Applied and Environmental Microbiology最新文献

{"title":"Glycophenotyping of mutants of <i>Lacticaseibacillus paracasei</i> by lectin microarray.","authors":"Emi Suzuki, Masaki Serata, Tomoyuki Sako, Sumie Sato, Tohru Iino, Hiroaki Tateno, Jun Hirabayashi","doi":"10.1128/aem.01707-24","DOIUrl":"10.1128/aem.01707-24","url":null,"abstract":"<p><p>We previously identified a gene cluster of <i>Lacticaseibacillus paracasei</i> strain Shirota (YIT 9029) for cell surface long-chain polysaccharides (LCPS-1) biosynthesis, which modulates YIT 9029 activity to induce cytokine production in immune cells, and showed that a lectin microarray can be useful for distinguishing the profile of bacterial cell-surface polysaccharide (PS) structures. Therefore, we isolated disruptive mutant strains of 51 genes predicted to be involved in cell wall PS biosynthesis in YIT 9029. Their binding profiles to lectins in conjunction with their binding abilities to YIT 9029-specific monoclonal antibody (MAb) were compared. The mutants defective in binding to the MAb all had defects within the <i>cps1</i> gene cluster. Some mutants were partially bound to MAb, indicating that these genes may influence the synthesis and maturation of LCPS-1. An advanced lectin microarray analyzed the cell surface glycosylation properties of YIT 9029 and its mutants. YIT 9029 bound to a rhamnose (Rha)-specific lectin CSA, and three additional lectins, including an O-glycan binder (rDiscoidin II) and two mannose (Man)-binders (rOrysata and rBanana). Lectin binding specificity was confirmed by a gene complementation assay for the <i>cps1C</i> gene and a carbohydrate inhibition assay. When the binding profiles of individual <i>cps1A</i> through <i>cps1J</i> knockout mutants were compared, typical and specific binding profile patterns were observed, in which some similarities in the functions of each gene could be predicted. In conclusion, the combined use of lectin microarray and a YIT 9029 mutant strain library is a powerful tool for identifying unknown bacterial gene functions related to the cell surface glycome.IMPORTANCEPreviously, only a limited number of methods have been available for studying mutations in bacterial cell surface polysaccharide structures in relation to gene function. In this study, we focused on the lectin-binding properties of <i>Lacticaseibacillus paracasei</i> YIT 9029 (wild type; WT) and investigated the lectin-binding capabilities of 51 cell wall biosynthesis gene disruption strains using lectin microarrays. The results indicated that lectin-binding properties in gene-disrupted strains varied significantly with the presence or absence of long-chain polysaccharides (LCPS-1), ranging from similar to WT to distinctly different. The use of lectin microarrays in conjunction with the YIT 9029 mutant library has been shown to be a highly effective method for identifying the functions of unknown bacterial genes related to cell-surface glycomes. This innovative approach to glycophenotyping allows for the determination of cell wall glycomes associated with bacterial gene functions using lectin microarrays.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0170724"},"PeriodicalIF":3.7,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366308/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590316","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":"Quantification of airborne fungal antigens by ELISA and comparison to molecular biological and classical methods.","authors":"C-E Pogner, M Gorfer, M Raulf, J Strauss, I Sander","doi":"10.1128/aem.00163-25","DOIUrl":"10.1128/aem.00163-25","url":null,"abstract":"<p><p>Airborne fungal spores are recognized for their human health impact, yet dose-response relationships remain undefined despite decades of bioaerosol sampling and analysis. In this article, we quantify immunologically active compounds, using six fungal-specific enzyme-linked immunosorbent assays (ELISAs) and compare them with cultivation, spore counting, and quantitative PCR (qPCR), using identical filter extract aliquots, various concentrations, single-organism aerosols, and mixes, in a controlled environment. Results showed high agreement between ELISAs and spore counting. By contrast, CFU enumeration and qPCR showed lower correlation with the other methods. Results of ELISAs showed high reproducibility of technical replicates and sampling duplicates, whereas CFU and qPCR results had high deviations. ELISA detection limits ranged from 10 to 100 spores/mL for larger spores (<i>Cladosporium herbarum</i>, <i>Aspergillus amstelodami</i>) and from 103 to 104 spores/mL for smaller spores (<i>Aspergillus amoenus</i>, <i>Aspergillus fumigatus</i>, <i>Penicillium chrysogenum</i>). The <i>Wallemia sebi</i> and the <i>Penicillium chrysogenum</i> ELISAs cross-reacted to <i>Aspergillus protuberus</i> or <i>Aspergillus amstelodami</i>, respectively. The spore dust production method influenced the spore germination rate and qPCR results significantly. By contrast, ELISA results remain unchanged, with the exception of the <i>W. sebi</i> ELISA. Quantitative spore counting was challenged by mixtures of species with morphologically similar spores from different fungal groups. In conclusion, the ELISA method is found suitable for fungal antigen quantification of air samples, provided the assays are sufficiently sensitive and specific, and germination evaluation is not required for risk assessment, leading to <i>C. herbarum</i> and <i>A. amstelodami</i> ELISA recommendations.</p><p><strong>Importance: </strong>Bioaerosol detection and analysis is an ongoing field of research. Although various methodologies are used for collection and analysis, there is no single method available to close the knowledge gap between exposure and health impact. For airborne fungal material, the standard analysis method remains cultivation. With molecular technology advancing in the field, both methods can only show the exposure to living, cultivatable, or total fungal cells in the airborne environment. To close the gap between airborne concentrations and impact on the human body, recognition of the allergenic potential is necessary. Therefore, we evaluated six fungal-specific ELISAs to make them ready for application in field studies and compared them to cultivation, spore counting, and molecular genetic methods. We are confident that in the future antigen-recognizing methods like the tested ELISAs will enable moving from particle detection toward detection of the disease-causing agent.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0016325"},"PeriodicalIF":3.7,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366363/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144641596","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":"Genomic analysis reveals two dominant strains of <i>Ornithobacterium rhinotracheale</i> in Austria and Hungary with distinct multidrug resistance profiles.","authors":"Nicola Palmieri, Claudia Hess, Boglárka Pollák, Tibor Magyar, Krisztina Pinter, Marianna Doman, Ivana Bilic, Michael Hess","doi":"10.1128/aem.00569-25","DOIUrl":"10.1128/aem.00569-25","url":null,"abstract":"<p><p><i>Ornithobacterium rhinotracheale</i> (ORT) is an emerging pathogen that poses significant challenges to commercial poultry production due to respiratory and systemic infections, leading to economic losses. Increasing multidrug resistance further complicates effective treatment strategies. Here, we present the first large-scale genomic analysis of ORT isolates from Europe, focusing on 94 newly sequenced isolates from Austria and Hungary. Phylogenetic analysis revealed two dominant clades, O1 and O2, which included isolates from both regions, indicating a lack of geographic segregation. Both clades display high genetic similarity, indicating that each represents a single strain. Notably, Clade O1 appears to be specific to Europe and exhibits higher resistance to several antibiotics compared to Clade O2. Genome-wide association studies and database screening identified resistance genes linked to beta-lactam antibiotics (<i>ccrA</i>/<i>orr</i>) and tylosin (<i>ermF</i>/<i>ermD</i>). Despite the widespread presence of <i>tetX</i> and <i>tetQ</i>, these genes did not consistently predict tetracycline resistance. Furthermore, we identified the insertion sequences IS<i>4351</i> and IS<i>1380</i> as key mobile elements mediating the co-localization of <i>tetX</i> and <i>ermF</i>/<i>ermD</i> resistance genes within ORT isolates of Clade O1. These findings enhance our understanding of ORT's genetic diversity, strain distribution, and resistance mechanisms, providing a basis for improved monitoring, vaccine development, and targeted interventions. The limited genetic variability observed in our data set underscores the challenges of identifying resistance genes and highlights the need for novel approaches to fully elucidate resistance mechanisms.IMPORTANCE<i>Ornithobacterium rhinotracheale</i> (ORT) is a bacterial pathogen that causes significant respiratory and systemic disease in poultry, leading to economic losses worldwide. By sequencing and comparing 94 isolates from Austria and Hungary, we discovered two major ORT strains circulating in these regions. One strain is unique to Europe and carries multiple antibiotic resistance genes on a mobile element, underscoring the need for careful antibiotic use. This study is the first large-scale genomic analysis of European ORT isolates, revealing how these strains spread and evolve over time. Our findings offer valuable insights for improving diagnostic methods, guiding vaccine development, and designing targeted strategies to manage ORT infections in commercial poultry flocks.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0056925"},"PeriodicalIF":3.7,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366310/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673804","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":"Historic mine waste contains diverse microbial communities that reflect waste type and geochemistry.","authors":"Mackenzie B Best, Zohreh Kazemi Motlagh, Virginia T McLemore, Daniel S Jones","doi":"10.1128/aem.00434-25","DOIUrl":"10.1128/aem.00434-25","url":null,"abstract":"<p><p>Waste rock and tailings left behind by historic mining operations can contain substantial critical mineral resources. However, over the decades and centuries, since these deposits were emplaced, microbial communities developed that can catalyze rock weathering and elemental cycling, which could have impacted the economic resources but also might be harnessed for future biomining or other metal recovery efforts. Here, we combined microbial cell counting, rRNA gene and transcript sequencing, and whole rock geochemistry to compare the composition and abundance of microbial communities from five inactive mine sites in south-central New Mexico that contain critical minerals. While acidic seeps and adits at the sites contained organisms commonly found in acid rock drainage and bioleaching operations, these organisms were only present at very low abundance in the waste rock and tailings, which were instead dominated by bacteria and archaea that are related to inorganic nitrogen- and organic carbon-oxidizing taxa. Generally, rRNA transcript libraries contain many of the same organisms as rRNA gene libraries, indicating that most of these populations are active. Differences among total and active microbial communities correspond to waste rock geochemistry, including concentrations of sulfur, iron, and other variables such as copper, lead, and rare earth elements. Nevertheless, many of the rRNA gene and transcript sequences in these deposits were from groups without cultured representatives, and these unknown microorganisms are likely important for biogeochemical cycling over the long lifetime of these waste deposits. We also discuss recommendations for microbiological assessment of similar large historic mine waste deposits.</p><p><strong>Importance: </strong>New Mexico has a long history of mining, with hundreds of mining districts across the state, many of which contain inactive operations with historic tailings and waste rock. Because metallurgical processing was in its infancy when most of these mines were active, they contain substantial metal resources in tailings and waste rock that could be used to support domestic demand for critical minerals. We found that microbial communities associated with these deposits do not represent typical bioleaching communities, and instead are dominated by taxa not typically associated with mine waste. However, the deposits did contain rare iron and sulfur-cycling taxa that could catalyze metal mobilization, as well as active populations of novel microorganisms that are likely important for biogeochemical cycling. These microbial communities could represent important resources for bioremediation and other biotechnological applications to recover valuable elements from these and other historic mine wastes.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0043425"},"PeriodicalIF":3.7,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366339/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144697449","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":"Reply to Almeida, \"Unreliable evidence to support a vector regulation hypothesis for <i>Xylella fastidiosa</i>-leafhopper interactions\".","authors":"Elaine A Backus, Holly J Shugart","doi":"10.1128/aem.00889-25","DOIUrl":"10.1128/aem.00889-25","url":null,"abstract":"","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0088925"},"PeriodicalIF":3.7,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366342/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144752108","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":"Slow food for lactobacilli: characterization of 1,2-propanediol metabolism in <i>Levilactobacillus parabrevis</i> FUA3697 in sourdough.","authors":"Vi D Pham, Michael G Gänzle","doi":"10.1128/aem.01207-25","DOIUrl":"https://doi.org/10.1128/aem.01207-25","url":null,"abstract":"<p><p>Some lactobacilli convert lactate to acetate and 1,2-propanediol in the stationary phase of growth, but the key enzyme of the pathway, lactaldehyde dehydrogenase, has not been characterized in any of the <i>Lactobacillales</i>. It was, therefore, the aim of this study to characterize lactate to 1,2-propanediol conversion in <i>Levilactobacillus parabrevis</i> FUA3697. The strain converted lactate to 1,2-propanediol during 14 days of incubation. The concentration of 1,2-propanediol was higher in media with maltose, glucose, and fructose as carbon sources when compared to arabinose; the addition of lactate increased the 1,2-propanediol formation. The 1,2-propanediol formation was higher in sourdough than in laboratory media and higher in sorghum sourdoughs than in wheat sourdoughs. The construction of a mutant strain <i>Lv. parabrevis</i> FUA3697Δ<i>aldA</i> confirmed that AldA is responsible for the conversion, as the mutant strain did not produce 1,2-propanediol. Competition experiments demonstrated that the disruption of <i>aldA</i> slightly decreased the competitiveness in wheat sourdoughs but not in sorghum sourdoughs. After incubation of the strains over 28 days at 4°C, the wild-type strain resumed growth and acidification faster than the <i>aldA</i>-deficient isogenic mutant. In summary, lactate conversion to acetate and 1,2-propanediol maintains slow metabolic activity over weeks or even months, thus increasing the ecological fitness.IMPORTANCEThe genes coding for lactate conversion to 1,2-propanediol are relatively broadly distributed in heterofermentative lactobacilli and also present in few homofermentative lactobacilli. To date, the conversion has been verified experimentally only in <i>Lentilactobacillus buchneri</i>, few other lentilactobacilli and, more recently, <i>Levilactobacillus lettrarii</i>. 1,2-Propanediol is a substrate for further conversion to propionic acid. The metabolic pathway contributes to spoilage of pickles and cider but is considered a beneficial metabolic trait in silage and sourdough fermentations. Our results document that lactobacilli using this pathway can be employed for improved activity and competitiveness of starter cultures that are distributed under refrigerated conditions.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0120725"},"PeriodicalIF":3.7,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144939255","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":"Key findings from 15 years of <i>Mangrovibacter</i> research: a generalist bacterium beyond endophytes.","authors":"Hong Soon Chin, Narendrakumar Ravi Varadharajulu, Kah Cheng Teo, Peter Chiew Hing Cheong, Sen-Lin Tang","doi":"10.1128/aem.02479-24","DOIUrl":"10.1128/aem.02479-24","url":null,"abstract":"<p><p>Since the discovery of <i>Mangrovibacter plantisponsor</i> in 2010, research on <i>Mangrovibacters</i> (MGBs) has stagnated. Although laboratories worldwide have isolated various MGB strains and deposited their 16S rDNA sequences in the NCBI database, a limited understanding of MGBs has resulted in only a few publications from these collections. Recent advancements in metagenomic technology have revealed the presence of MGBs in a broader range of habitats. Most microbiomes exhibit low MGB abundance (typically <1%). Even in environments with higher prevalence, such as salt-tolerant aerobic granular sludge (75%), the gut of superworms fed with polyurethane (22%), or fermented foods like mandai (16%), the functional roles of MGBs remain unclear. Through meticulous curation of publications and data from MicrobeAtlas and AMIBASE, MGBs can be classified as free living, endophytic, or zoonotic. Recent evidence suggests their presence in food sources and potential interactions with humans. Current studies confirm the coexistence of MGBs with humans. This review underscores the phenotypic features and genomic foundations of MGBs, highlighting attributes such as endophytic behavior, diverse metabolite utilization, tolerance to salinity and pH, metal homeostasis, biofilm formation, and bioremediation potential. Insights are derived from the analysis of four MGB genomes deposited in NCBI since 2014, along with three newly reported genomes in 2024. Experimental and genetic evidence suggests that MGBs act as \"generalist microbes\" capable of thriving in diverse nutrient sources and harsh environments. This review elucidates prospective research trajectories and highlights numerous potential commercial applications of MGBs, emphasizing the need for further investigation into their roles and benefits.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0247924"},"PeriodicalIF":3.7,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366330/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144599189","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":"Metabolic engineering of <i>Saccharomyces cerevisiae</i> for <i>de novo</i> biosynthesis of hydroxytyrosol and salidroside.","authors":"Jingfang Sun, Lingling Zhu, Liuping Duan, Furong Li, Shuai Guo, Jinlei Bian, Lin Yang","doi":"10.1128/aem.00712-25","DOIUrl":"10.1128/aem.00712-25","url":null,"abstract":"<p><p>Hydroxytyrosol and salidroside are phenylethanol compounds with significant industrial applications but limited availability due to low-yield natural extraction and complex chemical synthesis. In this study, <i>Saccharomyces cerevisiae</i> was engineered to achieve efficient <i>de novo</i> biosynthesis of these compounds. A tyrosol-producing strain (ZYT1) was optimized to produce 571.8 mg/L tyrosol, which served as the yeast chassis cell for hydroxytyrosol synthesis. By integrating <i>PaHpaB</i> and <i>EcHpaC</i>, strain ZYHT1 produced 304.4 mg/L hydroxytyrosol in shake-flask fermentation, which increased to 677.6 mg/L in a 15 L bioreactor after auxotrophic repair. For salidroside production, glycosyltransferase <i>RrU8GT33</i> was introduced into ZYT1, yielding strain ZYSAL1 with 48.4 mg/L salidroside. Enhancing UDP-glucose supply using truncated sucrose synthase (<i>tGuSUS1</i>) led to strain ZYSAL9+3, which achieved 1,021.0 mg/L in shake flasks and 18.9 g/L in fed-batch fermentation. This work demonstrates the scalable production of hydroxytyrosol and salidroside in yeast, providing a basis for industrial applications and advancing synthetic biology approaches for natural product biosynthesis.</p><p><strong>Importance: </strong>Hydroxytyrosol and salidroside are valuable natural compounds with strong antioxidant, anti-inflammatory, and neuroprotective properties, widely used in pharmaceuticals, cosmetics, and health supplements. However, traditional extraction from plants is inefficient, and chemical synthesis is costly and environmentally unfriendly. In this study, we engineered <i>Saccharomyces cerevisiae</i>, a common yeast, to efficiently produce these compounds from simple carbon sources such as glucose and sucrose. By optimizing key biosynthetic pathways, improving cofactor supply, and enhancing sucrose metabolism, we achieved high production levels suitable for industrial applications. Our work provides a sustainable and scalable microbial platform for producing hydroxytyrosol and salidroside, reducing reliance on plant extraction and chemical synthesis. This research advances the field of microbial biotechnology by demonstrating how engineered yeast can serve as a green factory for valuable bioactive compounds, opening new possibilities for large-scale production and commercial use.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0071225"},"PeriodicalIF":3.7,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366309/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144641595","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":"Rumen Synergistota: new insights into their role in mimosine and fluoroacetate toxicity of ruminant livestock.","authors":"Christopher S McSweeney, Michael Halliday, Roderick I Mackie","doi":"10.1128/aem.00380-25","DOIUrl":"10.1128/aem.00380-25","url":null,"abstract":"<p><p>This paper examines several rumen bacteria in the Synergistota phylum, specifically focusing on their potential to detoxify harmful compounds found in plants grazed by ruminants. Synergistota bacteria ferment amino acids for energy, while rumen <i>Synergistes jonesii</i> from which the phylum was named, can also metabolize toxins found in the forage plant <i>Leucaena leucocephala</i> (leucaena). Specifically, <i>S. jonesii</i> is able to detoxify mimosine, a non-protein amino acid in leucaena, by converting it into less harmful metabolites. Historically, <i>S. jonesii</i> was introduced to ruminants in Australia to mitigate leucaena toxicity based on the notion that the bacterium was absent on this continent. Recent studies indicate geographic variations in <i>S. jonesii's</i> presence and effectiveness, suggesting that strain variability may impact its detoxification efficacy. PCR-based assays have improved the detection of <i>S. jonesii</i>, revealing its widespread distribution in Australia and globally, but often low abundance in ruminant microbiomes. Additionally, other rumen Synergistota species (<i>Cloacibacillus porcorum</i> and <i>Pyramidobacter piscolens</i>) have recently been isolated and identified as agents for metabolizing fluoroacetate, another toxin present in Australian flora. These bacteria degrade fluoroacetate through a novel molecular mechanism of reductive dehalogenation, thus producing fluoride ions and acetate as byproducts. This mechanism has been detected in soil and contaminated groundwater but not the rumen. These findings underscore the ecological importance of Synergistota bacteria in reducing plant toxicity in ruminants. Ongoing research is recommended to isolate new strains, optimize rumen populations of these bacteria, and further understand the molecular pathways involved in toxin degradation to enhance detoxification capabilities in ruminant populations.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0038025"},"PeriodicalIF":3.7,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366334/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144648373","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":"Distinct strategies of soil bacterial generalists and specialists in temperate deciduous broad-leaved forests.","authors":"Xueying Li, Haixia Li, Senlin Wang, Huiping Zhang, Yizhen Shao, Yun Chen, Zhiliang Yuan","doi":"10.1128/aem.00992-25","DOIUrl":"10.1128/aem.00992-25","url":null,"abstract":"<p><p>Based on global biotic homogenization, habitat generalists and specialists play an important role in maintaining the stability of ecosystems. However, limited information is available about the assembly processes and co-occurrence patterns of soil bacterial habitat specialists and generalists in forest ecosystems, particularly their response mechanisms to environmental factors. In this study, high-throughput sequencing technology was used to investigate the role of the ecological assemblage processes of soil bacterial habitat specialists and generalists and their role in maintaining the stability of the symbiotic network in temperate deciduous broad-leaved forests (China). The results showed that compared with specialists, the diversity of bacterial habitat generalists was lower, but their distribution ranges and environmental niche breadth were wider. Results from the null and neutral models indicate that, compared to deterministic processes, the community assembly of habitat generalists and specialists is more strongly influenced by stochastic processes, with generalists exhibiting a higher degree of stochasticity than specialists. Network analysis results showed that habitat specialists played a greater role in maintaining the stability of the bacterial co-occurrence network than the generalists. In addition, bacterial habitat specialists were more likely to be affected by light and spatial feature vectors than generalists. These findings provide a novel perspective for understanding the assembly processes and diversity maintenance mechanisms of the forest soil bacterial community.</p><p><strong>Importance: </strong>Limited information is available about bacterial specialists and generalists in forests. Generalists were more affected by stochastic processes than specialists. Specialists played a more important role in network stability than generalists. Light and spatial vectors had stronger effects on specialists than generalists.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0099225"},"PeriodicalIF":3.7,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366338/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144741011","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}