Archives of Microbiology最新文献

{"title":"Generation and validation of a versatile inducible multiplex CRISPRi system to examine bacterial regulation in the Euprymna-Vibrio fischeri symbiosis","authors":"Brian Lynn Pipes,&nbsp;Michele Kiyoko Nishiguchi","doi":"10.1007/s00203-025-04354-8","DOIUrl":"10.1007/s00203-025-04354-8","url":null,"abstract":"<div><p>The <i>Vibrio fischeri</i>—<i>Euprymna scolopes</i> symbiosis has become a powerful animal—microbe model system to examine the genetic underpinnings of symbiont development and regulation. Although there has been a number of elegant bacterial genetic technologies developed to examine this symbiosis, there is still a need to develop more sophisticated methodologies to better understand complex regulatory pathways that lie within the association. Therefore, we have developed a suite of CRISPR interference (CRISPRi) vectors for inducible repression of specific <i>V. fischeri</i> genes associated with symbiotic competence. The suite utilizes both Tn7-integrating and shuttle vector plasmids that allow for inducible expression of CRISPRi dCas9 protein along with single-guide RNAs (sgRNA) modules. We validated this CRISPRi tool suite by targeting both exogenous (an introduced mRFP reporter) and endogenous genes (<i>luxC</i> in the bioluminescence producing <i>lux</i> operon, and f<i>lrA</i>, the major regulatory gene controlling flagella production). The suite includes shuttle vectors expressing both single and multiple sgRNAs complementary to the non-template strand of multiple targeted genetic loci, which were effective in inducible gene repression, with significant reductions in targeted gene expression levels. <i>V. fischeri</i> cells harboring a version of this system targeting the <i>luxC</i> gene and suppressing the production of luminescence were used to experimentally validate the hypothesis that continuous luminescence must be produced by the symbiont in order to maintain the symbiosis at time points longer than the known 24-h limit. This robust new CRISPRi genetic toolset has broad utility and will enhance the study of <i>V. fischeri</i> genes, bypassing the need for gene disruptions by standard techniques of allelic knockout-complementation-exchange and the ability to visualize symbiotic regulation in vivo.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 7","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00203-025-04354-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144074109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RsmG methylation of 16S rRNA affects the function of ribosomal protein uS12","authors":"Trevor W. Bell,&nbsp;Rowan M. Turner,&nbsp;Amanda M. Merryman,&nbsp;Juliana J. Joseph,&nbsp;Steven T. Gregory,&nbsp;Michael O’Connor","doi":"10.1007/s00203-025-04349-5","DOIUrl":"10.1007/s00203-025-04349-5","url":null,"abstract":"<div><p>The RsmG methyltransferase modifies G527 in bacterial 16S rRNA and its inactivation confers low level streptomycin resistance. In contrast, high level streptomycin resistance typically requires specific alterations in ribosomal protein uS12 or 16S rRNA. Here, we have asked if <i>rsmG</i> inactivation alters the phenotypes of any of a collection of randomly-generated <i>Escherichia coli</i> uS12 mutants. While several uS12 mutants show moderately increased resistance to streptomycin when <i>rsmG</i> is inactivated (MIC = 10–40 µg/ml), a uS12 R85H/<i>rsmG</i>-inactivated strain uniquely displays very high resistance (MIC &gt; 1,024 µg/ml). Additional genetic selections showed that <i>rsmG</i> null mutations combined with specific alterations in uS12 can generate streptomycin-dependence, or pseudo-dependence, in addition to resistance. Moreover, growth of several of these mutants on high concentrations of streptomycin is conditional on <i>rsmG</i> inactivation. Thus, loss of m⁷G527 methylation affects the streptomycin phenotypes of distinct uS12 mutants and identifies an additional route to high-level streptomycin resistance in bacteria.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 7","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144073616","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Endophytes of Zingiberaceae: distribution and bioactivity of their bioactive metabolites","authors":"Nor Hazwani Mohd Hasali,&nbsp;Muhammad Shahbaz,&nbsp;Jaya Seelan Sathiya Seelan,&nbsp;Nazirul Azam Ibrahim,&nbsp;Christophe Wiart,&nbsp;Nivaarani Arumugam,&nbsp;Mohammed Abdus Salam,&nbsp;Muneeb M. Musthafa,&nbsp;Suganthi Appalasamy","doi":"10.1007/s00203-025-04335-x","DOIUrl":"10.1007/s00203-025-04335-x","url":null,"abstract":"<div><p>The endophytes associated with the Zingiberaceae family have demonstrated remarkable potential in various biological activities through their bioactive compounds that are useful for both medical and agricultural purposes. Additionally, isolated secondary metabolites from symbiotic microbes associated with this family of plants have shown promising results in various biological activities such as antifungal, anticancer, antidiabetic, anti-inflammatory, and antibacterial. This review focuses on the bioactive metabolites of Zingiberaceae endophytes with their potential biological activities against different pathogens as well as the production of phytohormones that promote plant growth. Furthermore, bibliometric analysis revealed the current key trends and collaborative works in this field. Additionally, the bibliometric analysis also explored a total of 75 relevant publications from the Scopus database that India is the most contributing country in this field with 38.7% of the total reported research work. The bibliometric approach helps uncover new research gaps by identifying emerging trends, underexplored topics, and collaborative networks, providing insights into areas that require further investigation and development. Notably, <i>Streptomyces</i> spp. have been commonly reported as potent endophytes, generating bioactive substances such as Vanillin and Resacetophenone with strong antibacterial activities. Significant knowledge gaps still exist, and with evolving therapeutic potential, this could offer a wide opportunity for new studies to emerge.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 6","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143938312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the oral bacteria-oral lichen planus connection: mechanisms, clinical implications and future directions","authors":"Wei-long Zhang,&nbsp;Lian-pin Yu,&nbsp;Wei Zhou,&nbsp;Xue Wang,&nbsp;Juan Du","doi":"10.1007/s00203-025-04342-y","DOIUrl":"10.1007/s00203-025-04342-y","url":null,"abstract":"<div><p>Oral lichen planus (OLP) is a prevalent T-cell mediated inflammatory-immune disease with uncertain etiology. Recently, there is emerging evidence suggesting that oral bacteria may exert a prominent role in the onset and development of OLP. They might promote the initiation and progression of OLP by disrupting the oral epithelia, invading the lamina propria, stimulating pro-inflammatory cytokines production and inducing immune dysfunction. In this review, we will focus on the possible mechanisms of oral bacteria contributing to occurrence and development of OLP, and provide new insights into the bacteria-related diagnosis, prevention and treatment strategies for OLP.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 6","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143938417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impacts of PAR and UV radiation on diurnal photosynthesis performance, pigment composition, and antioxidant function of the hot-spring cyanobacterium Nostoc sp. strain VKB02","authors":"Megha Jaiswal,&nbsp;Nasreen Amin,&nbsp;Vinod K. Kannaujiya","doi":"10.1007/s00203-025-04338-8","DOIUrl":"10.1007/s00203-025-04338-8","url":null,"abstract":"<div><p>Diurnal oscillations are 24 h clock, that synchronize organisms biological functions based on the daily environmental fluctuation. Continuous increase in ultraviolet radiation have been shown to affect the biological clock of cyanobacteria. The present investigation deals with the 12/12 h of light/dark effects of PAR and PAB (PAR + UVA + UVB) irradiations on ecophysiology and defense management of a hot-spring cyanobacterium <i>Nostoc</i> sp. strain VKB02. The alternative L/D exposure of PAR showed increase in growth and pigment compositions. However, PAB radiation has significantly decreased within the same parameters after the L1 phase except for carotenoid and APC, while PE and PC recovered till the D2 phase corresponding to the counter light phase. The pigments destruction also resulted in Chl <i>a</i> fluorescence (F_v/F_m, F_v׳/F_m׳, Y(II), rETR) emission decline. In addition, PAB exposure accelerated free radicals generation with induced protein oxidation (RCG) and antioxidative enzymes (SOD, POD, CAT) as counteract defense during the light phase. The overall circadian regime facilitated the resynthesis fate of pigment-protein complexes and the mitigation of the high level of ROS production. This result suggests the unique survival strategy of the hot-spring cyanobacterium against ultraviolet radiation in a diurnal manner. This study also offers a deep understanding of the diurnal eco-physiological and biochemical responses of the cyanobacterium for the advancement in sustainable agricultural production with lower input in variable climate.</p><h3>Graphical Abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 6","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143938418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Endophytic fungi of Cynodon dactylon: a treasure trove of bioactive compounds","authors":"R. Nischitha,&nbsp;Sanjay K. Singh","doi":"10.1007/s00203-025-04296-1","DOIUrl":"10.1007/s00203-025-04296-1","url":null,"abstract":"<div><p><i>Cynodon dactylon</i> (L.) Pers., commonly known as Bermuda grass, is a medicinally significant plant recognized for its diverse pharmacological properties. Recent research highlights that its association with endophytic fungi contributes to the synthesis of bioactive secondary metabolites with immense therapeutic and agricultural potential. These fungal endophytes produce a wide spectrum of bioactive compounds, including antimicrobial, antioxidant, anticancer, immunosuppressive, and plant growth-promoting agents, positioning them as valuable resources for drug discovery and sustainable biotechnological applications. Despite their vast potential, the biodiversity, metabolic pathways, and functional significance of endophytic fungi in <i>C. dactylon</i> remain underexplored. This review consolidates the current knowledge on the isolation, identification, and characterization of endophytic fungi from <i>C. dactylon</i>, emphasizing their bioactive metabolites and pharmacological significance. Furthermore, it explores their biotechnological applications and the future scope of utilizing these fungi in pharmaceutical and agricultural advancements. Understanding the metabolic potential of these fungal endophytes can open new avenues for harnessing novel bioactive compounds, contributing to the development of innovative therapeutics and eco-friendly agricultural solutions.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 6","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143932327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pseudomonas aeruginosa biofilm: treatment strategies to combat infection","authors":"Rashmi Ramesh,&nbsp;N. D. Rekha,&nbsp;Shubha Gopal","doi":"10.1007/s00203-025-04346-8","DOIUrl":"10.1007/s00203-025-04346-8","url":null,"abstract":"<div><p><i>Pseudomonas aeruginosa</i> is an opportunistic human pathogenic bacterium that is a common cause of both acute and chronic infections. Multidrug-resistant <i>P. aeruginosa</i> poses a significant challenge to antibiotics and therapeutic approaches due to its pathogenicity, virulence, and biofilm-forming ability mediated by quorum sensing. Understanding the pathogenic mechanisms is essential for developing potential drug targets. In this regard, strategies aimed at combating the targeted inhibition of virulence, quorum sensing pathways, secretion systems, biofilm-associated two-component systems, and signalling system regulators (such as c-di-GMP) associated with biofilm formation are critical. Several new antimicrobial agents have been developed using these strategies, including antimicrobial peptides, bacteriophages, nanoantibiotics, photodynamics, and natural products, which are considered promising therapeutic tools. In this review, we address the concept of biofilms, their regulation, and recent treatment strategies to target <i>P. aeruginosa</i>, a clinically significant pathogen known for biofilm formation.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 6","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143932328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic insights into methanol utilization in Pichia pastoris lacking AOX genes under co-feeding conditions","authors":"Xueyun Zheng,&nbsp;Zhifang Ye,&nbsp;Jiao Gao,&nbsp;Yuechuo Hao,&nbsp;Cheng Li,&nbsp;Hongsen Xie,&nbsp;Ying Lin,&nbsp;Shuli Liang","doi":"10.1007/s00203-025-04339-7","DOIUrl":"10.1007/s00203-025-04339-7","url":null,"abstract":"<div><p>The methylotrophic yeast <i>Pichia pastoris</i> (<i>P. pastoris</i>) exhibits remarkable capability for methanol-driven protein biosynthesis, positioning it as an attractive platform for carbon-neutral biomanufacturing utilizing methanol as a renewable feedstock. However, challenges arising from methanol metabolism, particularly the accumulation of toxic formaldehyde intermediates, significantly hinder efficient methanol biotransformation. To address this limitation, we implemented a metabolic engineering strategy involving dual knockout of alcohol oxidase genes (<i>aox1</i> and <i>aox2</i>) combined with glycerol co-substrate supplementation. Using enhanced green fluorescent protein (EGFP) as a model heterologous product, we demonstrated that the ΔAOX1/2 strain achieved superior protein productivity in glycerol-methanol co-feeding cultures. Under optimized conditions (0.5% methanol + 0.4% glycerol), the engineered strain attained a biomass density of 38.5 (OD₆₀₀) and EGFP fluorescence intensity of 494,723 units, representing improvements of 32.8% and 53.6%, respectively, compared to the wild-type (WT) strain cultivated with 1% methanol alone. Transcriptome profiling revealed that the observed enhancement in protein synthesis originated from optimized methanol utilization through coordinated upregulation of both assimilatory and dissimilatory metabolic modules. This study demonstrates that alcohol oxidase suppression coupled with glycerol co-metabolism constitutes an effective strategy to alleviate methanol-derived metabolic stress while enhancing heterologous protein yields in <i>P. pastoris</i>.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 6","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143925707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification of CYP450 in Ganoderma lucidum and expression analysis of genes related to ganoderic acid synthesis","authors":"Xiaolu Li,&nbsp;Dong Liu,&nbsp;Bangxing Han,&nbsp;Shiping Huang,&nbsp;Hui Deng","doi":"10.1007/s00203-025-04344-w","DOIUrl":"10.1007/s00203-025-04344-w","url":null,"abstract":"<div><p>The biosynthesis mechanism of ganoderic acid, a class of secondary metabolites of <i>Ganoderma lucidum</i>, is currently unknown. Members of <i>G. lucidum</i>’s <i>CYP450</i> gene family were found in this study by genome-wide analysis. Determination of ganoderic acid content in Jilin, Zhejiang, Jinzhai, Fujian, Yunnan and Shandong regions was performed using high performance liquid chromatography. Expression of <i>CYP450</i> gene of <i>G. lucidum</i> from Jilin, Jinzhai and Shandong origins was analyzed by transcriptome sequencing. The findings indicated that, through comprehensive sequence analysis and functional annotation, 189 <i>CYP450</i> genes were detected in the <i>G. lucidum</i> genome, among which 34 <i>CYP450</i> genes were significantly differentially expressed in transcriptome analysis, and the gene expression was positively correlated with ganoderic acid content. Bioinformatics analysis predicted the conserved motifs, structural features, and subcellular localization of 189 <i>CYP</i> genes, revealing significant differences in gene structure and protein motif composition among <i>GlCYP450</i> family members. Subcellular localization revealed that they are located in the plasma membrane, cytoplasm, nucleus, mitochondria, peroxisome, endoplasmic reticulum, extracellular space, and cytoskeleton, suggesting that they have multiple functions. A number of cis-regulatory elements associated with stress responses and phytohormones were identified in the promoter regions of these genes. It demonstrates that ganoderic acid production has been significantly controlled by these <i>P450</i> genes. These findings offer a crucial theoretical foundation for a thorough comprehension of the process of ganoderic acid production, the bioinformatics role of <i>CYP450</i> genes in <i>G. lucidum</i>, and the selection and breeding of superior <i>G. lucidum</i> resources.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 6","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143919050","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Leaf transcriptomic responses to arbuscular mycorrhizal symbioses exerting growth depressions in tomato","authors":"Fengwei Diao,&nbsp;Ke Liu,&nbsp;Wenjing Wu,&nbsp;Jing Xu","doi":"10.1007/s00203-025-04343-x","DOIUrl":"10.1007/s00203-025-04343-x","url":null,"abstract":"<div><p>Arbuscular mycorrhizal (AM) fungi play important roles in sustainable agriculture, given that they provide multiple benefits for numerous crops. Conversely, negative plant growth effects induced by AM fungi are also occasionally observed. However, little information is available regarding the responses of symbiosis. In this study, compared with an absence of AM fungus inoculation, tomato seedlings inoculated with <i>Funneliformis mosseae</i> or <i>Rhizophagus intraradices</i> were characterized by reduced shoot and root growth. The two AM fungi decreased the carbon contents and the carbon-nitrogen ratios in shoots. To gain further insights into the underlying mechanisms, transcriptomic analyses were performed in the study. A total of 190 and 870 differentially expressed genes (DEGs) were identified in the <i>F. mosseae</i> vs. control and <i>R. intraradices</i> vs. control comparisons, respectively. KEGG enrichment analysis of the former 190 DEGs revealed significant enrichment of the “Protein processing in endoplasmic reticulum,” “Flavonoid biosynthesis,” “Flavone and flavonol biosynthesis,” and “Stilbenoid, diarylheptanoid, and gingerol biosynthesis” pathways, whereas “DNA replication,” “Photosynthesis - antenna proteins,” “Cutin, suberine, and wax biosynthesis,” “Protein processing in endoplasmic reticulum,” and “Glycerophospholipid metabolism” were identified as pathways significantly enriched with the latter 870 DEGs. GO functional analysis revealed that among both groups of DEGs, large numbers of genes were assigned the “Response to stimulus” term. Moreover, many of the enriched terms were associated with stimulus and stress response processes, including response to salt stress, heat, and reactive oxygen species. Therefore, the findings indicated that AM fungi may trigger defense-related responses in hosts, even though the symbioses performed growth depressions. These findings will contribute to advancing our current understanding of AM fungi.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 6","pages":""},"PeriodicalIF":2.3,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143918917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}