Microbes and Environments最新文献_第4页

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":"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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12213067/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Investigation of Microbial Community Shifts under the Mizumoto Japanese Traditional Sake Brewing Process Using Chemical Analyses and High-throughput Sequencing. 利用化学分析和高通量测序研究日本水本传统清酒酿造过程中微生物群落的变化。

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.ME23066

Shinnosuke Okuhama, Yuki Nakashima, Tsumugi Nakamoto, Masataka Aoki, Yuga Hirakata, Takashi Yamaguchi, Masataka Kusube

{"title":"Investigation of Microbial Community Shifts under the Mizumoto Japanese Traditional Sake Brewing Process Using Chemical Analyses and High-throughput Sequencing.","authors":"Shinnosuke Okuhama, Yuki Nakashima, Tsumugi Nakamoto, Masataka Aoki, Yuga Hirakata, Takashi Yamaguchi, Masataka Kusube","doi":"10.1264/jsme2.ME23066","DOIUrl":"10.1264/jsme2.ME23066","url":null,"abstract":"Over the past 10 centuries, sake brewing methods have been developed in stages, including doburoku, mizumoto, kimoto, yamahaimoto, and sokujyomoto. Mizumoto-sake is considered the oldest prototype. The brewing process involves lactic acid fermentation and multiple parallel saccharification and alcoholic fermentation by indigenous microbes, which has been operated based on a sense of craftsmanship. The processes involved lead to the creation of extreme conditions characterized by low pH levels and high alcohol concentrations. The characteristic feature of mizumoto-sake is that it begins with fermentation by indigenous lactic acid bacteria to produce acidic water for yeasts to ferment alcohol by inhibiting the growth of undesirable microbes. In the present study, we investigated changes in the microbial community and the transition of metabolites that affect taste and flavor during processes from the initiation of mizumoto-sake brewing to the final product. In the lactic acid fermentation phase, bacteria, including those in the genera Lactococcus, Leuconostoc, and Lactobacillus, produced lactic acid and contributed to the production of acidic water (pH of approximately 4) called soyashimizu. A heating process, known as \"Anka\", which increased the brewing temperature, then switched the relative abundance of 18S rRNA from 75.0% Pichia to 72.3% Saccharomycetaceae. Alcohol fermentation was accelerated by the Saccharomyces family (relative abundance: 89.8%), reaching alcohol concentrations >15%.","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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12213057/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144326163","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

Metabolic Potential and Microbial Diversity of Late Archean to Early Proterozoic Ocean Analog Hot Springs of Japan. 日本晚太古宙至早元古代海洋模拟温泉的代谢势和微生物多样性。

IF 2 4区环境科学与生态学

Microbes and Environments Pub Date : 2025-01-01 DOI: 10.1264/jsme2.ME24067

Fatima Li-Hau, Mayuko Nakagawa, Takeshi Kakegawa, L M Ward, Yuichiro Ueno, Shawn Erin McGlynn

{"title":"Metabolic Potential and Microbial Diversity of Late Archean to Early Proterozoic Ocean Analog Hot Springs of Japan.","authors":"Fatima Li-Hau, Mayuko Nakagawa, Takeshi Kakegawa, L M Ward, Yuichiro Ueno, Shawn Erin McGlynn","doi":"10.1264/jsme2.ME24067","DOIUrl":"10.1264/jsme2.ME24067","url":null,"abstract":"Circumneutral iron-rich hot springs may represent analogues of Neoarchean to Paleoproterozoic oceans of early Earth, potentially providing windows into ancient microbial ecology. Here we sampled five Japanese hot springs to gain insights into functional processes and taxonomic diversity in these analog environments. Amplicon and metagenomic sequencing confirm a hypothesis where taxonomy is distinct between sites and linked to the geochemical setting. Metabolic functions shared among the springs include carbon fixation via the reductive pentose phosphate cycle, nitrogen fixation, and dissimilatory iron oxidation/reduction. Among the sites, Kowakubi was unique in that it was dominated by Hydrogenophilaceae, a group known for performing hydrogen oxidation, motivating a hypothesis that H2 as an electron donor may shape community composition even in the presence of abundant ferrous iron. Evidence for nitrogen cycling across the springs included N2 fixation, dissimilatory nitrate reduction to ammonia (DNRA), and denitrification. The low-salinity springs Furutobe and OHK lacked evidence for ammonium oxidation by ammonia monooxygenase, but evidence for complete nitrification existed at Kowakubi, Jinata, and Tsubakiyama. In most sites, the microaerophilic iron-oxidizing bacteria from the Zetaproteobacteria or Gammaproteobacteria classes had higher relative abundances than Cyanobacteria. Microaerophilic iron oxidizers may outcompete abiotic Fe oxidation, while being fueled by oxy-phototrophic Cyanobacteria. Our data provide a foundation for considering which factors may have controlled productivity and elemental cycling as Earth's oceans became oxygenated at the onset of the Great Oxidation Event.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"40 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12501874/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144708056","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

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。

IF 2 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":2.0,"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

Accelerated Iron Corrosion by Microbial Consortia Enriched from Slime-like Precipitates from a Corroded Metal Apparatus Deployed in a Deep-sea Hydrothermal System. 部署在深海热液系统中的腐蚀金属装置产生的粘液状沉淀物中富集的微生物群加速了铁的腐蚀。

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.ME23089

Satoshi Wakai, Sanae Sakai, Tatsuo Nozaki, Masayuki Watanabe, Ken Takai

{"title":"Accelerated Iron Corrosion by Microbial Consortia Enriched from Slime-like Precipitates from a Corroded Metal Apparatus Deployed in a Deep-sea Hydrothermal System.","authors":"Satoshi Wakai, Sanae Sakai, Tatsuo Nozaki, Masayuki Watanabe, Ken Takai","doi":"10.1264/jsme2.ME23089","DOIUrl":"10.1264/jsme2.ME23089","url":null,"abstract":"Microbiologically influenced corrosion refers to the corrosion of metal materials caused or promoted by microorganisms. Although some novel iron-corrosive microorganisms have been discovered in various manmade and natural freshwater and seawater environments, microbiologically influenced corrosion in the deep sea has not been investigated in detail. In the present study, we collected slime-like precipitates composed of corrosion products and microbial communities from a geochemical reactor set on an artificial hydrothermal vent for 14.5 months, and conducted culture-dependent and -independent microbial community ana-lyses with corrosive activity measurements. After enrichment cultivation at 37, 50, and 70°C with zero-valent iron particles, some of the microbial consortia showed accelerated iron dissolution, which was approximately 10- to 50-fold higher than that of the abiotic control. In a comparative ana-lysis based on the corrosion acceleration ratio and amplicon sequencing of the 16S rRNA gene, three types of corrosion were estimated: the methanogen-induced type, methanogen-sulfate-reducing bacteria cooperative type, and sulfate-reducing Firmicutes-induced type. The methanogen-induced and methanogen-sulfate-reducing bacteria cooperative types were observed at 50°C, while the sulfate-reducing Firmicutes-induced type was noted at 37°C. The present results suggest the microbial components associated with microbiologically influenced corrosion in deep-sea hydrothermal systems, providing important insights for the development of future deep-sea resources with metal infrastructures.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"39 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11946385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141262284","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