Microbes and Environments最新文献

Gamma Ray-induced Mutations in pyrEF Genes in Frankia casuarinae Strain CcI3. γ射线诱导的木麻黄菌株CcI3 pyrEF基因突变

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.ME24062

Ken-Ichi Kucho, On Han, Miki Yunoki

引用次数: 0

Syntrophic Interaction between an Anoxygenic Photosynthetic Bacterium and a Tetrathionate-reducing Bacterium in Anaerobic Benzoate Degradation. 厌氧苯甲酸酯降解中无氧光合细菌和四硫酸还原细菌的共生相互作用。

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.ME24105

Miao He, Shin-Ichi Nishitani, Shin Haruta

{"title":"Syntrophic Interaction between an Anoxygenic Photosynthetic Bacterium and a Tetrathionate-reducing Bacterium in Anaerobic Benzoate Degradation.","authors":"Miao He, Shin-Ichi Nishitani, Shin Haruta","doi":"10.1264/jsme2.ME24105","DOIUrl":"10.1264/jsme2.ME24105","url":null,"abstract":"The present study exami-ned bacteria that anaerobically degrade the aromatic compound, benzoate, and obtained enrichment cultures from marine sediments under illumination. The enrichment culture contained anoxygenic photosynthetic bacteria and non-photosynthetic bacteria. The photosynthetic strain PS1, a purple sulfur bacterium in the genus Marichromatium, was unable to utilize benzoate; however, when combined with the non-photosynthetic bacterial isolate, Marinobacterium sp. strain BA1, the co-culture grew anaerobically on benzoate in the presence of thiosulfate or tetrathionate. Based on the metabolic profiles of the co-culture and axenic cultures, the following syntrophic interactions were proposed. Strain PS1 oxidizes thiosulfate as the electron source for photosynthesis to produce tetrathionate and relies on carbon dioxide produced through benzoate degradation by strain BA1. Strain BA1 oxidizes benzoate and reduces tetrathionate to provide thiosulfate to strain PS1 for photosynthetic carbon fixation. To the best of our knowledge, this is the first study to report anaerobic benzoate degradation in a photosynthetic co-culture through the syntrophic exchange of sulfur compounds.","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/PMC11946414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143616276","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

Categorization of Bacteria That Leak from Activated Sludge to Secondary Treated Water: Year-round Observations. 从活性污泥泄漏到二次处理水的细菌分类：全年观察。

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.ME24082

Egodaha G W Gunawardana, Tiffany Joan Sotelo, Kenshiro Oshima, Masahira Hattori, Takashi Mino, Hiroyasu Satoh

{"title":"Categorization of Bacteria That Leak from Activated Sludge to Secondary Treated Water: Year-round Observations.","authors":"Egodaha G W Gunawardana, Tiffany Joan Sotelo, Kenshiro Oshima, Masahira Hattori, Takashi Mino, Hiroyasu Satoh","doi":"10.1264/jsme2.ME24082","DOIUrl":"10.1264/jsme2.ME24082","url":null,"abstract":"The present study proposes a categorization of bacteria that leak from activated sludge processes to secondary treated water (STW). Bacterial populations in primary treated water (PTW), activated sludge (AS), STW, and the 0.2‍ ‍μm-filtrate of STW (FSTW) in a full-scale wastewater treatment plant with two treatment trains were observed for a period of one year using a 16S rRNA ana-lysis approach. The taxonomic groups detected were categorized as different \"leak types\" based on the read occupancies in PTW, AS, STW, and FSTW, where a leak type indicates the likelihood of a taxonomic group to leak to STW. Five leak types were introduced: \"LTE\", \"LTE-I\", \"LTEF\", \"LTF\", and \"NLT\", with \"LT\" for leak type, \"E\" for high read occupancy in STW or the effluent of secondary settling tanks, \"I\" for high read occupancy in PTW or influent to the AS process, \"F\" for high read occupancy in FSTW, and \"NLT\" for a smaller likelihood to leak. Representative taxonomic groups for each leak type were Neisseria and ABY1 for \"LTE\" Parcubacteria for \"LTEF\", Campylobacterota for \"LTE-I\", and Saccharimonadia, Bdellovibrionota, and some lineages in Comamonadaceae for \"LTF\". Although some taxonomic groups, such as Comamonadaceae, included different leak types, the categorization assigned to each taxonomic group was mostly consistent between the two treatment trains. The categorization scheme proposed herein may become a useful key for understanding the characteristics of bacteria that appear in AS and STW.","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/PMC11946410/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143639708","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

Impact of Inoculations with Indigenous Bradyrhizobium diazoefficiens Isolates on Productivity and Competition with Indigenous Bradyrhizobia in Adzuki Bean (Vigna angularis). 接种本地重氮缓生根瘤菌对小豆产量及与本地缓生根瘤菌竞争的影响

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.ME24069

Sokichi Shiro, Ryu Makihara, Shota Nakao, Masayuki Kadowaki, Yuichi Saeki

{"title":"Impact of Inoculations with Indigenous Bradyrhizobium diazoefficiens Isolates on Productivity and Competition with Indigenous Bradyrhizobia in Adzuki Bean (Vigna angularis).","authors":"Sokichi Shiro, Ryu Makihara, Shota Nakao, Masayuki Kadowaki, Yuichi Saeki","doi":"10.1264/jsme2.ME24069","DOIUrl":"10.1264/jsme2.ME24069","url":null,"abstract":"We herein exami-ned the inoculation effects of indigenous Bradyrhizobium diazoefficiens isolates on the growth and yield of adzuki beans and their competition with other bradyrhizobia using pot and field experiments. In the pot experiment, shoot nitrogen content was significantly higher following inoculations with AMP1 and Bd (a mixture of AN9 and AN20) than with the control. Furthermore, a correlation was observed between shoot nitrogen content and shoot dry weight. In the field experiment, the inoculating isolates did not significantly affect growth or yield. However, an interaction effect was observed in pod numbers and yield, suggesting that the effects of inoculation varied depending on the cultivar and inoculating isolate. In the correlation ana-lysis, pod number correlated with node number and nodule number. Similarly, yield correlated with shoot length, node number, nodule number, and pod number. Regarding competition between inoculated isolates and other strains, B. elkanii was dominant in pot and field experiments. To enhance the yield of adzuki bean through inoculations, it is necessary to overcome competition from indigenous B. elkanii and increase the occupancy rate of B. diazoefficiens isolates.","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/PMC11946408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143700873","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

Characterization of a Marine Bacterium Passing through a 0.1-μm Pore-sized Filter. 海洋细菌通过0.1 μm孔径过滤器的表征。

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.ME24014

Haruo Yamaguchi, Kazumasa Yamada

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

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

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