Microbes and Environments最新文献_第2页

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

Metagenomic Insights into Candidatus Scalindua in a Long-term Cultivated Marine Anammox Consortium: The Important Role of Tetrahydrofolate-mediated Carbon Fixation. 长期培养的海洋厌氧氨氧化菌群中褐藻的宏基因组研究：四氢叶酸介导的碳固定的重要作用。

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.ME25007

Thelwadanage Nadisha Tharangani Kumari Nawarathna, Naoki Fujii, Kohei Yamamoto, Kyohei Kuroda, Takashi Narihiro, Noriatsu Ozaki, Akiyoshi Ohashi, Tomonori Kindaichi

{"title":"Metagenomic Insights into Candidatus Scalindua in a Long-term Cultivated Marine Anammox Consortium: The Important Role of Tetrahydrofolate-mediated Carbon Fixation.","authors":"Thelwadanage Nadisha Tharangani Kumari Nawarathna, Naoki Fujii, Kohei Yamamoto, Kyohei Kuroda, Takashi Narihiro, Noriatsu Ozaki, Akiyoshi Ohashi, Tomonori Kindaichi","doi":"10.1264/jsme2.ME25007","DOIUrl":"10.1264/jsme2.ME25007","url":null,"abstract":"Marine anammox bacteria have been an exciting research area in recent years due to their high effectiveness in treating ammonia-containing saline wastewater. However, their direct implementation in the wastewater industry faces challenges due to slow growth, difficulty obtaining pure cultures, and their tendency to exist as part of an anammox consortium, interacting symbiotically with other bacteria. In the present study, 91 draft genome metagenome-assembled genomes (MAGs) from a long-term-operated reactor were recovered to clarify detailed symbiotic interactions within an anammox consortium. One marine anammox bacterial MAG, identified as Candidatus Scalindua, was successfully recovered and was abundant within the sampled microbial community. A comprehensive metabolic pathway ana-lysis revealed that Ca. Scalindua exhibited the complete anammox pathway and the Wood-Ljungdahl pathway for carbon fixation. The folate biosynthesis pathway in Ca. Scalindua was incomplete, lacking dihydrofolate reductase, a key enzyme for tetrahydrofolate (THF) production. The folate biopterin transporter, essential for transporting folate-related metabolites among coexisting bacteria, was identified exclusively in Ca. Scalindua. In addition, the impact of exogenously supplied THF on microbial activity and carbon uptake rates was investigated in batch experiments using 14C-labeled bicarbonate. The results obtained revealed that 2‍ ‍mg L-1 of exogenous THF resulted in a 43% increase in the carbon uptake rate, while anammox activity remained unaffected. The present results suggest that THF is a key intermediate for carbon fixation in Ca. Scalindua and may be essential for their growth.","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/PMC12213060/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144326164","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

Microbiome Associated with Polypedilum sp. (Diptera; Chironomidae), a Midge Adapted to an Extremely Acidic Environment. 双翅目蓼属微生物组；摇蚊科，一种适应极端酸性环境的蠓。

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.ME24090

Eita Nakanishi, Richard Cornette, Sachiko Shimura, Takahiro Kikawada

{"title":"Microbiome Associated with Polypedilum sp. (Diptera; Chironomidae), a Midge Adapted to an Extremely Acidic Environment.","authors":"Eita Nakanishi, Richard Cornette, Sachiko Shimura, Takahiro Kikawada","doi":"10.1264/jsme2.ME24090","DOIUrl":"10.1264/jsme2.ME24090","url":null,"abstract":"Chironomids (Diptera; Chironomidae), non-biting midges, are a highly diverse family of holometabolous insects, many of which are known for their tolerance to extreme environmental conditions, such as desiccation, pollution, and high acidity. The contribution of microbial symbionts to these adaptations was recently suggested. Therefore, we herein exami-ned the microbiome associated with the larvae of the undescribed acid-tolerant chironomid species, Polypedilum sp., which inhabits the Yukawa River (Gunma, Japan), an environment that is characterized by an extremely low pH (≤2) and high concentrations of heavy metal ions (including arsenic). Amplicon sequencing of the 16S rRNA gene revealed a distinct larval microbiome with a lower alpha diversity value and more enriched and specific bacterial taxa than the surrounding river water and detritus. Full-length 16S rRNA gene sequencing using nanopore long-read technology identified several previously undescribed operational taxonomic units (OTUs), among which OTU_Bacillaceae_Yukawa was consistently present in larvae reared in the laboratory for more than 4 months, suggesting persistent, possibly vertically transmitted, symbiosis. An inferred pathway ana-lysis suggested the contribution of the larval microbiome to host nutritional physiology. The possibly acid-sensitive OTU_Bacillaceae_Yukawa localized to midgut segments, indicating internal pH-buffered niches for microbial survival. These results provide novel insights into the ecology of acid-tolerant chironomids and lay the groundwork for further examinations of holobiont-based stress tolerance.","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/PMC12213058/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144369056","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

Isolation of a Tissierellaceae Bacterium Exhibiting a High Reduction Potential for Insoluble Indigo Dyes. 一种对不溶性靛蓝染料具有高还原潜力的组织菌科细菌的分离。

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.ME24104

Zhihao Tu, Isao Yumoto

{"title":"Isolation of a Tissierellaceae Bacterium Exhibiting a High Reduction Potential for Insoluble Indigo Dyes.","authors":"Zhihao Tu, Isao Yumoto","doi":"10.1264/jsme2.ME24104","DOIUrl":"https://doi.org/10.1264/jsme2.ME24104","url":null,"abstract":"In traditional indigo dyeing, water-insoluble indigo is anaerobically converted into soluble leuco-indigo via microbial reduction in alkaline dye suspensions, allowing its use as a fabric dye. Although various indigo-reducing bacteria have been isolated to date, culture-independent microbial community ana-lyses have suggested that bacteria belonging to uncultured clades also contribute to indigo reduction. Therefore, we aimed to isolate previously overlooked indigo-reducing bacteria using an unconventional culture method. We conducted enrichment cultures and single-colony isolation using a medium supplemented with sukumo, an indigo dye source derived from the composted leaves of indigo-containing plants, as the sole energy, carbon, and nitrogen sources. We isolated a previously uncultured bacterium belonging to the family Tissierellaceae, which had been predicted as a major indigo reducer in various indigo dyeing processes solely based on microbial community ana-lyses. The insoluble indigo-reducing activity of the Tissierellaceae isolate, strain TU-1 was significantly higher than that of known indigo-reducing bacteria. The addition of the culture supernatant of strain TU-1 enhanced the reduction of indigo powder by other indigo-reducing bacteria, with similar stimulatory effects to those of the insoluble electron mediator, anthraquinone. These results indicate that strain TU-1 possesses a high capacity for secreting electron mediators, conferring a significant reduction capacity for insoluble indigo. Further investigations, including the discovery of additional unknown indigo-reducing bacteria and the identification of the mediators they produce, will provide a more detailed understanding of the mechanisms underlying indigo reduction in practical dyeing processes.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"40 3","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144626693","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

Nitrogen-fixing Ability of a Thermophilic Sulfate-reducing Bacterium in the Genus Thermodesulfovibrio Isolated from a Terrestrial Hot Spring in Japan. 从日本陆生温泉中分离的嗜热硫酸盐还原菌的固氮能力。

IF 2 4区环境科学与生态学

Microbes and Environments Pub Date : 2025-01-01 DOI: 10.1264/jsme2.ME25030

Toko Hisano, Arisa Nishihara, Shin Haruta

引用次数: 0

Responses of Soil Bacteria Communities to Organic Material Application and Their Antagonistic Activity against Diaporthe destruens Causing Sweet Potato Foot Rot Disease. 土壤细菌群落对有机肥施用的响应及其对甘薯足腐病病原菌的拮抗活性

IF 2 4区环境科学与生态学

Microbes and Environments Pub Date : 2025-01-01 DOI: 10.1264/jsme2.ME25011

Zin Mar Soe, Masao Sakai, Sakura Kihara, Daisuke Fukahori, Masayuki Nakamura, Daisuke Ueno, Jun-Ichi Sakagami, Makoto Ikenaga

{"title":"Responses of Soil Bacteria Communities to Organic Material Application and Their Antagonistic Activity against Diaporthe destruens Causing Sweet Potato Foot Rot Disease.","authors":"Zin Mar Soe, Masao Sakai, Sakura Kihara, Daisuke Fukahori, Masayuki Nakamura, Daisuke Ueno, Jun-Ichi Sakagami, Makoto Ikenaga","doi":"10.1264/jsme2.ME25011","DOIUrl":"https://doi.org/10.1264/jsme2.ME25011","url":null,"abstract":"Sweet potato foot rot disease caused by Diaporthe destruens (formerly Plenodomus destruens) severely affects the yield and quality of sweet potatoes. To gain basic knowledge on regulating the pathogen using indigenous soil bacteria, the following organic materials were applied to potted soils collected from a sweet potato field contaminated with D. destruens: Kuroihitomi (compost made from shochu waste and chicken manure), Soil-fine (material made by adsorbing shochu waste on rice bran), and rice bran. Soil samples were periodically collected during an incubation for bacterial colony counts and a community ana-lysis using a meta 16S amplicon ana-lysis. The number of bacterial colonies was significantly higher with the Soil-fine and rice bran treatments and slightly higher with the Kuroihitomi treatment than with a chemical fertilizer as the control, and then gradually decreased over time. An amplicon ana-lysis showed that the Soil-fine and rice bran treatments increased the relative abundance of Streptomycetaceae and Micrococcaceae belonging to Actinobacteria and Burkholderiaceae belonging to Beta-proteobacteria. The Kuroihitomi treatment also increased the relative abundance of Streptomycetaceae. The dominant amplicon sequencing variant (ASV) sequences among these families were affiliated with the genera Kitasatospora, Arthrobacter, and Paraburkholderia. Bacteria with sequences identical to these ASVs were isolated from the incubated soils using selective media for dual culture assays. Bacterial isolates in a cluster of Kitasatospora exhibited antagonistic activity against D. destruens. The present results suggest that combining organic materials with antagonistic bacteria may be an effective approach to regulating the growth of D. destruens.","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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145015716","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

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

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

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