Microbes and Environments最新文献

{"title":"Transcriptional Regulation of Methanol Dehydrogenases in the Methanotrophic Bacterium Methylococcus capsulatus Bath by Soluble and Insoluble Lanthanides.","authors":"Ruoyun Xie, Motoko Takashino, Kensuke Igarashi, Wataru Kitagawa, Souichiro Kato","doi":"10.1264/jsme2.ME23065","DOIUrl":"10.1264/jsme2.ME23065","url":null,"abstract":"<p><p>The effects of soluble and insoluble lanthanides on gene expression in Methylococcus capsulatus Bath were investigated. Genes for lanthanide-containing methanol dehydrogenases (XoxF-MDHs) and their calcium-containing counterparts (MxaFI-MDHs) were up- and down-regulated, respectively, by supplementation with soluble lanthanide chlorides, indicating that M. capsulatus has the \"lanthanide switch\" observed in other methanotrophs. Insoluble lanthanide oxides also induced the lanthanide switch and were dissolved by the spent medium of M. capsulatus, suggesting the presence of lanthanide-chelating compounds. A transcriptome ana-lysis indicated that a gene cluster for the synthesis of an enterobactin-like metal chelator contributed to the dissolution of insoluble lanthanides.</p>","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"38 4","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10728633/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138806899","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":"Unique Rhizobial Communities Dominated by Bradyrhizobium liaoningense and Bradyrhizobium ottawaense were Found in Vegetable Soybean Nodules in Osaka Prefecture, Japan.","authors":"Chikage Minakata, Sawa Wasai-Hara, Satori Fujioka, Shuji Sano, Atsushi Matsumura","doi":"10.1264/jsme2.ME22081","DOIUrl":"10.1264/jsme2.ME22081","url":null,"abstract":"<p><p>Vegetable soybean (Glycine max [L.]) is mainly consumed in Asian countries, but has recently attracted attention worldwide due to its high nutritional value. We aimed to identify the indigenous rhizobia of vegetable soybean in Yao City, Osaka Prefecture, Japan, and to clarify the relationships between the rhizobial community and soil environmental factors. Soil samples were collected from 12 vegetable soybean cultivation fields under two different conditions (six greenhouses and six open fields) in Yao City with different varieties of vegetable soybean. A total of 217 isolates were obtained from the nodules and clustered into nine operational taxonomic units (OTUs) with 97% homology based on the 16S-23S rRNA internal transcribed spacer (ITS) region. A phylogenetic ana-lysis showed that OTUs were closely related to Bradyrhizobium liaoningense, B. ottawaense, B. elkanii, and other Bradyrhizobium species and were dominant in this order. B. liaoningense was widely found in sampled sites and accounted for 50.7% of all isolates, while B. ottawaense was mostly limited to open fields. This rhizobial community differed from Japanese soybean rhizobia, in which B. diazoefficiens, B. japonicum, and B. elkanii were dominant. These results imply the characteristic differences among host plants or regional specialties. A non-metric multidimensional scaling (NMDS) ana-lysis revealed the significant impact of soil pH and the contents of Ca, Mg, Mn, total nitrogen (TN), and total carbon (TC) on the distribution of rhizobia. B. liaoningense was detected in soils with a neutral pH, and high TN and low Mn contents increased its abundance. The present study provides novel insights into Japanese rhizobia and potentially novel resources for sustainable agriculture.</p>","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"38 2","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10308233/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9783457","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":"Potential of Predatory Bacteria to Colonize the Duckweed Microbiome and Change Its Structure: A Model Study Using the Obligate Predatory Bacterium, Bacteriovorax sp. HI3.","authors":"Daisuke Inoue,&nbsp;So Nakamura,&nbsp;Tomomi Sugiyama,&nbsp;Michihiko Ike","doi":"10.1264/jsme2.ME23040","DOIUrl":"10.1264/jsme2.ME23040","url":null,"abstract":"Modifying the duckweed microbiome is a major challenge for enhancing the effectiveness of duckweed-based wastewater treatment and biomass production technologies. We herein examined the potential of the exogenous introduction of predatory bacteria to change the duckweed microbiome. Bacteriovorax sp. HI3, a model predatory bacterium, colonized the core of the Lemna microbiome, and its predatory behavior changed the microbiome structure, which correlated with colonization density. These results reveal that bacterial predatory interactions may be important drivers that shape the duckweed microbiome, suggesting their potential usefulness in modifying the microbiome.","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"38 3","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10522839/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10209672","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":"Deep Subseafloor Biogeochemical Processes and Microbial Populations Potentially Associated with the 2011 Tohoku-oki Earthquake at the Japan Trench Accretionary Wedge (IODP Expedition 343).","authors":"Shinsuke Kawagucci,&nbsp;Sanae Sakai,&nbsp;Eiji Tasumi,&nbsp;Miho Hirai,&nbsp;Yoshihiro Takaki,&nbsp;Takuro Nunoura,&nbsp;Masafumi Saitoh,&nbsp;Yuichiro Ueno,&nbsp;Naohiro Yoshida,&nbsp;Takazo Shibuya,&nbsp;James Clifford Sample,&nbsp;Tomoyo Okumura,&nbsp;Ken Takai","doi":"10.1264/jsme2.ME22108","DOIUrl":"https://doi.org/10.1264/jsme2.ME22108","url":null,"abstract":"<p><p>Post-mega-earthquake geochemical and microbiological properties in subseafloor sediments of the Japan Trench accretionary wedge were investigated using core samples from Hole C0019E, which was drilled down to 851‍ ‍m below seafloor (mbsf) at a water depth of 6,890 m. Methane was abundant throughout accretionary prism sediments; however, its concentration decreased close to the plate boundary decollement. Methane isotope systematics indicated a biogenic origin. The content of mole-cular hydrogen (H₂) was low throughout core samples, but markedly increased at specific depths that were close to potential faults predicted by logging-while-drilling ana-lyses. Based on isotopic systematics, H₂ appeared to have been abundantly produced via a low-temperature interaction between pore water and the fresh surface of crushed rock induced by earthquakes. Subseafloor microbial cell density remained constant at approximately 10⁵‍ ‍cells‍ ‍mL^-1. Amplicon sequences revealed that predominant members at the phylum level were common throughout the units tested, which also included members frequently found in anoxic subseafloor sediments. Metabolic potential assays using radioactive isotopes as tracers revealed homoacetogenic activity in H₂-enriched core samples collected near the fault. Furthermore, homoacetogenic bacteria, including Acetobacterium carbinolicum, were isolated from similar samples. Therefore, post-earthquake subseafloor microbial communities in the Japan Trench accretionary prism appear to be episodically dominated by homoacetogenic populations and potentially function due to the earthquake-induced low-temperature generation of H₂. These post-earthquake microbial communities may eventually return to the steady-state communities dominated by oligotrophic heterotrophs and hydrogenotrophic and methylotrophic methanogens that are dependent on refractory organic matter in the sediment.</p>","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"38 2","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10308235/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9731375","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":"Novel Insights into Microbial Behavior Gleaned Using Microfluidics.","authors":"Kohei Takahashi,&nbsp;Xiaojie Li,&nbsp;Tatsuki Kunoh,&nbsp;Ryo Nagasawa,&nbsp;Norio Takeshita,&nbsp;Andrew S Utada","doi":"10.1264/jsme2.ME22089","DOIUrl":"https://doi.org/10.1264/jsme2.ME22089","url":null,"abstract":"<p><p>Microorganisms develop into communities in nearly every environmental niche, which is typically replete with micrometer-scale gaps and features. In each of these habitats, microorganisms adapt to and are affected by their physical environment. Conventional culture methods use glass bottom dishes or millimeter-scale flow cells, which poorly mimic the complexity of natural micrometer-scale environments; therefore, the limitations associated with the creation of microbe-scale environments with granularity hinder the ability to examine their ecological behavior. Microfluidics is a tool that is increasingly being used to study microorganisms because it enables the manipulation of micrometer-scale flows while simultaneously facilitating real-time and live-cell imaging. In this review, we discuss several insights into the behavior of bacteria and fungi that were gained through the adoption of microfluidics to control complex micrometer-scale environments. We also discuss the potential of the increased adoption of this tool.</p>","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"38 5","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9166089","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":"Analysis of the Bacterial Flora of Substrates Used for the Cultivation of Agaricus bisporus: Relationship between Clostridia and Yield.","authors":"Daishin Tomikawa,&nbsp;Hiroshi Okuda","doi":"10.1264/jsme2.ME22041","DOIUrl":"10.1264/jsme2.ME22041","url":null,"abstract":"<p><p>Agaricus bisporus has a high nutritional value and health benefits and its popularity is increasing among vegans and health-conscious consumers, indicating the need for its stable production. Therefore, we examined the bacterial flora of the substrates used to produce A. bisporus using a 16S rRNA gene ana-lysis and discussed the relationship between the bacterial flora and yield. The results obtained showed that A. bisporus yield slightly decreased with an increase in the abundance of Clostridia in substrates after primary fermentation. Lactobacillus showed little or no relationship with A. bisporus yield. Clostridia was identified as an indicator of A. bisporus yield.</p>","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"38 3","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10522844/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9843960","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":"Bioformulations Derived from Enterobacter sp. NRRU-N13 and Oligochitosan Alleviate Drought Stress in Thai Jasmine Rice (Oryza sativa L. var. KDML105).","authors":"Thanakorn Saengsanga, Nutthida Phakratok, Tarntip Rattana","doi":"10.1264/jsme2.ME23025","DOIUrl":"10.1264/jsme2.ME23025","url":null,"abstract":"<p><p>Climate change is predicted to increase the length, severity, and frequency of drought, which limits plant development by changing various physiological and biochemical processes. Therefore, the present study investigated the effects of drought stress on indole-3-acetic and exopolysaccharide production by Enterobacter sp. NRRU-N13, developed bioformulations of plant growth-promoting Enterobacter sp. NRRU-N13, and evaluated the synergistic effects of these bioformulations in combination with different chitosans on the physiological responses of rice under drought stress. Drought stress inhibited the biosynthesis of indole-3-acetic and exopolysaccharides by Enterobacter sp. NRRU-N13. The viability and stability of Enterobacter sp. NRRU-N13 in bioformulations ranged between 4.70 and 5.70 log CFU g^-1 after 80 days at an ambient temperature. Oligochitosan and chitosan at 40‍ ‍mg L^-1 were appropriate concentrations for improving rice seedling growth, namely, plant height, root length, shoot and root fresh weights, biomass, and the vigor index (P<0.05). The abilities of these bioformulations, in combination with oligochitosan and chitosan, to alleviate drought stress in rice were examined. The results obtained revealed that the combined application of oligochitosan (40‍ ‍mg L^-1) and the FON13 bioformulation (filter cake+40‍ ‍mg kg^-1 oligochitosan+10% Enterobacter sp. NRRU-N13) exerted the strongest synergistic effects to alleviate drought stress in rice plants by increasing ascorbate peroxidase and catalase activities, chlo-rophyll concentrations, and relative water content and suppressing proline accumulation and electrolyte leakage from rice plants under drought stress. The present results indicate that the application of oligochitosan combined with these bioformulations effectively improved plant physiology and development. Therefore, the combined application of oligochitosan and a bioformulation of Enterobacter sp. NRRU-N13 is recommended to alleviate drought stress in rice plants.</p>","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"38 4","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10728635/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71424882","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":"Effects of Co-existing Heterotrophs on Physiology of and Nitrogen Metabolism in Autotrophic Nitrite-oxidizing Candidatus Nitrotoga.","authors":"Hiroto Ide, Kento Ishii, Yu Takahashi, Hirotsugu Fujitani, Satoshi Tsuneda","doi":"10.1264/jsme2.ME23076","DOIUrl":"10.1264/jsme2.ME23076","url":null,"abstract":"<p><p>Interactions between autotrophic nitrifiers and heterotrophs have attracted considerable attention in microbial ecology. However, the mechanisms by which heterotrophs affect the physiological activity of and nitrogen metabolism in autotrophic nitrite oxidizers remain unclear. We herein focused on nitrite-oxidizing Candidatus Nitrotoga and compared an axenic culture including only Ca. Nitrotoga with a co-culture of both Ca. Nitrotoga and Acidovorax in physiological experiments and transcriptomics. In the co-culture with Acidovorax, nitrite consumption by Ca. Nitrotoga was promoted, and some genes relevant to nitrogen metabolism in Ca. Nitrotoga were highly expressed. These results provide insights into the mechanisms by which co-existing heterotrophs affect autotrophic nitrifiers.</p>","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"38 4","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10728634/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138806815","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 Lactic Acid Bacteria from Fermented Fish (pla-paeng-daeng) and Their Cholesterol-lowering and Immunomodulatory Effects.","authors":"Engkarat Kingkaew,&nbsp;Hiroshi Konno,&nbsp;Yoshihito Hosaka,&nbsp;Wongsakorn Phongsopitanun,&nbsp;Somboon Tanasupawat","doi":"10.1264/jsme2.ME22044","DOIUrl":"https://doi.org/10.1264/jsme2.ME22044","url":null,"abstract":"<p><p>The cholesterol-lowering and immunomodulatory effects and probiotic properties of 25 lactic acid bacteria (LAB) isolated from fermented fish (pla-paeng-daeng) in Thailand were examined in the present study. Based on their phenotypic and genetic characteristics, LAB were identified as Lactiplantibacillus pentosus (Group I, 6 isolates), Lactiplantibacillus argentoratensis (Group II, 1 isolate), Limosilactobacillus fermentum (Group III, 2 isolates), Companilactobacillus pabuli (Group IV, 4 isolates), Companilactobacillus farciminis (Group V, 5 isolates), Companilactobacillus futsaii (Group VI, 6 isolates), and Enterococcus lactis (Group VII, 1 isolate). Lactiplantibacillus pentosus PD3-1 and PD9-2 and Enterococcus lactis PD3-2 exhibited bile salt hydrolase (BSH) activities. The percentage of cholesterol assimilated by all isolates ranged between 21.40 and 54.07%. Bile salt hydrolase-producing isolates tolerated acidic and bile conditions and possessed adhesion properties. They also exerted immunomodulatory effects that affected the production of interleukin-12 (IL-12), interferon-γ (IFN-γ), human β-defensin-2 (hBD-2), and nitric oxide (NO). These isolates meet standard probiotic requirements and exert beneficial effects.</p>","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"38 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10037097/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9728963","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":"Diversity of the Hydroxylamine Oxidoreductase (HAO) Gene and Its Enzyme Active Site in Agricultural Field Soils.","authors":"Tsubasa Ohbayashi, Yong Wang, Luciano Nobuhiro Aoyagi, Shintaro Hara, Kanako Tago, Masahito Hayatsu","doi":"10.1264/jsme2.ME23068","DOIUrl":"10.1264/jsme2.ME23068","url":null,"abstract":"<p><p>Nitrification is a key process in the biogeochemical nitrogen cycle and a major emission source of the greenhouse gas nitrous oxide (N₂O). The periplasmic enzyme hydroxylamine oxidoreductase (HAO) is involved in the oxidation of hydroxylamine to nitric oxide in the second step of nitrification, producing N₂O as a byproduct. Its three-dimensional structure demonstrates that slight differences in HAO active site residues have inhibitor effects. Therefore, a more detailed understanding of the diversity of HAO active site residues in soil microorganisms is important for the development of novel nitrification inhibitors using structure-guided drug design. However, this has not yet been examined. In the present study, we investigated hao gene diversity in beta-proteobacterial ammonia-oxidizing bacteria (β-AOB) and complete ammonia-oxidizing (comammox; Nitrospira spp.) bacteria in agricultural fields using a clone library ana-lysis. A total of 1,949 hao gene sequences revealed that hao gene diversity in β-AOB and comammox bacteria was affected by the fertilizer treatment and field type, respectively. Moreover, hao sequences showed the almost complete conservation of the six HAO active site residues in both β-AOB and comammox bacteria. The diversity of nitrifying bacteria showed similarity between hao and amoA genes. The nxrB amplicon sequence revealed the dominance of Nitrospira cluster II in tea field soils. The present study is the first to reveal hao gene diversity in agricultural soils, which will accelerate the efficient screening of HAO inhibitors and evaluations of their suppressive effects on nitrification in agricultural soils.</p>","PeriodicalId":18482,"journal":{"name":"Microbes and Environments","volume":"38 4","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10728637/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138806755","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}