cascade of signaling responses in organisms that significantly affect photosynthetic efficiency and photomorphogenesis in autotrophs, while also influencing behavioral patterns and activity rhythms of heterotrophs. Despite its importance, the mechanisms by which mixotrophs respond to photoperiod changes remain largely unexplored. It is crucial for understanding metabolic plasticity how mixotrophs respond to light availability and make optimal decisions during diurnal transitions by regulating their autotrophic and osmotrophic pathways. Therefore, this study focused on &lt;i&gt;Ochromonas gloeopara&lt;/i&gt;, a eukaryotic protist capable of both photoautotrophic and osmotrophic growth, aiming to explore the metabolic strategies of mixotrophs in response to changes in photoperiod. The results showed the following. (i) Under autotrophic conditions, the optimal photoperiod for photosynthetic efficiency in &lt;i&gt;Ochromonas&lt;/i&gt; was approximately 12 h of light exposure, while prolonged light exposure beyond this duration reduced photosynthetic investment and efficiency, accompanied by an increase in heat dissipation to prevent photodamage. (ii) Under osmotrophic conditions, &lt;i&gt;O. gloeopara&lt;/i&gt; adapted to prolonged light exposure by reducing. The reliance on external organic carbon sources and enhancing photosynthetic capacity, thereby shifting towards a more autotrophic metabolic mode. This study systematically elucidates the nutritional strategies of mixotrophic &lt;i&gt;O. gloeopara&lt;/i&gt; in response to photoperiod changes at the levels of population dynamics, photosynthetic physiology, and carbon acquisition pathways, deepening our understanding of the response to photoperiodic changes in mixotrophs. These findings provide important theoretical insights for understanding the functional roles of mixotrophs in ecosystems and for accurately predicting changes in global carbon cycles.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Mixotrophs possess flexible metabolism modes and multiple ecological roles, making them sensitive to environmental changes. Due to their widespread distribution and unique nutritional strategy, they serve as key functional groups in marine and freshwater ecosystems, with significant roles in global biogeochemical cycles. Photoperiod, a critical environmental cue, regulates circadian rhythms and may influence the metabolic strategies of mixotrophs. Therefore, this study focused on how the mixotrophic microorganisms &lt;i&gt;Ochromonas gloeopara&lt;/i&gt; adjusted autotrophic and osmotrophic pathways in response to photoperiodic changes. These findings highlight the metabolic flexibility of mixotrophic organisms in response to photoperiodic changes, providing new insight on how mixotrophs regulate the flow of materials and reshape the food web structures. This research offers valuable and innovative perspectives for understanding the functional roles of mixotrophic microorganisms in ecosystems, wit","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0103225"},"PeriodicalIF":3.9,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473794","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":"Phenotypic analysis of various <i>Clostridioides difficile</i> ribotypes reveals consistency among core processes.","authors":"Merilyn A Beebe, Daniel Paredes-Sabja, Larry K Kociolek, César Rodríguez, Joseph A Sorg","doi":"10.1128/aem.00964-25","DOIUrl":"10.1128/aem.00964-25","url":null,"abstract":"<p><p><i>Clostridioides difficile</i> infections (CDI) cause almost 300,000 hospitalizations per year, of which ~15%-30% are the result of recurring infections. The prevalence and persistence of CDI in hospital settings have resulted in an extensive collection of <i>C. difficile</i> clinical isolates and their classification, typically by ribotype. While much of the current literature focuses on one or two prominent epidemic ribotypes (e.g., RT027), recent years have seen several other ribotypes dominate the clinical landscape (e.g., RT106 and RT078). Some ribotypes are associated with severe disease and/or increased recurrence rates, but why certain ribotypes are more prominent or harmful than others remains unknown. Because <i>C. difficile</i> has a large, open pan-genome, this observed relationship between ribotype and clinical outcome could be a result of the genetic diversity of <i>C. difficile</i>. Thus, we hypothesize that the core biological processes of <i>C. difficile</i> are conserved across ribotypes/clades. We tested this hypothesis by observing the growth kinetics, sporulation, germination, production of toxin A and toxin B, bile acid sensitivity, bile salt hydrolase activity, and surface motility of 15 strains belonging to various ribotypes spanning each known <i>C. difficile</i> clade. In viewing these phenotypes across each strain, we see that core phenotypes (growth, germination, sporulation, and resistance to bile salt toxicity) are remarkably consistent across clades/ribotypes. This suggests that variations observed in the clinical setting may be due to unidentified factors in the accessory genome or due to unknown host factors.IMPORTANCE<i>Clostridioides difficile</i> infections impact thousands of individuals every year, many of whom experience recurring infections. Clinical studies have reported an unexplained correlation between some clades/ribotypes of <i>C. difficile</i> and disease severity/recurrence. Here, we demonstrate that <i>C. difficile</i> strains across major clades/ribotypes are consistent in their core phenotypes. This suggests that such phenotypes are not responsible for variations in disease severity/recurrence and are ideal targets for the development of therapeutics meant to treat <i>C. difficile</i>-related infections.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0096425"},"PeriodicalIF":3.9,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473793","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}