Applied and Environmental Microbiology最新文献

{"title":"Flagellum-driven motility enhances <i>Pseudomonas aeruginosa</i> biofilm formation by altering cell orientation.","authors":"Guanju Wei, Jessica-Jae S Palalay, Joseph E Sanfilippo, Judy Q Yang","doi":"10.1128/aem.00821-25","DOIUrl":"10.1128/aem.00821-25","url":null,"abstract":"<p><p>Bacterial motility plays a crucial role in biofilm development, yet the underlying mechanism remains not fully understood. Here, we demonstrate that the flagellum-driven motility of <i>Pseudomonas aeruginosa</i> enhances biofilm formation by altering the orientation of bacterial cells, an effect controlled by shear stress rather than shear rate. By tracking wild-type <i>P. aeruginosa</i> and its non-motile mutants in a microfluidic channel, we demonstrate that while non-motile cells align with the flow, many motile cells can orient toward the channel sidewalls, enhancing cell surface attachment and increasing biofilm cell density by up to 10-fold. Experiments with varying fluid viscosities further demonstrate that bacterial swimming speed decreases with increasing fluid viscosity, and the cell orientation scales with the shear stress rather than shear rate. Our results provide a quantitative framework to predict the role of motility in the orientation and biofilm development under different flow conditions and viscosities.IMPORTANCEBiofilms are ubiquitous in rivers, water pipes, and medical devices, impacting the environment and human health. While bacterial motility plays a crucial role in biofilm development, a mechanistic understanding remains limited, hindering our ability to predict and control biofilms. Here, we reveal how the motility of <i>Pseudomonas aeruginosa</i>, a common pathogen, influences biofilm formation through systematically controlled microfluidic experiments with confocal and high-speed microscopy. We demonstrate that the orientation of bacterial cells is controlled by shear stress. While non-motile cells primarily align with the flow, many motile cells overcome the fluid shear forces and reorient toward the channel sidewalls, increasing biofilm cell density by up to 10-fold. Our findings provide insights into how bacterial transition from free-swimming to surface-attached states under varying flow conditions, emphasizing the role of cell orientation in biofilm establishment. These results enhance our understanding of bacterial behavior in flow environments, informing strategies for biofilm management and control.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0082125"},"PeriodicalIF":3.9,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12285247/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144551786","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":"Ultrahigh-throughput screening of environmental bacteria for proteolytic activity using droplet-based microfluidics.","authors":"Akihiro Nakamura, Yoshiyuki Suzuki, Nobuyuki Homma, Yosuke Shida, Rikako Sato, Hiroaki Takaku, Wataru Ogasawara","doi":"10.1128/aem.00109-25","DOIUrl":"10.1128/aem.00109-25","url":null,"abstract":"<p><p>Exploration of diverse microbial sources, particularly environmental bacteria, is needed to identify novel and efficient peptidases/proteases that can be used in a variety of industrial applications. However, conventional function-based screening methods are inefficient and preclude the use of diverse microbial resources. This study illustrates a revolutionary approach to microbial screening using droplet-based microfluidics and fluorescence-activated droplet sorting that targets endopeptidases. Droplet-based microfluidic systems are a powerful tool for culturing microorganisms and for detecting microbial functions inside droplets with ultra-high throughput. However, droplet-based microfluidics for screening the proteolytic activity of environmental bacteria at a large scale remains largely unexplored. Here, we screened approximately 630,000 microorganisms in 6 h and obtained four species with high peptidase activity using droplet-based microfluidics. Furthermore, we isolated an Asp-specific endopeptidase from the isolated bacteria <i>Lysobacter soli</i> and showed that its activity was 2.4-fold higher than that of the related commercially available enzyme. The successful isolation of Asp-specific peptidase with superior activity in a short period of time compared to existing alternatives underscores the efficacy of droplet-based microfluidics for function-based microbial screening.</p><p><strong>Importance: </strong>As global efforts to reduce environmental impact progress, realization of the significance of biomanufacturing bio-based products has risen, increasing the demand for microbial-based manufacturing. Producing diverse bio-based products through biomanufacturing requires isolating suitable host organisms from environmental sources and screening them for essential genetic characteristics. Efficient screening methods based on microbial activity and functionality are thus essential to significantly expand the scope of bio-based products. Here, we demonstrate the development of a highly efficient screening system for functional screening of environmental bacteria using a droplet-based microfluidic device. This platform enables the streamlined isolation of microbial strains and acquisition of genetic resources from the environment and is tailored to specific microbial activities and functions. In this study, we have demonstrated the efficacy of this droplet-based method for functional screening and have shown its potential for scalability to industrial levels for advancing bio-based production.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0010925"},"PeriodicalIF":3.9,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12285256/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144282136","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":"Enzymatic property and stabilization mechanism of LysBT1, a novel polyextremotolerant endolysin with a C-terminal S-layer homology domain.","authors":"Yu Li, Ke Luo, Chaofeng Jiang, Yihao Zhang, Yong Yang, Yitong Yao, Huai Li, Fei Gan, Xiao-Feng Tang, Bing Tang","doi":"10.1128/aem.00867-25","DOIUrl":"10.1128/aem.00867-25","url":null,"abstract":"<p><p>Phage-encoded endolysins are getting increasing attention because of their potential to serve as alternative antimicrobials to combat antibiotic-resistant bacteria. Here, we report a novel endolysin LysBT1, which is encoded by a prophage of thermophilic <i>Brevibacillus thermoruber</i> WF146 and comprises an N-acetylmuramoyl-L-alanine amidase domain and an S-layer homology (SLH) domain not found in known endolysins. LysBT1 is not only extremely thermostable, retaining more than 60% activity after 1 h incubation at 95°C, but also highly stable over a wide pH range of 4.0-11.0. Moreover, the thermostability of LysBT1 could be enhanced by EDTA or reducing agents. Although none of the seven cysteine residues of LysBT1 participate in disulfide bond formation, six of them, including the catalytic Zn²⁺-coordinating Cys156, are involved in stabilizing the enzyme at elevated temperatures. The SLH domain contributes to the thermostability of LysBT1 and mediates cell surface binding of the enzyme to facilitate enzymatic lysis of strain WF146 cells via increasing local enzyme concentration around the substrate. LysBT1 is capable of trimerization, where the SLH domains are predicted to form a three-prong spindle-like trimer similar to that in S-layer proteins. The SLH domain of LysBT1 could bind to cell surfaces of both Gram-positive and Gram-negative bacteria. LysBT1 can lyse not only Gram-positive strain WF146, <i>Geobacillus stearothermophilus</i>, and <i>Bacillus subtilis</i> but also Gram-negative <i>Escherichia coli</i> and <i>Acinetobacter baumannii</i> with the aid of EDTA or citric acid. EDTA also facilitates LysBT1 to lyse <i>Bacillus cereus</i>, probably because EDTA-induced disorganization of the S-layer allows LysBT1 to access and hydrolyze the peptidoglycan.IMPORTANCEThe emergence of antibiotic-resistant bacteria has led to an urgent requirement to develop novel antimicrobials, and endolysins are regarded as ideal alternatives to antibiotics. The thermostability of endolysins plays an important role in the feasibility of enzymatic bacteriolysis. However, reports on thermostable endolysins are limited, and little is known about their stabilization mechanisms. Our results demonstrate that the thermophile-derived prophage endolysin LysBT1 is highly thermostable and functional under polyextreme (multiple forms of stress) conditions, enabling the enzyme to lyse both Gram-positive and Gram-negative bacteria in synergy with outer membrane permeabilizer. Moreover, we found that the unique S-layer homology domain of LysBT1 contributes to the stability, activity, oligomerization, and cell-wall binding ability of the enzyme. This study not only characterizes a novel endolysin but also provides new clues about the stabilization mechanisms of endolysins.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0086725"},"PeriodicalIF":3.9,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12285257/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144282233","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":"Influence of the pili of <i>Lacticaseibacillus rhamnosus</i> GG on its encapsulation and survival in mixed protein-starch gels assembled by <i>in situ</i> fermentation.","authors":"Tana Hernandez-Barrueta, Silvia Lorena Amaya-Llano, Nitin Nitin","doi":"10.1128/aem.00248-25","DOIUrl":"10.1128/aem.00248-25","url":null,"abstract":"<p><p>Preserving the viability of probiotics during storage and gastrointestinal digestion poses a significant challenge in the development of effective probiotic formulations. Thus, this study developed an <i>in situ</i> fermentation approach to encapsulate the probiotic <i>Lacticaseibacillus rhamnosus</i> GG (LGG) in a mixed whey protein/modified starch gel and evaluated (i) the role of the pili on gel formation and on the effectiveness of the gel to maintain cell viability during simulated digestion, and (ii) the storage stability of the encapsulated probiotics. Kinetic data of gels made with the wild-type (WT) or a pilus-depleted mutant (Δ<i>spaCBA</i>) strain showed a rapid <i>in situ</i> gel formation (<30 min) at room temperature after inoculating the polymeric mixture, driven by <i>in situ</i> fermentation and independently of the piliation of the cells. After simulated gastrointestinal digestion, the viability of encapsulated WT cells was ~3 log higher than free WT cells (<i>P</i> value 7 × 10^-4) and ~0.6 times higher than encapsulated Δ<i>spaCBA</i> cells (<i>P</i> value 9 × 10^-3). A higher release of Δ<i>spaCBA</i> vs WT cells from the gels was quantified, and confocal microscopy revealed the aggregation of Δ<i>spaCBA</i> but not WT cells within the gel cavities. These findings suggest the pili-dependent retention of LGG within the gel contributes to its protective effect. Finally, the hydrated gels sustained counts of LGG of 7.76-6.69 log CFU/g (depending on the relative humidity) during 2 months of storage at room temperature. In summary, bacteria-to-matrix interactions might influence the survival of probiotics during delivery, and the protein/starch gels could represent a cost-effective alternative for unrefrigerated storage and delivery of probiotics.</p><p><strong>Importance: </strong>Many probiotic formulations struggle to maintain the viability of microbial cells over time and during their passage through the gastrointestinal tract. This has led to the development of encapsulation strategies for probiotics, most of which are either costly to implement or damage the cells during the encapsulation process. To overcome these limitations, this work developed a rapid fermentation-based approach to encapsulate probiotics in protein/starch gels as a strategy to keep the cells alive during storage and digestion. Moreover, this work explored the role of interactions between bacterial cells and their encapsulation matrix on the formation of the gels and in the protection the gels provided in maintaining the viability of cells during simulated digestion. Developing this <i>in situ</i> fermentation approach for the encapsulation of probiotics and understanding the bacteria-matrix interactions will lead to the development of more effective probiotic products that can be easily deployed in low-resource settings.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0024825"},"PeriodicalIF":3.9,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12285250/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144273972","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":"Landscape-scale endophytic community analyses in replicated grapevine stands reveal that dieback disease is unlikely to be caused by specific fungal communities.","authors":"Vinciane Monod, Valérie Hofstetter, Olivier Viret, Vivian Zufferey, Katia Gindro, Daniel Croll","doi":"10.1128/aem.00782-25","DOIUrl":"10.1128/aem.00782-25","url":null,"abstract":"<p><p>Tree diebacks are complex and multifactorial diseases with suspected biotic and abiotic components. Microbiome effects on plant health are challenging to assess due to the complexity of fungal and bacterial communities. Grapevine wood dieback is the main threat to sustainable production worldwide, and no causality with microbial species has been established despite long-standing claims of fungal drivers. Here, we aimed to test the hypothesis that grapevine esca disease progression has reproducible drivers in the fungal species community. For this, we analyzed a set of 21 vineyards planted simultaneously with a single susceptible cultivar to provide unprecedented replication at the landscape scale. We sampled a total of 496 plants at the graft union across vineyards in 2 different years to perform deep amplicon sequencing analyses of the fungal communities inhabiting grapevine trunks. The communities were highly diverse with a total of 4,129 amplified sequence variants assigned to 697 distinct species. We detected trunk fungal community shifts over years of sampling, vineyards and climatic conditions, as well as disease status. However, we detect no specific fungal species driving symptom development across vineyards, contrary to long-standing expectations. The high degree of environmental standardization in the decade-long experimental plots and the well-powered replication provide the clearest evidence yet that grapevine wood dieback is most likely caused by environmental factors rather than specific pathogens. Furthermore, our study shows how landscape-scale replicated field surveys allow for powerful hypothesis testing for complex dieback disease drivers and prioritize future research directions.IMPORTANCETree diebacks are complex diseases suspected to be caused by both biological and environmental drivers. Grapevine wood dieback is a major threat to vineyards worldwide, but no specific microbial species have been experimentally implicated, despite claims that fungi are causing the symptoms. Here, we tested whether the progression of grapevine esca disease is driven by specific fungal species. We analyzed 21 long-established vineyards planted at the same time with the same susceptible grape variety to ensure consistent conditions. Over the years, we observed changes in the fungal communities inhabiting the trunk depending on the vineyard, climate, and disease status. However, contrary to expectations, we did not detect any specific fungal species that consistently could cause symptoms across the vineyards. The high level of environmental control and replication in our study provides strong evidence that grapevine wood dieback is more likely caused by environmental factors rather than specific pathogens.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0078225"},"PeriodicalIF":3.9,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12285245/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144332362","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 microbiome profiles on vaginally inserted polypropylene midurethral mesh slings compared to vaginal, urinary, and skin microbiomes.","authors":"Nazish Abbas, Thomas Willmott, Paul M Campbell, Gurdeep Singh, Maya Basu, Fiona Reid, Andrew J McBain","doi":"10.1128/aem.02463-24","DOIUrl":"10.1128/aem.02463-24","url":null,"abstract":"<p><p>Midurethral slings are widely used in the treatment of stress urinary incontinence in women. However, little is known about the microbiomes that develop on these implants, their relationship to the urinary and vaginal microbiomes, or their potential role in mesh-related complications. In this study, we characterized the microbiomes of explanted midurethral slings and examined associations with clinical complications. Seventy-four women provided a total of 397 samples, including explanted mesh, urine, and swabs from the vagina and groin or suprapubic skin. Participants were categorized into clinical groups: chronic pain, vaginal mesh exposure, lower urinary tract perforation, or recurrent incontinence (control group). Samples underwent 16S rRNA gene sequencing. The mesh microbiome was dominated by Firmicutes, Proteobacteria, and Actinobacteria, with <i>Enterococcus</i> particularly abundant. Microbial diversity was significantly higher in mesh samples compared to vaginal and skin swabs, but not urine. The mesh microbiome was compositionally distinct from the urinary, vaginal, and skin microbiomes, potentially reflecting vaginal microbiome alterations due to urinary incontinence at the time of implantation. Differences in microbial diversity in mesh and skin samples among women with pain suggest a possible microbial contribution to mesh complications. These findings demonstrate the presence of distinct, site-specific microbial communities on explanted midurethral slings, with potential implications for understanding mesh-related complications.IMPORTANCEStress urinary incontinence commonly affects women, and effective treatment is essential. Midurethral mesh slings have provided effective relief; however, long-term complications such as chronic pain, vaginal mesh exposure, and lower urinary tract perforation have emerged. The pathophysiology of these complications is not well understood but is thought to involve a heightened inflammatory response to mesh implants. The local microbiome may contribute to this inflammation. We have shown that the mesh samples harbored a distinct microbiome and that differences in microbial composition may be associated with mesh complications. Understanding the role of specific bacteria in modulating host responses may offer new insights into the pathogenesis of mesh complications and inform future clinical approaches.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0246324"},"PeriodicalIF":3.9,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12285226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473851","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":"Evaluation of the efficient propagation of <i>Rhizophagus intraradices</i> and its inoculation effects on rice.","authors":"Feng Shi, Xinghao Wang, Xue He, Tianle Xu, Mingguo Jiang, Wei Chang, Fuqiang Song","doi":"10.1128/aem.00558-25","DOIUrl":"10.1128/aem.00558-25","url":null,"abstract":"<p><p>Arbuscular mycorrhizal fungi (AMF) are a key group of fungi closely associated with agricultural production within soil microbial communities. However, large-scale propagation of AMF inoculum faces various challenges, limiting our ability to obtain and utilize these inocula on a broad scale. To address this, we designed a monolayer mesh cultivation system employing a hydroponic approach for propagating arbuscular mycorrhizal fungi, specifically <i>Rhizophagus intraradices</i>. We conducted a comparative analysis of quality and inoculation efficiency between the water culture inoculum (w-Ri) and traditional soil-based inoculum (s-Ri). Our findings revealed the following. (i) The propagation cycle of w-Ri inoculum is 35 days and only 23% of the 150-day cycle required for s-Ri inoculum. (ii) The spore density, viability, and purity of w-Ri inoculum are 5.25 times, 1.09 times, and 1.26 times higher, respectively, than those of s-Ri inoculum. (iii) The w-Ri inoculants demonstrate effects on enhancing rice biomass, root morphology, and photosynthesis that are consistent with those of the s-Ri inoculants, while requiring only 10% of the application rate of the s-Ri inoculants. These results provide crucial theoretical references for establishing a pure and efficient arbuscular mycorrhizal fungus propagation system and its promotion and application.IMPORTANCEThe development of a monolayer mesh hydroponic cultivation system for propagating <i>Rhizophagus intraradices</i> offers a significant advancement in overcoming the challenges of large-scale AMF inoculum production, which is critical for enhancing agricultural sustainability. The comparative analysis of water culture-based (w-Ri) and traditional soil-based (s-Ri) inoculum demonstrates the superior efficiency of the w-Ri system in terms of propagation speed, spore density, and inoculum quality, highlighting its potential for large-scale application in farming practices. The findings that w-Ri inoculants are equally effective in promoting plant growth while requiring only a fraction of the application rate of s-Ri inoculants underscore the potential for reducing both cost and environmental impact in agricultural inoculation practices.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0055825"},"PeriodicalIF":3.9,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12285234/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crucial roles of intracellular cyclic di-GMP in impacting the genes important for extracellular electron transfer by <i>Geobacter metallireducens</i>.","authors":"Yongguang Jiang, Lin Sun, Lingyu Hou, Yidan Hu, Zhou Jiang, Yiran Dong, Hao Song, Liang Shi","doi":"10.1128/aem.00727-25","DOIUrl":"10.1128/aem.00727-25","url":null,"abstract":"<p><p>To investigate the roles of intracellular c-di-GMP in bacterial extracellular electron transfer (EET), three <i>Geobacter metallireducens</i> strains with high (Gme-H), intermediate (Gme-C), and low (Gme-L) intracellular levels of c-di-GMP were constructed via the synthetic biology approach. Compared to Gme-C, Gme-H showed similar Fe(III) reduction rates, formed thicker biofilms on conductive and nonconductive surfaces, and produced more electricity, but showed delayed ability for electricity production. Gme-L formed thinner biofilms on nonconductive surfaces and reduced Fe(III)-citrate faster, but showed slower reduction of ferrihydrite in comparison to Gme-C. Although it produced electricity much faster, Gme-L produced less electricity and formed slightly less amounts of biofilms on anodes, as compared to Gme-C. The mRNA levels of multiple genes encoding <i>c</i>-type cytochromes (<i>c</i>-Cyts) and extracellular pilin protein PilA-N were differentially regulated in Gme-L or Gme-H in comparison to that in Gme-C. Expressions of the genes for PilA-N and extracellular <i>c</i>-Cyt Gmet2896 were increased by high c-di-GMP. Low c-di-GMP increased the gene expressions of the porin-cytochromes in the outer membrane. Further investigation also identified new c-di-GMP-regulated genes directly involved in the EET of <i>G. metallireducens</i>, such as those for the <i>c</i>-Cyts of extracellular Gmet0601, the periplasmic Gmet1703 and Gmet1809 on the cytoplasmic membrane, as deletions of these genes impaired bacterial reductions of extracellular ferrihydrite and anode. Thus, intracellular c-di-GMP impacted multiple genes of <i>G. metallireducens</i> whose protein products might transfer electrons from the cytoplasmic membrane, through the periplasm, across the outer membrane to and in the extracellular environment.IMPORTANCEBis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is ubiquitous in bacterial cells where it regulates a variety of bacterial processes, which range from biofilm formation, bacterial virulence to cell cycle progression. However, its role in regulating bacterial extracellular electron transfer is much less characterized. This investigation shows the crucial roles of intracellular c-di-GMP in impacting the extracellular electron transfer of the Gram-negative bacterium <i>Geobacter metallireducens</i>. The gene expressions of the multiheme <i>c</i>-type cytochromes in the bacterial cytoplasmic membrane, periplasm, outer membrane, and extracellular environment, as well as the gene expression of extracellular pilin protein PilA-N, are all impacted by c-di-GMP. Although how it impacts the expression of these genes is currently unclear, c-di-GMP affects the entire extracellular electron transfer process of <i>G. metallireducens</i> from the cytoplasmic membrane, through the periplasm and across the outer membrane to and in the extracellular environment.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0072725"},"PeriodicalIF":3.9,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12285248/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214733","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":"Compartment-specific microbial communities highlight the ecological roles of fungi in a subtropical seagrass ecosystem.","authors":"Xiao Wang, Jiawei Chen, Sangwook Lee, Zhicheng Ju, Anirban Akhand, Hongbin Liu","doi":"10.1128/aem.00606-25","DOIUrl":"10.1128/aem.00606-25","url":null,"abstract":"<p><p>Plant-associated compartments provide habitats for various microbes. Seagrasses are the only submerged marine angiosperms. However, the simultaneous investigation of fungi and prokaryotes inhabiting different seagrass-associated compartments is limited, and much remains to be learned about the functional roles of seagrass fungi. We examined the diversity, composition, and networks of fungal and prokaryotic communities in multiple compartments associated with the seagrass <i>Halophila ovalis</i> to shed light on the significance of fungi in the seagrass ecosystem. Seagrass compartments primarily differentiated the microbial communities. Notably, the root and rhizome tissues of visually healthy <i>H. ovalis</i> exhibited a very narrow, single-species dominated and enriched fungal spectrum, leading us to hypothesize the possible establishment of a symbiotic relationship between the Lulworthiaceae mycobiont, <i>Halophilomyces hongkongensis</i>, and the seagrass host. In addition, the Vibrionaceae family, represented by the genus <i>Vibrio</i>, emerged as the most abundant prokaryotic taxon enriched in the roots/rhizomes, showing exclusive positive correlations with <i>H. hongkongensis</i> within the tissues, implying a cross-kingdom reciprocal interaction between these taxa in the endosphere of <i>H. ovalis</i>. Fungal-prokaryotic interdomain network analysis identified <i>H. hongkongensis</i> as a keystone taxon, essential for coordinating microbial interactions in <i>H. ovalis</i>-associated compartments, while robustness analysis of interdomain networks suggested fungi plays a more crucial role in sustaining the network structures of <i>H. ovalis</i> inner tissues compared to surrounding compartments. These findings provide valuable insights into the seagrass-fungi relationship and emphasize the importance of fungi in the seagrass ecosystem.IMPORTANCEAlthough plant-associated microbes are key determinants of plant health, fitness, and stress resilience, microbial communities associated with seagrasses remain poorly understood compared to those in land plants, particularly concerning the diversity and ecological roles of their fungal associates. Our work provides a comprehensive assessment of fungal and prokaryotic communities across multiple above- and below-ground compartments associated with <i>Halophila ovalis</i>, the most widespread seagrass species in Hong Kong, through a year-round sampling. Our findings reveal compartment-specific patterns in diversity, network topology, and stability of microbial communities, highlighting the critical roles of fungi in seagrass-associated microbial networks and advancing our understanding of plant-fungal interactions in the marine environment.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0060625"},"PeriodicalIF":3.9,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12285264/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537835","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Salinity-driven shifts in estuarine viral community composition and diversity near the Shenzhen coast.","authors":"Sarfraz Hussain, Xiaomeng Wang, Cong Pan, Songze Chen, Jiajia Xie, Nazia Mahtab, Shengwei Hou, Shuangfei Li","doi":"10.1128/aem.00407-25","DOIUrl":"10.1128/aem.00407-25","url":null,"abstract":"<p><p>Estuarine viral communities play a key role in microbial dynamics and ecosystem functioning. However, how viruses adapt to the highly dynamic estuarine environments remains largely underexplored. This study uses viromic sequencing to investigate the DNA viruses in estuarine water samples adjacent to the Shenzhen coast. Samples were divided into two major groups based on variations in quantified water parameters, corresponding to low-salinity and high-salinity waters. A total of 16,497 viral operational taxonomic units (vOTUs) were recovered, of which 85.59% were identified as novel viruses. β-diversity of viral communities supported the partition of samples based on salinity, and viral α-diversity differed significantly between low and high salinity. Taxonomically, Caudoviricetes dominated across all sites, with Myoviridae and Podoviridae more abundant in low salinity sites and Siphoviridae and Baculoviridae more abundant in high salinity sites. Gammaproteobacteria and Bacteroidota were the dominant host taxa, with distinct shifts in host abundance across the salinity gradient. Functional analysis revealed the abundant auxiliary metabolic genes involved in lipid, nucleotide, cofactor, and polysaccharide metabolisms. In particular, the alginate-degrading polysaccharide lyase family 6 was particularly abundant at high salinity sites. These results suggested that environmental factors, particularly salinity, shape the genomic diversity of estuarine viruses, which may further impact the biogeochemical processes in estuarine ecosystems.IMPORTANCEEstuaries are highly dynamic ecosystems with strong environmental fluctuations, particularly in salinity and nutrients. This study highlights how environmental factors shape viral diversity and function by examining viral populations across the salinity gradient, providing new insights into viral dynamics in these ecosystems. We identified novel viruses and viral-encoded auxiliary metabolic genes in estuarine samples, including the discovery of a previously unreported viral alginate lyase gene that was abundant at high salinity sites, which sheds light on the ecological role of viruses in nutrient cycling and ecosystem partition. In addition, the study provides valuable information on distinct viral populations and virus-host interactions across the salinity gradient, which are essential for predicting ecosystem responses to salinity changes. These findings provide important implications for a broader understanding of microbial and viral ecology in estuarine ecosystems.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0040725"},"PeriodicalIF":3.9,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12285232/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}