Microbes and Environments最新文献

{"title":"Fusarium Fungi Produce Nitrous Oxide (N₂O) from Nitrite (NO₂^-) in a Model Pot System Simulating the Soybean Rhizosphere.","authors":"Makoto Moriuchi, Keiichi Kuzunuki, Fumio Ikenishi, Reiko Sameshima, Akira Nakagiri, Sakae Toyoda, Chie Katsuyama, Kaori Kakizaki, Manabu Itakura, Naohiro Yoshida, Yuichi Suwa, Kiwamu Minamisawa","doi":"10.1264/jsme2.ME24092","DOIUrl":"https://doi.org/10.1264/jsme2.ME24092","url":null,"abstract":"<p><p>Nitrous oxide (N₂O) is a key atmospheric greenhouse gas that contributes to global warming, with anthropogenic N₂O emissions from agriculture being a particular concern. Among agricultural sources, unknown soil organisms in the legume rhizosphere emit N₂O from degraded root nodules. To discriminate between fungal and bacterial N₂O emissions, we adopted an isotopomer ana-lysis, which provides site preference values (the difference in ¹⁵N abundance of the central and terminal N atoms in the N₂O molecule). The addition of nitrite instead of nitrate to soybean nodulated roots significantly increased SP_N2O from -3.5‰ to 4.2‰ in a pot system. Moreover, a mutation of the nirK gene (encoding dissimilatory nitrite reductase) in symbiotic bradyrhizobia significantly increased SP_N2O from 4.2‰ to 13.9‰ with nitrite. These results suggest that nitrite-utilizing N₂O emissions via fungal denitrification occurred in the model pot system of the soybean rhizosphere. Microscopic observations showed fungal hyphae and crescent spores around N₂O-emitting nodules. Therefore, we isolated single spores from soybean nodules under a microscope. A phylogenetic ana-lysis revealed that all 12 fungal isolates were Fusarium species, which exist in soybean field soil. When these isolates were cultivated in glycerol-peptone medium supplemented with nitrate or nitrite (1‍ ‍mM), 11 of the 12 isolates strongly converted nitrite to N₂O; however, no N₂O emissions were noted in the presence of nitrate. A ¹⁵N-nitrite tracer experiment revealed that one N₂O molecule was derived exclusively from two molecules of nitrite (NO₂^-) in the fungal culture. These results suggest that nitrite-utilizing Fusarium fungi mediate N₂O emissions in the soybean rhizosphere.</p>","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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144025718","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}

{"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":"<p><p>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.</p>","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}

{"title":"Gamma Ray-induced Mutations in pyrEF Genes in Frankia casuarinae Strain CcI3.","authors":"Ken-Ichi Kucho, On Han, Miki Yunoki","doi":"10.1264/jsme2.ME24062","DOIUrl":"10.1264/jsme2.ME24062","url":null,"abstract":"<p><p>Frankia spp. are multicellular actinobacteria with the ability to fix atmospheric dinitrogen (N₂). Frankia fixes N₂ not only in the free-living state, but also in root-nodule symbioses with more than 200 plant species called actinorhizal plants. In the present study, we isolated mutants of the pyrE (orotate phosphoribosyltransferase) and pyrF (orotidine-5'-phosphate decarboxylase) genes in Frankia casuarinae strain CcI3 using gamma rays as a mutagen and systematically identified the types of mutations that occurred in these genes. pyrEF mutants were isolated as uracil auxotrophs using the antimetabolite 5-fluoroorotic acid. We elucidated the nucleotide sequences of the pyrEF genes in 32 uracil auxotrophs, and detected eight substitutions, 17 single-nucleotide deletions, and seven large insertions. Large insertions were insertion sequences (IS elements); four belonged to the IS4 family, two to the IS66 family, and one to the IS110 family. This is the first study to demonstrate the mobilization of IS elements in the Frankia genome.</p>","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/PMC11946415/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143616274","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}

{"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":"<p><p>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.</p>","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}

{"title":"Prevalence, Symbiosis with Rickettsia, and Transmission of Tomato yellow leaf curl virus of Invasive Bemisia tabaci MED Q2 in Japan.","authors":"Akiko Fujiwara, Hiroki Hagiwara, Maiko Tsuchimoto, Tsutomu Tsuchida","doi":"10.1264/jsme2.ME24095","DOIUrl":"https://doi.org/10.1264/jsme2.ME24095","url":null,"abstract":"<p><p>The whitefly, Bemisia tabaci, is a notorious insect pest that transmits plant pathogenic viruses to a wide range of economically important crops. An invasive genetic group of B. tabaci, Mediterranean Q2 (MED Q2), has recently spread to Europe, USA, and Asia. In the present study, we investigated the prevalence of MED Q2 in Japanese agricultural sites and found that its distribution has expanded since it was initially detected in 2013. A polymerase chain reaction ana-lysis revealed that all MED Q2 individuals were infected with Rickettsia. Rickettsia titers increased during nymphal development, presumably in response to the nutritional needs of the host. A fluorescence in situ hybridization ana-lysis revealed that Rickettsia was densely located near Portiera-containing bacteriocytes at all growth stages. Therefore, Rickettsia may play an important role, such as supplying nutrients to the host, in cooperation with Portiera. Transfer experiments indicated that MED Q2 was as effective a vector for Tomato yellow leaf curl virus as MED Q1 and, thus, is a high-risk agricultural pest. These results provide important insights into the biology and ecology of invasive MED Q2 to effectively control its spread and minimize its impact on crops.</p>","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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143971501","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}

{"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":"<p><p>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.</p>","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}

{"title":"Characterization of a Marine Bacterium Passing through a 0.1-μm Pore-sized Filter.","authors":"Haruo Yamaguchi, Kazumasa Yamada","doi":"10.1264/jsme2.ME24014","DOIUrl":"10.1264/jsme2.ME24014","url":null,"abstract":"<p><p>The present study aimed to isolate and characterize a marine bacterium capable of passing through a 0.1-μm pore-sized filter (0.1-μm filter). Sediment suspension samples were filtered through 0.1-μm filters, inoculated into sterile media, and incubated. Isolated SspURN76 belonged to Saccharospirillum, according to 16S rRNA gene sequencing, and showed a very slender shape. The minimum cell size of SspURN76 was 0.09×3.2‍ ‍μm. These morphological features of SspURN76 were likely responsible for its passage through 0.1-μm filters. Based on the results obtained herein, marine bacteria may be present in 0.1-μm filtered fractions.</p>","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/PMC11946411/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586281","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}

{"title":"A HPLC-based Method for Counting the Genome Copy Number of Cells Allows the Production of a High-quality Mock Community of Bacterial Cells.","authors":"Yoshifumi Ohyama, Takamasa Miura, Masataka Furukawa, Mamiko Shimamura, Yuki Asami, Atsushi Yamazoe, Yoshihito Uchino, Hiroko Kawasaki","doi":"10.1264/jsme2.ME24076","DOIUrl":"https://doi.org/10.1264/jsme2.ME24076","url":null,"abstract":"<p><p>Improving the reliability of a metagenomic sequencing ana-lysis requires the use of control samples, known as mock communities. Therefore, mock communities must be prepared with high accuracy and reproducibility, which is particularly challenging for cellular mock communities. In the present study, we prepared a cellular mock community consisting of bacterial strains representative of the human and surrounding environmental microbiomes to demonstrate the suitability of a HPLC-based method that measures the genome number of cells. This method proved to be more accurate and reproducible for preparing cellular mock communities than traditional cell counting-based enumeration methods.</p>","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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144025091","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}

{"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":"<p><p>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.</p>","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}

{"title":"Group-specific Quantification of mcrA genes of Methanogenic Archaea and \"Candidatus Methanoperedens\" by Digital PCR.","authors":"Takeshi Watanabe, Atsuya Endo, Rio Hamada, Rina Shinjo, Susumu Asakawa","doi":"10.1264/jsme2.ME24097","DOIUrl":"https://doi.org/10.1264/jsme2.ME24097","url":null,"abstract":"<p><p>Digital PCR is a technique that quantifies target genes based on the absence or presence of the targets in PCR amplicons. The present study exami-ned group-specific probes for the quantification of mcrA genes in six methanogenic archaeal groups and \"Candidatus Methanoperedens\" by digital PCR with the universal primers ML-f and ML-r. A digital PCR ana-lysis of paddy field soil detected all the targets, with the dominant and minor groups being Methanomicrobiales and Methanobrevibacter spp., respectively (10⁷ and 10⁴ copies [g dry soil]^-1). This method has the potential to reveal the dynamics of specific methanogenic archaeal groups in the environment.</p>","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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143989859","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}