Microbes and Environments最新文献_第2页

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

Vertical Distribution and Seasonal Patterns of Candidatus Nitrotoga in a Sub-Alpine Lake. 亚阿尔卑斯湖中尼特罗加菌的垂直分布和季节模式

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.ME23086

Albin Alfreider, Manuel Harringer

引用次数: 0

Successful Isolation of Diverse Verrucomicrobiota Strains through the Duckweed-Microbes Co-cultivation Method. 通过浮萍-微生物共培养法成功分离出多种疣状微生物菌株

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.me24019

Yasuhiro Tanaka,Erina Tozawa,Tomoki Iwashita,Yosuke Morishita,Hideyuki Tamaki,Tadashi Toyama,Masaaki Morikawa,Yoichi Kamagata,Kazuhiro Mori

{"title":"Successful Isolation of Diverse Verrucomicrobiota Strains through the Duckweed-Microbes Co-cultivation Method.","authors":"Yasuhiro Tanaka,Erina Tozawa,Tomoki Iwashita,Yosuke Morishita,Hideyuki Tamaki,Tadashi Toyama,Masaaki Morikawa,Yoichi Kamagata,Kazuhiro Mori","doi":"10.1264/jsme2.me24019","DOIUrl":"https://doi.org/10.1264/jsme2.me24019","url":null,"abstract":"The \"duckweed-microbes co-cultivation method\" is a microbial isolation technique that effectively recovers diverse microbes, including rarely cultivated bacterial phyla, from environmental samples. In this method, aseptic duckweed and microbes collected from an environmental sample are co-cultivated for several days, and duckweed-associated microbes are then isolated from its roots using a conventional agar plate-based cultivation method. We herein propose several improvements to the method in order to specifically obtain members of the rarely cultivated bacterial phylum, Verrucomicrobiota. In systems using river water as the inoculum, the marked enrichment of Verrucomicrobiota was observed after 10 days of co-cultivation, particularly in the roots and co-cultivated media. We also successfully isolated 44 strains belonging to subdivisions 1, 3, and 4 of the phylum Verrucomicrobiota from these systems. This was achieved by changing the concentration of nitrogen in the co-cultivation medium, which is known to affect duckweed growth and/or metabolism, and by subjecting the fronds and co-cultivated media as well as the roots after co-cultivation to microbial isolation.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"13 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142209416","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

Effects of NaCl Treatment on Root Nodule Formation, Isoflavone Secretion in Soybean, and Nodulation Gene Expression in Rhizobia. NaCl处理对大豆根瘤形成、异黄酮分泌及根瘤菌根瘤基因表达的影响

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.ME24023

Yoshikazu Nitawaki, Takaaki Yasukochi, Shinya Naono, Akihiro Yamamoto, Yuichi Saeki

{"title":"Effects of NaCl Treatment on Root Nodule Formation, Isoflavone Secretion in Soybean, and Nodulation Gene Expression in Rhizobia.","authors":"Yoshikazu Nitawaki, Takaaki Yasukochi, Shinya Naono, Akihiro Yamamoto, Yuichi Saeki","doi":"10.1264/jsme2.ME24023","DOIUrl":"10.1264/jsme2.ME24023","url":null,"abstract":"We herein investigated the effects of salt (NaCl) stress on soybean nodulation by rhizobial strains. We specifically exami-ned: (1) the effects of NaCl on nodule maturity and positioning by inoculating three rhizobial strains (Bradyrhizobium diazoefficiens USDA110T, Bradyrhizobium elkanii USDA31, and Sinorhizobium fredii USDA191) onto soybean variety CNS, (2) the effects of the NaCl treatment on isoflavones (daidzein and genistein) secretion by CNS, (3) the effects of the NaCl treatment on gene expression induced by daidzein and genistein in rhizobia, and (4) the effects of the NaCl treatment on rhizobial growth. The results obtained were as follows: (1) the NaCl treatment delayed nodule development and reduced nodulation on the primary root following the USDA110T inoculation, minimal sensitivity regarding nodule formation in the USDA 31 inoculation, and significantly increased the mature nodule number and nodules on the primary root following the USDA 191 inoculation. (2) The NaCl treatment significantly reduced the secretion of daidzein from soybean roots, but did not significantly affect that of genistein. (3) NaCl treatment induced a significant decrease in genistein-induced nodC expression in USDA110T, but not in USDA31, and also caused a significant reduction in daidzein-induced nodC expression, but not genistein-induced expression, in USDA191. (4) NaCl treatment reduced survivability under acidic conditions, but increased survivability under saline-alkaline conditions for USDA191 than bradyrhizobia. These results indicate that saline conditions give S. fredii a competitive advantage over Bradyrhizobium during soybean infection.","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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11821761/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142877440","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

Comprehensive Insights into Potential Metabolic Functions of Myxococcota in Activated Sludge Systems. 粘球菌在活性污泥系统中潜在代谢功能的综合见解。

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.ME24068

Hazuki Kurashita, Masashi Hatamoto, Shun Tomita, Takashi Yamaguchi, Takashi Narihiro, Kyohei Kuroda

{"title":"Comprehensive Insights into Potential Metabolic Functions of Myxococcota in Activated Sludge Systems.","authors":"Hazuki Kurashita, Masashi Hatamoto, Shun Tomita, Takashi Yamaguchi, Takashi Narihiro, Kyohei Kuroda","doi":"10.1264/jsme2.ME24068","DOIUrl":"10.1264/jsme2.ME24068","url":null,"abstract":"Myxobacteria, belonging to the phylum Myxococcota, are ubiquitous in soil, marine, and other environments. A recent metagenomic sequencing ana-lysis showed that Myxococcota are predominant in activated sludge systems; however, their metabolic traits remain unclear. In the present study, we exami-ned the potential biological functions of 46 metagenomic bins of Myxococcota reconstructed from activated sludge samples from four municipal sewage treatment plants. The results obtained showed that most Myxococcota bins had an almost complete set of genes associated with glycolysis and the TCA cycle. The Palsa-1104 and Polyangiales bins contained the glycoside hydrolase GH5 and peptidase M23, which are presumably involved in lysis of the cell wall and cellular cytoplasm, suggesting that some Myxococcota from activated sludge prey on other microorganisms. The cell contact-dependent predatory functions of Myxococcus xanthus are conserved in the family Myxococcaceae, but not in other families. Two bins belonging to Palsa-1104 had phototrophic gene clusters, indicating the potential for heterotrophic and autotrophic metabolism by these microbes. In assessments of the social behavior of Myxococcota in activated sludge, the FruA gene and C-signal gene, which are involved in the regulation of fruiting body formation, were lacking in Myxococcota bins, suggesting their inability to form fruiting bodies. In addition, multiple bins of Myxococcota had novel secondary metabolite biosynthesis gene clusters that may be used for the predation of other bacteria in activated sludge. Our metagenome-based ana-lyses provide novel insights into the microbial interactions associated with Myxococcota in activated sludge ecosystems.","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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11821767/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142932115","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

Two Distinct Enzymes Have Both Phytoene Desaturase and 3,4-Desaturase Activities Involved in Carotenoid Biosynthesis by the Extremely Halophilic Archaeon Haloarcula japonica. 两种不同的酶同时具有植物烯去饱和酶和 3,4-去饱和酶的活性，它们参与了极嗜卤古菌 Haloarcula japonica 的类胡萝卜素生物合成。

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.ME24004

Rie Yatsunami, Ai Ando, Nobuhiro Miyoko, Ying Yang, Shinichi Takaichi, Satoshi Nakamura

{"title":"Two Distinct Enzymes Have Both Phytoene Desaturase and 3,4-Desaturase Activities Involved in Carotenoid Biosynthesis by the Extremely Halophilic Archaeon Haloarcula japonica.","authors":"Rie Yatsunami, Ai Ando, Nobuhiro Miyoko, Ying Yang, Shinichi Takaichi, Satoshi Nakamura","doi":"10.1264/jsme2.ME24004","DOIUrl":"10.1264/jsme2.ME24004","url":null,"abstract":"The extremely halophilic archaeon Haloarcula japonica accumulates the C50 carotenoid, bacterioruberin (BR). To reveal the BR biosynthetic pathway, unidentified phytoene desaturase candidates were functionally characterized in the present study. Two genes encoding the potential phytoene desaturases, c0507 and d1086, were found from the Ha. japonica genome sequence by a homology search using the Basic Local Align Search Tool. Disruption mutants of c0507 and d1086 and their complemented strains transformed with expression plasmids for c0507 and d1086 were subsequently constructed. High-performance liquid chromatography (HPLC) ana-lyses of carotenoids produced by these strains revealed that C0507 and D1086 were both bifunctional enzymes with the same activities as both phytoene desaturase (CrtI) and 3,4-desaturase (CrtD). C0507 and D1086 complemented each other during BR biosynthesis in Ha. japonica. This is the first study to identify two distinct enzymes with both CrtI and CrtD activities in an extremely halophilic archaeon.","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":"141175540","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

Metagenomic Insights into Ecophysiology of Zetaproteobacteria and Gammaproteobacteria in Shallow Zones within Deep-sea Massive Sulfide Deposits. 元基因组学对深海大型硫化物矿床浅层区 Zetaproteobacteria 和 Gammaproteobacteria 生态生理学的启示。

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.ME23104

Nao Masuda, Shingo Kato, Moriya Ohkuma, Kazuyoshi Endo

{"title":"Metagenomic Insights into Ecophysiology of Zetaproteobacteria and Gammaproteobacteria in Shallow Zones within Deep-sea Massive Sulfide Deposits.","authors":"Nao Masuda, Shingo Kato, Moriya Ohkuma, Kazuyoshi Endo","doi":"10.1264/jsme2.ME23104","DOIUrl":"https://doi.org/10.1264/jsme2.ME23104","url":null,"abstract":"Deep-sea massive sulfide deposits serve as energy sources for chemosynthetic ecosystems in dark, cold environments even after hydrothermal activity ceases. However, the vertical distribution of microbial communities within sulfide deposits along their depth from the seafloor as well as their ecological roles remain unclear. We herein conducted a culture-independent metagenomic ana-lysis of a core sample of massive sulfide deposits collected in a hydrothermally inactive field of the Southern Mariana Trough, Western Pacific, by drilling (sample depth: 0.52‍ ‍m below the seafloor). Based on the gene context of the metagenome-assembled genomes (MAGs) obtained, we showed the metabolic potential of as-yet-uncultivated microorganisms, particularly those unique to the shallow zone rich in iron hydroxides. Some members of Gammaproteobacteria have potential for the oxidation of reduced sulfur species (such as sulfide and thiosulfate) to sulfate coupled to nitrate reduction to ammonia and carbon fixation via the Calvin-Benson-Bassham (CBB) cycle, as the primary producers. The Zetaproteobacteria member has potential for iron oxidation coupled with microaerobic respiration. A comparative ana-lysis with previously reported metagenomes from deeper zones (~2‍ ‍m below the seafloor) of massive sulfide deposits revealed a difference in the relative abundance of each putative primary producer between the shallow and deep zones. Our results expand knowledge on the ecological potential of uncultivated microorganisms in deep-sea massive sulfide deposits and provide insights into the vertical distribution patterns of chemosynthetic ecosystems.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"39 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11427306/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142349767","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

The Discovery of Membrane Vesicle Biogenesis in the Polyhydroxybutyrate-non-producing Mutant Strain of Cupriavidus necator H16. 在不产生多羟基丁酸的突变株中发现膜囊泡的生物生成过程。

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.ME24007

Sangho Koh, Michio Sato, Hiromi Matsusaki, Seiichi Taguchi

引用次数: 0

Polyethylene Biodegradation by an Artificial Bacterial Consortium: Rhodococcus as a Competitive Plastisphere Species. 人工细菌联盟对聚乙烯的生物降解：罗氏球菌是一种具有竞争力的塑球菌种。

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.ME24031

Jyothi Priya Putcha, Wataru Kitagawa

{"title":"Polyethylene Biodegradation by an Artificial Bacterial Consortium: Rhodococcus as a Competitive Plastisphere Species.","authors":"Jyothi Priya Putcha, Wataru Kitagawa","doi":"10.1264/jsme2.ME24031","DOIUrl":"10.1264/jsme2.ME24031","url":null,"abstract":"Polyethylene (PE), a widely used recalcitrant synthetic polymer, is a major global pollutant. PE has very low biodegradability due to its rigid C-C backbone and high hydrophobicity. Although microorganisms have been suggested to possess PE-degrading enzymes, our understanding of the PE biodegradation process and its overall applicability is still lacking. In the present study, we used an artificial bacterial consortium for PE biodegradation to compensate for the enzyme availability and metabolic capabilities of individual bacterial strains. Consortium members were selected based on available literature and preliminary screening for PE-degrading enzymes, including laccases, lipases, esterases, and alkane hydroxylases. PE pellets were incubated with the consortium for 200 days. A next-generation sequencing ana-lysis of the consortium community of the culture broth and on the PE pellet identified Rhodococcus as the dominant bacteria. Among the Rhodococcus strains in the consortium, Rhodococcus erythropolis was predominant. Scanning electron microscopy (SEM) revealed multilayered biofilms with bacteria embedded on the PE surface. SEM micrographs of PE pellets after biofilm removal showed bacterial pitting and surface deterioration. Multicellular biofilm structures and surface biodeterioration were observed in an incubation of PE pellets with R. erythropolis alone. The present study demonstrated that PE may be biodegraded by an artificially constructed bacterial consortium, in which R. erythropolis has emerged as an important player. The results showing the robust colonization of hydrophobic PE by R. erythropolis and that it naturally possesses and extracellularly expresses several target enzymes suggest its potential as a host for further improved PE biodeterioration by genetic engineering technology using a well-studied host-vector system.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"39 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11427307/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141860202","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

Methanotrophic Communities and Cultivation of Methanotrophs from Rice Paddy Fields Fertilized with Pig-livestock Biogas Digestive Effluent and Synthetic Fertilizer in the Vietnamese Mekong Delta. 越南湄公河三角洲使用猪-牲畜沼气消化废水和合成肥料施肥的稻田中的甲烷营养群落和甲烷滋养菌的培养。

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.ME24021

Huynh Van Thao, Mitsunori Tarao, Hideshige Takada, Tomoyasu Nishizawa, Tran Sy Nam, Nguyen Van Cong, Do Thi Xuan

{"title":"Methanotrophic Communities and Cultivation of Methanotrophs from Rice Paddy Fields Fertilized with Pig-livestock Biogas Digestive Effluent and Synthetic Fertilizer in the Vietnamese Mekong Delta.","authors":"Huynh Van Thao, Mitsunori Tarao, Hideshige Takada, Tomoyasu Nishizawa, Tran Sy Nam, Nguyen Van Cong, Do Thi Xuan","doi":"10.1264/jsme2.ME24021","DOIUrl":"10.1264/jsme2.ME24021","url":null,"abstract":"Biogas digestive effluent (BDE) has been applied to rice fields in the Vietnamese Mekong Delta (VMD). However, limited information is available on the community composition and isolation of methanotrophs in these fields. Therefore, the present study aimed (i) to clarify the responses of the methanotrophic community in paddy fields fertilized with BDE or synthetic fertilizer (SF) and (ii) to isolate methanotrophs from these fields. Methanotrophic communities were detected in rhizospheric soil at the rice ripening stage throughout 2 cropping seasons, winter-spring (dry) and summer-autumn (wet). Methanotrophs were isolated from dry-season soil samples. Although the continued application of BDE markedly reduced net methane oxidation potential and the copy number of pmoA genes, a dissimilarity ordination ana-lysis revealed no significant difference in the methanotrophic community between BDE and SF fields (P=0.167). Eleven methanotrophic genera were identified in the methanotrophic community, and Methylosinus and Methylomicrobium were the most abundant, accounting for 32.3-36.7 and 45.7-47.3%, respectively. Type-I methanotrophs (69.4-73.7%) were more abundant than type-II methanotrophs (26.3-30.6%). Six methanotrophic strains belonging to 3 genera were successfully isolated, which included type I (Methylococcus sp. strain BE1 and Methylococcus sp. strain SF3) and type II (Methylocystis sp. strain BE2, Methylosinus sp. strain SF1, Methylosinus sp. strain SF2, and Methylosinus sp. strain SF4). This is the first study to examine the methanotrophic community structure in and isolate several methanotrophic strains from BDE-fertilized fields in VMD.","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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11821765/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142365801","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