Microbes and Environments最新文献_第2页

Microbial Community Structure of Mesophilic and Low-temperature Partial Nitrification-anammox Reactors: Distribution and Functional Roles of the Core Microbiome. 中温和低温部分硝化-厌氧氨氧化反应器微生物群落结构：核心微生物群的分布和功能作用

IF 2.1 4区环境科学与生态学

Microbes and Environments Pub Date : 2025-01-01 DOI: 10.1264/jsme2.ME25001

Mamoru Oshiki, Kohei Takahashi, Seiya Kawasaki, Hyungmin Choi, Jihye Park, Kwiyong Kim, Hyokwan Bae, Satoshi Okabe, Changsoo Lee

引用次数: 0

Massive RNA Editing in Ascetosporean Mitochondria. ascetospore线粒体中的大量RNA编辑。

IF 2.1 4区环境科学与生态学

Microbes and Environments Pub Date : 2025-01-01 DOI: 10.1264/jsme2.ME24070

Akinori Yabuki, Chihaya Fujii, Euki Yazaki, Akihiro Tame, Keiko Mizuno, Yumiko Obayashi, Yoshitake Takao

{"title":"Massive RNA Editing in Ascetosporean Mitochondria.","authors":"Akinori Yabuki, Chihaya Fujii, Euki Yazaki, Akihiro Tame, Keiko Mizuno, Yumiko Obayashi, Yoshitake Takao","doi":"10.1264/jsme2.ME24070","DOIUrl":"10.1264/jsme2.ME24070","url":null,"abstract":"Ascetosporeans are parasitic protists of invertebrates. A deep sequencing ana-lysis of species within the orders Mikrocytida, Paramyxida, and Haplosporida using metagenomic approaches revealed that their mitochondria were functionally reduced and their organellar genomes were lacking. Ascetosporeans belonging to the order Paradinida have not been sequenced, and the nature of their mitochondria remains unclear. We herein established two cultures of Paradinida and conducted DNA and RNA sequencing ana-lyses. The results obtained indicate that mitochondrial function in paradinids was not reduced and their organellar genomes were retained. In contrast, their mitochondrial genomes were involved in massive A-to-I and C-to-U substitution types of RNA editing. All edits in protein-coding genes were nonsynonymous substitutions, and likely had a restorative function against negative mutations. Furthermore, we detected possible sequences of DYW type of pentatricopeptide repeat (PPR-DYW) protein and a homologue of adenosine deaminase acting on RNA (ADAR-like), which are key enzymes for C-to-U and A-to-I substitutions, respectively. An immunofluorescence ana-lysis showed that ADAR-like of paradinids may specifically localize within mitochondria. These results expand our knowledge of the diversity and complexity of organellar RNA editing phenomena.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"40 1","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11946409/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143639744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Size Distribution and Pathogenic Potential of Culturable Airborne Clostridium spp. in a Suburb of Toyama City, Japan. 日本富山市郊区可培养空气中梭状芽孢杆菌的大小分布和致病潜力。

IF 2.1 4区环境科学与生态学

Microbes and Environments Pub Date : 2025-01-01 DOI: 10.1264/jsme2.ME24078

Makoto Seki, Reika Iwamoto, Jianjian Hou, So Fujiyoshi, Fumito Maruyama, Yukihiro Furusawa, Shigehiro Kagaya, Akihiro Sakatoku, Shogo Nakamura, Daisuke Tanaka

{"title":"Size Distribution and Pathogenic Potential of Culturable Airborne Clostridium spp. in a Suburb of Toyama City, Japan.","authors":"Makoto Seki, Reika Iwamoto, Jianjian Hou, So Fujiyoshi, Fumito Maruyama, Yukihiro Furusawa, Shigehiro Kagaya, Akihiro Sakatoku, Shogo Nakamura, Daisuke Tanaka","doi":"10.1264/jsme2.ME24078","DOIUrl":"10.1264/jsme2.ME24078","url":null,"abstract":"Clostridium spp. are anaerobic, Gram-positive, spore-forming bacteria comprising more than 150 species, some of which are important pathogens of humans and animals. Members of this genus have been isolated from a number of environments, but are rarely found in the atmosphere. In the present study, we exami-ned culturable airborne Clostridium spp. and clarified their pathogenicity. We obtained 19 culturable Clostridium isolates from size-fractionated samples collected at a suburban site in Toyama, central Japan. Culturable Clostridium spp. were detected in particles larger than 1.1‍ ‍μm, and the size distribution peaked at 2.1-3.3‍ ‍μm, corresponding to the spore size of Clostridium spp. More Clostridium spp. were detected in coarse particles >2.1‍ ‍μm not only by culture methods, but also by 16S rRNA gene amplicon sequencing. Whole-genome sequencing (WGS) identified seven Clostridium species, among which Clostridium perfringens was predominant. Moreover, WGS revealed that C. perfringens isolates harbored many virulence and antibiotic resistance genes with the potential to cause gas gangrene. The detection and characterization of potential airborne pathogens are crucial for preventing the spread of diseases caused by these pathogens. To the best of our knowledge, this is the first study to demonstrate that anaerobic Clostridium spp. may be transported under aerobic conditions in the atmosphere and pose potential risks to human health.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"40 1","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11946412/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143256125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Biocontrol of Phytophthora Root and Stem Rot and Growth Promotion of Soybean Plants by the Rhizobacterium Enterobacter pseudoroggenkampii Strain GVv1 Isolated from Vicia villosa Roth. 假根坎皮根际肠杆菌GVv1对大豆根茎腐病的防生及促生作用

IF 2.1 4区环境科学与生态学

Microbes and Environments Pub Date : 2025-01-01 DOI: 10.1264/jsme2.ME24089

Juan Taboadela-Hernanz, Yuichiro Ikagawa, Kosei Yamauchi, Yui Minoshima, Haruhisa Suga, Masafumi Shimizu

{"title":"Biocontrol of Phytophthora Root and Stem Rot and Growth Promotion of Soybean Plants by the Rhizobacterium Enterobacter pseudoroggenkampii Strain GVv1 Isolated from Vicia villosa Roth.","authors":"Juan Taboadela-Hernanz, Yuichiro Ikagawa, Kosei Yamauchi, Yui Minoshima, Haruhisa Suga, Masafumi Shimizu","doi":"10.1264/jsme2.ME24089","DOIUrl":"https://doi.org/10.1264/jsme2.ME24089","url":null,"abstract":"Phytophthora root and stem rot (PRSR) caused by Phytophthora sojae is a major concern for global soybean production. To identify a bacterial biocontrol agent against PRSR, 73 rhizobacterial strains were isolated from wild and cultivated legumes and screened for their protective activities against PRSR in pot experiments. Strain GVv1 was selected for its consistent protective effect through repeated pot experiments. The protective effect of this strain was similar to that of the fungicide mancozeb-metalaxyl. A dual-culture assay showed that GVv1 produced antifungal metabolites effective against P. sojae. To evaluate the potential adaptability of GVv1 to the soybean rhizosphere environment, its growth was exami-ned in soybean root exudates and nutrient medium, both supplemented with daidzein, an antimicrobial isoflavone secreted by soybean roots. GVv1 proliferated using soybean root exudates and had sufficient tolerance to daidzein to colonize the soybean rhizosphere. The plant growth-promoting effect of GVv1 on soybean plants was also investigated. GVv1 significantly increased shoot and root dry weights, indicating its plant growth-promoting activity. In vitro assays showed that GVv1 produced indole-3-acetic acid, siderophores, and 1-aminocyclopropane-1-carboxylate deaminase and solubilized insoluble phosphates. A taxonogenomic ana-lysis of the draft genome identified GVv1 as Enterobacter pseudoroggenkampii with high similarity (98.32% average nucleotide identity) to E. pseudoroggenkampii strain 155092T. To the best of our knowledge, this is the first study to report the biocontrol and plant growth-promoting activities of E. pseudoroggenkampii.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"40 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144004879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cell cycle perturbation uncouples mitotic progression and invasive behavior in a post-mitotic cell. 细胞周期扰动解除了有丝分裂进程与有丝分裂后细胞侵袭行为之间的联系。

4区环境科学与生态学

Microbes and Environments Pub Date : 2024-02-07 DOI: 10.1101/2023.03.16.533034

Michael A Q Martinez, Chris Z Zhao, Frances E Q Moore, Callista Yee, Wan Zhang, Kang Shen, Benjamin L Martin, David Q Matus

{"title":"Cell cycle perturbation uncouples mitotic progression and invasive behavior in a post-mitotic cell.","authors":"Michael A Q Martinez, Chris Z Zhao, Frances E Q Moore, Callista Yee, Wan Zhang, Kang Shen, Benjamin L Martin, David Q Matus","doi":"10.1101/2023.03.16.533034","DOIUrl":"10.1101/2023.03.16.533034","url":null,"abstract":"The acquisition of the post-mitotic state is crucial for the execution of many terminally differentiated cell behaviors during organismal development. However, the mechanisms that maintain the post-mitotic state in this context remain poorly understood. To gain insight into these mechanisms, we used the genetically and visually accessible model of C. elegans anchor cell (AC) invasion into the vulval epithelium. The AC is a terminally differentiated uterine cell that normally exits the cell cycle and enters a post-mitotic state, initiating contact between the uterus and vulva through a cell invasion event. Here, we set out to identify the set of negative cell cycle regulators that maintain the AC in this post-mitotic, invasive state. Our findings revealed a critical role for CKI-1 (p21CIP1/p27KIP1) in redundantly maintaining the post-mitotic state of the AC, as loss of CKI-1 in combination with other negative cell cycle regulators-including CKI-2 (p21CIP1/p27KIP1), LIN-35 (pRb/p107/p130), FZR-1 (Cdh1/Hct1), and LIN-23 (β-TrCP)-resulted in proliferating ACs. Remarkably, time-lapse imaging revealed that these ACs retain their ability to invade. Upon examination of a node in the gene regulatory network controlling AC invasion, we determined that proliferating, invasive ACs do so by maintaining aspects of pro-invasive gene expression. We therefore report that the requirement for a post-mitotic state for invasive cell behavior can be bypassed following direct cell cycle perturbation.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10871222/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88287778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Ferrihydrite Addition Activated Geobacteraceae, the Most Abundant Iron-reducing Diazotrophs, and Suppressed Methanogenesis by Heterogeneous Methanogens in Xylan-amended Paddy Soil Microcosms. 在添加了木聚糖的水稻田土壤微生态系统中，添加亚铁能激活最丰富的铁还原重氮菌--革囊菌，并抑制异型甲烷菌的甲烷生成。

IF 2.2 4区环境科学与生态学

Microbes and Environments Pub Date : 2024-01-01 DOI: 10.1264/jsme2.me24028

Yoko Masuda,Mitsutaka Chihara,Keishi Senoo

引用次数: 0

Author's correction: Relationship Between Rumen Microbial Composition and Fibrolytic Isozyme Activity During the Biodegradation of Rice Straw Powder Using Rumen Fluid. 作者的更正：利用瘤胃液生物降解稻草粉过程中瘤胃微生物组成与纤维分解异构酶活性之间的关系。

IF 2.1 4区环境科学与生态学

Microbes and Environments Pub Date : 2024-01-01 DOI: 10.1264/jsme2.ME23041e

Shuhei Takizawa, Ryoki Asano, Kenichi Abe, Yasuhiro Fukuda, Yasunori Baba, Riku Sakurai, Chika Tada, Yutaka Nakai

引用次数: 0

A Novel Strain of the Cyanobacterial Growth-promoting Bacterium, Rhodococcus sp. AF2108, Enhances the Growth of Synechococcus elongatus. 一株新的蓝细菌促生长菌红球菌AF2108促进长聚球菌生长。

IF 2.1 4区环境科学与生态学

Microbes and Environments Pub Date : 2024-01-01 DOI: 10.1264/jsme2.ME24050

Pei Yu Tan, Yuta Kato, Masaaki Konishi

引用次数: 0

How Do Thermophiles Organize Their Genomes? 嗜热菌如何组织基因组？

IF 2.1 4区环境科学与生态学

Microbes and Environments Pub Date : 2024-01-01 DOI: 10.1264/jsme2.ME23087

Naomichi Takemata

引用次数: 0

Comparative Genomics and Characterization of Shigella flexneri Isolated from Urban Wastewater. 从城市污水中分离出的柔性志贺氏菌的比较基因组学及其特征。

IF 2.1 4区环境科学与生态学

Microbes and Environments Pub Date : 2024-01-01 DOI: 10.1264/jsme2.ME23105

Sarmishta Mukhopadhyay, Meesha Singh, Mahashweta Mitra Ghosh, Santanu Chakrabarti, Sayak Ganguli

{"title":"Comparative Genomics and Characterization of Shigella flexneri Isolated from Urban Wastewater.","authors":"Sarmishta Mukhopadhyay, Meesha Singh, Mahashweta Mitra Ghosh, Santanu Chakrabarti, Sayak Ganguli","doi":"10.1264/jsme2.ME23105","DOIUrl":"10.1264/jsme2.ME23105","url":null,"abstract":"Shigella species are a group of highly transmissible Gram-negative pathogens. Increasing reports of infection with extensively drug-resistant varieties of this stomach bug has convinced the World Health Organization to prioritize Shigella for novel therapeutic interventions. We herein coupled the whole-genome sequencing of a natural isolate of Shigella flexneri with a pangenome ana-lysis to characterize pathogen genomics within this species, which will provide us with an insight into its existing genomic diversity and highlight the root causes behind the emergence of quick vaccine escape variants. The isolated novel strain of S. flexneri contained ~4,500 protein-coding genes, 57 of which imparted resistance to antibiotics. A comparative pan-genomic ana-lysis revealed genomic variability of ~64%, the shared conservation of core genes in central metabolic processes, and the enrichment of unique/accessory genes in virulence and defense mechanisms that contributed to much of the observed antimicrobial resistance (AMR). A pathway ana-lysis of the core genome mapped 22 genes to 2 antimicrobial resistance pathways, with the bulk coding for multidrug efflux pumps and two component regulatory systems that are considered to work synergistically towards the development of resistance phenotypes. The prospective evolvability of Shigella species as witnessed by the marked difference in genomic content, the strain-specific essentiality of unique/accessory genes, and the inclusion of a potent resistance mechanism within the core genome, strengthens the possibility of novel serotypes emerging in the near future and emphasizes the importance of tracking down genomic diversity in drug/vaccine design and AMR governance.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"39 2","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220449/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141262282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0