Microbes and Environments最新文献

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

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

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.ME23087

Naomichi Takemata

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

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 2.2 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":"https://doi.org/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":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Formation of Biogenic Manganese Oxide Nodules on Hyphae of a New Fungal Isolate of Periconia That Immobilizes Aqueous Copper. 可固定水溶液中的铜的一种新的 Periconia 真菌分离菌丝上生物氧化锰结节的形成。

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.ME23102

Shihori Tsushima, Yuma Nishi, Ryo Suzuki, Masaru Tachibana, Robert A Kanaly, Jiro F Mori

{"title":"Formation of Biogenic Manganese Oxide Nodules on Hyphae of a New Fungal Isolate of Periconia That Immobilizes Aqueous Copper.","authors":"Shihori Tsushima, Yuma Nishi, Ryo Suzuki, Masaru Tachibana, Robert A Kanaly, Jiro F Mori","doi":"10.1264/jsme2.ME23102","DOIUrl":"10.1264/jsme2.ME23102","url":null,"abstract":"Mn(II)-oxidizing microorganisms are considered to play significant roles in the natural geochemical cycles of Mn and other heavy metals because the insoluble biogenic Mn oxides (BMOs) that are produced by these microorganisms adsorb other dissolved heavy metals and immobilize them as precipitates. In the present study, a new Mn(II)-oxidizing fungal strain belonging to the ascomycete genus Periconia, a well-studied plant-associating fungal genus with Mn(II)-oxidizing activity that has not yet been exami-ned in detail, was isolated from natural groundwater outflow sediment. This isolate, named strain TS-2, was confirmed to oxidize dissolved Mn(II) and produce insoluble BMOs that formed characteristic, separately-located nodules on their hyphae while leaving major areas of the hyphae free from encrustation. These BMO nodules also adsorbed and immobilized dissolved Cu(II), a model analyte of heavy metals, as evidenced by elemental mapping ana-lyses of fungal hyphae-BMO assemblages using a scanning electron microscope with energy-dispersive X-ray spectroscopy (SEM-EDX). Analyses of functional genes within the whole genome of strain TS-2 further revealed the presence of multiple genes predicted to encode laccases/multicopper oxidases that were potentially responsible for Mn(II) oxidation by this strain. The formation of BMO nodules may have functioned to prevent the complete encrustation of fungal hyphae, thereby enabling the control of heavy metal concentrations in their local microenvironments while maintaining hyphal functionality. The present results will expand our knowledge of the physiological and morphological traits of Mn(II)-oxidizing Periconia, which may affect the natural cycle of heavy metals through their immobilization.","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/PMC11220447/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141311062","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

Root Colonization by Trichoderma atroviride Triggers Induced Systemic Resistance Primarily Independent of the Chitin-mediated Signaling Pathway in Arabidopsis. 拟南芥中atroviride木霉定殖诱导的系统性抗性主要独立于几丁质介导的信号通路。

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.ME24038

Ayae Sakai, Hisako Yamagata, Keigo Naito, Mai Yoshioka, Takaya Tominaga, Shinsuke Ifuku, Hironori Kaminaka

{"title":"Root Colonization by Trichoderma atroviride Triggers Induced Systemic Resistance Primarily Independent of the Chitin-mediated Signaling Pathway in Arabidopsis.","authors":"Ayae Sakai, Hisako Yamagata, Keigo Naito, Mai Yoshioka, Takaya Tominaga, Shinsuke Ifuku, Hironori Kaminaka","doi":"10.1264/jsme2.ME24038","DOIUrl":"https://doi.org/10.1264/jsme2.ME24038","url":null,"abstract":"Beneficial root endophytic fungi induce systemic responses, growth promotion, and induced systemic resistance (ISR) in colonized host plants. The soil application of chitin, a main component of fungal cell walls, also systemically induces disease resistance. Therefore, chitin recognition and its downstream signaling pathway mediate ISR triggered by beneficial fungi colonizing the root. The present study compared systemic disease resistance and transcriptional responses induced by Trichoderma, a representative beneficial root endophytic fungus, and chitin in Arabidopsis. Significant plant growth promotion was observed under root colonization by the three beneficial fungi tested: Trichoderma atroviride, Serendipita indica, and S. vermifera. Only T. atroviride and S. indica triggered ISR against the necrotrophic fungal pathogen Alternaria brassicicola. Induced systemic resistance triggered by T. atroviride was compromised in the chitin-receptor mutant, whereas systemic resistance caused by the soil application of chitin was not. A transcriptome ana-lysis demonstrated that chitin-regulated genes were mostly shared with those regulated by T. atroviride; however, many of the latter were specific. The commonly enriched gene ontologies for these genes indicated that the T. atroviride inoculation and chitin application systemically controlled similar transcriptional responses, mainly associated with cell wall functions. Therefore, Trichoderma may trigger ISR primarily independent of the chitin-mediated signaling pathway; however, chitin and Trichoderma may systemically induce similar cellular functions aboveground.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"39 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142932118","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

DiGAlign: Versatile and Interactive Visualization of Sequence Alignment for Comparative Genomics. DiGAlign：用于比较基因组学的多功能交互式可视化序列比对。

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.ME23061

Yosuke Nishimura, Kohei Yamada, Yusuke Okazaki, Hiroyuki Ogata

引用次数: 0