Journal of Basic Microbiology最新文献

{"title":"Small Interfering RNA Mediated Messenger RNA Knockdown in the Amphibian Pathogen Batrachochytrium dendrobatidis","authors":"Rebecca J. Webb,&nbsp;Alexandra A. Roberts,&nbsp;Catherine Rush,&nbsp;Lee F. Skerratt,&nbsp;Mark L. Tizard,&nbsp;Lee Berger","doi":"10.1002/jobm.202400081","DOIUrl":"10.1002/jobm.202400081","url":null,"abstract":"<p>RNA interference (RNAi) has not been tested in the pandemic amphibian pathogen, <i>Batrachochytrium dendrobatidis</i>, but developing this technology could be useful to elucidate virulence mechanisms, identify therapeutic targets, and may present a novel antifungal treatment option for chytridiomycosis. To manipulate and decipher gene function, rationally designed small interfering RNA (siRNA) can initiate the destruction of homologous messenger RNA (mRNA), resulting in the “knockdown” of target gene expression. Here, we investigate whether siRNA can be used to manipulate gene expression in <i>B. dendrobatidis</i> via RNAi using differing siRNA strategies to target genes involved in glutathione and ornithine synthesis. To determine the extent and duration of mRNA knockdown, target mRNA levels were monitored for 24–48 h after delivery of siRNA targeting glutamate–cysteine ligase, with a maximum of ~56% reduction in target transcripts occurring at 36 h. A second siRNA design targeting glutamate-cysteine ligase also resulted in ~53% knockdown at this time point. siRNA directed toward a different gene target, ornithine decarboxylase, achieved 17% reduction in target transcripts. Although no phenotypic effects were observed, these results suggest that RNAi is possible in <i>B. dendrobatidis</i>, and that gene expression can be manipulated in this pathogen. We outline ideas for further optimization steps to increase knockdown efficiency to better harness RNAi techniques for control of <i>B. dendrobatidis.</i></p>","PeriodicalId":15101,"journal":{"name":"Journal of Basic Microbiology","volume":"64 8","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jobm.202400081","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141528452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhancing Agricultural Sustainability Through Rhizomicrobiome: A Review","authors":"Prateek Ranjan Behera,&nbsp;Kishan Kumar Behera,&nbsp;Gangadhar Sethi,&nbsp;B. Jeberlin Prabina,&nbsp;A. Thoyajakshi Bai,&nbsp;B. S. Sipra,&nbsp;Varanasi Adarsh,&nbsp;Sasmita Das,&nbsp;Kanhu Charan Behera,&nbsp;Lakshmi Singh,&nbsp;Mihir Kumar Mishra,&nbsp;Maheswari Behera","doi":"10.1002/jobm.202400100","DOIUrl":"10.1002/jobm.202400100","url":null,"abstract":"<div>\u0000 \u0000 <p>Sustainable agriculture represents the responsible utilization of natural resources while safeguarding the well-being of the natural environment. It encompasses the objectives of preserving the environment, fostering economic growth, and promoting socioeconomic equality. To achieve sustainable development for humanity, it is imperative to prioritize sustainable agriculture. One significant approach to achieving this transition is the extensive utilization of microbes, which play a crucial role due to the genetic reliance of plants on the beneficial functions provided by symbiotic microbes. This review focuses on the significance of rhizospheric microbial communities, also known as the rhizomicrobiome (RM). It is a complex community of microorganisms that live in the rhizosphere and influence the plant's growth and health. It provides its host plant with various benefits related to plant growth, including biocontrol, biofertilization, phytostimulation, rhizoremediation, stress resistance, and other advantageous properties. Yet, the mechanisms by which the RM contributes to sustainable agriculture remain largely unknown. Investigating this microbial population presents a significant opportunity to advance toward sustainable agriculture. Hence, this study aims to provide an overview of the diversity and applications of RM in sustainable agriculture practices. Lately, there has been growing momentum in various areas related to rhizobiome research and its application in agriculture. This includes rhizosphere engineering, synthetic microbiome application, agent-based modeling of the rhizobiome, and metagenomic studies. So, developing bioformulations of these beneficial microorganisms that support plant growth could serve as a promising solution for future strategies aimed at achieving a new green revolution.</p>\u0000 </div>","PeriodicalId":15101,"journal":{"name":"Journal of Basic Microbiology","volume":"64 11","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141426954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Isolation, Plant Growth-Promoting Properties, and Whole-Genome Sequence of a Novel Paenibacillus Species","authors":"Dinh Minh Tran,&nbsp;To Uyen Huynh,&nbsp;Tu Oanh Do,&nbsp;Anh Dzung Nguyen","doi":"10.1002/jobm.202400119","DOIUrl":"10.1002/jobm.202400119","url":null,"abstract":"<div>\u0000 \u0000 <p>This work aimed to isolate and characterize a novel chitin-degrading bacterium from Yok Don National Park, Vietnam, for crop production studies. Among the chitinolytic isolates, strain YSY-4.3 was selected, which grew rapidly and produced a large halo around the colony. 16S rDNA analysis indicated that the strain is a novel species in the genus <i>Paenibacillus</i>, and an in vitro evaluation showed that the strain produced phytohormones (IAA, GA3, and zeatin), biofilms, and siderophores; possessed cellulase; and exerted antifungal activity. The whole genome of the strain was 5,628,400 bp with 49.3% GC content, 5056 coding sequences, 48 tRNA, and 1 rRNA. It shared the highest values of digital DNA–DNA hybridization (67.4%) and average nucleotide identity (89.54%) with those of <i>Paenibacillus woosongensis</i> B2_4 (CP126084.1), suggesting a novel species. Of the coding sequences, 4287 proteins were identified by COG, and 2561 were assigned by KEGG. The genome contained at least 51 genes involved in plant growth and resistance to heavy-metal toxicity and 359 carbohydrate-active enzymes. The chitinolytic system of the strain was composed of 15 enzymes, among them, PsChiC, which contained a GH18 catalytic domain and a GH5 catalytic domain, had not been previously reported. In addition, the genome possessed 15 gene clusters encoding antimicrobial metabolites, 10 of which are possible novel clusters. This study expands knowledge regarding novel chitinolytic bacteria from Yok Don National Park and provides a valuable gene resource for future studies.</p>\u0000 </div>","PeriodicalId":15101,"journal":{"name":"Journal of Basic Microbiology","volume":"64 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141419291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Influence of Geothermal Fumaroles in Driving the Microbial Community Dynamics and Functions of Adjacent Ecosystems","authors":"Aslia Asif,&nbsp;Jung-Sheng Chen,&nbsp;Gwo-Jong Hsu,&nbsp;Bashir Hussain,&nbsp;Viji Nagarajan,&nbsp;Suprokash Koner,&nbsp;Shih-Wei Huang,&nbsp;Bing-Mu Hsu","doi":"10.1002/jobm.202400157","DOIUrl":"10.1002/jobm.202400157","url":null,"abstract":"<div>\u0000 \u0000 <p>Growing evidence suggests that the hydrochemical properties of geothermal fumaroles may play a crucial role in shaping the diversity and functions of microbial communities in various environments. In the present study, the impact of geothermal furaneols on the microbial communities and their metabolic functions across the rock-soil-plant continuum was explored considering varying distances from the fumarole source. The results revealed that bacterial phylum Proteobacteria was predominant in all sample types, except in the 10 m rock sample, irrespective of the sampling distance. Archaeal phyla, such as Euryarchaeota and Crenarchaeota, were more prevalent in rock and soil samples, whereas bacterial phyla were more prevalent in plant samples. Thermoacidophilic archaeons, including <i>Picrophilus</i>, <i>Ferroplasma</i>, and <i>Thermogymnomonas</i> were dominant in rocks and soil samples of 1 and 5 m distances; acidophilic mesophiles, including <i>Ferrimicrobium</i> and <i>Granulicella</i> were abundant in the rhizoplane samples, whereas rhizosphere-associated microbes including <i>Pseudomonas</i>, <i>Pedobacter, Rhizobium</i>, and <i>Novosphingobium</i> were found dominant in the rhizosphere samples. The functional analysis highlighted the higher expression of sulfur oxidative pathways in the rock and soil samples; dark iron oxidation and nitrate/nitrogen respiratory functions in the rhizosphere samples. The findings underscore microbial adaptations across the rock-soil-plant continuum, emphasizing the intricate relationship between geothermal fumaroles and microbial communities in adjacent ecosystems. These insights offer a crucial understanding of the evolution of microbial life and highlight their pivotal roles in shaping ecosystem dynamics and functions.</p></div>","PeriodicalId":15101,"journal":{"name":"Journal of Basic Microbiology","volume":"64 8","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141300743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cover: Journal of Basic Microbiology. 6/2024","authors":"","doi":"10.1002/jobm.202470051","DOIUrl":"https://doi.org/10.1002/jobm.202470051","url":null,"abstract":"<p><b>Cover illustration:</b></p><p>Plaque and TEM images of mycobacteriophages.</p><p>(Photo: Sunil K. Raman, Pharmaceutics and Pharmacokinetic Division, CSIR-Central Drug Research Institute, Lucknow, and UB Lab, Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Kalkaji, New Delhi, India)\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":15101,"journal":{"name":"Journal of Basic Microbiology","volume":"64 6","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jobm.202470051","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141245723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Issue Information: Journal of Basic Microbiology. 6/2024","authors":"","doi":"10.1002/jobm.202470052","DOIUrl":"https://doi.org/10.1002/jobm.202470052","url":null,"abstract":"","PeriodicalId":15101,"journal":{"name":"Journal of Basic Microbiology","volume":"64 6","pages":""},"PeriodicalIF":3.1,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jobm.202470052","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141245724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First report of betalain production from endolichenic Bacillus sp. LDAB-1 from Dirinaria aegilita: Insights from novel quantification methodology of image processing","authors":"Karthikumar Sankar,&nbsp;Karl Joseph Samuel,&nbsp;Shyam Kumar Rajaram,&nbsp;Ponmurugan Karuppiah,&nbsp;Govindasami Periyasami,&nbsp;Gopalu Karunakaran","doi":"10.1002/jobm.202300721","DOIUrl":"10.1002/jobm.202300721","url":null,"abstract":"<div>\u0000 \u0000 <p>Pigments are widely used in food supplements envisaging attractive colors along with health benefits. The desired advancements in the nutraceutical and antioxidant properties of pigments utilized in food products necessitate the search for novel additives. The present study is the first in the field to report the pigment-producing endolichenic bacteria, <i>Bacillus</i> sp. LDAB-1 from <i>Dirinaria aegilita</i>. Morphological, biochemical, and molecular characterization of the bacterium emphasizes that ideal pigment production occurs when utilizing sucrose and sodium nitrate. The pigment was salted out and dialyzed for further qualitative characterization using ultraviolet–visible, fluorescence, and Fourier transform infrared spectra and the results corroborated the presence of betalains. The antioxidant activity of betalain is closer to the efficiency of α-tocopherol, which confers the pigment properties for antioxidant and nutraceutical significance. An optimal methodology for pigment affirmation is an issue when using an alternative methodology. Hence, the present assessment employs a comparative analysis of findings from both a spectrophotometric method and image processing technology encompassing RGB, CMYK, YCbCr, and <i>L</i>*<i>a</i>*<i>b</i>* color space models. Amongst these, the <i>L</i>*<i>a</i>*<i>b</i>* model potentially provides an effective modality for determining the pigment concentration. Bland–Altman plot analysis indicates similar consistency levels in betalain quantification by both methods at 95% confidence intervals, affirming the integrity and consistency of color image processing technology. Consequently, the present study represents novelty and innovativeness in reporting endolichenic <i>Bacillus</i> sp. LDAB-1 from <i>D. aegilita</i> and a rational image optimization protocol for pigment elucidation characteristics.</p>\u0000 </div>","PeriodicalId":15101,"journal":{"name":"Journal of Basic Microbiology","volume":"64 9","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141199398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unearthing the therapeutic benefits of culinary-medicinal mushrooms for humans: Emerging sustainable bioresources of 21st century","authors":"Lebin Thomas,&nbsp;Payal Mago","doi":"10.1002/jobm.202400127","DOIUrl":"10.1002/jobm.202400127","url":null,"abstract":"<p>Global interest in mushroom farming techniques has grown in the last few years. Despite not making up a large amount of the human diet at the moment, the nutritional worth of mushrooms has prompted their usage. The three main segments of the global mushroom industry are wild, culinary (edible), and medicinal mushrooms. The quality food that mushrooms provide can be utilized to build agricultural ecosystems that are more sustainable for increasing productivity and enhancing the effectiveness of resource usage. This is mostly because mushrooms can be utilized for the recycling of biomass and remains from crop production. Culinary-medicinal mushrooms are becoming more and more important because of their nutrient density, dietary value, and health advantages. Given its many bioactive components, which include polysaccharides, proteins, vitamins, minerals, dietary fiber, and secondary metabolites, mushrooms have been utilized extensively as health foods. These mushrooms exhibit pharmacological activities and possess prebiotic and antibacterial capabilities. This review provides information on the latest advancements in the sustainable cultivation of mushrooms, particularly with nontraditional substrates, and their potential therapeutic uses. Furthermore, some of the newest developments and difficulties in the production of mushrooms are explored.</p>","PeriodicalId":15101,"journal":{"name":"Journal of Basic Microbiology","volume":"64 8","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141075669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phytochemical inhibitors from Leucas aspera against the target proteins induced by Trichophyton mentagrophytes using computational techniques","authors":"Monalisha Giri,&nbsp;Sagarika Parida","doi":"10.1002/jobm.202400112","DOIUrl":"10.1002/jobm.202400112","url":null,"abstract":"<p>Dermatophytosis is a cutaneous infection that is able to degrade the keratinized tissues of the animal/human body, like skin, nails, and hair, causing chronic or subacute infection with the contact of some specific fungal strains. <i>Trichophyton mentagrophytes</i> are the most potential fungal pathogen causing dermatophytoses. The present study focuses on computationally based in silico antifungal activity of selected phytocompounds of <i>Leucas aspera</i> (Willd.) Link. against dermatophytic fungus, <i>T. mentagrophytes</i>. Validation and screening of derived phytocompounds is performed using Lipinski rule of five and toxicity test through Protox-II. Five target genes involved in dermatophytosis, induced by <i>T. mentagrophytes</i> are retrieved from the UniProt Database, and the corresponding proteins such as glucan 1,3-beta-glucosidase ARB_02797, Probable class II chitinase ARB_00204, squalene monooxygenase, actin, and ubiquitin are selected for in silico study. Three-dimensional structures of the target protein were computationally determined and validated through modeling tools and techniques due to the lack of validated protein structures in the database. Then, these proteins are used for in silico molecular docking through the AutoDock Vina tool to find out the promising phytocompounds. This study could be utilized in designing more effective drugs against <i>T. mentagrophytes</i>. Based on this work, a plant-based natural alternative can be added to the treatment of dermatophytosis rather than synthetic supplements.</p>","PeriodicalId":15101,"journal":{"name":"Journal of Basic Microbiology","volume":"64 7","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141070982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Special issue: Fungal ecology","authors":"Erika Kothe","doi":"10.1002/jobm.202400267","DOIUrl":"10.1002/jobm.202400267","url":null,"abstract":"","PeriodicalId":15101,"journal":{"name":"Journal of Basic Microbiology","volume":"64 7","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141070983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}