Microbes and Environments最新文献_第7页

Risk Evaluation of Verticillium Wilt on Cabbage Grown in Soil Reused from Sediment Basins. 泥沙盆地回用土壤对白菜黄萎病风险评价

IF 2 4区环境科学与生态学

Microbes and Environments Pub Date : 2025-01-01 DOI: 10.1264/jsme2.ME25017

Hiroyuki Yamada, Masahito Banba, Keisuke Hoshino, Yukari Nakatsuji, Kentaro Ikeda

引用次数: 0

A HPLC-based Method for Counting the Genome Copy Number of Cells Allows the Production of a High-quality Mock Community of Bacterial Cells. 一种基于高效液相色谱的细胞基因组拷贝数计数方法可以产生高质量的模拟细菌细胞群落。

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.ME24076

Yoshifumi Ohyama, Takamasa Miura, Masataka Furukawa, Mamiko Shimamura, Yuki Asami, Atsushi Yamazoe, Yoshihito Uchino, Hiroko Kawasaki

引用次数: 0

Degradation of N-acylhomoserine Lactone Quorum-sensing Signals by Azorhizobium caulinodans, a Stem Nodule-forming Symbiont in Sesbania rostrata. 山田菁茎结共生体氮根根菌对n -酰基高丝氨酸内酯群体感应信号的降解

IF 2 4区环境科学与生态学

Microbes and Environments Pub Date : 2025-01-01 DOI: 10.1264/jsme2.ME25060

Tomohiro Morohoshi, Kio Murakami, Nobutaka Someya

引用次数: 0

Group-specific Quantification of mcrA genes of Methanogenic Archaea and "Candidatus Methanoperedens" by Digital PCR. 产甲烷古菌和“Methanoperedens Candidatus Methanoperedens”mcrA基因的群体特异性定量分析。

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.ME24097

Takeshi Watanabe, Atsuya Endo, Rio Hamada, Rina Shinjo, Susumu Asakawa

引用次数: 0

Role of Formate Chemoreceptor in Pseudomonas syringae pv. tabaci 6605 in Tobacco Infection. 甲酸化学受体在丁香假单胞菌中的作用。烟草侵染中的烟草6605。

IF 2 4区环境科学与生态学

Microbes and Environments Pub Date : 2025-01-01 DOI: 10.1264/jsme2.ME25019

Phuoc Quy Thang Nguyen, Yuta Watanabe, Hidenori Matsui, Nanami Sakata, Yoshiteru Noutoshi, Kazuhiro Toyoda, Yuki Ichinose

{"title":"Role of Formate Chemoreceptor in Pseudomonas syringae pv. tabaci 6605 in Tobacco Infection.","authors":"Phuoc Quy Thang Nguyen, Yuta Watanabe, Hidenori Matsui, Nanami Sakata, Yoshiteru Noutoshi, Kazuhiro Toyoda, Yuki Ichinose","doi":"10.1264/jsme2.ME25019","DOIUrl":"10.1264/jsme2.ME25019","url":null,"abstract":"Chemotaxis is essential for infection by plant pathogenic bacteria. The causal agent of tobacco wildfire disease, Pseudomonas syringae pv. tabaci 6605 (Pta6605), is known to cause severe leaf disease and is highly motile. The requirement of chemotaxis for infection has been demonstrated through the inoculation of mutant strains lacking chemotaxis sensory component proteins. Pta6605 possesses 54 genes that encode chemoreceptors (known as methyl-accepting chemotaxis proteins, MCPs). Chemoreceptors are classified into several groups based on the type and localization of ligand-binding domains (LBD). Cache LBD-type chemoreceptors have been reported to recognize formate in several bacterial species. In the present study, we identified Cache_3 Cache_2 LBD-type Mcp26 encoded by Pta6605_RS00335 as a chemoreceptor for formate using a quantitative capillary assay, and named it McpF. Although the deletion mutant of mcpF (ΔmcpF) retained attraction to 1% yeast extract, its chemotactic response to formate was markedly reduced. Swimming and swarming motilities were also impaired in the mutant. To investigate the effects of McpF on bacterial virulence, we conducted inoculations on tobacco plants using several methods. The ΔmcpF mutant exhibited weaker virulence in flood and spray assays than wild-type and complemented strains, highlighting not only the involvement of McpF in formate recognition, but also its critical role in leaf entry during the early stages of infection.","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/PMC12501870/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144708057","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

Differential Responses of Soil Ammonia-oxidizing Bacterial and Archaeal Communities to Land-use Changes in Zambia. 赞比亚土壤氨氧化细菌和古细菌群落对土地利用变化的差异响应

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.ME24049

Takamitsu Ohigashi, Suzumi Mori, Kanako Tago, Tsubasa Ohbayashi, Shintaro Hara, Yoshitaka Uchida

{"title":"Differential Responses of Soil Ammonia-oxidizing Bacterial and Archaeal Communities to Land-use Changes in Zambia.","authors":"Takamitsu Ohigashi, Suzumi Mori, Kanako Tago, Tsubasa Ohbayashi, Shintaro Hara, Yoshitaka Uchida","doi":"10.1264/jsme2.ME24049","DOIUrl":"10.1264/jsme2.ME24049","url":null,"abstract":"Soil nutrient loss from intensive farming is a critical issue in sub-Saharan Africa that affects food security. While soil microbial nitrification supplies available nitrogen, excessive nitrification leads to nitrogen loss. However, the species driving nitrification and their functions in this region remain largely unknown. Therefore, we investigated the responses of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities to land-use changes in Zambia and their relationship with nitrification potential. Soil samples were collected from three sites in Zambia that all had neighboring natural and farmed (maize) lands. We measured nitrification potential, quantified AOB and AOA, and analyzed these communities by targeting the ammonia monooxygenase subunit A (amoA) gene, which encodes a key enzyme in nitrification. Nitrification potential was 1.51-fold higher in farmlands than in natural lands. AOB abundance tended to be greater in farmlands, whereas AOA abundance was smaller. Farming changed the AOB community structure, increasing Nitrosospira cluster 3a.2 at the three sites, while minor site-specific responses were also observed. In contrast, the AOA community structure was not significantly different between land uses, but varied among sites, with cluster NS-ζ being more prominent in one site with neutral soil (pH 7.64) than in the other sites (pH 5.70 and 5.71). These results suggest that AOA species were generally vulnerable to farming, decreasing in abundance without structural changes, while some AOB species increased, driving changes in their community structure. These insights are fundamental for understanding soil nitrogen depletion due to microbial changes under farming and are crucial for developing sustainable land-use practices in sub-Saharan Africa.","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/PMC11946413/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143639743","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

A Rechargeable Biomineral Induced by the Sulfate-reducing Bacterium Nitratidesulfovibrio sp. HK-II. 硫酸盐还原菌Nitratidesulfovibrio sp. HK-II诱导的可充电生物矿物。

IF 2 4区环境科学与生态学

Microbes and Environments Pub Date : 2025-01-01 DOI: 10.1264/jsme2.ME24022

Yui Arashi, Hiroki Mochihara, Hiroko Kubota, Kei Suzuki, Yusuke Chiba, Yutaka Kato, Toshihiro Kogure, Ryota Moriuchi, Hideo Dohra, Yuto Nakamura, Yosuke Tashiro, Hiroyuki Futamata

{"title":"A Rechargeable Biomineral Induced by the Sulfate-reducing Bacterium Nitratidesulfovibrio sp. HK-II.","authors":"Yui Arashi, Hiroki Mochihara, Hiroko Kubota, Kei Suzuki, Yusuke Chiba, Yutaka Kato, Toshihiro Kogure, Ryota Moriuchi, Hideo Dohra, Yuto Nakamura, Yosuke Tashiro, Hiroyuki Futamata","doi":"10.1264/jsme2.ME24022","DOIUrl":"10.1264/jsme2.ME24022","url":null,"abstract":"A sulfate-reducing bacterium was isolated from the anode surface of a microbial fuel cell (MFC) producing a high current density. 16S rRNA gene ana-lyses showed that the isolate was affiliated with the genus Nitratidesulfovibrio, and the strain was named HK-II. When Nitratidesulfovibrio sp. strain HK-II was incubated anaerobically under sulfate-reducing conditions with Fe(III) citrate, a black precipitate formed. The resulting black precipitate was investigated using multidisciplinary methods. An X-ray diffraction (XRD) ana-lysis revealed that the black precipitate was mainly composed of mackinawite. A cyclic voltammetry ana-lysis showed clear redox peaks, and biogenic mackinawite possessed rechargeable properties. The XRD ana-lysis also showed that the form of the rechargeable biogenic mineral induced by strain HK-II (RBM-II) was changed by discharge and recharge treatments. Field-emission transmission electron microscopy revealed that lepidocrocite and amorphous iron oxide formed from mackinawite under discharged conditions, and the three mineral types were intermingled via charge and discharge cycles. Physicochemical parameters regularly changed under the treatments, suggesting that discharge occurred via iron oxidation followed by sulfur reduction and vice versa. These results indicate that sulfur dynamics are important key processes in charge and discharge mechanisms. MFCs equipped with lactate, strain HK-II, and an anode containing RBM-II consumed lactate under open-circuit conditions, after which MFCs generated a higher current density under reclosed-circuit conditions. These results demonstrate that RBM-II is a rechargeable material that enables the capture of electrons produced by bacterial cells and is useful for enhancing the performance of MFCs.","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/PMC12501878/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553963","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

Identification of Arbuscular Mycorrhizal Fungal Isolates using MiSeq Sequencing. 利用MiSeq测序技术鉴定丛枝菌根真菌分离株。

IF 2 4区环境科学与生态学

Microbes and Environments Pub Date : 2025-01-01 DOI: 10.1264/jsme2.ME25040

Ryo Ohtomo

{"title":"Identification of Arbuscular Mycorrhizal Fungal Isolates using MiSeq Sequencing.","authors":"Ryo Ohtomo","doi":"10.1264/jsme2.ME25040","DOIUrl":"10.1264/jsme2.ME25040","url":null,"abstract":"The standardization of strain identification methods is essential for effectively managing the genetic resources of arbuscular mycorrhizal (AM) fungi. Due to their highly polymorphic rRNA sequence and multinucleate nature, conventional strain identification using a single sequence of the rRNA region is often inadequate for these fungi. Therefore, the present study exami-ned the use of genetic diversity information obtained through high-throughput sequencing to improve the strain identification of AM fungal isolates. Five previously reported primer pairs were used to amplify a portion of the rRNA region from DNA extracted from AM fungal spores, which was then sequenced using the Illumina MiSeq platform. The majority of amplicon sequence variants (ASVs) matched the same strain as the source isolate. A cluster anal-ysis indicated that strains of the same species generally grouped together, demonstrating the method's effectiveness for species-level identification. Furthermore, a phylogenetic anal-ysis revealed some strain-specific ASVs that may be valuable for differentiating between different strains within the same species. Based on these results, it is feasible to develop a reliable identification protocol for AM fungal isolates using MiSeq sequencing.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"40 4","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12727196/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145534511","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

Analysis of Soil Microbial Features in a Rice Paddy Field with High Methane Emissions. 高甲烷排放稻田土壤微生物特征分析

IF 2 4区环境科学与生态学

Microbes and Environments Pub Date : 2025-01-01 DOI: 10.1264/jsme2.ME25044

Yoriko Sakai, Ichiro Uezono, Makoto Shibuya, Noriko Oura, Shigeto Sudo

引用次数: 0

Marked Genome Reduction Driven by a Parasitic Lifestyle: Two Complete Genomes of Endosymbiotic Bacteria Possibly Hosted by a Dinoflagellate. 由寄生生活方式驱动的标记基因组减少：可能由鞭毛藻宿主的内共生细菌的两个完整基因组。

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.ME25005

Takuro Nakayama, Ryo Harada, Akinori Yabuki, Mami Nomura, Kogiku Shiba, Kazuo Inaba, Yuji Inagaki

{"title":"Marked Genome Reduction Driven by a Parasitic Lifestyle: Two Complete Genomes of Endosymbiotic Bacteria Possibly Hosted by a Dinoflagellate.","authors":"Takuro Nakayama, Ryo Harada, Akinori Yabuki, Mami Nomura, Kogiku Shiba, Kazuo Inaba, Yuji Inagaki","doi":"10.1264/jsme2.ME25005","DOIUrl":"10.1264/jsme2.ME25005","url":null,"abstract":"Bacteria with endosymbiotic lifestyles often show marked genome reduction. While the shrinkage of genomes in intracellular symbionts of animals, including parasitic bacteria, has been extensively exami-ned, less is known about symbiotic bacteria associated with single-celled eukaryotes. We herein report the genomes of two novel gammaproteobacterial lineages, RS3 and XS4, identified as putative parasitic endosymbionts of the dinoflagellate Citharistes regius. Phylogenetic ana-lyses suggest that RS3 and XS4 belong to the family Fastidiosibacteraceae within the order Beggiatoales, forming independent lineages therein. The genomes of RS3 and XS4 are 529 and 436‍ ‍kbp in size, respectively, revealing marked reductions from related bacterial genomes. XS4, which has a very reduced genome with a low GC content, uses a different genetic code, in which UGA assigned tryptophan. The small genomes of RS3 and XS4 encode a limited number of proteins, retaining only approximately 20% of the predicted ancestral proteome. Metabolic reconstruction suggests that RS3 and XS4 are parasitic symbionts that are heavily dependent on their host for essential metabolites. Furthermore, we found that the ancestor of both genomes likely acquired an ADP:ATP antiporter gene via horizontal gene transfer, an event that may have enabled their evolution as energy parasites by facilitating the acquisition of ATP from their host. These results on novel bacteria with highly reduced genomes expand our understanding of the phylogenetic and genomic diversities of endosymbiotic bacteria in protists.","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/PMC12213064/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144225884","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