Applied and Environmental Microbiology最新文献

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RB-TnSeq elucidates dicarboxylic-acid-specific catabolism in β-proteobacteria for improved plastic monomer upcycling. RB-TnSeq阐明了β-变形菌中二羧酸特异性分解代谢,以改善塑料单体的升级循环。
IF 3.7 2区 生物学
Applied and Environmental Microbiology Pub Date : 2025-09-22 DOI: 10.1128/aem.00924-25
Allison N Pearson, Julie M Lynch, Cindy N Ho, Graham A Hudson, Jacob B Roberts, Javier Menasalvas, Aaron A Vilchez, Matthew R Incha, Matthias Schmidt, Aindrila Mukhopadhyay, Adam M Deutschbauer, Mitchell G Thompson, Patrick M Shih, Jay D Keasling
{"title":"RB-TnSeq elucidates dicarboxylic-acid-specific catabolism in β-proteobacteria for improved plastic monomer upcycling.","authors":"Allison N Pearson, Julie M Lynch, Cindy N Ho, Graham A Hudson, Jacob B Roberts, Javier Menasalvas, Aaron A Vilchez, Matthew R Incha, Matthias Schmidt, Aindrila Mukhopadhyay, Adam M Deutschbauer, Mitchell G Thompson, Patrick M Shih, Jay D Keasling","doi":"10.1128/aem.00924-25","DOIUrl":"https://doi.org/10.1128/aem.00924-25","url":null,"abstract":"<p><p>Dicarboxylic acids are key components of many polymers and plastics, making them a target for both engineered microbial degradation and sustainable bioproduction. In this study, we generated a comprehensive data set of functional evidence for the genetic basis of dicarboxylic and fatty acid metabolism using randomly barcoded transposon sequencing (RB-TnSeq). We identified four β-proteobacteria that displayed robust growth with dicarboxylic acid sole carbon source and cultured their mutant libraries with dicarboxylic and fatty acids with carbon chain lengths from C3 to C12. The resulting fitness data suggested that dicarboxylic and fatty acid metabolisms are largely distinct, and different sets of β-oxidation genes are required for catabolizing dicarboxylic versus fatty acids of the same carbon chain lengths. In addition, we identified transcriptional regulators and transporters with strong fitness phenotypes related to dicarboxylic acid utilization. In <i>Ralstonia sp</i>. UNC404CL21Col (<i>R. CL21</i>), we deleted two transcriptional repressors to improve its utilization of short-chain dicarboxylic acids. We exploited the diacid-utilizing catabolism of <i>R. CL21</i> to upcycle a mock mixture of the dicarboxylic acids produced when polyethylene is oxidized. After introducing a heterologous indigoidine production pathway, this engineered <i>Ralstonia</i> produced 0.56 ± 0.02 g/L indigoidine from a mixture of dicarboxylic acids as a carbon source, demonstrating the potential of <i>R. CL21</i> to upcycle plastic wastes to products derived from tricarboxylic acid (TCA) cycle intermediates.</p><p><strong>Importance: </strong>Upcycling the carbon in plastic wastes to value-added products is a promising approach to address the plastic waste and climate crises, and dicarboxylic acid metabolism is an important facet of several approaches. Improving our understanding of the genetic basis of this metabolism has the potential to uncover new enzymes and genetic parts for engineered pathways involving dicarboxylic acids. Our data set is the most comprehensive interrogation of dicarboxylic acid catabolism to date, and this work will be of utility to researchers interested in both plastics bioproduction and upcycling applications.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0092425"},"PeriodicalIF":3.7,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111734","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}
引用次数: 0
Comparative antibacterial activity of N-terminal and C-terminal domains of a recombinant endolysin against Cutibacterium acnes. 重组内溶素n端和c端结构域对痤疮表皮杆菌的抑菌活性比较。
IF 3.7 2区 生物学
Applied and Environmental Microbiology Pub Date : 2025-09-22 DOI: 10.1128/aem.01168-25
Jae-Hyuk Lee, Muhammad Adeel Hasnain, Jung-Ho Park, Wonho Choi, Gi-Seong Moon
{"title":"Comparative antibacterial activity of N-terminal and C-terminal domains of a recombinant endolysin against <i>Cutibacterium acnes</i>.","authors":"Jae-Hyuk Lee, Muhammad Adeel Hasnain, Jung-Ho Park, Wonho Choi, Gi-Seong Moon","doi":"10.1128/aem.01168-25","DOIUrl":"https://doi.org/10.1128/aem.01168-25","url":null,"abstract":"<p><p>Endolysins are promising antibacterial agents due to their selective antibacterial activity and minimal risk of resistance. The antibacterial activity of individual domains of endolysins from anti-<i>Cutibacterium acnes</i> phages remains unexplored. In this study, a recombinant endolysin from <i>C. acnes</i> phage CAP 10-3 and its N-terminal and C-terminal domains were tested against <i>C. acnes</i> KCTC 3314 and KCTC 3320 using turbidity reduction and live cell count methods. Starting with an initial OD<sub>600</sub><b>≈</b>1, a 3 h treatment with 50 µg/mL of the N-terminal domain (N1) reduced OD<sub>600</sub> to 0.395 (KCTC 3314) and 0.324 (KCTC 3320), while that of full-length (FL) reduced OD<sub>600</sub> to 0.547 and 0.474, respectively. Correspondingly, N1 reduced viable counts by 1.13-1.35 log, whereas FL showed 0.94-0.95 log reduction, confirming N1's stronger bactericidal effect. C-terminal domain exhibited minimal changes in both OD<sub>600</sub> and cell count values. N1's lytic effect was further confirmed by morphology analysis. Therefore, the N-terminal domain was further characterized for its activity and specificity. It showed dose-dependent activity against both <i>C. acnes</i> strains, but it had no significant effect on <i>Staphylococcus aureus</i> KCTC 3881 and only weak activity against <i>Staphylococcus epidermidis</i> CJNU 0702 at high concentrations (100 µg/mL). These findings highlight the N-terminal domain's potential as a selective anti-<i>C</i>. <i>acnes</i> agent with minimal impact on skin flora, supporting its suitability for protein-based antimicrobial therapeutics and cosmetic applications.IMPORTANCE<i>Cutibacterium acnes</i> is known to play a significant role in the pathology of acne vulgaris and several other disorders. Conventional methods of treating <i>C. acnes</i> infections using antibiotics face an ever-aggravating antibiotic resistance challenge. Endolysins present a promising alternative with advantages such as specificity and low-to-no chances of resistance. The current study compares the antibacterial activity of the full length as well as its N- and C-terminal domains of an endolysin from phage CAP 10-3. In addition, the dose-dependent effect and specificity of the N-terminal domain (which showed the most significant anti-<i>C</i>. <i>acnes</i> activity) are also explained. These findings can pave the way for developing alternative peptide-based anti-<i>C</i>. <i>acnes</i> therapeutics.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0116825"},"PeriodicalIF":3.7,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145111766","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}
引用次数: 0
Dissecting the antibacterial functions of the T6SS-2 cluster in Xanthomonas oryzae for environment and plant protection. 解析米黄单胞菌T6SS-2簇的抑菌功能及其对环境和植物保护的意义。
IF 3.7 2区 生物学
Applied and Environmental Microbiology Pub Date : 2025-09-19 DOI: 10.1128/aem.01021-25
Zhi-Min Tan, Xin Zheng, Jingtong Su, Jin-Sheng Liu, Xiaoye Liang, Tong-Tong Pei, Tao Dong
{"title":"Dissecting the antibacterial functions of the T6SS-2 cluster in <i>Xanthomonas oryzae</i> for environment and plant protection.","authors":"Zhi-Min Tan, Xin Zheng, Jingtong Su, Jin-Sheng Liu, Xiaoye Liang, Tong-Tong Pei, Tao Dong","doi":"10.1128/aem.01021-25","DOIUrl":"https://doi.org/10.1128/aem.01021-25","url":null,"abstract":"<p><p>Plant pathogens pose a serious threat to global food security, and the excessive use of chemical pesticides has raised significant ecological concerns. Harnessing microbial competition presents a promising green technology for crop protection. In this study, we examined the functions of the type VI secretion system (T6SS), a crucial microbial competition tool, in <i>Xanthomonas oryzae</i> pv. <i>oryzae</i> strain PXO99A. PXO99A exhibited significant antibacterial activities dependent on its T6SS-2 cluster. Using genome, secretome, and functional analysis, we systematically predicted T6SS-associated effectors, detected the expression of five putative effectors, and functionally validated the toxicity of a VasX_N family effector PXO_00500 and its immunity protein PXO_RS08595. We further show that PXO99A uses its T6SS-2 to kill a broad range of plant and animal pathogens <i>in vitro</i> and <i>in planta</i>. Inactivation of the T3SS functions abolished virulence but had little effect on the T6SS-2-dependent antibacterial activities. Finally, we demonstrated that the avirulent T3SS-defective mutant is effective in protecting tomatoes from <i>Pseudomonas syringae</i> co-infection. Collectively, these results highlight an effective biocontrol strategy for plant protection.</p><p><strong>Importance: </strong>The growing concerns over the toxicity, environmental impact, and resistance associated with chemical pesticides underscore the urgent need for alternative pathogen management strategies. In this study, we introduce an innovative approach of \"turning waste into treasure\" by repurposing plant pathogens as biocontrol-like agents. By elucidating the virulence and antimicrobial functions of <i>Xanthomonas oryzae</i>, we demonstrate that an avirulent mutant can employ its T6SS to effectively combat a broad spectrum of human and plant pathogens. Furthermore, its ability to protect tomato plants underscores its significant potential for sustainable agricultural practices.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0102125"},"PeriodicalIF":3.7,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084619","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}
引用次数: 0
Diel cycle of lanthanide-dependent methylotrophy by TMED127/Methylaequorales bacteria in oligotrophic surface seawater. 低营养表层海水中TMED127/Methylaequorales细菌镧系依赖甲基化的双循环
IF 3.7 2区 生物学
Applied and Environmental Microbiology Pub Date : 2025-09-19 DOI: 10.1128/aem.01181-25
Jennifer B Glass, Leilani N Warters, Abdulaziz M Alajlan
{"title":"Diel cycle of lanthanide-dependent methylotrophy by TMED127/Methylaequorales bacteria in oligotrophic surface seawater.","authors":"Jennifer B Glass, Leilani N Warters, Abdulaziz M Alajlan","doi":"10.1128/aem.01181-25","DOIUrl":"https://doi.org/10.1128/aem.01181-25","url":null,"abstract":"<p><p>Methanol, the simplest alcohol, has long been known to be a key energy and carbon source for soil and plant-associated bacteria and fungi and is increasingly recognized as an important substrate for marine bacteria. Lanthanide-dependent methanol dehydrogenases (encoded by the gene <i>xoxF</i>) have been shown to be key catalysts for methylotrophy in many environments, yet the identity of the most transcriptionally active methylotrophs in open ocean waters (\"Clade X\") has remained elusive. Here, we show that \"Clade X\" methylotrophs belong to the deep-branching alphaproteobacterial order TMED127, which we propose be renamed \"Methylaequorales\": \"methyl\" for \"methylotrophic metabolism\" and \"aequor\" for \"ocean surface,\" as these bacteria are most transcriptionally active near the sea surface. TMED127/Methylaequorales are present in surface waters of tropical and subtropical oceans throughout the global ocean. They have small, streamlined genomes (~1.5 Mb) and appear to be obligate methylotrophs that use the serine cycle for carbon assimilation. They display a diel pattern of <i>xoxF5</i> and glucose dehydrogenase (<i>gdh</i>) transcription, peaking in the late afternoon, in oligotrophic surface water of the Sargasso Sea. Several other highly transcribed genes of unknown function had no homologs outside of TMED127/Methylaequorales genomes. Our findings illuminate an overlooked marine methylotrophic bacterium and predict a diel cycle of methanol production in surface seawater by an unknown pathway.</p><p><strong>Importance: </strong>Methanol metabolism is increasingly recognized as an important process in the marine carbon cycle, yet the identity and metabolism of the microorganisms mediating methylotrophy in the open ocean have remained unknown. This study reveals that bacteria in the TMED127 order of Alphaproteobacteria, renamed here as \"Methylaequorales,\" abundantly transcribe the key gene for lanthanide-dependent methylotrophy in oligotrophic surface waters of the world's oceans. TMED127/Methylaequorales likely require methanol as a carbon and energy source and display a diel pattern of transcription of key genes for methylotrophy that peaks in the late afternoon. These findings motivate future studies on the mechanisms of methanol production in surface seawater.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0118125"},"PeriodicalIF":3.7,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084632","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}
引用次数: 0
Microbial ecology of acidic, biogenic gypsum: community structure and distribution of extremophiles on freshly formed and relict sulfate deposits in a hydrogen sulfide-rich cave. 酸性生物石膏的微生物生态学:富硫化氢洞穴中新形成和残留硫酸盐沉积物中极端微生物的群落结构和分布
IF 3.7 2区 生物学
Applied and Environmental Microbiology Pub Date : 2025-09-19 DOI: 10.1128/aem.01397-25
Zoë E Havlena, Katherine Lucero, Heather V Graham, Jennifer C Stern, Scott D Wankel, Maurizio Mainiero, Daniel S Jones
{"title":"Microbial ecology of acidic, biogenic gypsum: community structure and distribution of extremophiles on freshly formed and relict sulfate deposits in a hydrogen sulfide-rich cave.","authors":"Zoë E Havlena, Katherine Lucero, Heather V Graham, Jennifer C Stern, Scott D Wankel, Maurizio Mainiero, Daniel S Jones","doi":"10.1128/aem.01397-25","DOIUrl":"10.1128/aem.01397-25","url":null,"abstract":"<p><p>Sulfate minerals are abundant on the Martian surface, and many of these evaporite deposits are thought to have precipitated from acidic fluids. On Earth, gypsum (CaSO<sub>4</sub>•2H<sub>2</sub>O) and other sulfates sometimes form under acidic conditions, so exploring the extremophilic life that occurs in these mineral environments can help evaluate the astrobiological potential of acid sulfate depositional settings. Here, we characterized the microbial communities associated with acidic gypsum deposits in a sulfuric acid cave, where sulfate precipitation is driven by sulfide-oxidizing bacteria and archaea. We used 16S rRNA gene sequencing and cell counts to characterize gypsum-associated microorganisms in freshly formed and relict deposits throughout the cave, to test how microbial community composition and abundance would vary with distance from the sulfidic water table and with the concentration of H<sub>2</sub>S(<i>g</i>) and other gases in the cave atmosphere. We found that actively forming gypsum in the lower cave levels was colonized by low-diversity communities that have few cells compared to other environments in the cave. The most abundant taxa were <i>Acidithiobacillus, Metallibacterium, Mycobacteria</i>, and three different <i>Thermoplasmatales</i>-group archaea, which occupied distinct niches based on proximity to sulfidic streams and the concentration of gases in the cave air. By contrast, deposits in older cave levels had more diverse communities that were distinct from those associated with freshly formed gypsum and likely represent a community reliant on different energy resources. These findings show that acidic sulfate deposits serve as habitats for extremophilic microorganisms and broaden our knowledge of the life associated with terrestrial sulfates.</p><p><strong>Importance: </strong>Gypsum and other sulfate salts are common on Mars, and many of these deposits are thought to have formed from acidic fluids early in the planet's history. Understanding the life that survives and thrives in similar environments on Earth is therefore crucial for evaluating whether these Martian sulfates are or ever were habitable. One such environment where acidic gypsum occurs is in sulfuric acid caves, where extremophilic microorganisms drive the precipitation of sulfate minerals by oxidizing hydrogen sulfide gas from the cave atmosphere. Here, we characterized the communities of microorganisms on freshly formed and ancient gypsum in the Frasassi Caves and found that the gypsum deposits hosted microbial communities that changed based on chemical energy availability and the age of the gypsum. Our findings underscore the importance of chemical and microbiological interactions in shaping habitable niches and provide context for searching for past or present life in acidic Martian sulfates.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0139725"},"PeriodicalIF":3.7,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084818","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}
引用次数: 0
The hidden life of Xylella: mining the NCBI Sequence Read Archive reveals potential new species, host plants, and infected areas for this elusive bacterial plant pathogen. 木杆菌的隐藏生活:挖掘NCBI序列读取档案揭示了这种难以捉摸的细菌植物病原体的潜在新物种,寄主植物和感染区域。
IF 3.7 2区 生物学
Applied and Environmental Microbiology Pub Date : 2025-09-19 DOI: 10.1128/aem.00913-25
Martial Briand, Marie-Agnès Jacques, Jessica Dittmer
{"title":"The hidden life of <i>Xylella</i>: mining the NCBI Sequence Read Archive reveals potential new species, host plants, and infected areas for this elusive bacterial plant pathogen.","authors":"Martial Briand, Marie-Agnès Jacques, Jessica Dittmer","doi":"10.1128/aem.00913-25","DOIUrl":"https://doi.org/10.1128/aem.00913-25","url":null,"abstract":"<p><p>New crop disease outbreaks can occur when phytopathogenic bacterial pathogens acquire new traits, switch to a new host plant, or are introduced into new geographic areas. Therefore, the rapid detection of a pathogen in a new environment and/or in a new host plant is essential to mitigate disease outbreaks. However, bacteria with a wide plant host range, many asymptomatic hosts, and slow symptom development can sometimes remain unnoticed for years. This is the case for the vector-borne xylem-inhabiting bacterium <i>Xylella fastidiosa</i> known to infect hundreds of plant species worldwide and its sister species <i>X. taiwanensis</i>, currently thought to be restricted to Taiwan. To investigate whether the two <i>Xylella</i> species are already present in other parts of the world, potentially in unrecognized host species, we performed an in-depth data mining of raw sequence data available in the NCBI Sequence Read Archive. This led to the identification of 62 datasets from diverse plant and insect samples from around the world. Furthermore, nine draft and one circular <i>Xylella</i> genome could be assembled from these datasets. Our results reveal several potential new host plants and previously unrecognized infected areas in the Americas, Africa, and Southeast Asia. Moreover, the newly assembled genomes represent several new strains of both <i>X. fastidiosa</i> and <i>X. taiwanensis</i> as well as an additional <i>Xylella</i> species infecting wild rice. Taken together, our work extends our knowledge on the genetic diversity, host range, and global distribution of the genus <i>Xylella</i> and can orient surveillance programs towards new regions and host plants.IMPORTANCEThe rapid detection of a pathogen in a new environment and/or in a new host plant is essential to mitigate disease outbreaks. However, bacteria with a wide plant host range, many asymptomatic hosts, and slow symptom development can sometimes remain unnoticed for years. In this work, we used an in-depth screening of publicly available raw sequencing data as an alternative approach to investigate the distribution of the xylem-inhabiting bacteria <i>Xylella fastidiosa</i> and <i>X. taiwanensis</i> across the world. Our results reveal several potential new host plants and previously unrecognized infected areas in the Americas, Africa, and Southeast Asia. Moreover, we provide evidence, including a complete genome sequence, for a third <i>Xylella</i> species infecting wild rice. This work extends our knowledge of the genetic diversity, plant host range, and global distribution of the genus <i>Xylella</i> in natural environments and motivates surveillance programs in so-far-neglected biomes, regions, and host plants.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0091325"},"PeriodicalIF":3.7,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084780","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}
引用次数: 0
How sequencing technology shapes our understanding of river water microbiomes and resistomes: a comparative study. 测序技术如何塑造我们对河水微生物组和抗性组的理解:一项比较研究。
IF 3.7 2区 生物学
Applied and Environmental Microbiology Pub Date : 2025-09-19 DOI: 10.1128/aem.01723-25
Jialin Hu, J Chris Blazier, Anna Gitter, Lucas F Gregory, Terry J Gentry
{"title":"How sequencing technology shapes our understanding of river water microbiomes and resistomes: a comparative study.","authors":"Jialin Hu, J Chris Blazier, Anna Gitter, Lucas F Gregory, Terry J Gentry","doi":"10.1128/aem.01723-25","DOIUrl":"https://doi.org/10.1128/aem.01723-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;River ecosystems are vital for supporting biodiversity and supplying freshwater, but are increasingly impacted by microbial pollution, including the spread of antibiotic resistance genes (ARGs), which poses growing public health concerns. While high-throughput sequencing technologies have advanced our ability to study microbial communities and resistomes, their varying capabilities and biases require comparative analysis. In this study, we compared three sequencing approaches-Illumina 16S rRNA amplicon, Illumina shotgun metagenomics, and Oxford Nanopore-based long-read metagenomics-to profile microbial communities, ARGs, and virulence factors (VFs) in 48 river water samples. All methods identified Proteobacteria and Actinobacteria as dominant phyla, but substantial differences emerged at finer taxonomic levels. Long-read metagenomics and 16S data showed greater consistency at the genus level, while Illumina metagenomics differed, detecting more potential pathogens and fewer native freshwater taxa. For ARG and VF profiling, unassembled Illumina data yielded higher diversity and abundance, but assembled Illumina data showed comparable results to long-read metagenomics data in terms of dominant genes and host associations. Although Illumina provides high sensitivity, the use of short reads and associated assembly limitations can compromise functional accuracy. In contrast, long-read metagenomics facilitates gene-level resolution and direct host linkage, providing a more comprehensive understanding of environmental microbiomes. Our findings highlight the strengths and limitations of each method and support Oxford Nanopore technology (ONT)-based long-read metagenomic sequencing as a cost-effective and informative tool for high-resolution taxonomic and functional analysis of complex environmental samples.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Accurate characterization of microbial communities and their functional traits, such as antibiotic resistance, is essential for evaluating water quality and associated public health risks. However, the selection of sequencing methods can substantially influence the detection and interpretation of microbial community composition and functional potential in environmental samples. By directly comparing amplicon, short-read metagenomic, and long-read metagenomic sequencing across 48 freshwater samples collected across different sites and time points, this study builds upon earlier work that typically focused on only two methods or less complex communities. It provides a comparative evaluation of three widely used sequencing approaches, demonstrating how methodological differences affect the resolution and reliability of taxonomic and functional profiling in complex environmental microbiomes. By highlighting the strengths and limitations of each platform, these findings enhance our understanding of how sequencing strategy shapes environmental microbiome analyses and contributes to evidence-based method selection in ","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0172325"},"PeriodicalIF":3.7,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084841","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}
引用次数: 0
Refining microbial biomarker identification in rumen microbiome studies: a viability PCR-based approach. 改进瘤胃微生物组研究中的微生物生物标志物鉴定:一种基于生存力pcr的方法。
IF 3.7 2区 生物学
Applied and Environmental Microbiology Pub Date : 2025-09-19 DOI: 10.1128/aem.01429-25
Woohyung Lee, Geonwoo Kim, Tansol Park
{"title":"Refining microbial biomarker identification in rumen microbiome studies: a viability PCR-based approach.","authors":"Woohyung Lee, Geonwoo Kim, Tansol Park","doi":"10.1128/aem.01429-25","DOIUrl":"https://doi.org/10.1128/aem.01429-25","url":null,"abstract":"<p><p>The rumen microbiome significantly affects host performance, influencing feed efficiency, nitrogen utilization, and methane emission. However, conventional DNA-based marker gene sequencing cannot distinguish between viable and non-viable microbes, leading to inaccurate microbiota analyses. Viability PCR (v-PCR) with propidium monoazide (PMA) can inhibit DNA amplification from membrane-compromised cells, allowing the detection of viable microbes in rumen cultures. Therefore, this study aims to identify conditions for applying PMA in rumen culture experiments using qPCR and to examine its effect on the rumen microbial community using 16S rRNA gene sequencing in standard <i>in vitro</i> experiments. PMA treatment conditions were applied using a fivefold inoculum dilution, 100  µM PMA concentration, 30 min dark incubation, and 20 min light exposure, validated by a decrease in absolute abundance in heat-treated samples. When applied to <i>in vitro</i> rumen experiments, PMA treatment reduced bacterial evenness and induced shifts in key bacterial and archaeal taxa. Additionally, it affected major functional profiles of the microbiota. PMA treatment increased the relative abundance of <i>Ruminobacter</i> [log fold change (LFC) = 0.52] and <i>Succinivibrio</i> (LFC = 0.68) at 0 h (no incubation), along with <i>Ruminobacter</i> (LFC = 0.83) after 24 h of incubation, while decreasing that of <i>Xylanibacter</i> (LFC = -0.39) at 24 h. These shifts align with those of RNA-based studies showing higher Succinivibrionaceae abundance than Prevotellaceae, supporting the effectiveness of PMA in capturing active microbial dynamics. PMA-based v-PCR offers a reliable alternative to RNA-based methods, improving microbial community assessments and facilitating the identification of viability-associated microbial biomarkers in rumen studies.IMPORTANCEThis study identifies the optimal conditions for applying propidium monoazide (PMA) in <i>in vitro</i> rumen experiments to selectively amplify DNA from viable microorganisms while suppressing amplification from nonviable ones. PMA-based viability PCR (v-PCR) improves the accuracy of microbial community analysis by selectively detecting viable microorganisms, addressing the limitations of conventional DNA-based methods. Additionally, this approach provides a potential cost-effective alternative to RNA-based analyses, offering a practical tool for studying rumen microbial ecology.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0142925"},"PeriodicalIF":3.7,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084833","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}
引用次数: 0
Decoding Collimonas pratensis PMB3(1) responses during biotite interaction and dissolution: a multi-omics and geochemical perspective. 解码黑云母相互作用和溶解过程中Collimonas pratensis PMB3(1)的响应:多组学和地球化学视角。
IF 3.7 2区 生物学
Applied and Environmental Microbiology Pub Date : 2025-09-19 DOI: 10.1128/aem.00704-25
Laura Picard, Marie-Pierre Turpault, Jean Armengaud, Stéphane Uroz
{"title":"Decoding <i>Collimonas pratensis</i> PMB3(1) responses during biotite interaction and dissolution: a multi-omics and geochemical perspective.","authors":"Laura Picard, Marie-Pierre Turpault, Jean Armengaud, Stéphane Uroz","doi":"10.1128/aem.00704-25","DOIUrl":"https://doi.org/10.1128/aem.00704-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Mineral weathering bacteria are known to mobilize the nutrients entrapped in minerals using acidification- and chelation-driven mineral weathering (MWe) mechanisms. Through these mechanisms, bacteria are expected to play important roles in soil nutrient cycling and tree nutrition. Among the most effective MWe bacteria identified, &lt;i&gt;Collimonas&lt;/i&gt; are particularly interesting due to their occurrence in the rhizosphere and their ability to acidify their environment using a glucose methanol choline oxidoreductase and to mobilize iron using malleobactin. Until now, the regulations of these functions according to nutrient availability and presence/absence of minerals remain uncharacterized, as does the potential involvement of other direct and indirect MWe mechanisms. In this context, we investigated how the solution chemistry and the functions expressed by strain PMB3(1) were regulated according to the concentrations of iron and magnesium and the presence/absence of biotite. Transcriptomics and proteomics dual approach highlighted that under nutrient-depleted conditions and in the absence of biotite, strain PMB3(1) increased the expression of genes and abundance of proteins related to osmoprotection, stress, and iron mobilization. On the contrary, in the presence of biotite, an upregulation of genes and proteins associated with surface sensing, motility, chemotaxis, transport, acidification, and iron storage was observed. These new findings represent a crucial first step in understanding the regulatory processes and mechanisms employed by &lt;i&gt;Collimonas&lt;/i&gt; during its interaction with and weathering of biotite. They show that bacteria respond to nearby minerals in more complex ways than simply reacting to a lack of nutrients.IMPORTANCEMinerals and rocks represent reactive interfaces at the geochemical level and a particular habitat at the microbial level. They are, however, usually considered inert substrata, although they represent 80% of the soil composition. The works performed on interactions between minerals and bacteria have mainly considered anoxic processes and microorganisms and poorly soil heterotrophs. In this context, our understanding of the role of soil minerals and rocks in soil fertility and the relative contribution and the molecular mechanisms employed by effective mineral weathering bacterial communities remain poorly documented. The combined use in our study of transcriptomics, proteomics, and geochemical analyses permitted filling this gap. The new findings obtained here suggest that minerals impact the global metabolism and the effectiveness at weathering of the strain &lt;i&gt;Collimonas pratensis&lt;/i&gt; PMB3(1). They also reveal that the behavior exhibited by this bacterial strain extends beyond a mere reaction to the lack of nutrients. The complex interactions occurring between the physicochemical properties of these minerals and the activities of the MWe bacteria we observed &lt;i&gt;in vitro&lt;/i&gt; offer a new view of the relative impo","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0070425"},"PeriodicalIF":3.7,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084611","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}
引用次数: 0
Evidence of ESBL plasmid transfer and selective persistence of multiple host-associated Escherichia coli isolates in a chicken cecal fermentation model. 鸡盲肠发酵模型中ESBL质粒转移和多种宿主相关大肠杆菌分离株选择性持久性的证据。
IF 3.7 2区 生物学
Applied and Environmental Microbiology Pub Date : 2025-09-19 DOI: 10.1128/aem.00822-25
J Leng, M Ferrandis-Vila, R Oldenkamp, J W Mehat, A S Fivian-Hughes, S Kumar Tiwari, B Van der Putten, V Trung Nguyen, A Bethe, J Clark, P Singh, T Semmler, S Schwarz, J Alvarez, N T Hoa, M Bootsma, C Menge, C Berens, C Schultsz, J M Ritchie, R M La Ragione
{"title":"Evidence of ESBL plasmid transfer and selective persistence of multiple host-associated <i>Escherichia coli</i> isolates in a chicken cecal fermentation model.","authors":"J Leng, M Ferrandis-Vila, R Oldenkamp, J W Mehat, A S Fivian-Hughes, S Kumar Tiwari, B Van der Putten, V Trung Nguyen, A Bethe, J Clark, P Singh, T Semmler, S Schwarz, J Alvarez, N T Hoa, M Bootsma, C Menge, C Berens, C Schultsz, J M Ritchie, R M La Ragione","doi":"10.1128/aem.00822-25","DOIUrl":"https://doi.org/10.1128/aem.00822-25","url":null,"abstract":"<p><p>The guts of animals and humans harbor diverse microbial communities that are regularly exposed to bacteria originating from food, water, and their surroundings. Species such as <i>Escherichia coli</i> are adept at colonizing multiple hosts, along with surviving in the environment. By encoding pathogenic traits and transmissible forms of antimicrobial resistance (AMR), <i>E. coli</i> can also pose a zoonotic risk. Our understanding of the factors that govern host residency is limited. Here, we used a chicken cecal fermentation model to study survival and the AMR transfer potential of 17 host-associated extended-spectrum β-lactamase (ESBL)-producing <i>E. coli</i> isolates. Vessels containing chicken cecal contents were stabilized for 4 days before the addition of a cocktail comprising ESBL-producing <i>E. coli</i> obtained from human, cattle, pig, and chicken hosts. Consecutive sampling showed that pig and cattle-associated isolates persisted in most vessels, although the recovery of all isolates declined over time. Increasing the inoculum dose or adding ceftiofur helped to stabilize populations of ESBL <i>E. coli</i> within the vessels, although this did not result in outgrowth of resistant populations in all vessels. Sequencing revealed that most new ESBL-producing <i>E. coli</i> recovered during the study acquired a <i>bla</i><sub>CTX-M-1</sub> plasmid from a single ESBL <i>E. coli</i> included in the cocktail that lacked host-specific traits (generalist). Our data highlight that isolate-specific differences in the <i>E. coli</i> genome composition likely explain the persistence of specific clones and efficiency of plasmid transfer, both of which could impact the spread of AMR in complex communities.IMPORTANCEThere are few insights into how host-associated <i>Escherichia coli</i> behave within the gut environment of other hosts. <i>E. coli</i> isolates that are immigrants to the gastrointestinal system of humans and animals have the potential to transfer their resistance to other native bacteria. A better understanding of this process is needed to assess how the gastrointestinal environment could serve as a reservoir and a melting pot of new, multidrug-resistant <i>E. coli</i> isolates.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0082225"},"PeriodicalIF":3.7,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084604","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}
引用次数: 0
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