Applied and Environmental Microbiology最新文献

{"title":"Surveillance of Japanese encephalitis virus in piggery effluent and environmental samples: a complementary tool for outbreak detection.","authors":"Warish Ahmed, Metasebia Gebrewold, David T Williams, Jianning Wang, Wendy J M Smith, Leah G Starick, Regina Fogarty, Kirsty Richards, Stuart L Simpson","doi":"10.1128/aem.00895-25","DOIUrl":"10.1128/aem.00895-25","url":null,"abstract":"<p><p>Japanese encephalitis virus (JEV) is an emerging public health and biosecurity concern in Australia, with recent human cases and detections in mosquitoes and pigs across multiple states highlighting the risk to susceptible human and animal populations. While traditional surveillance methods such as mosquito trapping, sentinel chicken programs, and direct testing of pig specimens remain essential, monitoring effluents offers a valuable complementary approach for detecting infections within livestock herds. This study presents the first evidence of JEV in Australian piggery effluents and environmental waters, demonstrating the feasibility of effluent and environmental water surveillance for JEV monitoring. Effluent and environmental samples from multiple piggery sites were analyzed using real-time reverse transcription polymerase chain reaction, revealing the presence of JEV genetic fragments in solid and liquid fractions of effluents at three farms, with corresponding veterinary cases in some herds. Viral RNA was detected more frequently in the solid fraction of effluent samples, aligning with previous findings on the partitioning behavior of mosquito-borne viruses. The detection of JEV in environmental water from an excavated area highlights the potential for transmission via mosquito vectors. These findings demonstrate the value of effluent monitoring as an additional tool for JEV surveillance in piggery settings, supporting potential early warning systems and mitigation strategies. Integrating effluent-based monitoring with traditional surveillance approaches could improve livestock-industry-related disease detection, risk assessments, and response efforts for human and animal health in both endemic regions and areas where livestock diseases are emerging. Wastewater and effluent surveillance may have important applications for the management of a wide range of emerging animal diseases.IMPORTANCEThis study presents the first evidence of JEV detection in Australian piggery effluents, establishing effluent surveillance as a valuable complementary tool for monitoring viral pathogens in animal herds. Our findings support the integration of effluent monitoring with traditional surveillance systems to improve early warning capabilities, enhance biosecurity, and mitigate risks to both human and animal health.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0089525"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442344/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144939248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regulation of iron homeostasis by Fur and atypical response regulator SsoR via derepressor-inhibitor oscillation in <i>Shewanella oneidensis</i>.","authors":"Kaiyue Jie, Xinyue Liu, Jiyuan Hou, Peilu Xie, Jiaxin Tang, Haichun Gao","doi":"10.1128/aem.01230-25","DOIUrl":"10.1128/aem.01230-25","url":null,"abstract":"<p><p>Iron is a vital cofactor for enzymes essential to many biological processes, yet in excess, it poses a danger to all living organisms. In order to ensure survival and proliferation under fluctuating environmental iron levels, bacteria evolve sophisticated regulatory systems to maintain iron homeostasis. Unlike master regulator Fur, a large portion of other players remains poorly defined. Here, we characterized the physiological impacts of atypical phosphorylation-independent response regulator SsoR of <i>Shewanella oneidensis</i>, a γ-proteobacterium renowned for metabolic versatility. By combining transcriptomics, proteomics, and transposon screening, we discovered that the SsoR loss impairs growth and decreases cytochrome <i>c</i> content under iron-limited conditions. Further investigations revealed that the defects can be attributed to lowered heme and iron levels, a consequence of elevated Fur production. Together, our findings suggest that SsoR and Fur constitute a derepressing-inhibiting oscillation system in maintaining iron homeostasis, providing a new composite view of regulator dynamics during the regulation of iron homeostasis in bacteria.IMPORTANCE<i>Shewanella</i> comprises a large group of bacteria that are ubiquitous, ecologically widespread, and metabolically versatile, having enormous potential in biotechnology, environmental remediation, and energy production. These characteristics and applications are crucially determined by a myriad of iron-containing proteins, whose activity depends on the intricate regulation of iron homeostasis. Our study reveals that a derepressing-inhibiting oscillation system composed of Fur and atypical phosphorylation-independent response regulator SsoR plays a key role in the regulation of iron homeostasis at the transcription level. The loss of either results in altered production of the other, leading to disruption of iron homeostasis, which is harmful to the cell, especially under iron-limited conditions. This study deepens our understanding of the interacting dynamics of multiple regulators in iron homeostasis.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0123025"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144939825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Testing the priming effect in the deep ocean: are microorganisms too starved to consume recalcitrant organic carbon?","authors":"Richard LaBrie, Corday R Selden, Nagissa Mahmoudi","doi":"10.1128/aem.01204-25","DOIUrl":"https://doi.org/10.1128/aem.01204-25","url":null,"abstract":"<p><p>Deep ocean dissolved organic carbon (DOC) is one of the largest pools of reduced carbon on Earth. Many DOC compounds escape microbial degradation and persist for thousands of years in the ocean. Although many hypotheses have been proposed, the mechanisms responsible for this long-term stability remain unresolved. Heterotrophic microorganisms in the deep ocean are energetically starved and exhibit low metabolic activity. Here, we investigated whether the severe energy limitation in deep-sea environments acts as a barrier to microbial degradation of DOC. We hypothesized that alleviating this energetic barrier through the addition of labile compounds (i.e., the priming effect) could stimulate microbial consumption of DOC. We conducted 62-day bottle incubations with deep seawater from the Southern Ocean that were amended with simple organic carbon, nitrogen, and/or phosphorus-containing compounds. We tracked DOC concentration, cell abundance, and microbial community structure over the course of the experiment. Our results show no evidence of a priming effect regardless of the priming compound. Interestingly, priming compounds were selected for distinct microbial populations even when the compounds were chemically similar. <i>Pseudoalteromonas</i> and <i>Pseudomonas</i> were enriched across all amended bottles, and their competition for labile substrates likely contributed to observed variations in DOC consumption. Our results suggest that the persistence of DOC is not driven by the energetic state of deep-sea microorganisms. These findings indicate that inputs of fresh carbon to the deep ocean are unlikely to trigger extensive degradation of the existing DOC pool, reinforcing its role as a stable long-term reservoir of carbon.IMPORTANCEThe oceans store vast amounts of dissolved organic carbon (DOC) that can resist microbial degradation for thousands of years. The mechanisms that underlie the long-term stability of DOC in the ocean are still debated. Microorganisms in this environment exhibit low metabolic activity and are energetically starved. We tested whether the microbial degradation of DOC could be stimulated through the addition of labile compounds. Surprisingly, alleviating energetic constraints did not stimulate the consumption of deep ocean DOC. Additionally, our results suggest that competition among taxa is an important constraint on dissolved organic carbon consumption, with implications for ecosystem processing. Our study suggests that the long-term stability of deep ocean DOC reflects inherent chemical or structural resistance to microbial degradation, rather than ecological or energetic constraints. This finding is also of consequence for ongoing geoengineering efforts that aim to remove atmospheric carbon by increasing carbon export to the deep sea.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0120425"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074398","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":"Potential of a constitutive-UPR and histone deacetylase A-deficient <i>Saccharomyces cerevisiae</i> strain for biomolecule production.","authors":"Yuki Ishiwata-Kimata, Phuong Thi Mai Nguyen, Maya Sugimoto, Yukio Kimata","doi":"10.1128/aem.00644-25","DOIUrl":"10.1128/aem.00644-25","url":null,"abstract":"<p><p>The endoplasmic reticulum (ER) is an organelle responsible for the production of secretory proteins and lipid molecules. In many ascomycetous yeasts, including <i>Saccharomyces cerevisiae</i>, <i>HAC1</i> mRNA undergoes splicing to yield <i>HAC1</i>i mRNA (\"i\" denotes induced), which is translated into the nuclear transcription factor Hac1 upon ER dysfunction. The extensive transcriptome change triggered by Hac1 is called the unfolded protein response (UPR), which leads to ER enforcement. As an unregulated UPR continuously elevates ER activity and size, <i>S. cerevisiae</i> cells exhibit increased production of secretory proteins and lipid molecules when Hac1 is constitutively and artificially expressed. While this technique holds promise for industrial bioproduction, it has a notable drawback, as cells strongly expressing Hac1 exhibit slow growth, making it difficult to handle and store them. To address this issue, in this study, we searched for fast-growing mutants of <i>HAC1</i>i cells carrying the <i>HAC1</i>i sequence at the <i>HAC1</i> locus to express Hac1 constitutively. We found that histone deacetylase A (HDA)-deficient mutations, including <i>Δhda3</i>, accelerated the growth of Hac1-expressing cells. Despite their increased growth rate, <i>Δhda3HAC1</i>i cells showed stronger expression of prominent UPR target genes related to ER function than <i>HAC1</i>i cells. Moreover, <i>Δhda3HAC1</i>i cells carried a structurally complex and expanded ER and exhibited high-yield production of triglycerides and of different heterologous model biomolecules, β-carotene and Taka amylase A. In conclusion, we propose that combining artificial Hac1 expression with mutations that affect the chromosomal status holds promise for optimizing yeast-based bioproduction systems.IMPORTANCEThe production of commercially valuable biomolecules using genetically modified <i>Saccharomyces cerevisiae</i> is an important biotechnological process that has been partly industrialized. Because secretory proteins and many lipid molecules are produced in and/or from the endoplasmic reticulum (ER), their production is expected to be improved by artificial enhancement of ER functions. This can be accomplished by artificial and constitutive expression of the nuclear transcription factor Hac1. In wild-type cells, Hac1 is induced upon ER dysfunction and upregulates its functions. A major drawback of cells artificially overexpressing Hac1 is their slow-growing phenotype. Here, we showed that the growth of artificially Hac1-expressing cells is fastened by histone deacetylase A-deficient mutations, leading to efficient biomolecule production. Our study provides an intriguing example of how the properties of a genetically modified yeast strain can be improved by a mutation that alters its chromosomal status.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0064425"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442391/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144793304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Long-term impacts of untreated dairy manure on the microbiome and Shiga toxin-producing <i>Escherichia coli</i> persistence in agricultural soil.","authors":"Taylor K S Richter, Michael Kauffman, Mark K Mammel, David W Lacher, Gireesh Rajashekara, Susan R Leonard","doi":"10.1128/aem.00447-25","DOIUrl":"10.1128/aem.00447-25","url":null,"abstract":"<p><p>Biological soil amendments of animal origin (BSAAO) improve the soil health of agricultural fields for plant growth. However, as natural reservoirs for bacterial foodborne pathogens, BSAAO application can introduce and support microbes of public health concern, such as pathogenic Shiga toxin-producing <i>Escherichia coli</i> (STEC), in agricultural soils. Using shotgun metagenomic sequencing, this project investigated the microbiome of soil with and without BSAAO, focusing on STEC and the <i>E. coli</i> population over time alongside changes in the soil microbiome and soil abiotic properties. Two farms in Ohio, one using an untreated dairy manure amendment and one that does not use a BSAAO, were sampled for over a year for metagenomic analysis of the soil microbiome. All manure samples were positive for <i>stx</i> genes, indicating the presence of STEC. Impacts of the manure on the soil lasted four weeks by several measures including higher <i>E. coli</i> diversity and more frequent STEC detection. Outside of these four weeks post-amendment, Shiga toxin genes (<i>stx</i>) were identified periodically in both fields throughout the year. STEC detection significantly correlated with higher <i>in silico E. coli</i> O-serogroup diversity, as well as lower soil cation exchange capacity and concentrations of calcium, magnesium, and organic nitrogen. Differential abundance analysis of the soil metagenomes identified several taxa influenced by amendment but did not identify taxa correlated with detection of <i>stx</i> genes. This work provides insights into the timing of and ecological factors associated with STEC persistence in the agricultural environment.IMPORTANCEShiga toxin-producing <i>E. coli</i> (STEC), including <i>E. coli</i> O157:H7, is a major etiological agent of foodborne human disease outbreaks associated with fresh produce and can be transferred to produce via contaminated agricultural soil. Given the devastating impacts of foodborne STEC outbreaks on public health and growers, it is necessary to understand the longevity of the impacts of manure application on the pathogen risk in the soil as well as better understand the ecological and environmental conditions that contribute to STEC survival in the agricultural soil environment. This work expands upon the knowledge of conditions that support STEC persistence in the produce-growing environment and its longevity following amendment in commercial fields with naturally occurring STEC contamination.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0044725"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442374/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144793303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Elucidating the metabolic pathway and initial degradation gene for <i>p</i>-chloro-<i>m</i>-xylenol biodegradation in <i>Rhodococcus pyridinivorans</i> DMU114.","authors":"Liang Zhao, Jia Shi, Jingwei Wang, Hao Zhou, Dan Xu, Qiao Ma","doi":"10.1128/aem.00984-25","DOIUrl":"10.1128/aem.00984-25","url":null,"abstract":"<p><p>The antimicrobial agent <i>p</i>-chloro-<i>m</i>-xylenol (PCMX), an emerging environmental pollutant, poses ecological risks; however, its biodegradation mechanisms remain unresolved. Here, we elucidate the metabolic pathway and functional genes involved in the initial catabolic step of PCMX in a newly isolated bacterium, <i>Rhodococcus pyridinivorans</i> DMU114. Pure-culture and synthetic consortium assays confirmed the pivotal role of <i>Rhodococcus</i> in PCMX degradation, despite its relatively low abundance in the PCMX-enriched consortium. Genomic analysis and heterologous expression identified a constitutively expressed flavin-dependent monooxygenase CxyAB as the key enzyme initiating PCMX degradation. High-resolution liquid chromatography-mass spectrometry and nuclear magnetic resonance analyses demonstrated that strain DMU114 degraded PCMX via a potential three-step pathway: <i>ortho</i>-hydroxylation to 4-chloro-3,5-dimethylcatechol, dechlorination to 2-hydroxy-3,5-dimethyl-[1,4]benzoquinone, and dual <i>meta</i>- and <i>ortho</i>-cleavage of the aromatic ring. Homologs of CxyA are phylogenetically widespread in environmentally relevant genera, including <i>Streptomyces</i>, <i>Pseudomonas</i>, <i>Klebsiella</i>, and <i>Rhodococcus</i>, indicating their potential role in natural PCMX attenuation. This work provides the first genetic dissection of PCMX mineralization, offering critical insights into its environmental fates and bioremediation strategies targeting antimicrobial contaminants.</p><p><strong>Importance: </strong>The widespread use of the antimicrobial agent <i>p</i>-chloro-<i>m</i>-xylenol (PCMX) in consumer products has raised environmental concerns due to its aquatic toxicity. However, the microbial mechanisms driving its natural breakdown remain poorly understood. This study reveals how a newly isolated bacterium, <i>Rhodococcus pyridinivorans</i> DMU114, mineralizes PCMX, a process critical for mitigating its ecological risks. This study, for the first time, elucidates the PCMX's complete degradation pathway and identifies the functional genes for its initial conversion step. The degradation gene identified is widespread in environmentally relevant bacteria, suggesting that natural ecosystems may already harbor the potential to neutralize PCMX contamination. These findings advance our ability to predict PCMX's environmental fate and provide a foundation for engineering microbial solutions to combat antimicrobial pollution.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0098425"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442393/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144871067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome evolution of <i>Acinetobacter baylyi</i> ADP1 during laboratory domestication: acquired mutations impact competence and metabolism.","authors":"Isaac Gifford, Meghna R Vergis, Jeffrey E Barrick","doi":"10.1128/aem.00936-25","DOIUrl":"10.1128/aem.00936-25","url":null,"abstract":"<p><p>The bacterium <i>Acinetobacter baylyi</i> is a model organism known for its extreme natural competence and metabolic versatility. It is capable of taking up environmental DNA at a high rate across all growth phases. The type strain ADP1 was created by random mutagenesis of a precursor strain, BD4, to prevent it from forming cell chains in culture. ADP1 has since been distributed between research groups over several decades and acquired subsequent mutations during this time. In this study, we compare the genome sequences of <i>A. baylyi</i> BD4 and its modern descendants to identify and understand the effects of mutations acquired and engineered during its domestication. We demonstrate that the ADP1 variants in use today differ in their competence, growth on different carbon sources, and autoaggregation. In addition, we link the global carbon storage regulator CsrA and a transposon insertion that removes its C-terminal domain specifically to changes in both overall competence and an almost complete loss of competence during the stationary phase. Reconstructing the history of ADP1 and the diversity that has evolved in the variants currently in use improves our understanding of the desirable properties of this experimentally and industrially important bacterium and suggests ways that its reliability can be improved through further genome engineering.IMPORTANCE<i>Acinetobacter baylyi</i> ADP1 is a bacterial chassis of interest to microbiologists in academia and industry due to its extreme natural competence and wide metabolic range. Its ability to take up DNA from its environment makes it straightforward to efficiently edit its chromosome. We identify and characterize mutations that have been passed down to modern strains of ADP1 from the initial work in the 1960s, as well as subsequent mutations and genome edits separating strains in use by different research groups today. These mutations, including one in a global regulator (CsrA), have significant phenotypic consequences that have affected the reproducibility and consistency of experiments reported in the literature. We link a mutation in this global regulator to unexpected changes in natural competence. We also show that domesticated <i>A. baylyi</i> strains have impaired growth on a variety of carbon sources.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0093625"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144871069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PlyCYU endolysin targeting <i>Streptococcus agalactiae</i> exhibits a CHAP activity and a glucosaminidase domain mediating multimerization.","authors":"Sakunrat Ubonprasert, Wachiraporn Wachiradusit, Wichai Pornthanakasem, Warangkhana Songsungthong, Aritsara Jaruwat, Sasina Premjaichon, Tanaporn Uengwetwanit, Rinrada Suntivich, Konrawee Thananon, Kanyarat Suksomjaisaman, Jeerus Sucharitakul, Chutathip Puyprom, Tamonwan Lotangchanintra, Kanokwan Salamteh, Kittikhun Wangkanont, Channarong Rodkhum, Wonnop Visessanguan, Pimchai Chaiyen, Penchit Chitnumsub, Ubolsree Leartsakulpanich","doi":"10.1128/aem.01872-24","DOIUrl":"10.1128/aem.01872-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Bacteriophage endolysins are attractive alternatives to antibiotics owing to their rapid action, host specificity, and unlikeliness of resistance development. Here, bioinformatic analysis of &lt;i&gt;Streptococcus suis&lt;/i&gt; prophage sequences identified an endolysin, named PlyCYU, containing two putative catalytic domains-an N-terminal amidase_5 and a C-terminal glucosaminidase (Lyz2) domain-with two CW_7 family cell wall binding motifs. PlyCYU exhibited bactericidal activity against &lt;i&gt;Streptococcus agalactiae&lt;/i&gt;, &lt;i&gt;Streptococcus dysgalactiae&lt;/i&gt;, and &lt;i&gt;Streptococcus uberis,&lt;/i&gt; with a minimum bactericidal concentration (MBC) range of 1.25 µM-40 µM, and retained bactericidal activity against &lt;i&gt;S. agalactiae&lt;/i&gt; serotype II in ultra-high-temperature-processed milk (MBC 2.5 µM). Site-directed mutagenesis indicated that the amidase_5 domain was catalytically active and exhibited a cysteine-, histidine-dependent amidohydrolase/peptidase (CHAP) activity with the catalytic residues Cys34 and His99. Subdomain truncation analysis showed that PlyCYU214 and PlyCYU277, comprising the CHAP domain with one and two CW_7 motifs, respectively, conferred bactericidal activity, but lower than that of PlyCYU, while cyuLyz2 alone showed no activity. Notably, the bacteriolytic activity of PlyCYU277 was enhanced when cyuLyz2 was present. Agreeably, reducing sugars were detected in &lt;i&gt;S. agalactiae&lt;/i&gt; lysis by PlyCYU and PlyCYU277 combined with cyuLyz2, but not by CHAP-inactive variants (PlyCYU-Cys34Ala/Ser and PlyCYU-His99Ala), PlyCYU277, and cyuLyz2 alone. This implied that cyuLyz2 action is CHAP dependent. Size exclusion chromatography (SEC) coupled with multi-angle light scattering and SEC-UV revealed PlyCYU and cyuLyz2 are homomultimers, whereas PlyCYU214 and PlyCYU277 are monomers. Therefore, the cyuLyz2 domain is important for the quaternary structure and the maximal activity of PlyCYU. Altogether, this study established PlyCYU endolysin as a potential antibiotic alternative against &lt;i&gt;Streptococcus&lt;/i&gt;.IMPORTANCE&lt;i&gt;Streptococcus agalactiae&lt;/i&gt; is a major pathogen responsible for severe neonatal infections, bovine mastitis, and streptococcosis in fish. The increasing prevalence of multidrug-resistant bacteria presses the urgent need to discover antibiotic alternatives. Bacteriophage-derived endolysins represent a promising solution due to their ability to specifically and rapidly kill target bacteria and be less likely to develop resistance. Here, we identified and characterized a novel endolysin, PlyCYU, with potent bactericidal activity against different &lt;i&gt;Streptococcus&lt;/i&gt; species, including &lt;i&gt;S. agalactiae&lt;/i&gt;, &lt;i&gt;S. dysgalactiae&lt;/i&gt;, and &lt;i&gt;S. uberis&lt;/i&gt;, isolated from bovine and fish sources. This study also demonstrated the relationships between the structure assembly and activity of PlyCYU. PlyCYU forms a multimer, facilitated by its glucosaminidase (cyuLyz2) domain, for maximal activity. Altogether, we revealed that PlyCYU is a promising candidat","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0187224"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442389/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144871073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Asphaltene biotransformation by a novel enzyme thiol peroxidase from <i>Micrococcus</i> sp. IITD107.","authors":"Nidhi Patil, Preeti Srivastava","doi":"10.1128/aem.00151-25","DOIUrl":"10.1128/aem.00151-25","url":null,"abstract":"<p><p>Asphaltenes are known to cause high density and viscosity in heavy crude oil. The gene for thiol peroxidase was found to be present in five members of the nine-membered bacterial consortium able to biotransform about 75% of asphaltenes. Here, we report cloning, expression, purification, and detailed characterization of a thiol peroxidase enzyme from one of the consortium members, <i>Micrococcus</i> sp. IITD107. Asphaltene was treated with the crude cell lysate obtained after overexpression of thiol peroxidase from heterologous host <i>Escherichia coli</i> as well as with purified enzyme. A significant reduction in the major peaks obtained by gas chromatography mass spectrometry (GC-MS) of asphaltene was observed, corresponding to small polyaromatic hydrocarbons such as benzaldehyde, phenol-methylethylidene, benzenepropionic acid, and linear aliphatic chains such as heptadecane, tetradecane, octadecane, etc. Changes in the structure of asphaltene were also observed in the Fourier transform infrared spectroscopy and nuclear magnetic resonance spectra. The elemental analysis determined around 60% reduction in sulfur and 69% reduction in nitrogen. A decrease in aromaticity of asphaltene was also observed. Scanning electron microscopy imaging of the treated asphaltene fraction captured during the course of biotransformation revealed formation of pores in the structure. This is the first report demonstrating the use of thiol peroxidase for asphaltene biotransformation. The enzyme can also be used for the biological synthesis of porous carbon, which has not been reported to date.IMPORTANCEHeavy crude oil is abundant but contains asphaltene, which results in its high density and viscosity, making it unsuitable for commercial application. The removal of asphaltene leads to a reduction in heaviness of the oil and renders it light and suitable for commercialization. Asphaltene is a complex and large polyaromatic hydrocarbon consisting of several heteroatoms. The use of enzymatic biotransformation of asphaltene aids in breaking down the complex molecule into smaller moieties without affecting the calorific value. This study helps in identifying a novel enzyme thiol peroxidase for biotransformation of asphaltene and valorization of asphaltene to synthesize porous carbon.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0015125"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442351/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144939806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-genome sequencing characterization of silver-resistant bacteria from the outfall of wastewater treatment plants and effluent-receiving rivers.","authors":"Yubing Xia, Haichen Wang, Jun Li, Haolan Wang, Yuyao Wang, Yongmei Hu, Fengjun Xia, Mingxiang Zou","doi":"10.1128/aem.00022-25","DOIUrl":"10.1128/aem.00022-25","url":null,"abstract":"<p><p>The excessive use of silver compounds has led to the environmental dissemination of silver resistance genes. However, little is known about the epidemiology of silver-resistant bacteria in the environment. Wastewater treatment plants (WWTPs) link the clinical settings with the natural environment and serve as a major pathway for silver entering the natural environment. However, their role in the dissemination of silver resistance genes remains unclear. This study investigated the characteristics of silver-resistant bacteria in the vicinity of four WWTPs to assess their environmental impact. Water and sediment samples were collected from the WWTP outfalls and downstream rivers. Among 22 silver-resistant strains obtained through plate screening, the majority were <i>Klebsiella</i> spp., followed by <i>Escherichia</i> spp. and <i>Kluyvera</i> spp. Notably, ST23 and ST2464 were the predominant sequence types (multilocus sequence typing) identified among the <i>Klebsiella pneumoniae</i> isolates. Antimicrobial susceptibility testing and whole-genome sequencing were performed to identify environmental heavy metal and antibiotic-resistant genes. Whole-genome sequencing revealed the presence of the <i>sil</i> and <i>pco</i> operons, which together formed the copper homeostasis and silver resistance island. The silver resistance gene sequences varied. Various heavy metal resistance genes, including <i>mer</i> and <i>ars</i>, were detected in the strains, as were a diverse array of plasmid types, including IncFIB(K) and repB(R1701), and <i>fosA</i> and <i>β</i>-lactamase encoding genes. Taken together, the findings underscore the coexistence of silver resistance genes with multiple heavy metal resistance genes in wastewater bacteria, highlighting the environmental implications of silver usage. Efforts should be directed toward restricting silver usage, improving WWTP purification methods to safeguard human and environmental health.</p><p><strong>Importance: </strong>The misuse of silver compounds has led to an increasing presence of silver-resistant microorganisms in the environment, which cannot be completely eliminated in wastewater treatment plants, allowing them to enter the environment and pose risks to environmental safety and human health. However, research on the epidemiology of silver-resistant bacteria in wastewater and their whole-genome sequencing remains limited. Our findings explain that silver-resistant bacteria from the environment often possess resistance to other heavy metals, share genetic similarities, and possess the potential for widespread transmission. Furthermore, these bacteria may enter clinical settings through environmental pathways, posing a risk to human health.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0002225"},"PeriodicalIF":3.7,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12442373/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144783315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}