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Zhu X, Deng Y, Liu Y. Methylocystis dominates methane oxidation in glacier foreland soil at elevated temperature. FEMS Microbiol Lett 2024; 371:fnae011. [PMID: 38366911 DOI: 10.1093/femsle/fnae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/01/2023] [Accepted: 02/15/2024] [Indexed: 02/19/2024] Open
Abstract
Methane-oxidizing bacteria (methanotrophs) play an important role in mitigating methane emissions in various ecological environments, including cold regions. However, the response of methanotrophs in these cold environments to extreme temperatures above the in-situ temperature has not been thoroughly explored. Therefore, this study collected soil samples from Longxiazailongba (LXZ) and Qiangyong (QY) glacier forelands and incubated them with 13CH4 at 35°C under different soil water conditions. The active methanotroph populations were identified using DNA stable isotope probing (DNA-SIP) and high throughput sequencing techniques. The results showed that the methane oxidation potential in LXZ and QY glacier foreland soils was significantly enhanced at an unusually high temperature of 35°C during microcosm incubations, where abundant substrate (methane and oxygen) was provided. Moreover, the influence of soil water conditions on this potential was observed. Interestingly, Methylocystis, a type II and mesophilic methanotroph, was detected in the unincubated in-situ soil samples and became the active and dominant methanotroph in methane oxidation at 35°C. This suggests that Methylocystis can survive at low temperatures for a prolonged period and thrive under suitable growth conditions. Furthermore, the presence of mesophilic methanotrophs in cold habitats could have potential implications for reducing greenhouse gas emissions in warming glacial environments.
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Affiliation(s)
- Xinshu Zhu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
- College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yongcui Deng
- School of Geography, Nanjing Normal University, Nanjing 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing 210023, China
| | - Yongqin Liu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
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Miyadera T, Kojima H, Fukui M. Methyloradius palustris gen. nov., sp. nov., a methanol-oxidizing bacterium isolated from snow. Arch Microbiol 2021; 203:5715-5721. [PMID: 34476514 DOI: 10.1007/s00203-021-02559-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/22/2021] [Accepted: 08/24/2021] [Indexed: 12/29/2022]
Abstract
A novel methylotrophic bacterium, strain Zm11T, was isolated from reddish brown snow collected in a moor in Japan. Cells of the isolate were Gram-stain-negative, motile, and rod-shaped (0.6-0.7 × 1.2-2.7 μm). Growth was observed at 5-32 °C with an optimum growth temperature of 25-28 °C. The pH range for growth was 5.4-7.8 with an optimum pH of 6.8. The strain utilized only methanol as carbon and energy sources for aerobic growth. The major cellular fatty acids (> 40% of total) were summed feature 3 (C16:1ω7c and/or C16:1ω6c) and C16: 0. The predominant quinone was Q-8, and major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The complete genome of strain Zm11T is composed of a circular chromosome (2,800,413 bp), with G + C content of 46.4 mol%. Phylogenetic analyses were conducted based on the 16S rRNA gene sequence and conserved proteins encoded in the genome. The results of analyses indicate that strain Zm11T is a member of the family Methylophilaceae but does not belong to any existing genus. On the basis of its genomic and phenotypic properties, strain Zm11T (= DSM111909T = NBRC114766T) is proposed as the type strain of a new species in a new genus, Methyloradius palustris gen. nov., sp. nov.
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Affiliation(s)
- Takeshi Miyadera
- Graduate School of Environmental Science, Hokkaido University, Kita-10, Nishi-5, Kita-ku, Sapporo, 060-0810, Japan.,The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan
| | - Hisaya Kojima
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan.
| | - Manabu Fukui
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan
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Vieira S, Huber KJ, Neumann-Schaal M, Geppert A, Luckner M, Wanner G, Overmann J. Usitatibacter rugosus gen. nov., sp. nov. and Usitatibacter palustris sp. nov., novel members of Usitatibacteraceae fam. nov. within the order Nitrosomonadales isolated from soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 33433313 DOI: 10.1099/ijsem.0.004631] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Members of the metabolically diverse order Nitrosomonadales inhabit a wide range of environments. Two strains affiliated with this order were isolated from soils in Germany and characterized by a polyphasic approach. Cells of strains 0125_3T and Swamp67T are Gram-negative rods, non-motile, non-spore-forming, non-capsulated and divide by binary fission. They tested catalase-negative, but positive for cytochrome c-oxidase. Both strains form small white colonies on agar plates and grow aerobically and chemoorganotrophically on SSE/HD 1 : 10 medium, preferably utilizing organic acids and proteinaceous substrates. Strains 0125_3T and Swamp67T are mesophilic and grow optimally without NaCl addition at slightly alkaline conditions. Major fatty acids are C16 : 1 ω7c, C16 : 0 and C14 : 0. The major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyglycerol. The predominant respiratory quinone is Q-8. The G+C content for 0125_3T and Swamp67T was 67 and 66.1 %, respectively. The 16S rRNA gene analysis indicated that the closest relatives (<91 % sequence similarity) of strain 0125_3T were Nitrosospira multiformis ATCC 25196T, Methyloversatilis universalis FAM5T and Denitratisoma oestradiolicum AcBE2-1T, while Nitrosospira multiformis ATCC 25196T, Nitrosospira tenuis Nv1T and Nitrosospira lacus APG3T were closest to strain Swamp67T. The two novel strains shared 97.4 % 16S rRNA gene sequence similarity with one another and show low average nucleotide identity of their genomes (83.8 %). Based on the phenotypic, chemotaxonomic, genomic and phylogenetic analysis, we propose the two novel species Usitatibacter rugosus sp. nov (type strain 0125_3T=DSM 104443T=LMG 29998T=CECT 9241T) and Usitatibacter palustris sp. nov. (type strain Swamp67T=DSM 104440T=LMG 29997T=CECT 9242T) of the novel genus Usitatibacter gen. nov., within the novel family Usitatibacteraceae fam. nov.
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Affiliation(s)
- Selma Vieira
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Katharina J Huber
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Alicia Geppert
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Manja Luckner
- Department of Biology I, Biozentrum Ludwig Maximilian University of Munich, Großhaderner Str. 2-4, 82152, Planegg-Martinsried, Germany
| | - Gerhard Wanner
- Department of Biology I, Biozentrum Ludwig Maximilian University of Munich, Großhaderner Str. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jörg Overmann
- Braunschweig University of Technology, Spielmanstraße 7, 38106 Braunschweig, Germany.,Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
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Mohamed AMHA, Sorokin VV, Skladnev DA, Shevlyagina NV, Zhukhovitsky VG, Pshenichnikova AB. Biosynthesis of Silver Nanoparticles by Methylophilus quaylei, Characterization and Its Impact on Established Biofilms. BIONANOSCIENCE 2020. [DOI: 10.1007/s12668-020-00780-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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Alok D, Annapragada H, Singh S, Murugesan S, Singh NP. Symbiotic nitrogen fixation and endophytic bacterial community structure in Bt-transgenic chickpea (Cicer arietinum L). Sci Rep 2020; 10:5453. [PMID: 32214159 PMCID: PMC7096491 DOI: 10.1038/s41598-020-62199-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/10/2020] [Indexed: 01/11/2023] Open
Abstract
Symbiotic nitrogen fixation (SNF) of transgenic grain legumes might be influenced either by the site of transgene integration into the host genome or due to constitutive expression of transgenes and antibiotic-resistant marker genes. The present investigation confirmed proper nodulation of five tested Bt-chickpea events (IPCa2, IPCa4, IPCT3, IPCT10, and IPCT13) by native Mesorhizobium under field environment. Quantitative variations for nodulation traits among Bt-chickpea were determined and IPCT3 was found superior for nodule number and nodule biomass. Diversity, as well as richness indices, confirmed the changes in bacterial community structure of root and root-nodules from Bt-chickpea events IPCa2 and IPCT10. Especially, Gram-positive bacteria belonging to Firmicutes and Actinobacteria were selectively eliminated from root colonization of IPCa2. Richness indices (CHAO1 and ACE) of the root-associated bacterial community of IPCa2 was 13-14 times lesser than that of parent cv DCP92-3. Root nodule associated bacterial community of IPCT10 was unique with high diversity and richness, similar to the roots of non-Bt and Bt-chickpea. It indicated that the root nodules of IPCT10 might have lost their peculiar characteristics and recorded poor colonization of Mesorhizobium with a low relative abundance of 0.27. The impact of Bt-transgene on bacterial community structure and nodulation traits should be analyzed across the years and locations to understand and stabilize symbiotic efficiency for ecosystem sustainability.
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Affiliation(s)
- Das Alok
- Division of Plant Biotechnology, Indian Institute of Pulses Research, Kalyanpur, Kanpur, India
| | - Harika Annapragada
- Division of Basic Sciences, Indian Institute of Pulses Research, Kalyanpur, Kanpur, India
| | - Shilpa Singh
- Division of Basic Sciences, Indian Institute of Pulses Research, Kalyanpur, Kanpur, India
| | - Senthilkumar Murugesan
- Division of Basic Sciences, Indian Institute of Pulses Research, Kalyanpur, Kanpur, India.
| | - Narendra Pratap Singh
- Division of Plant Biotechnology, Indian Institute of Pulses Research, Kalyanpur, Kanpur, India
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7
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Sorokin VV, Pshenichnikova AB, Kalenov SV, Suyasov NA, Skladnev DA. Comparison of the Wild-Type Obligate Methylotrophic Bacterium Methylophilus quaylei and its Isogenic Streptomycin-Resistant Mutant via Metal Nanoparticle Generation. Biol Trace Elem Res 2020; 193:564-573. [PMID: 31073700 PMCID: PMC6944653 DOI: 10.1007/s12011-019-01740-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 04/22/2019] [Indexed: 11/16/2022]
Abstract
Metal nanoparticles synthesized by green methods with the use of microorganisms are currently one of the most closely studied types of nanomaterials. It has accurately been shown that the characteristics of metal nanoparticles generated in the presence of different bacteria vary. For the two isogenic strains of obligate methylotrophic bacteria of the wild type (M. quaylei MTT) and its streptomycin-resistant mutant (M. quaylei SMR), the pleiotropic character of streptomycin resistance mutation in the SMR cells has been revealed. It has been shown that both cultures can generate silver nanoparticles. There is a dramatic difference in the formation of palladium nanoparticles, which are formed only in the presence of cells of the streptomycin-resistant mutant M. quaylei SMR. This study shows that closely related isogenic strains of obligate methylotrophic bacteria can be distinguished by the spectra of biogenic nanoparticles of two noble metals. While palladium nanoparticles are only generated by the cells of the streptomycin-resistant mutant M. quaylei SMR, biogenic silver nanoparticles can be generated from both cultures. Thus, the assessment of the ability of microorganisms to form biogenic nanoparticles of different metals allows the revelation of subtle metabolic differences of even close cultures.
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Affiliation(s)
- Vladimir V Sorokin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, Bld. 2 Leninsky Ave., Moscow, Russia
| | - Anna B Pshenichnikova
- Department of Biotechnology and Industrial Pharmacy, MIREA - Russian Technological University, 86 Vernadsky Avenue, Moscow, Russia
| | - Sergei V Kalenov
- Department of Biotechnology, Faculty of Biotechnology and Industrial Ecology, D.I. Mendeleyev University of Chemical Technology of Russia, 9 Miusskaya Square, Moscow, Russia.
| | - Nikolay A Suyasov
- Department of Biotechnology, Faculty of Biotechnology and Industrial Ecology, D.I. Mendeleyev University of Chemical Technology of Russia, 9 Miusskaya Square, Moscow, Russia
| | - Dmitry A Skladnev
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, Bld. 2 Leninsky Ave., Moscow, Russia
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8
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Pseudomethylobacillus aquaticus gen. nov., sp. nov., a new member of the family Methylophilaceae isolated from an artificial reservoir. Int J Syst Evol Microbiol 2019; 69:3551-3559. [DOI: 10.1099/ijsem.0.003661] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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9
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Mohamed AM, Vladimirovna SN, Grigorievich ZV, Borisovna PA, Ivanovich SV. Sodium Oleate Increases Ampicillin Sensitivity in Methylophilus quaylei Biofilms on Teflon and Polypropylene. Curr Pharm Biotechnol 2019; 20:261-270. [DOI: 10.2174/1389201020666190222191656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/14/2019] [Accepted: 02/14/2019] [Indexed: 01/22/2023]
Abstract
Background:Drug combination is a new therapy to improve antibiotic deficiency treatment towards biofilm resistance.Objective:This study was conducted to determine the potential effect of sodium oleate to inhibit established biofilms of two strains, methylotrophic bacteria Methylophilus quaylei in combination with ampicillin. Minimum inhibitory concentration (MIC) of ampicillin was determined and added in combination with sodium oleate and examined on planktonic and established biofilms of two strains M. quaylei were characterized by different properties of cell surface hydrophobicity.Methods:The effect on biofilms was evaluated by the number of colony forming units (CFUs), crystal violet assay, light and scanning electron microscopy.Results:The study demonstrates that sodium oleate has a promoting activity against planktonic growth of M. quaylei strains and has a slight inhibitory effect on biofilm. Addition of sodium oleate enhances the bactericidal effect of ampicillin against biofilm cells. Combination of ampicillin 0.1 mg/ml (MIC) and sodium oleate 0.03 mg/ml showed a remarkable destruction effect on established biofilms.Discussion:Combination of ampicillin 0.1 mg/ml (MIC) and sodium oleate 0.03 mg/ml showed a remarkable destruction effect on established biofilms. Overall, results indicated that sodium oleate in combination with ampicillin enhances the inhibition of M. quaylei biofilms and this combination can be utilized for combating bacterial biofilm resistance.Conclusion:Overall, results indicated that sodium oleate in combination with ampicillin enhances the inhibition of M. quaylei biofilms and this combination can be utilized for combating bacterial biofilm resistance.
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Affiliation(s)
- Abir M.H.A. Mohamed
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
| | - Shevlyagina N. Vladimirovna
- Gamaleya Federal Research Centre for Microbiology and Immunology of the Ministry of Public Health, Moscow, Russian Federation
| | - Zhukhovitsky V. Grigorievich
- Gamaleya Federal Research Centre for Microbiology and Immunology of the Ministry of Public Health, Moscow, Russian Federation
| | - Pshenichnikova A. Borisovna
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
| | - Shvets V. Ivanovich
- Department of Biotechnology and Industrial Pharmacy, M.V. Lomonosov Institute of Fine Chemical Technologies, MIREA-Russian Technological University, 119571 Moscow, Russian Federation
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Kaparullina EN, Agafonova NV, Trotsenko YA, Doronina NV. Methylophilus aquaticus sp. nov., a New Aerobic Methylotrophic Bacterium Isolated from a Freshwater Reservoir. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718050119] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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11
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Oren A, Garrity GM. List of novel names and novel combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2017; 67:2075-2078. [DOI: 10.1099/ijsem.0.002122] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - George M. Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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Jin D, Zhao S, Zheng N, Bu D, Beckers Y, Denman SE, McSweeney CS, Wang J. Differences in Ureolytic Bacterial Composition between the Rumen Digesta and Rumen Wall Based on ureC Gene Classification. Front Microbiol 2017; 8:385. [PMID: 28326079 PMCID: PMC5339240 DOI: 10.3389/fmicb.2017.00385] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/23/2017] [Indexed: 11/13/2022] Open
Abstract
Ureolytic bacteria are key organisms in the rumen producing urease enzymes to catalyze the breakdown of urea to ammonia for the synthesis of microbial protein. However, little is known about the diversity and distribution of rumen ureolytic microorganisms. The urease gene (ureC) has been the target gene of choice for analysis of the urea-degrading microorganisms in various environments. In this study, we investigated the predominant ureC genes of the ureolytic bacteria in the rumen of dairy cows using high-throughput sequencing. Six dairy cows with rumen fistulas were assigned to a two-period cross-over trial. A control group (n = 3) were fed a total mixed ration without urea and the treatment group (n = 3) were fed rations plus 180 g urea per cow per day at three separate times. Rumen bacterial samples from liquid and solid digesta and rumen wall fractions were collected for ureC gene amplification and sequencing using Miseq. The wall-adherent bacteria (WAB) had a distinct ureolytic bacterial profile compared to the solid-adherent bacteria (SAB) and liquid-associated bacteria (LAB) but more than 55% of the ureC sequences did not affiliate with any known taxonomically assigned urease genes. Diversity analysis of the ureC genes showed that the Shannon and Chao1 indices for the rumen WAB was lower than those observed for the SAB and LAB (P < 0.01). The most abundant ureC genes were affiliated with Methylococcaceae, Clostridiaceae, Paenibacillaceae, Helicobacteraceae, and Methylophilaceae families. Compared with the rumen LAB and SAB, relative abundance of the OTUs affiliated with Methylophilus and Marinobacter genera were significantly higher (P < 0.05) in the WAB. Supplementation with urea did not alter the composition of the detected ureolytic bacteria. This study has identified significant populations of ureolytic WAB representing genera that have not been recognized or studied previously in the rumen. The taxonomic classification of rumen ureC genes in the dairy cow indicates that the majority of ureolytic bacteria are yet to be identified. This survey has expanded our knowledge of ureC gene information relating to the rumen ureolytic microbial community, and provides a basis for obtaining regulatory targets of ureolytic bacteria to moderate urea hydrolysis in the rumen.
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Affiliation(s)
- Di Jin
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural SciencesBeijing, China; Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, University of LiègeGembloux, Belgium; Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture (Beijing), Institute of Animal Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural SciencesBeijing, China; Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture (Beijing), Institute of Animal Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Nan Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural SciencesBeijing, China; Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture (Beijing), Institute of Animal Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Dengpan Bu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences Beijing, China
| | - Yves Beckers
- Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, University of Liège Gembloux, Belgium
| | - Stuart E Denman
- Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St. Lucia QLD, Australia
| | - Christopher S McSweeney
- Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St. Lucia QLD, Australia
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural SciencesBeijing, China; Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture (Beijing), Institute of Animal Science, Chinese Academy of Agricultural SciencesBeijing, China
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Chen R, Luo YH, Chen JX, Zhang Y, Wen LL, Shi LD, Tang Y, Rittmann BE, Zheng P, Zhao HP. Evolution of the microbial community of the biofilm in a methane-based membrane biofilm reactor reducing multiple electron acceptors. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:9540-9548. [PMID: 26841777 DOI: 10.1007/s11356-016-6146-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 01/20/2016] [Indexed: 06/05/2023]
Abstract
Previous work documented complete perchlorate reduction in a membrane biofilm reactor (MBfR) using methane as the sole electron donor and carbon source. This work explores how the biofilm's microbial community evolved as the biofilm stage-wise reduced different combinations of perchlorate, nitrate, and nitrite. The initial inoculum, carrying out anaerobic methane oxidation coupled to denitrification (ANMO-D), was dominated by uncultured Anaerolineaceae and Ferruginibacter sp. The microbial community significantly changed after it was inoculated into the CH4-based MBfR and fed with a medium containing perchlorate and nitrite. Archaea were lost within the first 40 days, and the uncultured Anaerolineaceae and Ferruginibacter sp. also had significant losses. Replacing them were anoxic methanotrophs, especially Methylocystis, which accounted for more than 25 % of total bacteria. Once the methanotrophs became important, methanol-oxidizing denitrifying bacteria, namely, Methloversatilis and Methylophilus, became important in the biofilm, probably by utilizing organic matter generated by the metabolism of methanotrophs. When methane consumption was equal to the maximum-possible electron-donor supply, Methylomonas, also an anoxic methanotroph, accounted for >10 % of total bacteria and remained a major part of the community until the end of the experiments. We propose that aerobic methane oxidation coupled to denitrification and perchlorate reduction (AMO-D and AMO-PR) directly oxidized methane and reduced NO3 (-) to NO2 (-) or N2O under anoxic condition, producing organic matter for methanol-assimilating denitrification and perchlorate reduction (MA-D and MA-PR) to reduce NO3 (-). Simultaneously, bacteria capable of anaerobic methane oxidation coupled to denitrification and perchlorate reduction (ANMO-D and ANMO-PR) used methane as the electron donor to respire NO3 (-) or ClO4 (-) directly. Graphical Abstract ᅟ.
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Affiliation(s)
- Ran Chen
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yi-Hao Luo
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jia-Xian Chen
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yin Zhang
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Zhejiang University, Hangzhou, Zhejiang, China
| | - Li-Lian Wen
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Zhejiang University, Hangzhou, Zhejiang, China
- MOE Key Laboratory of Environmental Remediation and Ecosystem Health, Zhejiang University, Hangzhou, China
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Ling-Dong Shi
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Youneng Tang
- Department of Civil and Environmental Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, FL, 32310-6046, USA
| | - Bruce E Rittmann
- Swette Center for Environmental Biotechnology, Biodesign Institute at Arizona State University, P.O. Box 875701, Tempe, AZ, 85287-5701, USA
| | - Ping Zheng
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Zhejiang University, Hangzhou, Zhejiang, China
- MOE Key Laboratory of Environmental Remediation and Ecosystem Health, Zhejiang University, Hangzhou, China
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - He-Ping Zhao
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Zhejiang University, Hangzhou, Zhejiang, China.
- MOE Key Laboratory of Environmental Remediation and Ecosystem Health, Zhejiang University, Hangzhou, China.
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China.
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Draft Genome Sequence of Methanol-Utilizing Methylophilus sp. Strain OH31, Isolated from Pond Sediment in Hokkaido, Japan. GENOME ANNOUNCEMENTS 2014; 2:2/2/e00274-14. [PMID: 24723716 PMCID: PMC3983305 DOI: 10.1128/genomea.00274-14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Methylophilus sp. strain OH31 was isolated from the sediment of the Ohno pond at Hokkaido University. Strain OH31 utilizes methanol as its energy source. Here, we present the draft genome sequence of Methylophilus sp. strain OH31.
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Wei ZS, Li HQ, He JC, Ye QH, Huang QR, Luo YW. Removal of dimethyl sulfide by the combination of non-thermal plasma and biological process. BIORESOURCE TECHNOLOGY 2013; 146:451-456. [PMID: 23954717 DOI: 10.1016/j.biortech.2013.07.114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 07/20/2013] [Accepted: 07/25/2013] [Indexed: 06/02/2023]
Abstract
A bench scale system integrated with a non-thermal plasma (NTP) and a biotricking filtration (BTF) unit for the treatment of gases containing dimethyl sulfide (DMS) was investigated. DMS removal efficiency in the integrated system was up to 96%. Bacterial communities in the BTF were assessed by PCR-DGGE, which play the dominant role in the biological processes of metabolism, sulfur oxidation, sulfate-reducing and carbon oxidation. The addition of ozone from NTP made microbial community in BTF more complicated and active for DMS removal. The NTP oxidize DMS to simple compounds such as methanol and carbonyl sulfide; the intermediate organic products and DMS are further oxidized to sulfate, carbon dioxide, water vapors by biological degradation. These results show that NTP-BTF is achievable and open new possibilities for applying the integrated with NTP and BTF to odour gas treatment.
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Affiliation(s)
- Z S Wei
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510275, China.
| | - H Q Li
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510275, China
| | - J C He
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510275, China
| | - Q H Ye
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510275, China
| | - Q R Huang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510275, China
| | - Y W Luo
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510275, China
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Madhaiyan M, Poonguzhali S, Senthilkumar M, Pragatheswari D, Lee KC, Lee JS. Methylobacillus rhizosphaerae sp. nov., a novel plant-associated methylotrophic bacterium isolated from rhizosphere of red pepper. Antonie van Leeuwenhoek 2012; 103:475-84. [DOI: 10.1007/s10482-012-9828-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 10/06/2012] [Indexed: 11/25/2022]
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17
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Saimmai A, Rukadee O, Onlamool T, Sobhon V, Maneerat S. Characterization and Phylogenetic Analysis of Microbial Surface Active Compound-Producing Bacteria. Appl Biochem Biotechnol 2012; 168:1003-18. [DOI: 10.1007/s12010-012-9836-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 08/06/2012] [Indexed: 11/25/2022]
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18
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Liu R, Yu Z, Zhang H, Yang M, Shi B, Liu X. Diversity of bacteria and mycobacteria in biofilms of two urban drinking water distribution systems. Can J Microbiol 2012; 58:261-70. [DOI: 10.1139/w11-129] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, to give insight into the bacterial diversity of biofilms from full-scale drinking water distribution systems (DWDSs), the bacterial community compositions of biofilms from two urban DWDSs (Guangzhou and Beijing, China) were determined using a 16S rRNA gene library technique. Meanwhile, the occurrence and diversity of mycobacteria were also analyzed by a Mycobacterium -specific hsp gene assay. The biofilms from the full-scale DWDSs have complex bacterial populations. Proteobacteria was the common and predominant group in all biofilm samples, in agreement with previous reports. The community structures of bacteria at the three sites in Guangzhou DWDS were significantly different, despite the similar physicochemical properties of portable water. Some abundant and peculiar bacterial phylotypes were noteworthy, including Methylophilus , Massilia , and Planomicrobium , members of which are rarely found in DWDSs and their roles in DWDS biofilms are still unclear. The diversity of Mycobacterium species in biofilm samples was rather low. Mycobacterium arupense and Mycobacterium gordonae were the primary Mycobacterium species in Guangzhou and Beijing biofilms, respectively, indicating that M. arupense may be more resistant to chloride than M. gordonae.
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Affiliation(s)
- Ruyin Liu
- College of Environmental and Resource Sciences, Graduate University of Chinese Academy of Sciences, 100049 Beijing, People’s Republic of China
| | - Zhisheng Yu
- College of Environmental and Resource Sciences, Graduate University of Chinese Academy of Sciences, 100049 Beijing, People’s Republic of China
| | - Hongxun Zhang
- College of Environmental and Resource Sciences, Graduate University of Chinese Academy of Sciences, 100049 Beijing, People’s Republic of China
| | - Min Yang
- Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People’s Republic of China
| | - Baoyou Shi
- Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People’s Republic of China
| | - Xinchun Liu
- College of Environmental and Resource Sciences, Graduate University of Chinese Academy of Sciences, 100049 Beijing, People’s Republic of China
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19
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Otman SAM, Pshenichnikova AB, Shvets VI. Effect of exogenous fatty acids on the growth and production of exopolysaccharides of obligately methylotrophic bacterium Methylophilus quaylei. APPL BIOCHEM MICRO+ 2012. [DOI: 10.1134/s0003683812020093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Doronina NV, Gogleva AA, Trotsenko YA. Methylophilus glucosoxydans sp. nov., a restricted facultative methylotroph from rice rhizosphere. Int J Syst Evol Microbiol 2012; 62:196-201. [DOI: 10.1099/ijs.0.024620-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two restricted facultatively methylotrophic strains, designed BT and P, were isolated from rice roots. The isolates were strictly aerobic, Gram-negative, asporogenous, mesophilic, neutrophilic, motile rods that multiplied by binary fission and were able to synthesize indole-3-acetate. The cellular fatty acid profiles of the two strains were dominated by C16 : 0, C16 : 1ω7c and C16 : 0 2-OH. The major ubiquinone was Q-8. The predominant phospholipids were phosphatidylethanolamine and phosphatidylglycerol. Cardiolipin (diphosphatidylglycerol) was absent. The two strains assimilated methanol carbon at the level of formaldehyde via the ribulose monophosphate cycle (2-keto-3-deoxy-6-phosphogluconate variant). They lacked α-ketoglutarate dehydrogenase and glutamate dehydrogenase. They assimilated ammonium via the glutamate cycle enzymes glutamine synthetase and glutamate synthase. The DNA G+C contents of strains BT and P were 52.5 and 51.5 mol% (T
m), respectively. The level of DNA–DNA reassociation between these strains was 78 %, indicating that they belong to one species. Phylogenetic analysis of strain BT based on 16S rRNA and methanol dehydrogenase (mxaF) gene sequences showed a high level of similarity to members of the genus Methylophilus. As the two isolates were clearly distinct from all recognized members of the genus Methylophilus based on phenotypic data and levels of DNA–DNA relatedness (30–46 %), they are considered to represent a novel species, for which the name Methylophilus glucosoxydans sp. nov. is proposed; the type strain is BT ( = VKM B-1607T = CCUG 59685T = DSM 5898T).
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Affiliation(s)
- Nina V. Doronina
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences and Pushchino State University, Pushchino, Moscow Region 142290, Russia
| | - Anna A. Gogleva
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences and Pushchino State University, Pushchino, Moscow Region 142290, Russia
| | - Yuri A. Trotsenko
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences and Pushchino State University, Pushchino, Moscow Region 142290, Russia
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21
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Terekhova EA, Stepicheva NA, Pshenichnikova AB, Shvets VI. Stearic acid methyl ester: A new extracellular metabolite of the obligate methylotrophic bacterium Methylophilus quaylei. APPL BIOCHEM MICRO+ 2010. [DOI: 10.1134/s0003683810020079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Gogleva AA, Kaparullina EN, Doronina NV, Trotsenko YA. Methylophilus flavus sp. nov. and Methylophilus luteus sp. nov., aerobic, methylotrophic bacteria associated with plants. Int J Syst Evol Microbiol 2009; 60:2623-2628. [PMID: 20023062 DOI: 10.1099/ijs.0.019455-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Novel yellow, obligately methylotrophic and restricted facultatively methylotrophic bacteria, respectively designated strains Ship(T) and Mim(T), with the ribulose monophosphate pathway of C(1) assimilation are described. Cells were strictly aerobic, Gram-negative, asporogenous, non-motile rods that multiply by binary fission, were mesophilic and neutrophilic and synthesized indole-3-acetic acid and exopolysaccharide. The predominant cellular fatty acids were C(16 : 0) and C(16 : 1). The major ubiquinone was Q-8. The predominant phospholipids were phosphatidylethanolamine and phosphatidylglycerol; diphosphatidylglycerol was absent. The two strains lacked α-ketoglutarate dehydrogenase and glutamate dehydrogenase. They assimilated ammonium via the glutamate cycle enzymes glutamine synthetase and glutamate synthase. The DNA G+C contents of strains Ship(T) and Mim(T) were 50.7 and 54.5 mol% (T(m)), respectively. The level of 16S rRNA gene sequence similarity between these strains was very high (99.8 %) but they shared a low level of DNA-DNA relatedness (44 %). Based on 16S rRNA gene sequence analysis and low levels of DNA-DNA relatedness with the type strains of recognized species of the genus Methylophilus (31-36 %), strains Ship(T) and Mim(T) are considered to represent novel species of the genus Methylophilus, for which the names Methylophilus flavus sp. nov. (type strain Ship(T) =DSM 23073(T) =VKM B-2547(T) =CCUG 58411(T)) and Methylophilus luteus sp. nov. (type strain Mim(T) =DSM 22949(T) =VKM B-2548(T) =CCUG 58412(T)) are proposed.
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Affiliation(s)
- Anna A Gogleva
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences and Pushchino State University, Pushchino, Moscow region 142290, Russia
| | - Elena N Kaparullina
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences and Pushchino State University, Pushchino, Moscow region 142290, Russia
| | - Nina V Doronina
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences and Pushchino State University, Pushchino, Moscow region 142290, Russia
| | - Yuri A Trotsenko
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences and Pushchino State University, Pushchino, Moscow region 142290, Russia
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23
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Kalyuzhnaya MG, Bowerman S, Lara JC, Lidstrom ME, Chistoserdova L. Methylotenera mobilis gen. nov., sp. nov., an obligately methylamine-utilizing bacterium within the family Methylophilaceae. Int J Syst Evol Microbiol 2007; 56:2819-2823. [PMID: 17158982 DOI: 10.1099/ijs.0.64191-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel obligate methylamine utilizer (strain JLW8(T)), isolated from Lake Washington sediment, was characterized taxonomically. The isolate was an aerobic, Gram-negative bacterium. Cells were rod-shaped and motile by means of a single flagellum. Reproduction was by binary fission and no resting bodies were formed. Growth was observed within a pH range of 5-8.5, with optimum growth at pH 7.5. It utilized methylamine as a single source of energy, carbon and nitrogen. Methylamine was oxidized via methylamine dehydrogenase and formaldehyde was assimilated via the ribulose monophosphate cycle. The cellular fatty acid profile was dominated by C(16 : 0)omega7c and C(16 : 0) and the major phospholipid was phosphatidylethanolamine. The DNA G+C content was 54 mol%. 16S rRNA gene sequence analysis indicated that the new isolate was closely related (97-98 % similarity) to a broad group of sequences from uncultured or uncharacterized Betaproteobacteria, but only distantly related (93-96 % similarity) to known methylotrophs of the family Methylophilaceae. Strain JLW8(T) (=ATCC BAA-1282(T)=DSM 17540(T)) is proposed as the type strain of a novel species in a new genus within the family Methylophilaceae, Methylotenera mobilis gen. nov., sp. nov.
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Affiliation(s)
- Marina G Kalyuzhnaya
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Sarah Bowerman
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Jimmie C Lara
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Mary E Lidstrom
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Ludmila Chistoserdova
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
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