Microbes and Environments最新文献

{"title":"Nitrifying Communities in Biological Nitrogen Removal Processes at Tropical Municipal Wastewater Treatment Plants.","authors":"Liang Feng, Jia Xing Loi, Joana Séneca, Petra Pjevac, Faidzul Hakim Adnan, Gek Cheng Ngoh, Bee Chin Khor, Alijah Mohd Aris, Mamoru Oshiki, Holger Daims, Adeline Seak May Chua","doi":"10.1264/jsme2.ME25036","DOIUrl":"https://doi.org/10.1264/jsme2.ME25036","url":null,"abstract":"<p><p>Nitrifying communities in activated sludge play a crucial role in biological nitrogen removal processes in municipal wastewater treatment plants. While extensive research has been conducted in temperate regions, limited information is available on nitrifiers in tropical regions. The present study investigated all currently known nitrifying communities in two full-scale municipal wastewater treatment plants in Malaysia operated under low-dissolved oxygen (DO) (0.2-0.7‍ ‍mg‍ ‍DO‍ ‍L^-1) or high-DO (2.0-5.5‍ ‍mg‍ ‍DO‍ ‍L^-1) conditions at 30°C. The core nitrifiers in the municipal wastewater treatment plants were Nitrosomonas (ammonia-oxidizing bacteria, AOB), Nitrospira (nitrite-oxidizing or complete ammonia-oxidizing, comammox, bacteria), and ammonia-oxidizing archaea (AOA) as identified by a 16S rRNA gene amplicon sequencing ana-lysis and corroborated by 16S rRNA-targeted fluorescence in situ hybridization. A quantitative polymerase chain reaction (qPCR) targeting ammonia monooxygenase subunit A (amoA) genes revealed stable populations of comammox Nitrospira and AOB in both wastewater treatment plants. AOA were detected in only one of the plants and their population sizes fluctuated, with higher temporary abundance under high-DO conditions. These results provide important insights into the composition and dynamics of nitrifying communities in tropical municipal wastewater treatment plants.</p>","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":"145033697","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":"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":"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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12213065/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of the Fecal Microbiota from Long-term Captive and Newly Captured Whale Sharks (Rhincodon typus).","authors":"Takaomi Ito, Takao Segawa, Kazuto Takasaki, Takahiro Matsudaira, Itsuki Kiyatake, Hiroyuki Irino, Yu Nakajima","doi":"10.1264/jsme2.ME25023","DOIUrl":"https://doi.org/10.1264/jsme2.ME25023","url":null,"abstract":"<p><p>Despite its ecological importance, the gut microbiota of whale sharks (Rhincodon typus) remains poorly understood. Therefore, the present study exami-ned how environmental differences affect the fecal microbiota by comparing long-term captive and newly captured individuals. Fecal samples were collected over time from four long-term captive and two newly captured whale sharks, with seawater also being sampled from their respective tanks. Using 16S rRNA sequencing, 12,497 amplicon sequence variants (ASVs) were identified, including 6,976 classified as major ASVs. There were no significant differences in alpha diversity indexes between long-term captive and newly captured sharks; however, the latter showed slightly larger variance in four indexes. The ASV count per individual was slightly lower in long-term captive sharks than in their newly captured counterparts. In long-term captive individuals, Photobacterium was highly abundant. Conversely, Ureaplasma was dominant in newly captured individuals, but was barely detected in long-term captive sharks. Although alpha diversity did not differ significantly between the groups, a beta diversity ana-lysis showed clear distinctions. The high abundance of Ureaplasma in newly captured sharks suggests its involvement in nitrogen metabolism, possibly through urea recycling. Although further research is needed to clarify the taxonomic position and ecological functions of these Ureaplasma populations, the present study provides key insights for the conservation of wild whale sharks and improving health management for captive individuals.</p>","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":"145206859","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":"Amplicon Analysis of Dictean Cave Microbial Communities and Essential Oils as a Mild Biocide.","authors":"Olga Martzoukou, Alexandra Oikonomou, Sotiris Amillis, Dimitris G Hatzinikolaou","doi":"10.1264/jsme2.ME24115","DOIUrl":"https://doi.org/10.1264/jsme2.ME24115","url":null,"abstract":"<p><p>Naturally occurring caves are sites of significant cultural value, while also displaying the unique biodiversity of associated microbiomes that may provide an untapped source of potentially beneficial organisms. However, the touristic exploitation of show caves may ultimately result in the biodeterioration of speleothems, primarily through the introduction and establishment of alien microbiota or the uncontrolled growth of indigenous species, exacerbated by the use of artificial lighting. These habitat characteristics are present in the Dictean cave, also known as \"Diktaion Andron\", a highly visited cave in eastern Crete, Greece, which was regarded in ancient Greek mythology as one of the putative sites of the birth of Zeus. Therefore, an efficient approach to controlling these ecological niches without irreversibly disturbing microbial diversity is needed, and essential oils are currently being investigated as a mild cleaning method. The present study exami-ned the microbial diversity of the Dictean cave using 16S and 18S rRNA gene amplicon sequencing and methods for quantitative metabolic activity estimations and also investigated the application of a formulation containing specific essential oils as a mild cleaning method. Amplicon sequencing ana-lyses revealed distinct profiles among the different sample sites, with species of the genera Pseudomonas, Sporosarcina, Butiauxella, Glutamicibacter, Paenibacillus, Mortierella, and Jenufa being the most abundant, while uncharacterized microorganisms were also detected. The single simultaneous application of a formulation of 0.2% (v/v) oregano and 0.4% (v/v) cinnamon essential oils was effective at significantly reducing microbial metabolic activity by up to 89.2% within 24 h, without adversely affecting the coloration of speleothems.</p>","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":"145138072","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":"Physiological and Genomic Characterization of Oligotrophic Nitrobacter Isolated from a Forest Soil in Japan.","authors":"Yoichiro Kobayashi, Takuya Ninomiya, Yuki Shiraishi, Ayano Kaneko, Megumi Kuroiwa, Yuichi Suwa, Hirotsugu Fujitani","doi":"10.1264/jsme2.ME24114","DOIUrl":"10.1264/jsme2.ME24114","url":null,"abstract":"<p><p>Nitrite is a key intermediate in global nitrogen cycles. It has been widely recognized that the accumulation of nitrite is often not appreciable in environments, and nitrite concentrations in canonical media for the cultivation of nitrite-oxidizing bacteria (NOB) in laboratories may not be low enough to recover oligotrophic NOB. We herein report the isolation, physiology, and genomics of oligotrophic NOB from a Japanese forest soil. NOB in soil samples were enumerated using the most probable number method with a medium containing urea for enriching oligotrophic NOB. Urea was completely converted into nitrate, and nitrite was not detected in any nitrifier-positive tubes cultivated after 9‍ ‍weeks of incubation. After subculturing NOB several times in a medium supplemented with 1‍ ‍mM nitrite and performing the extinction-dilution procedure, a novel strain oxidizing nitrite to nitrate was obtained and designated as strain CN101, which was affiliated with the genus Nitrobacter at the 16S rRNA gene level. The half-saturation constant of strain CN101 was lower than other known Nitrobacter strains, suggesting that Nitrobacter strains do not always exhibit low affinity for nitrite. The complete genome of strain CN101 included a larger number of nitrite/nitrate transporters than other Nitrobacter strains, which may serve as tools for flexibly adapting to varying nitrite concentrations in soils. Therefore, the physiological and genomic characteristics of strain CN101 will expand knowledge of the ecologically important but understudied genus Nitrobacter.</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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12213059/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144326165","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":"Improvements in the Duckweed-Microbe Co-cultivation Method for the Stable and Efficient Isolation of Rarely Cultivated Bacteria Using Microfilter Membranes.","authors":"Yosuke Morishita, Tomoki Iwashita, Manabu Kanno, Hideyuki Tamaki, Yoichi Kamagata, Tadashi Toyama, Kazuhiro Mori, Masaaki Morikawa, Yasuhiro Tanaka","doi":"10.1264/jsme2.ME24075","DOIUrl":"https://doi.org/10.1264/jsme2.ME24075","url":null,"abstract":"<p><p>We recently proposed a novel microbial isolation technique, the \"duckweed-microbe co-cultivation method\", for isolating a wide variety of microbes, including rarely cultivated microbes. This method involves the inoculation of aseptic duckweed with environmental microbes followed by co-cultivation for a set period. Plants and their surrounding medium are then used as microbial sources for isolation in the conventional agar plate method. In the present study, we improved the method by using microfilter membranes (pore sizes of 0.8-1.2‍ ‍μm) to pretreat microbial inocula, which increased the isolation efficiency of rarely cultivated microbes representing the phylum Verrucomicrobiota.</p>","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":"144960359","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":"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":"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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12213066/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}