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Epsilon-Caprolactam- and Nylon Oligomer-Degrading Bacterium Brevibacterium epidermidis BS3: Characterization and Potential Use in Bioremediation. Microorganisms 2023; 11:microorganisms11020373. [PMID: 36838338 PMCID: PMC9966071 DOI: 10.3390/microorganisms11020373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/16/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
epsilon-Caprolactam (Caprolactam, CAP), a monomer of the synthetic non-degradable polymer nylon-6, is the major wastewater component in the production of caprolactam and nylon-6. Biological treatment of CAP, using microbes could be a potent alternative to the current waste utilization techniques. This work focuses on the characterization and potential use of caprolactam-degrading bacterial strain BS3 isolated from soils polluted by CAP production wastes. The strain was identified as Brevibacterium epidermidis based on the studies of its morphological, physiological, and biochemical properties and 16S rRNA gene sequence analysis. This study is the first to report the ability of Brevibacterium to utilize CAP. Strain BS3 is an alcalo- and halotolerant organism, that grows within a broad range of CAP concentrations, from 0.5 up to 22.0 g/L, optimally at 1.0-2.0 g/L. A caprolactam biodegradation experiment using gas chromatography showed BS3 to degrade 1.0 g/L CAP over 160 h. In contrast to earlier characterized narrow-specific CAP-degrading bacteria, strain BS3 is also capable of utilizing linear nylon oligomers (oligomers of 6-aminohexanoic acid), CAP polymerization by-products, as sole sources of carbon and energy. The broad range of utilized toxic pollutants, the tolerance for high CAP concentrations, as well as the physiological properties of B. epidermidis BS3, determine the prospects of its use for the biological cleanup of CAP and nylon-6 production wastes that contain CAP, 6-aminohexanoic acid, and low molecular weight oligomer fractions.
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Dubinina G, Leshcheva N, Mikheeva N, Spring S, Neumann-Schaal M, Shcherbakova V, Grabovich M. Description of Oceanispirochaeta crateris sp. nov. and reclassification of Spirochaeta perfilievii as Thiospirochaeta perfilievii gen. nov., comb. nov. Int J Syst Evol Microbiol 2020; 70:6373-6380. [DOI: 10.1099/ijsem.0.004544] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A novel obligately anaerobic spirochete strain K2T was isolated from bottom marine sediments at Crater Bay of Yankicha Island (Kuril Islands, Russia). Strain K2T had helical shape and Gram-negatively stained. The optimal growth conditions were as follows: the optimum temperature was 28–30 °C with range 5–34 °C; optimal pH at 7.0–7.5 with range of 6.8–8.5; NaCl optimum at 3–3.5 % (w/v) and range of 1–7 % (w/v). Strain K2T was catalase- and oxidase-negative. Glucose fermentation products were acetate, lactate, ethanol, CO2, H2. The major fatty acids were C14 : 0, iso-C13 : 0, iso-C15:0, C14 : 0 DMA, iso-C15 : 0 DMA. The G+C content of genomic DNA was 43.2 mol%. Phylogenetic analyses of 16S rRNA genes showed that strain K2T belonged to the genus
Oceanispirochaeta
of the family
Spirochaetaceae
. The 16S rRNA gene sequence similarity of strain K2T and
O. litoralis
DSM 2029T and
O. sediminicola
DSM 104770T was 96 and 94 %, respectively. Based on the results of our study, we propose the name Oceanispirochaeta crateris sp. nov.; type strain K2T (=DSM 16308T=VKM B-3266T). Also, the taxonomic status of Spirochaeta perfilevii was revised: 16S rRNA genes sequence showed less than 89 % similarity to nearest phylogenetic neighbours. Therefore, we proposed to separate this species into a novel genus Thiospirochaeta - T. perfilievii gen. nov., comb. nov.
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Affiliation(s)
- Galina Dubinina
- Federal State Institution Federal Research Centre Fundamentals of Biotechnology of the Russian Academy of Sciences, Prospect 60-letiya Oktyabrya, 7/2, 117312 Moscow, Russia
| | - Natalia Leshcheva
- Federal State Institution Federal Research Centre Fundamentals of Biotechnology of the Russian Academy of Sciences, Prospect 60-letiya Oktyabrya, 7/2, 117312 Moscow, Russia
| | - Natalia Mikheeva
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, Voronezh 394018, Russia
| | - Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Junior Research Group Bacterial Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Viktoria Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, the Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, pr. Nauki 5, Pushchino Moscow region, 142290, Russia
| | - Margarita Grabovich
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, Voronezh 394018, Russia
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Methylopila carotae sp. nov., a facultative methylotroph, isolated from a root of Daucus carota L. Antonie van Leeuwenhoek 2019; 112:1307-1316. [DOI: 10.1007/s10482-019-01263-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/06/2019] [Indexed: 10/27/2022]
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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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Agafonova NV, Kaparullina EN, Doronina NV, Trotsenko YA. Methylobacillus caricis sp. nov., an obligate methylotroph isolated from roots of sedge (Carex sp.). Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717060042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Dubinina G, Savvichev A, Orlova M, Gavrish E, Verbarg S, Grabovich M. Beggiatoa leptomitoformis sp. nov., the first freshwater member of the genus capable of chemolithoautotrophic growth. Int J Syst Evol Microbiol 2017; 67:197-204. [PMID: 27902215 DOI: 10.1099/ijsem.0.001584] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strain of filamentous sulfur bacteria was isolated from freshwater spring contaminated with residential and agricultural wastewater in Moscow region, Russia. According to the results of phylogenetic analysis, strain D-402T belonged to the genus Beggiatoa within the family Beggiatoaceae of the class Gammaproteobacteria. Within the genus Beggiatoa, strain D-402T was most closely related to Beggiatoa alba strains. Strain D-402T had a DNA G+C content 42.1 mol%. The DNA-DNA hybridization value between strain D-402T and Beggiatoa alba strain B15LD was 33 %. Predominant fatty acids were C18 : 1 (46.1 and 53.3 %), C16 : 0 (15.5 and 16.2 %) and C16 : 1 (32.9 and 25.4 %) for strains D-402T and B15LD, respectively. In contrast to known representatives of Beggiatoa, strain D-402T was capable of chemolithoautotrophic growth with sulfide and thiosulfate as electron donors. Oxidation of sulfide and thiosulfate was accompanied by deposition of sulfur globules within the cells. Strain D-402T was capable of heterotrophic growth. The strain was capable of using different organic compounds, sulfur compounds and hydrogen as electron donors. Based on these observations, strain D-402T is considered as a representative of a species Beggiatoa leptomitoformis sp. nov. of the genus Beggiatoa. The type strain is D-402T (=DSM 14946T=UNIQEM U 779T).
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Affiliation(s)
- Galina Dubinina
- Federal State Institution 'Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences', Prospect 60-letiya Oktyabrya, 7/2, 117312 Moscow, Russia
| | - Alexander Savvichev
- Federal State Institution 'Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences', Prospect 60-letiya Oktyabrya, 7/2, 117312 Moscow, Russia
| | - Maria Orlova
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, Voronezh 394018, Russia
| | | | - Suzanne Verbarg
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Margarita Grabovich
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, Voronezh 394018, Russia
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Kaparullina EN, Trotsenko YA, Doronina NV. Methylobacillus methanolivorans sp. nov., a novel non-pigmented obligately methylotrophic bacterium. Int J Syst Evol Microbiol 2017; 67:425-431. [DOI: 10.1099/ijsem.0.001646] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Elena N. Kaparullina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow region 142290, Russian Federation
| | - Yuri A. Trotsenko
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow region 142290, Russian Federation
| | - Nina V. Doronina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Moscow region 142290, Russian Federation
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Dubinina G, Grabovich M, Leshcheva N, Gronow S, Gavrish E, Akimov V. Spirochaeta sinaica sp. nov., a halophilic spirochaete isolated from a cyanobacterial mat. Int J Syst Evol Microbiol 2015; 65:3872-3877. [DOI: 10.1099/ijsem.0.000506] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strain of free-living obligately anaerobic, halophilic spirochaete, SLT, was isolated from a sample of a cyanobacterial mat of the hypersaline Solar Lake, Sinai shore. The strain had motile helical cells, 0.35–0.40 × 6–10 μm. Strain SLT exhibited high resistance to NaCl among known halophilic spirochaetes growing at NaCl concentrations from 2 to 12 % (optimum growth at 7 %). The strain grew at temperatures from 10 to 32 °C (optimum at 28 °C) and pH from 6 to 8.5 (optimum at pH 7.0–7.5). Carbohydrates, but not alcohols, organic acids or nitrogenous compounds (peptone, yeast extract and amino acids), were used as energy substrates for growth. Ethanol, acetate, lactate, H2 and CO2 were the products of glucose fermentation. Sulfide was produced in the presence of S0 or thiosulfate in the medium. The DNA G+C content was 44.7 mol%. Based on 16S rRNA gene sequence analysis, strain SLT clustered within the genus Spirochaeta, exhibiting 94.2 and 93.7 % similarity with its closest relatives, Spirochaeta bajacaliforniensis DSM 160554T and Spirochaeta smaragdinae DSM 11293T, respectively; similarity with other species did not exceed 86 %. The phenotypic and chemotaxonomic characteristics of the strain, as well as the results of phylogenetic analysis support the classification of strain SLT as representing a novel species of the genus Spirochaeta, for which the name Spirochaeta sinaica sp. nov. is proposed. The type strain is SLT ( = DSM 14994 = UNIQEM U 783).
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Affiliation(s)
- Galina Dubinina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, , Prospekt 60-letiya Oktyabrya, 7/2, Moscow, 117312, Russia
| | - Margarita Grabovich
- Faculty of Biology and Soil Science, Voronezh State University, Universitetskaya Pl., 1, Voronezh, 394893, Russia
| | - Nataliya Leshcheva
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, , Prospekt 60-letiya Oktyabrya, 7/2, Moscow, 117312, Russia
| | - Sabine Gronow
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Ekaterina Gavrish
- Department of Biology, , Northeastern University, Boston, MA 02115, USA
| | - Vladimir Akimov
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, , Prospekt 60-letiya Oktyabrya, 7/2, Moscow, 117312, Russia
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospekt Nauki, 5, Pushchino, 142290, Russia
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Agafonova NV, Kaparullina EN, Doronina NV, Trotsenko YA. Methylopila turkiensis sp. nov., a new aerobic facultatively methylotrophic phytosymbiont. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715040025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Poroshina MN, Trotsenko YA, Doronina NV. Methylobrevis pamukkalensis gen. nov., sp. nov., a halotolerant restricted facultative methylotroph isolated from saline water. Int J Syst Evol Microbiol 2015; 65:1321-1327. [PMID: 25667389 DOI: 10.1099/ijs.0.000105] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic halotolerant restricted facultatively methylotrophic bacterium was isolated from a saline hot spring in Pamukkale, Turkey, and designated strain PK2(T). The cells of this strain were Gram-stain-negative, asporogenous, motile short rods multiplying by binary fission. They utilized methanol, methylamine and mannitol as carbon and energy sources. The organism grew optimally at 30 °C in media containing 85 mM NaCl and at pH 7.5-8.0. C1 compounds were assimilated via the isocitrate-lyase-positive variant of the serine pathway. Poly-β-hydroxybutyrate and the compatible solute ectoine were found in the cells. The dominant phospholipids were phosphatidylethanolamine and phosphatidylmonomethylethanolamine. The major cellular fatty acids of methanol-grown cells were C(18 : 1)ω7 and C(16 : 1)ω7c. The main ubiquinone was Q-10. The DNA G+C content was 67.9 mol% (T(m)). The 16S rRNA gene sequence suggests that strain PK2(T) is affiliated with the order Rhizobiales within the class Alphaproteobacteria , being most closely related to Mesorhizobium gobiense CCBAU 83330(T) (94% similarity). A novel genus and species, Methylobrevis pamukkalensis gen. nov., sp. nov., is proposed on the basis of phenotypic and genotypic data, with PK2(T) (VKM B-2849(T) = JCM 30229(T)) as the type strain.
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Affiliation(s)
- Maria N Poroshina
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region 142290, Russia
| | - Yuri A Trotsenko
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region 142290, Russia
| | - Nina V Doronina
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region 142290, Russia
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Wang L, Zhou Z, Wu G, Chen M, Lin M, Zhang W, Chen W. Falsirhodobacter deserti sp. nov., isolated from sandy soil. Int J Syst Evol Microbiol 2014; 65:650-655. [PMID: 25424484 DOI: 10.1099/ijs.0.068262-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, heterotrophic, rod-shaped bacterium, designated strain W402(T), was isolated from an enrichment culture of a Tamarix ramosissima rhizosphere soil sample from the Xinjiang desert in the PR China. Analysis of the almost-complete 16S rRNA gene sequence showed that the isolate was phylogenetically related to a species of the genus Falsirhodobacter, having a close relationship to Falsirhodobacter halotolerans JA744(T) (97 % similarity). However, DNA-DNA relatedness between W402(T) and F. halotolerans JA744(T) was 43.2±1.2 %. Strain W402(T) grew in 0-10 % (w/v) NaCl. The temperature and pH ranges for growth were 10-40 °C and pH 5.5-10.0, respectively. Optimal growth occurred at 1-3 % (w/v) NaCl, 30 °C and pH 7.0. The predominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 61.4 %), C18 : 0 (9.8 %) and 11-methyl C18 : 1ω7c (8.2 %). The major quinone of strain W402(T) was Q-10. Phosphatidylethanolamine was predominant in the polar lipid profile. The DNA G+C content of strain W402(T) was 67.3 mol%. Taken together, these results confirm that W402(T) represents a novel species of the genus Falsirhodobacter, for which the name Falsirhodobacter deserti sp. nov. is proposed. The type strain is W402(T) ( = ACCC 05851(T) = KCTC 32408(T)).
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Affiliation(s)
- Lin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, PR China
| | - Zhengfu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Gang Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Wuling Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an 710069, PR China
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Esikova TZ, Akatova EV, Taran SA. Bacteria that degrade low-molecular linear epsilon-caprolactam oligomers. APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s0003683814050044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Jiang S, Chen M, Su S, Yang M, Li A, Zhang C, Lin M, Zhang W, Luo X. Sphingobacterium arenae sp. nov., isolated from sandy soil. Int J Syst Evol Microbiol 2013; 64:248-253. [PMID: 24052628 DOI: 10.1099/ijs.0.051706-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, Gram-stain-negative, non-motile, non-spore-forming, short rod-shaped, aerobic bacterium designated H-12(T) was isolated from a mixed sandy soil sample collected from Xinjiang, China. Strain H-12(T) grew at 20-37 °C (optimum, 30 °C), pH 7.0-11.0 (optimum, pH 8.5) on TGY medium with 0-5 % NaCl (w/v). 16S rRNA gene sequence analysis indicated that strain H-12(T) shared sequence similarities with Sphingobacterium composti DSM 18850(T) (90.0 %). Strain H-12(T) showed a low level of DNA-DNA relatedness to Sphingobacterium composti DSM 18850(T) (45.5 %). The predominant isoprenoid quinone of strain H-12(T) was MK-7 and the major polar lipid was phosphatidylethanolamine. The predominant cellular fatty acids were C16:1ω7c and/or C16 : 1ω6c, iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0, C16 : 0 3-OH and iso-C15 : 0 3-OH. DNA G+C content of strain H-12(T) was 44.15 mol%. On the basis of phenotypic, genetic and phylogenetic data, strain H-12(T) is proposed to be a representative of a novel species of the genus Sphingobacterium, for which the name Sphingobacterium arenae sp. nov. is suggested and the type strain is H-12(T) ( = ACCC 05758(T) = KCTC 32294(T)).
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Affiliation(s)
- Shijie Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,Life Science and Engineering College, Southwest University of Science and Technology, Mianyang, Sichuan 621010, PR China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Shiyou Su
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Mingkun Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Aihua Li
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, PR China
| | - Chen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xuegang Luo
- Life Science and Engineering College, Southwest University of Science and Technology, Mianyang, Sichuan 621010, PR China
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Doronina NV, Kaparullina EN, Trotsenko YA. Methyloversatilis thermotolerans sp. nov., a novel thermotolerant facultative methylotroph isolated from a hot spring. Int J Syst Evol Microbiol 2013; 64:158-164. [PMID: 24048869 DOI: 10.1099/ijs.0.055046-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A newly isolated facultatively methylotrophic bacterium (strain 3t(T)) was investigated. Cells of the isolate were Gram-stain-negative, asporogenous, non-motile rods that multiplied by binary fission. The strain utilized methanol, methylamine and a variety of multicarbon compounds as carbon and energy sources. Growth occurred at pH 6.5-8.5 (optimally at 7.0-7.5) and at 10-45 °C (optimally at 30-37 °C). The major fatty acids of methanol-grown cells were C16 : 1ω7c and C16 : 0. The predominant phospholipids were phosphatidylethanolamine and phosphatidylglycerol. The major ubiquinone was Q-8. Strain 3t(T) possessed pyrroloquinoline quinone (PQQ)-linked methanol dehydrogenase and assimilated C1 units at the level of formaldehyde and CO2 via the serine cycle. The DNA G+C content of the strain was 63.6 mol% (Tm). On the basis of 16S rRNA gene sequence similarity (98.1 %) and rather low DNA-DNA relatedness (30 %) with the type strain of the type species of the genus Methyloversatilis (Methyloversatilis universalis FAM5(T)), and physiological and biochemical characteristics, the isolate was classified as a representative of a new species of the genus and named Methyloversatilis thermotolerans 3t(T) ( = VKM B-2692(T) = CCUG 61694(T) = DSM 25156(T)).
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Affiliation(s)
- Nina V Doronina
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences Pushchino, Moscow region 142290, Russia
| | - Elena N Kaparullina
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences Pushchino, Moscow region 142290, Russia
| | - Yuri A Trotsenko
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences Pushchino, Moscow region 142290, Russia
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15
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Doronina NV, Poroshina MN, Kaparullina EN, Ezhov VA, Trotsenko YA. Methyloligella halotolerans gen. nov., sp. nov. and Methyloligella solikamskensis sp. nov., two non-pigmented halotolerant obligately methylotrophic bacteria isolated from the Ural saline environments. Syst Appl Microbiol 2013; 36:148-54. [PMID: 23351489 DOI: 10.1016/j.syapm.2012.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 12/07/2012] [Accepted: 12/10/2012] [Indexed: 11/16/2022]
Abstract
Two newly isolated halotolerant obligately methylotrophic bacteria (strains C2(T) and SK12(T)) with the serine pathway of C1 assimilation are described. The isolates are strictly aerobic, Gram negative, asporogenous, non-motile rods, forming rosettes, multiplying by binary fission. Mesophilic and neutrophilic, accumulate intracellularly compatible solute ectoine and poly-β-hydroxybutyrate. The novel strains are able to grow at 0 up to 16% NaCl (w/v), optimally at 3-5% NaCl. The major cellular fatty acids are C18:1ω7c and C19:0cyc and the prevailing quinone is Q-10. The predominant phospholipids are phosphatidylcholine, phosphatidylglycerol, phosphatidyldimethylethanolamine and phosphatidylethanolamine. Assimilate NH4(+) by glutamate dehydrogenase and via the glutamate cycle (glutamine synthetase and glutamate synthase). The DNA G+C contents of strains C2(T) and SK12(T) are 60.9 and 60.5 mol% (Tm), respectively. 16S rRNA gene sequence similarity between the two new isolates are 99% but below 94% with other members of the Alphaproteobacteria thus indicating that they can be assigned to a novel genus Methyloligella. Rather low level of DNA-DNA relatedness (53%) between the strains C2(T) and SK12(T) indicates that they represent two separate species of the new genus, for which the names Methyloligella halotolerans gen. nov., sp. nov. and Methyloligella solikamskensis sp. nov. are proposed. The type strain of Methyloligella halotolerans is C2(T) (=VKM B-2706(T)=CCUG 61687(T)=DSM 25045(T)) and the type strain of Methyloligella solikamskensis is SK12(T) (=VKM B-2707(T)=CCUG 61697(T)=DSM 25212(T)).
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Affiliation(s)
- Nina V Doronina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.
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Yan Y, Chen H, Xu W, He Q, Zhou Q. Enhancement of biochemical methane potential from excess sludge with low organic content by mild thermal pretreatment. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2012.10.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Doronina NV, Kaparullina EN, Bykova TV, Trotsenko YA. Methylopila musalis sp. nov., an aerobic, facultatively methylotrophic bacterium isolated from banana fruit. Int J Syst Evol Microbiol 2012; 63:1847-1852. [PMID: 22984139 DOI: 10.1099/ijs.0.042028-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A newly isolated, facultatively methylotrophic bacterium (strain MUSA(T)) was investigated. The isolate was strictly aerobic, Gram-stain-negative, asporogenous, motile, rod-shaped and multiplied by binary fission. The strain utilized methanol, methylamine and an apparently narrow range of multi-carbon compounds, but not methane, dichloromethane or CO2/H2, as the carbon and energy sources. Growth occurred at pH 5.5-9.5 (optimum, pH 7.0) and 16-40 °C (optimum, 28-30 °C). The major fatty acids of methanol-grown cells were C18 : 1ω7c, C18 : 0 and 11-methyl-C18 : 1ω7c . The predominant phospholipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and phosphatidylmonomethylethanolamine. The major ubiquinone was Q-10. The strain had methanol and methylamine dehydrogenases as well as the enzymes of the N-methylglutamate pathway (lyases of γ-glutamylmethylamide and N-methylglutamate). C1 assimilation occurs via the isocitrate lyase-negative serine pathway. Ammonium was assimilated by glutamate dehydrogenase and the glutamate cycle (glutamate synthase/glutamine synthetase). The DNA G+C content of the strain was 64.5 mol% (determined from the melting temperature). Based on 16S rRNA gene sequence similarity (97.0-98.9 %) and DNA-DNA relatedness (36-38 %) with representatives of the genus Methylopila (Methylopila capsulata IM1(T) and Methylopila jiangsuensis JZL-4(T)) the isolate was classified as a novel species of the genus Methylopila, for which the name Methylopila musalis sp. nov. is proposed. The type strain is MUSA(T) ( = VKM B-2646(T) = DSM 24986(T) = CCUG 61696(T)).
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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 Institute of Natural Sciences, 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 Institute of Natural Sciences, Pushchino, Moscow region 142290, Russia
| | - Tatjana V Bykova
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences and Pushchino State Institute of Natural Sciences, 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 Institute of Natural Sciences, Pushchino, Moscow region 142290, Russia
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Antony CP, Doronina NV, Boden R, Trotsenko YA, Shouche YS, Murrell JC. Methylophaga lonarensis sp. nov., a moderately haloalkaliphilic methylotroph isolated from the soda lake sediments of a meteorite impact crater. Int J Syst Evol Microbiol 2012; 62:1613-1618. [DOI: 10.1099/ijs.0.035089-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A moderately haloalkaliphilic methylotrophic bacterium possessing the ribulose monophosphate pathway for carbon assimilation, designated MPLT, was isolated from Lonar Lake sediment microcosms that were oxidizing methane for two weeks. The isolate utilized methanol and was an aerobic, Gram-negative, asporogenous, motile, short rod that multiplied by binary fission. The isolate required NaHCO3 or NaCl for growth and, although not auxotrophic for vitamin B12, had enhanced growth with vitamin B12. Optimal growth occurred with 0.5–2 % (w/v) NaCl, at 28–30 °C and at pH 9.0–10.0. The cellular fatty acid profile consisted primarily of straight-chain saturated C16 : 0 and unsaturated C16 : 1ω7c and C18 : 1ω7c. The major ubiquinone was Q-8. The dominant phospholipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Cells accumulated ectoine as the main compatible solute. The DNA G+C content was 50.0 mol%. The isolate exhibited 94.0–95.4 % 16S rRNA gene sequence similarity with the type strains of methylotrophs belonging to the genus
Methylophaga
and 31 % DNA–DNA relatedness with the reference strain,
Methylophaga alcalica
VKM B-2251T. It is proposed that strain MPLT represents a novel species, Methylophaga lonarensis sp. nov. (type strain MPLT = VKM B-2684T = MCC 1002T).
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Affiliation(s)
| | - Nina V. Doronina
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow 142290, Russia
| | - Rich Boden
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Yuri A. Trotsenko
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow 142290, Russia
| | - Yogesh S. Shouche
- Microbial Culture Collection, National Centre for Cell Science, Pune 411007, India
| | - J. Colin Murrell
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
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Chernousova EY, Belousova EV, Gavrish EY, Dubinina GA, Tourova TP, Grabovich MY. Molecular phylogeny and taxonomy of colorless, filamentous sulfur bacteria of the genus Thiothrix. Microbiology (Reading) 2012. [DOI: 10.1134/s0026261712030046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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20
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Kompantseva EI, Komova AV, Novikov AA, Kostrikina NA. Rhodovulum tesquicola sp. nov., a haloalkaliphilic purple non-sulfur bacterium from brackish steppe soda lakes. Int J Syst Evol Microbiol 2012; 62:2962-2966. [PMID: 22286907 DOI: 10.1099/ijs.0.035857-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains of purple non-sulfur bacteria (A-36s(T) and A-51s) were isolated from brackish steppe soda lakes of southern Siberia. Genetically, the isolates were related most closely to the type strains of Rhodovulum steppense and Rhodovulum strictum, from which they differed at the species level (98.5% 16S rRNA gene sequence similarity, 40-53% DNA-DNA relatedness). Cells of the two strains were ovoid to rod-shaped, 0.4-0.8 µm wide and 1.0-2.5 µm long, and motile by means of a polar flagellum. They contained internal photosynthetic membranes of vesicular type and photosynthetic pigments (bacteriochlorophyll a and carotenoids of the spheroidene series). The strains were obligate haloalkaliphiles, growing over wide ranges of salinity (0.3-10.0% NaCl) and pH (7.5-10.0), with growth optima at 1.0-3.0% NaCl and pH 8.5-9.0. Photoheterotrophic and chemoheterotrophic growth occurred with a number of organic compounds and biotin, p-aminobenzoate, thiamine and niacin as growth factors. No anaerobic respiration on nitrite, nitrate or fumarate and no fermentation were demonstrated. The strains grew photolithoautotrophically and chemolithoautotrophically with sulfide, sulfur and thiosulfate, oxidizing them to sulfate. Sulfide was oxidized via deposition of extracellular elemental sulfur. No growth with H(2) as the electron donor was observed. The major fatty acid was C(18:1) (78%). The major quinone was ubiquinone Q-10. The DNA G+C content of strain A-36s(T) was 65.4 mol% (T(m)). According to genotypic and phenotypic characteristics, the investigated strains were assigned to a novel species of the genus Rhodovulum, for which the name Rhodovulum tesquicola sp. nov. is proposed. The type strain is A-36s(T) ( = VKM B-2491(T) = ATCC BAA-1573(T)), which was isolated from steppe soda lake Sul'fatnoe (Zabaikal'skii Krai, southern Siberia, Russia).
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Affiliation(s)
- Elena I Kompantseva
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7-2, Moscow 117312, Russia
| | - Anastasia V Komova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7-2, Moscow 117312, Russia
| | - Andrey A Novikov
- Gubkin Russian State University of Oil and Gas, Leninskiy Prospect 65, Moscow 119991, Russia
| | - Nadezhda A Kostrikina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7-2, Moscow 117312, Russia
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21
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Methylobacillus arboreus sp. nov., and Methylobacillus gramineus sp. nov., novel non-pigmented obligately methylotrophic bacteria associated with plants. Syst Appl Microbiol 2011; 34:477-81. [DOI: 10.1016/j.syapm.2011.03.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 02/24/2011] [Accepted: 03/05/2011] [Indexed: 11/19/2022]
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22
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Plotnikova EG, Anan’ina LN, Krausova VI, Ariskina EV, Prisyazhnaya NV, Lebedev AT, Demakov VA, Evtushenko LI. Thalassospira permensis sp. nov., a new terrestrial halotolerant bacterium isolated from a naphthalene-utilizing microbial consortium. Microbiology (Reading) 2011. [DOI: 10.1134/s0026261711050109] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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23
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Sahin N, Tani A, Kotan R, Sedláček I, Kimbara K, Tamer AU. Pandoraea oxalativorans sp. nov., Pandoraea faecigallinarum sp. nov. and Pandoraea vervacti sp. nov., isolated from oxalate-enriched culture. Int J Syst Evol Microbiol 2011; 61:2247-2253. [DOI: 10.1099/ijs.0.026138-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five isolates, designated TA2, TA4, TA25T, KOxT and NS15T were isolated in previous studies by enrichment in mineral medium with potassium oxalate as the sole carbon source and were characterized using a polyphasic approach. The isolates were Gram-reaction-negative, aerobic, non-spore-forming rods. Phylogenetic analyses based on 16S rRNA and DNA gyrase B subunit (gyrB) gene sequences confirmed that the isolates belonged to the genus Pandoraea and were most closely related to Pandoraea sputorum and Pandoraea pnomenusa (97.2–99.7 % 16S rRNA gene sequence similarity). The isolates could be differentiated from their closest relatives on the basis of several phenotypic characteristics. The major cellular fatty acid profiles of the isolates comprised C16 : 0, C18 : 1ω7c, C17 : 0 cyclo and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). On the basis of DNA–DNA hybridization studies and phylogenetic analyses, the isolates represent three novel species within the genus Pandoraea, for which the names Pandoraea oxalativorans sp. nov. (TA25T = NBRC 106091T = CCM 7677T = DSM 23570T), Pandoraea faecigallinarum sp. nov. (KOxT = NBRC 106092T = CCM 2766T = DSM 23572T) and Pandoraea vervacti sp. nov. (NS15T = NBRC 106088T = CCM 7667T = DSM 23571T) are proposed.
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Affiliation(s)
| | - Akio Tani
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Recep Kotan
- Department of Plant Protection, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Ivo Sedláček
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kazuhide Kimbara
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
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24
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Zhou Z, Yuan M, Tang R, Chen M, Lin M, Zhang W. Corynebacterium deserti sp. nov., isolated from desert sand. Int J Syst Evol Microbiol 2011; 62:791-794. [PMID: 21571935 DOI: 10.1099/ijs.0.030429-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel coryneform bacterium, designated strain GIMN1.010T, was isolated from a sand sample collected in the desert in the west of China. Cells were Gram-stain-positive, non-spore-forming, catalase-positive, irregular rods. Comparative 16S rRNA gene sequence analysis demonstrated that strain GIMN1.010T belonged to the genus Corynebacterium and was related closely to Corynebacterium glutamicum ATCC 13032T (98.4 % similarity). However, the level of DNA-DNA relatedness between strain GIMN1.010T and C. glutamicum ATCC 13032T was only 22.4±1.72 %, showing that strain GIMN1.010T represented a genomic species distinct from C. glutamicum. On the basis of phenotypic and phylogenetic data, strain GIMN1.010T is considered to represent a novel species of the genus Corynebacterium, for which the name Corynebacterium deserti sp. nov. is proposed. The type strain is GIMN1.010T (=CCTCC AB 2010341T=NRRL B-59552).
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Affiliation(s)
- Zhengfu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Menglong Yuan
- College of Life Sciences, Beijing Normal University, 100875 Beijing, PR China.,Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Ran Tang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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25
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Ramette A, Frapolli M, Fischer-Le Saux M, Gruffaz C, Meyer JM, Défago G, Sutra L, Moënne-Loccoz Y. Pseudomonas protegens sp. nov., widespread plant-protecting bacteria producing the biocontrol compounds 2,4-diacetylphloroglucinol and pyoluteorin. Syst Appl Microbiol 2011; 34:180-8. [PMID: 21392918 DOI: 10.1016/j.syapm.2010.10.005] [Citation(s) in RCA: 191] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 10/18/2010] [Accepted: 10/20/2010] [Indexed: 10/18/2022]
Abstract
Fluorescent Pseudomonas strains producing the antimicrobial secondary metabolite 2,4-diacetylphloroglucinol (Phl) play a prominent role in the biocontrol of plant diseases. A subset of Phl-producing fluorescent Pseudomonas strains, which can additionally synthesize the antimicrobial compound pyoluteorin (Plt), appears to cluster separately from other fluorescent Pseudomonas spp. based on 16S rRNA gene analysis and shares at most 98.4% 16S rRNA gene sequence identity with any other Pseudomonas species. In this study, a polyphasic approach based on molecular and phenotypic methods was used to clarify the taxonomy of representative Phl(+) Plt(+) strains isolated from tobacco, cotton or wheat on different continents. Phl(+) Plt(+) strains clustered separately from their nearest phylogenetic neighbors (i.e. species from the 'P. syringae', 'P. fluorescens' and 'P. chlororaphis' species complexes) based on rpoB, rpoD or gyrB phylogenies. DNA-DNA hybridization experiments clarified that Phl(+) Plt(+) strains formed a tight genomospecies that was distinct from P. syringae, P. fluorescens, or P. chlororaphis type strains. Within Phl(+) strains, the Phl(+) Plt(+) strains were differentiated from other biocontrol fluorescent Pseudomonas strains that produced Phl but not Plt, based on phenotypic and molecular data. Discriminative phenotypic characters were also identified by numerical taxonomic analysis and siderotyping. Altogether, this polyphasic approach supported the conclusion that Phl(+) Plt(+) fluorescent Pseudomonas strains belonged to a novel species for which the name Pseudomonas protegens is proposed, with CHA0(T) (=CFBP 6595(T), =DSM 19095(T)) as the type strain.
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Affiliation(s)
- Alban Ramette
- Plant Pathology Group, Institute of Integrative Biology, Swiss Federal Institute of Technology (ETH), CH-8092 Zürich, Switzerland
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26
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Gridneva E, Chernousova E, Dubinina G, Akimov V, Kuever J, Detkova E, Grabovich M. Taxonomic investigation of representatives of the genus Sphaerotilus: descriptions of Sphaerotilus montanus sp. nov., Sphaerotilus hippei sp. nov., Sphaerotilus natans subsp. natans subsp. nov. and Sphaerotilus natans subsp. sulfidivorans subsp. nov., and an emended description of the genus Sphaerotilus. Int J Syst Evol Microbiol 2011; 61:916-925. [DOI: 10.1099/ijs.0.023887-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seven strains of the genus Sphaerotilus were obtained from natural thermal sulfide (strains D-501T, D-502, D-504, D-505 and D-507) and low-temperature ferrous (strain HST) springs and from an activated sludge system (strain D-380). These Sphaerotilus isolates and strains of Sphaerotilus natans obtained from the DSMZ (S. natans DSM 6575T, DSM 565 and DSM 566) were studied using a polyphasic taxonomic approach. All strains had Q-8 as the major quinone and C16 : 1ω7, C16 : 0 and C18 : 1ω7 as the major fatty acids. The DNA–DNA hybridization results and 16S rRNA, hsp60 and gyrB gene sequencing experiments showed that isolates D-501T, D-502, D-504, D-505, D-507 and D-380 were closely related to the type strain of S. natans DSM 6575T. However, strains D-501T, D-502, D-504, D-505 and D-507 significantly differed from the heterotrophic strain S. natans DSM 6575T by their capability for lithotrophic growth with reduced sulfur compounds as an electron donor for energy conservation and some other phenotypic features. For this reason, strains D-501T, D-502, D-504, D-505 and D-507 merit a separate taxonomic classification at the subspecies level. The name Sphaerotilus natans subsp. sulfidivorans subsp. nov. (type strain D-501T = DSM 22545T = VKM B-2573T) is proposed. The subspecies Sphaerotilus natans subsp. natans subsp. nov. is automatically created as a result of this proposal. Strain D-380 was phenotypically closely related to S. natans DSM 6575T. Strains D-380 and S. natans DSM 6575T were assigned to the subspecies Sphaerotilus natans subsp. natans subsp. nov. (type strain DSM 6575T = ATCC 13338T). The 16S rRNA, hsp60 and gyrB gene sequences obtained for strains HST and DSM 565 showed very low sequence similarity values of 97.3 %, 89.7 % and 88.4 %, respectively, with S. natans DSM 6575T. Strain HST shared 99 % DNA–DNA relatedness with strain
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Affiliation(s)
- Elena Gridneva
- Department of Biology, University of Voronezh, Universitetskaya pl. 1, 394006 Voronezh, Russia
| | - Elena Chernousova
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospect Nauki 5, 142290 Pushchino, Russia
- Department of Biology, University of Voronezh, Universitetskaya pl. 1, 394006 Voronezh, Russia
| | - Galina Dubinina
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - Vladimir Akimov
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospect Nauki 5, 142290 Pushchino, Russia
| | - Jan Kuever
- Department of Microbiology, Bremen Institute for Materials Testing, Paul-Feller Str. 1, D-28199 Bremen, Germany
| | - Ekaterina Detkova
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - Margarita Grabovich
- Department of Biology, University of Voronezh, Universitetskaya pl. 1, 394006 Voronezh, Russia
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27
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Dubinina G, Grabovich M, Leshcheva N, Rainey FA, Gavrish E. Spirochaeta
perfilievii sp. nov., an oxygen-tolerant, sulfide-oxidizing, sulfur- and thiosulfate-reducing spirochaete isolated from a saline spring. Int J Syst Evol Microbiol 2011; 61:110-117. [DOI: 10.1099/ijs.0.018333-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strain of fermenting, aerotolerant, chemo-organoheterotrophic spirochaete designated PT was isolated from a sulfur ‘Thiodendron’ mat in a saline spring at the Staraya Russa resort (Novgorod Region, Russia). Cells of strain PT exhibited a helical shape. The spirochaete required sulfide in the growth medium and was able to oxidize it non-enzymically to elemental sulfur via the interaction of H2O2 with sulfide and deposit it in the periplasmic space. Growth occurred at 4–32 °C (optimum at 28–30 °C), pH 6.0–8.5 (optimum pH 7.0–7.5), and in 0.1–1 M NaCl (optimum 0.35 M). The isolate used several sugars and polysaccharides as carbon or energy sources but did not use peptides, amino acids, organic acids or alcohols. The products of glucose fermentation were formate, acetate, ethanol, pyruvate, CO2 and H2. The genomic DNA G+C content was 41.7 mol%. 16S rRNA gene sequence analysis showed that strain PT fell within a group of species in the genus Spirochaeta, including Spirochaeta litoralis, S. isovalerica and S. cellobiosiphila, with which it shared less then 89 % sequence similarity. On the basis of its morphology, physiology and other phenotypic properties, as well as its phylogenetic position, the new isolate is considered to represent a novel species of the genus Spirochaeta, for which the name Spirochaeta perfilievii sp. nov. is proposed. The type strain is PT (=DSM 19205T =VKM B-2514T).
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Affiliation(s)
- Galina Dubinina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Pr. 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - Margarita Grabovich
- Faculty of Biology and Soil Science, Voronezh State University, Universitetskaya Pl., 1, Voronezh 394893, Russia
| | - Natalia Leshcheva
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Pr. 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - Frederick A. Rainey
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Ekaterina Gavrish
- Department of Biology, Northeastern University, Boston, MA 02115, USA
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Lu SE, Gross DC. Drippy Pod of White Lupine: A New Bacterial Disease Caused by a Pathovar of Brenneria quercina. PLANT DISEASE 2010; 94:1431-1440. [PMID: 30743385 DOI: 10.1094/pdis-05-10-0365] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Drippy pod is a unique bacterial disease of Mediterranean white lupine (Lupinus albus) that first appeared in commercial fields in Eastern Washington State in the mid-1980s. The disease is most noticeable in the field as water-soaked lesions on lupine pods that produce an abundance of whitish-colored ooze with a sticky and foamy consistency. As the disease progresses, yellowing of lupine plants occurs with ooze characteristically dripping down the infected pods and stems and solidifying. A gram-negative rod-shaped bacterium with facultative anaerobic growth was repeatedly isolated from infected lupine tissues, and subsequently confirmed by Koch's postulates to infect lupines. Physiological and biochemical tests, including the API 20E and 50CHE strip assays, showed a highly uniform phenotype for the lupine strains that was distinctive for the genus Brenneria and most closely resembled the oak pathogen Brenneria quercina. Furthermore, sequence analyses of the 16S rDNA gene and the 16S-23S intergenic region of lupine strains revealed the highest similarity (>97%) to the corresponding regions of B. quercina and less similarity to the next closest species, B. salicis. Fatty acid profiling demonstrated that lupine strains were qualitatively similar in composition to Brenneria spp., and supported placement of the drippy pod bacterium in the species B. quercina. Oak strains of B. quercina, however, did not incite drippy pod disease on lupine. Consequently, the lupine strains that cause bacterial drippy pod disease were classified as B. quercina pv. lupinicola pv. nov.
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Affiliation(s)
- Shi-En Lu
- Department of Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762
| | - Dennis C Gross
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843-2132
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29
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Kompantseva EI, Komova AV, Kostrikina NA. Rhodovulum steppense sp. nov., an obligately haloalkaliphilic purple nonsulfur bacterium widespread in saline soda lakes of Central Asia. Int J Syst Evol Microbiol 2010; 60:1210-1214. [DOI: 10.1099/ijs.0.014639-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seven strains of purple nonsulfur bacteria isolated from the shallow-water steppe soda lakes of the cryoarid zone of Central Asia formed a genetically homogeneous group within the genus Rhodovulum. The isolates were most closely related to Rhodovulum strictum, from which they differed at the species level (99.5 % 16S rRNA gene identity and 42–44 % DNA–DNA hybridization level). According to genotypic and phenotypic characteristics, the strains were assigned to a new species of the genus Rhodovulum, for which the name Rhodovulum steppense sp. nov. is proposed. Cells of all strains were ovoid to rod-shaped, 0.3–0.8 μm wide and 1–2.5 μm long, and motile by means of polar flagella. They contained internal photosynthetic membranes of the vesicular type and photosynthetic pigments (bacteriochlorophyll a and carotenoids of the spheroidene series). All strains were obligate haloalkaliphiles, growing within a wide range of salinity (0.3–10 %) and pH (7.5–10), with growth optima at 1–5 % NaCl and pH 8.5. Photo- and chemoheterotrophic growth occurred with a number of organic compounds and biotin, thiamine and niacin as growth factors. No anaerobic respiration on nitrite, nitrate or fumarate and no fermentation was demonstrated. Bacteria grew photo- and chemolithoautotrophically with sulfide, sulfur and thiosulfate, oxidizing them to sulfate. Sulfide was oxidized via deposition of extracellular elemental sulfur. No growth with H2 as electron donor was demonstrated. The major fatty acid was 18 : 1 (81.0 %). The major quinone was Q-10. The DNA G+C content was 66.1 mol% (T
m). The type strain, A-20sT (=VKM B-2489T =DSM 21153T), was isolated from soda lake Khilganta (Zabaikal'skii Krai, southern Siberia, Russia).
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Affiliation(s)
- Elena I. Kompantseva
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - Anastasia V. Komova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - Nadezhda A. Kostrikina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
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López MM, Roselló M, Llop P, Ferrer S, Christen R, Gardan L. Erwinia piriflorinigrans sp. nov., a novel pathogen that causes necrosis of pear blossoms. Int J Syst Evol Microbiol 2010; 61:561-567. [PMID: 20382791 DOI: 10.1099/ijs.0.020479-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eight Erwinia strains, isolated from necrotic pear blossoms in València, Spain, were compared with reference strains of Erwinia amylovora and Erwinia pyrifoliae, both of which are pathogenic to species of pear tree, and to other species of the family Enterobacteriaceae using a polyphasic approach. Phenotypic analyses clustered the novel isolates into one phenon, distinct from other species of the genus Erwinia, showing that the novel isolates constituted a homogeneous phenotypic group. Rep-PCR profiles, PCR products obtained with different pairs of primers and plasmid contents determined by restriction analysis showed differences between the novel strains and reference strains of E. amylovora and E. pyrifoliae. Phylogenetic analysis of 16S rRNA, gpd and recA gene sequences showed that the eight novel strains could not be assigned to any recognized species. On the basis of DNA-DNA hybridization studies, the novel isolates constituted a single group with relatedness values of 87-100 % to the designated type strain of the group, CFBP 5888(T). Depending on the method used, strain CFBP 5888(T) showed DNA-DNA relatedness values of between 22.7 and 50 % to strains of the closely related species E. amylovora and E. tasmaniensis. The DNA G+C contents of two of the novel strains, CFBP 5888(T) and CFBP 5883, were 51.1 and 50.5 mol%, respectively. On the basis of these and previous results, the novel isolates represent a novel species of the genus Erwinia, for which the name Erwinia piriflorinigrans sp. nov. is proposed. The type strain is CFBP 5888(T) (=CECT 7348(T)).
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Affiliation(s)
- María M López
- Instituto Valenciano de Investigaciones Agrarias (IVIA). Ctra. Moncada-Náquera, km. 4,5, 46113 Moncada, Valencia, Spain
| | - Montserrat Roselló
- Área de Protección Agroalimentaria, Conselleria de Agricultura, Pesca y Alimentación, Ctra. Alicante-València, km. 276,5, 46460 Silla, Valencia, Spain
| | - Pablo Llop
- Instituto Valenciano de Investigaciones Agrarias (IVIA). Ctra. Moncada-Náquera, km. 4,5, 46113 Moncada, Valencia, Spain
| | - Sergi Ferrer
- ENOLAB - Departament de Microbiologia i Ecologia, Universitat de València, Dr Moliner 50, E-46100 Burjassot, València, Spain
| | - Richard Christen
- UMR 6543 CNRS and Université de Nice Sophia Antipolis, Centre de Biochimie, Parc Valrose, 06108 Nice CEDEX 2, France
| | - Louis Gardan
- UMR de Pavé, INRA-INH-Université, BP 60057. 42, rue G. Morel, 49071 Beaucouzé CEDEX, France
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Lavrinenko K, Chernousova E, Gridneva E, Dubinina G, Akimov V, Kuever J, Lysenko A, Grabovich M. Azospirillum thiophilum sp. nov., a diazotrophic bacterium isolated from a sulfide spring. Int J Syst Evol Microbiol 2010; 60:2832-2837. [PMID: 20081019 DOI: 10.1099/ijs.0.018853-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel nitrogen-fixing strain, designated BV-S(T), was isolated from a sulfur bacterial mat collected from a sulfide spring of the Stavropol Krai, North Caucasus, Russia. Strain BV-S(T) grew optimally at pH 7.5 and 37°C. According to the results of phylogenetic analysis, strain BV-S(T) belonged to the genus Azospirillum within the family Rhodospirillaceae of the class Alphaproteobacteria. Within the genus Azospirillum, strain BV-S(T) was most closely related to Azospirillum doebereinerae GSF71(T), A. picis IMMIB TAR-3(T) and A. lipoferum ATCC 29707(T) (97.7, 97.7 and 97.4 % 16S rRNA gene sequence similarity, respectively). DNA-DNA relatedness between strain BV-S(T) and A. doebereinerae DSM 13131(T), A. picis DSM 19922(T) and A. lipoferum ATCC 29707(T) was 38, 55 and 42 %, respectively. Similarities between nifH sequences of strain BV-S(T) and members of the genus Azospirillum ranged from 94.5 to 96.8 %. Chemotaxonomic characteristics (quinone Q-10, major fatty acid C(18 : 1)ω7c and G+C content 67 mol%) were similar to those of members of the genus Azospirillum. In contrast to known Azospirillum species, strain BV-S(T) was capable of mixotrophic growth under microaerobic conditions with simultaneous utilization of organic substrates and thiosulfate as electron donors for energy conservation. Oxidation of sulfide was accompanied by deposits of sulfur globules within the cells. Based on these observations, strain BV-S(T) is considered as a representative of a novel species of the genus Azospirillum, for which the name Azospirillum thiophilum sp. nov. is proposed. The type strain is BV-S(T) (=DSM 21654(T) =VKM B-2513(T)).
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Affiliation(s)
- Ksenia Lavrinenko
- Department of Biology, University of Voronezh, Universitetskaya pl. 1, Voronezh 394006, Russia
| | - Elena Chernousova
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences and Pushchino State University, Pushchino, Moscow region, 142290, Russia.,Department of Biology, University of Voronezh, Universitetskaya pl. 1, Voronezh 394006, Russia
| | - Elena Gridneva
- Department of Biology, University of Voronezh, Universitetskaya pl. 1, Voronezh 394006, Russia
| | - Galina Dubinina
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Vladimir Akimov
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences and Pushchino State University, Pushchino, Moscow region, 142290, Russia
| | - Jan Kuever
- Department of Microbiology, Bremen Institute for Materials Testing, Paul-Feller-Strasse 1, D-28199 Bremen, Germany
| | - Anatoly Lysenko
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Margarita Grabovich
- Department of Biology, University of Voronezh, Universitetskaya pl. 1, Voronezh 394006, Russia
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Doronina NV, Kaparullina EN, Trotsenko YA, Nörtemann B, Bucheli-Witschel M, Weilenmann HU, Egli T. Chelativorans multitrophicus gen. nov., sp. nov. and Chelativorans oligotrophicus sp. nov., aerobic EDTA-degrading bacteria. Int J Syst Evol Microbiol 2009; 60:1044-1051. [PMID: 19666787 DOI: 10.1099/ijs.0.003152-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two previously isolated strains (DSM 9103(T) and LPM-4(T)) able to grow with EDTA (facultatively and obligately, respectively) as the source of carbon, nitrogen and energy were investigated in order to clarify their taxonomic positions. The strains were strictly aerobic, Gram-negative, asporogenous and non-motile rods that required biotin for growth. Reproduction occurred by binary fission. The strains were mesophilic and neutrophilic. Their major fatty acids were summed feature 7 (consisting of C(18 : 1)omega7c, C(18 : 1)omega9t and/or C(18 : 1)omega12t) and C(19 : 0) cyclo omega8c. The polyamine pattern revealed homospermidine as a major polyamine. Predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine and diphosphatidylglycerol. Mesorhizobium-specific ornithine lipid was absent. The predominant isoprenoid quinone was Q-10. The DNA G+C values were 60.8 and 63.1 mol% (T(m)) for strains LPM-4(T) and DSM 9103(T), respectively. The level of 16S rRNA gene sequence similarity between these EDTA-utilizers was 99.3 % while the DNA-DNA hybridization value was only 37 %. Both strains were phylogenetically related to members of the genera Aminobacter and Mesorhizobium (95-97 % sequence similarity). However, DNA-DNA hybridization values between the novel EDTA-degrading strains and Aminobacter aminovorans DSM 7048(T) and Mesorhizobium loti DSM 2626(T) were low (10-11 %). Based on their genomic and phenotypic properties, the new alphaproteobacterial strains are assigned to a novel genus, Chelativorans gen. nov., with the names Chelativorans multitrophicus sp. nov. (type strain DSM 9103(T)=VKM B-2394(T)) and Chelativorans oligotrophicus sp. nov. (type strain LPM-4(T)=VKM B-2395(T)=DSM 19276(T)).
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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
| | - 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
| | - 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
| | - Bernd Nörtemann
- Institute of Biochemical Engineering, Technische Universität Braunschweig, 38106, Germany
| | - Margarete Bucheli-Witschel
- Department of Environmental Microbiology, EAWAG (Swiss Federal Institute of Aquatic Science and Technology), 8600 Dubendorf, Switzerland
| | - Hans-Ueli Weilenmann
- Department of Environmental Microbiology, EAWAG (Swiss Federal Institute of Aquatic Science and Technology), 8600 Dubendorf, Switzerland
| | - Thomas Egli
- Department of Environmental Microbiology, EAWAG (Swiss Federal Institute of Aquatic Science and Technology), 8600 Dubendorf, Switzerland
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Sharma VK, Hobson PN. Properties of a cellulolyticSporolactobacillusand some non-sporing cellulolytic rods, presumptive clostridia, from an anaerobic digester. ACTA ACUST UNITED AC 2008. [DOI: 10.1111/j.1365-2672.1986.tb04285.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kim HG, Doronina NV, Trotsenko YA, Kim SW. Methylophaga aminisulfidivorans sp. nov., a restricted facultatively methylotrophic marine bacterium. Int J Syst Evol Microbiol 2007; 57:2096-2101. [PMID: 17766878 DOI: 10.1099/ijs.0.65139-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel restricted facultatively methylotrophic marine strain, MP(T), possessing the ribulose monophosphate pathway of C(1)-carbon compound assimilation was isolated from a seawater sample obtained from Mokpo, South Korea. The novel isolate is aerobic, Gram-negative, asporogenous and a non-motile short rod. It grows well on methanol, methylated amines, dimethylsulfide and DMSO. Optimal growth occurs with 3 % NaCl at 30 degrees C and pH 7.0. Fructose is utilized as a multicarbon source. Growth factors are not required and vitamin B(12) does not stimulate growth. The cellular fatty acid profile of the novel strain consists primarily of straight-chain saturated C(16 : 0) and unsaturated C(16 : 1) acids. The major ubiquinone is Q-8. The dominant phospholipids are phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content is 44.9 mol% (T(m)). Based on 16S rRNA gene sequence analysis and DNA-DNA relatedness (25-41 %) with the type strains of marine methylotrophs belonging to the genus Methylophaga, it is suggested that isolate MP(T) represents a novel species, Methylophaga aminisulfidivorans sp. nov. (type strain MP(T)=KCTC 12909(T)=VKM B-2441(T)=JCM 14647(T)).
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MESH Headings
- Aerobiosis
- Bacterial Typing Techniques
- Base Composition
- Carbon/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Dimethyl Sulfoxide/metabolism
- Fatty Acids/analysis
- Fructose/metabolism
- Genes, rRNA
- Hydrogen-Ion Concentration
- Korea
- Methanol/metabolism
- Methylamines/metabolism
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phospholipids/analysis
- Phylogeny
- Piscirickettsiaceae/classification
- Piscirickettsiaceae/genetics
- Piscirickettsiaceae/isolation & purification
- Piscirickettsiaceae/physiology
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Seawater/microbiology
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sodium Chloride/metabolism
- Sulfides/metabolism
- Temperature
- Ubiquinone/analysis
- Vitamin B 12/metabolism
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Affiliation(s)
- Hee Gon Kim
- Department of Biomaterials Engineering, Chosun University, Gwangju 501-759, South Korea
| | - Nina V Doronina
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Yuri A Trotsenko
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Si Wouk Kim
- Department of Environmental Engineering, Chosun University, Gwangju 501-759, South Korea
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Ivanova E, Doronina N, Trotsenko Y. Hansschlegelia plantiphila gen. nov. sp. nov., a new aerobic restricted facultative methylotrophic bacterium associated with plants. Syst Appl Microbiol 2007; 30:444-52. [PMID: 17481841 DOI: 10.1016/j.syapm.2007.03.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Indexed: 11/16/2022]
Abstract
A new genus, Hansschlegelia, and a new species, Hansschlegelia plantiphila, are proposed for three strains of methanol-utilizing bacteria isolated from lilac buds (strain S(1)(T)), linden buds (strain S(2)) and blue spruce needles (strain S(4)), which were selected in winter at -17 degrees C. These bacteria are aerobic, Gram-negative, colorless, non-motile short rods that multiply by binary fission and employ the ribulose bisphosphate (RuBP) and the serine pathways for C(1) assimilation. The strains have a limited number of growth substrates and use methanol, methylamine, formate, CO(2)/H(2) and glycerol as carbon and energy sources. Only strain S(1)(T) grows with ethanol and inulin. The strains are neutrophilic and mesophilic, and synthesize phytohormones (auxins and cytokinins) and vitamin B(12). Their major cellular fatty acids are saturated C(16:0), straight-chain, unsaturated C(18:1)(omega)(7) and cyclopropane C(19 cyc) acids. The main ubiquinone is ubiquinone-10 (Q-10). The dominant phospholipids are phosphatidylethanolamine, phosphatidylcholine and diphosphatidylglycerol (cardiolipin). The DNA G+C content is 68.5+/-0.2 mol%. The strains share almost identical 16S rRNA gene sequences, a high DNA-DNA hybridization value (72-86%) and represent a novel lineage of autotrophic methanol-utilizing bacteria within the Alphaproteobacteria. Collectively, these strains comprise a new genus and species H. plantiphila gen. nov., sp. nov., with strain S(1)(T) (VKM B-2347(T), NCIMB 14035(T)) as the type strain.
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Affiliation(s)
- Ekaterina Ivanova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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Anan’ina LN, Plotnikova EG, Gavrish EY, Demakov VA, Evtushenko LI. Salinicola socius gen. nov., sp. nov., a moderately halophilic bacterium from a naphthalene-utilizing microbial association. Microbiology (Reading) 2007. [DOI: 10.1134/s0026261707030095] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Mantelin S, Saux MFL, Zakhia F, Béna G, Bonneau S, Jeder H, de Lajudie P, Cleyet-Marel JC. Emended description of the genus Phyllobacterium and description of four novel species associated with plant roots: Phyllobacterium bourgognense sp. nov., Phyllobacterium ifriqiyense sp. nov., Phyllobacterium leguminum sp. nov. and Phyllobacterium brassicacearum sp. nov. Int J Syst Evol Microbiol 2006; 56:827-839. [PMID: 16585703 DOI: 10.1099/ijs.0.63911-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gram-negative bacteria were isolated from the rhizoplane of Brassica napus in France and from root nodules of Argyrolobium uniflorum, Astragalus algerianus and Lathyrus numidicus growing in the infra-arid zone of southern Tunisia. Based on phylogenetic analysis of the 16S rRNA gene sequences, the seven isolates belong to the Alphaproteobacteria and are related to Phyllobacterium myrsinacearum strains. The isolates formed three clusters; clusters A and C consist of Tunisian strains, whereas cluster B consists of two strains from Brassica napus from France. Phylogenetic reconstruction based on the atpD gene strongly supports their affiliation to the genus Phyllobacterium. DNA-DNA hybridizations revealed that (i) none of the isolates belong to the species P. myrsinacearum, (ii) clusters A and C represent two distinct genomospecies and (iii) the two strains of cluster B represent two separate genomospecies. Distinctive phenotypic features were deduced from numerical analysis of phenotypic data. Based on this polyphasic approach, four novel species are proposed: Phyllobacterium leguminum sp. nov. (type strain ORS 1419T = CFBP 6745T = LMG 22833T), Phyllobacterium ifriqiyense sp. nov. (type strain STM 370T = CFBP 6742T = LMG 22831T), Phyllobacterium brassicacearum sp. nov. (type strain STM 196T = CFBP 5551T = LMG 22836T) and Phyllobacterium bourgognense sp. nov. (type strain STM 201T = CFBP 5553T = LMG 22837T). The description of the genus Phyllobacterium is emended accordingly.
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Affiliation(s)
- Sophie Mantelin
- LSTM - Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 113, Campus International de Baillarguet TA 10/J, 34398 Montpellier Cedex 05, France
| | - Marion Fischer-Le Saux
- Institut National de la Recherche Agronomique, UMR 77, Pathologie Végétale, BP 60057, 49071 Beaucouzé cedex, France
| | - Frédéric Zakhia
- LSTM - Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 113, Campus International de Baillarguet TA 10/J, 34398 Montpellier Cedex 05, France
| | - Gilles Béna
- LSTM - Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 113, Campus International de Baillarguet TA 10/J, 34398 Montpellier Cedex 05, France
| | - Sophie Bonneau
- Institut National de la Recherche Agronomique, UMR 77, Pathologie Végétale, BP 60057, 49071 Beaucouzé cedex, France
| | - Habib Jeder
- Institut des Régions Arides, Nahal-Gabès, Tunisia
| | - Philippe de Lajudie
- LSTM - Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 113, Campus International de Baillarguet TA 10/J, 34398 Montpellier Cedex 05, France
| | - Jean-Claude Cleyet-Marel
- LSTM - Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 113, Campus International de Baillarguet TA 10/J, 34398 Montpellier Cedex 05, France
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Grabovich M, Gavrish E, Kuever J, Lysenko AM, Podkopaeva D, Dubinina G. Proposal of Giesbergeria voronezhensis gen. nov., sp. nov. and G. kuznetsovii sp. nov. and reclassification of [Aquaspirillum] anulus, [A.] sinuosum and [A.] giesbergeri as Giesbergeria anulus comb. nov., G. sinuosa comb. nov. and G. giesbergeri comb. nov., and [Aquaspirillum] metamorphum and [A.] psychrophilum as Simplicispira metamorpha gen. nov., comb. nov. and S. psychrophila comb. nov. Int J Syst Evol Microbiol 2006; 56:569-576. [PMID: 16514029 DOI: 10.1099/ijs.0.64027-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five Gram-negative, motile, spiral-shaped strains were isolated from a sulfide spring (D-412T), active sludge of wastewater (D-419T, D-420, D-424) and industrial wastewater (D-416). Comparative 16S rRNA gene sequence analysis showed that the isolates belong to the family Comamonadaceae, within the class Betaproteobacteria, but fall into a distinct cluster. On the basis of phenotypic, chemotaxonomic and phylogenetic data, a new genus, Giesbergeria gen. nov., is proposed, including five species. The type species of the genus is Giesbergeria voronezhensis sp. nov. (type strain D-419T=DSM 12825T=CIP 107340T=VKM B-2350T) and other novel members of the genus are Giesbergeria kuznetsovii sp. nov. (type strain D-412T=DSM 12827T=VKM B-2352T), Giesbergeria giesbergeri comb. nov. (basonym Aquaspirillum giesbergeri), Giesbergeria sinuosa comb. nov. (basonym Aquaspirillum sinuosum) and Giesbergeria anulus comb. nov. (basonym Aquaspirillum anulus). Using the same criteria, isolate D-416 (=DSM 12826) was identified as a strain of [Aquaspirillum] metamorphum. Strain D-416, the type strain of [A.] metamorphum and the type strain of [Aquaspirillum] psychrophilum form a distinct cluster within the family Comamonadaceae (97–97·2 % 16S rRNA gene sequence similarity) and share phenotypic and chemotaxonomic properties. Therefore, it is proposed that these strains are reclassified as members of a new genus, Simplicispira gen. nov., as Simplicispira metamorpha comb. nov. (the type species) and Simplicispira psychrophila comb. nov., respectively.
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Affiliation(s)
- Margarita Grabovich
- Department of Biochemistry and Plant Physiology, Faculty of Biology, Voronezh State University, Voronezh, Russia
| | - Ekaterina Gavrish
- All Russian Collection of Microorganisms (VKM), G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Jan Kuever
- Max-Planck-Institute for Marine Microbiology, Celsiusstraße 1, D-28359 Bremen, Germany
| | - Anatoly M Lysenko
- S. N. Winogradsky Institute of Microbiology of the Russian Academy of Sciences, Pr. 60-letiya Octyabrya 7/2, Moscow, 117811, Russia
| | - Daria Podkopaeva
- Department of Biochemistry and Plant Physiology, Faculty of Biology, Voronezh State University, Voronezh, Russia
| | - Galina Dubinina
- S. N. Winogradsky Institute of Microbiology of the Russian Academy of Sciences, Pr. 60-letiya Octyabrya 7/2, Moscow, 117811, Russia
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de Groot A, Chapon V, Servant P, Christen R, Saux MFL, Sommer S, Heulin T. Deinococcus deserti sp. nov., a gamma-radiation-tolerant bacterium isolated from the Sahara Desert. Int J Syst Evol Microbiol 2006; 55:2441-2446. [PMID: 16280508 DOI: 10.1099/ijs.0.63717-0] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two gamma- and UV-radiation-tolerant, Gram-negative, rod-shaped bacterial strains, VCD115T and VCD117, were isolated from a mixture of sand samples collected in the Sahara Desert in Morocco and Tunisia, after exposure of the sand to 15 kGy gamma radiation. Phylogenetic analysis based on 16S rRNA gene sequences and DNA-DNA hybridizations showed that VCD115T and VCD117 are members of a novel species belonging to the genus Deinococcus, with Deinococcus grandis as its closest relative. The DNA G+C contents of VCD115T and VCD117 are 59.8 and 60.6 mol%, respectively. The major fatty acids (straight-chain 15 : 1, 16 : 1, 17 : 1 and 16 : 0), polar lipids (dominated by phosphoglycolipids and glycolipids) and quinone type (MK-8) support the affiliation to the genus Deinococcus. The strains did not grow on rich medium such as trypticase soy broth (TSB), but did grow as whitish colonies on tenfold-diluted TSB. The genotypic and phenotypic properties allowed differentiation of VCD115T and VCD117 from recognized Deinococcus species. Strains VCD115T and VCD117 are therefore identified as representing a novel species, for which the name Deinococcus deserti sp. nov. is proposed, with the type strain VCD115T (=DSM 17065T=LMG 22923T).
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MESH Headings
- Africa, Northern
- Base Composition
- DNA, Bacterial/analysis
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Deinococcus/classification
- Deinococcus/genetics
- Deinococcus/isolation & purification
- Deinococcus/radiation effects
- Desert Climate
- Fatty Acids/analysis
- Gamma Rays
- Molecular Sequence Data
- Phylogeny
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/genetics
- Radiation Tolerance
- Temperature
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Affiliation(s)
- Arjan de Groot
- Laboratoire d'Écologie Microbienne de la Rhizosphère (LEMIR), UMR 6191 CNRS-CEA-Université de la Méditerranée, DSV-DEVM, CEA Cadarache, F-13108 Saint-Paul-Lez-Durance, France
| | - Virginie Chapon
- Laboratoire d'Écologie Microbienne de la Rhizosphère (LEMIR), UMR 6191 CNRS-CEA-Université de la Méditerranée, DSV-DEVM, CEA Cadarache, F-13108 Saint-Paul-Lez-Durance, France
| | - Pascale Servant
- Institut de Génétique et Microbiologie, UMR 8621 CNRS-Université Paris-Sud, LRC CEA 42V, Bâtiment 409, F-91405 Orsay cedex, France
| | - Richard Christen
- Biologie Virtuelle, UMR 6543 CNRS-Université de Nice, Parc Valrose, Centre de Biochimie, F-06108 Nice cedex 2, France
| | - Marion Fischer-Le Saux
- UMR de Pathologie Végétale INRA-INH-Université d'Angers, BP 60057, 42 rue Georges Morel, F-49071 Beaucouzé cedex, France
| | - Suzanne Sommer
- Institut de Génétique et Microbiologie, UMR 8621 CNRS-Université Paris-Sud, LRC CEA 42V, Bâtiment 409, F-91405 Orsay cedex, France
| | - Thierry Heulin
- Laboratoire d'Écologie Microbienne de la Rhizosphère (LEMIR), UMR 6191 CNRS-CEA-Université de la Méditerranée, DSV-DEVM, CEA Cadarache, F-13108 Saint-Paul-Lez-Durance, France
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Doronina N, Ivanova E, Trotsenko Y, Pshenichnikova A, Kalinina E, Shvets V. Methylophilus quaylei sp. nov., a new aerobic obligately methylotrophic bacterium. Syst Appl Microbiol 2005; 28:303-9. [PMID: 15997702 DOI: 10.1016/j.syapm.2005.02.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A new obligately methylotrophic bacterium (strain MTT) with the ribulose monophosphate pathway of carbon assimilation is described. The isolate, utilizing only methanol, is an aerobic, Gram-negative, asporogenous, non-motile short rod multiplying by binary fission. Its cellular fatty acids profile consists primarily of straight-chain saturated C16:0 and unsaturated C16:l acids. The major ubiquinone is Q-8. The dominant phospholipids are phosphatidylethanolamine and phosphatidylglycerol. Diphosphatidylglycerol (cardiolipin) is absent. Optimal growth conditions are 25-29 degree C, pH 6.5 - 7.5, 0.5% CH3OH and 0.05% NaCl. Strain MTT lacks alpha-ketoglutarate dehydrogenase, the glyoxylate shunt enzymes, and glutamate dehydrogenase. Ammonium is assimilated by the operation of the glutamate cycle enzymes: glutamine synthetase and glutamate synthase. An exopolysaccharide consisting of rhamnose, glucose and galactose is formed under nitrogen limitation. The G + C content of the DNA is 54.0 mol%. Based on 16S rDNA sequence analysis and DNA-DNA relatedness (29-34%) with type strains of the genus Methylophilus, the novel isolate was classified as a new species of this genus and named Methylophilus quaylei MTT (VKM B-2338T, DSMZ, etc.).
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Affiliation(s)
- Nina Doronina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Moscow region, Russian Federation
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41
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Perevalova AA, Svetlichny VA, Kublanov IV, Chernyh NA, Kostrikina NA, Tourova TP, Kuznetsov BB, Bonch-Osmolovskaya EA. Desulfurococcus fermentans sp. nov., a novel hyperthermophilic archaeon from a Kamchatka hot spring, and emended description of the genus Desulfurococcus. Int J Syst Evol Microbiol 2005; 55:995-999. [PMID: 15879224 DOI: 10.1099/ijs.0.63378-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An obligately anaerobic, hyperthermophilic, organoheterotrophic archaeon, strain Z-1312T, was isolated from a freshwater hot spring of the Uzon caldera (Kamchatka Peninsula, Russia). The cells were regular cocci, 1–4 μm in diameter, with one long flagellum. The cell envelope was composed of a globular layer attached to the cytoplasmic membrane. The temperature range for growth was 63–89 °C, with an optimum between 80 and 82 °C. The pH range for growth at 80 °C was 4·8–6·8, with an optimum at pH 6·0. Strain Z-1312Tgrew by hydrolysis and/or fermentation of a wide range of polymeric and monomeric substrates, including agarose, amygdalin, arabinose, arbutin, casein hydrolysate, cellulose (filter paper, microcrystalline cellulose, carboxymethyl cellulose), dextran, dulcitol, fructose, lactose, laminarin, lichenan, maltose, pectin, peptone, ribose, starch and sucrose. No growth was detected on glucose, xylose, mannitol or sorbitol. Growth products when sucrose or starch were used as the substrate were acetate, H2and CO2. Elemental sulfur, thiosulfate and nitrate added as potential electron acceptors for anaerobic respiration did not stimulate growth when tested with starch as the substrate. H2at 100 % in the gas phase did not inhibit growth on starch or peptone. The G+C content of the DNA was 42·5 mol%. 16S rRNA gene sequence analysis placed the isolated strain Z-1312Tas a member of the genusDesulfurococcus, where it represented a novel species, for which the nameDesulfurococcus fermentanssp. nov. (type strain Z-1312T=DSM 16532T=VKM V-2316T) is proposed.
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Affiliation(s)
- A A Perevalova
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - V A Svetlichny
- Lehrstuhl für Mikrobiologie, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - I V Kublanov
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - N A Chernyh
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - N A Kostrikina
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - T P Tourova
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - B B Kuznetsov
- Bioengineering Center, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/1, Moscow 117312, Russia
| | - E A Bonch-Osmolovskaya
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, Moscow 117312, Russia
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Roumagnac P, Gagnevin L, Gardan L, Sutra L, Manceau C, Dickstein ER, Jones JB, Rott P, Pruvost O. Polyphasic characterization of xanthomonads isolated from onion, garlic and Welsh onion (Allium spp.) and their relatedness to different Xanthomonas species. Int J Syst Evol Microbiol 2004; 54:15-24. [PMID: 14742454 DOI: 10.1099/ijs.0.02714-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial blight is an emerging disease that affects primarily onion, but also garlic and Welsh onion. The present study was undertaken to characterize the causative xanthomonad(s) by a polyphasic approach using a worldwide collection of 33 bacterial strains. Analysis of 16S rRNA gene sequence similarities indicated that the causal agent belongs to the campestris core in the genus Xanthomonas, which is in agreement with results of phenotypic characterization (analyses of carbon source utilization and fatty acid methyl esters). However, DNA-DNA hybridization, thermal stability of DNA reassociation and fluorescent amplified fragment length polymorphism analysis allowed the causal agent to be identified as a pathovar of Xanthomonas axonopodis.
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Affiliation(s)
- P Roumagnac
- CIRAD, UMR Peuplement végétaux et Bioagresseurs en Milieu Tropical CIRAD/Université de la Réunion, Ligne Paradis, 97410 Saint Pierre, Réunion Island, France
| | - L Gagnevin
- CIRAD, UMR Peuplement végétaux et Bioagresseurs en Milieu Tropical CIRAD/Université de la Réunion, Ligne Paradis, 97410 Saint Pierre, Réunion Island, France
| | - L Gardan
- UMR de Pathologie Végétale, INRA, Station de Pathologie Végétale, 42 rue Georges Morel, BP 57, 49071 Beaucouzé Cedex, France
| | - L Sutra
- UMR de Pathologie Végétale, INRA, Station de Pathologie Végétale, 42 rue Georges Morel, BP 57, 49071 Beaucouzé Cedex, France
| | - C Manceau
- UMR de Pathologie Végétale, INRA, Station de Pathologie Végétale, 42 rue Georges Morel, BP 57, 49071 Beaucouzé Cedex, France
| | - E R Dickstein
- Department of Plant Pathology, University of Florida, PO Box 110680, Gainesville, FL 32611-0680, USA
| | - J B Jones
- Department of Plant Pathology, University of Florida, PO Box 110680, Gainesville, FL 32611-0680, USA
| | - P Rott
- UMR 385 ENSAM-INRA-CIRAD, Biologie et Génétique des Interactions Plante-Parasite, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - O Pruvost
- CIRAD, UMR Peuplement végétaux et Bioagresseurs en Milieu Tropical CIRAD/Université de la Réunion, Ligne Paradis, 97410 Saint Pierre, Réunion Island, France
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Gardan L, Christen R, Achouak W, Prior P. Erwinia papayae sp. nov., a pathogen of papaya (Carica papaya). Int J Syst Evol Microbiol 2004; 54:107-113. [PMID: 14742466 DOI: 10.1099/ijs.0.02718-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial canker of papaya (Carica papaya) emerged during the 1980s in different islands of the Caribbean. Nineteen strains of Gram-negative, rod-shaped, non-spore-forming bacteria isolated from papaya were compared to 38 reference and type strains of phytopathogenic Enterobacteriaceae and related bacteria. Phylogenetic analysis of 16S rRNA gene sequences showed that the papaya strains belonged to the genus Erwinia. The DNA G+C content of strain CFBP 5189T, 52·5 mol%, is in the range of the genus Erwinia. The 19 papaya strains were all pathogenic to papaya and were differentiated clearly from type or reference strains of phytopathogenic enterobacteria and related bacteria by phenotypic tests. The papaya strains constituted a discrete DNA hybridization group, indicating that they belonged to a unique genomic species. Thus, strains pathogenic to papaya belong to a novel species for which the name Erwinia papayae sp. nov. is proposed, with the type strain CFBP 5189T (=NCPPB 4294T).
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Affiliation(s)
- Louis Gardan
- UMR de Pathologie Végétale INRA-INH-UNIVERSITE, BP 57, 42 rue G. Morel, 49071 Beaucouzé, France
| | - Richard Christen
- UMR 6543 CNRS and Université de Nice Sophia Antipolis, Centre de biochimie, Parc Valrose, 06108 Nice cedex 2, France
| | - Wafa Achouak
- CEA/Cadarache, DSV-DEVM, LEMIR, UMR 163 CNRS-CEA-Univ. Méditerranée, Saint Paul-lez-Durance, France
| | - Philippe Prior
- INRA, Station de Pathologie Végétale, Domaine St Maurice, BP 94, 84143, Montfavet, France
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Heulin T, Barakat M, Christen R, Lesourd M, Sutra L, De Luca G, Achouak W. Ramlibacter tataouinensis gen. nov., sp. nov., and Ramlibacter henchirensis sp. nov., cyst-producing bacteria isolated from subdesert soil in Tunisia. Int J Syst Evol Microbiol 2003; 53:589-594. [PMID: 12710631 DOI: 10.1099/ijs.0.02482-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ramlibacter gen. nov. is proposed for two aerobic, chemo-organotrophic, cyst-producing soil bacterial strains. These bacteria are Gram-negative, non-flagellated rods or cysts, isolated from subdesert soil in Tataouine, Tunisia. Phylogenetic analyses of the rrs sequences of the two strains showed that they do not constitute a robust clade at the genus level with any previously described bacteria and that they are a deep branch of a clade also grouping the genera Acidovorax and Hydrogenophaga within the beta-Proteobacteria. They belong to two different species, as verified by DNA-DNA hybridization (23.5% reassociation). The type species of the genus is Ramlibacter tataouinensis sp. nov., with the type strain TTB310T (=DSM 14655T =ATCC BAA-407T =LMG 21543T). The second species is Ramlibacter henchirensis sp. nov., with the type strain TMB834T (=DSM 14656T =ATCC BAA-408T =LMG 21542T). The G + C contents of R. tataouinensis and R. henchirensis are 69.6 and 66.6 mol%, respectively.
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Affiliation(s)
- Thierry Heulin
- CEA/Cadarache, DSV-DEVM, Laboratoire d'Ecologie Microbienne de la Rhizosphère UMR 163 CNRS-CEA-Univ. Méditerranée, F-13108 Saint-Paul-lez-Durance, France
| | - Mohamed Barakat
- CEA/Cadarache, DSV-DEVM, Laboratoire d'Ecologie Microbienne de la Rhizosphère UMR 163 CNRS-CEA-Univ. Méditerranée, F-13108 Saint-Paul-lez-Durance, France
| | - Richard Christen
- UMR 6078 CNRS-Université de Nice Sophia-Antipolis, Bât. Jean Maetz, F-06230 Villefranche-sur-mer, France
| | - Maurice Lesourd
- Service Commun de Microscopie Electronique, CNRS & Université d'Angers, rue Haute de Reculée, F-49045 Angers, France
| | - Laurent Sutra
- UMR 077 de Pathologie Végétale, INRA-INH-Université d'Angers, 42 rue Georges-Morel, BP 57, F-49071 Beaucouzé Cedex, France
| | - Gilles De Luca
- CEA/Cadarache, DSV-DEVM, Laboratoire d'Ecologie Microbienne de la Rhizosphère UMR 163 CNRS-CEA-Univ. Méditerranée, F-13108 Saint-Paul-lez-Durance, France
| | - Wafa Achouak
- CEA/Cadarache, DSV-DEVM, Laboratoire d'Ecologie Microbienne de la Rhizosphère UMR 163 CNRS-CEA-Univ. Méditerranée, F-13108 Saint-Paul-lez-Durance, France
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Doronina NV, Darmaeva TD, Trotsenko YA. Methylophaga alcalica sp. nov., a novel alkaliphilic and moderately halophilic, obligately methylotrophic bacterium from an East Mongolian saline soda lake. Int J Syst Evol Microbiol 2003; 53:223-229. [PMID: 12656177 DOI: 10.1099/ijs.0.02267-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A moderately haloalkaliphilic and obligately methylotrophic bacterium (strain M39T) with the ribulose monophosphate pathway of carbon assimilation is described. Cells of this methanol and methylamine utilizer are aerobic, Gram-negative, asporogenous, motile short rods, multiplying by binary fission. It is auxotrophic for vitamin B12 and requires NaHCO3 or NaCl for growth in alkaline medium. Its cellular fatty acid profile consists primarily of straight-chain saturated C16:0 and unsaturated C16:1 and C18:1 acids. The major ubiquinone is Q-8. The dominant phospholipids are phosphatidylethanolamine and phosphatidylglycerol. Diphosphatidylglycerol is also present. Optimal growth conditions are 25-29 degrees C, pH 9.0-9.5 and 3-4 % (w/v) NaCl. Cells accumulate the cyclic amino acid ectoine as the main compatible solute. The DNA G + C content is 48.3 mol%. Based on 16S rDNA sequence analysis and DNA-DNA relatedness (25-30 %) with the type strains of marine methylotrophs belonging to the genus Methylophaga, the novel isolate M39T (=VKM B-2251T =ATCC BAA-297T) was classified as the type strain of Methylophaga alcalica sp. nov.
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Affiliation(s)
- Nina V Doronina
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region 142290, Russia
| | - Tsyregma D Darmaeva
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region 142290, Russia
| | - Yuri A Trotsenko
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region 142290, Russia
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Doronina N, Darmaeva T, Trotsenko Y. Methylophaga natronica sp. nov., a new Alkaliphilic and Moderately Halophilic, Restricted-facultatively Methylotrophic Bacterium from Soda Lake of the Southern Transbaikal Region. Syst Appl Microbiol 2003; 26:382-9. [PMID: 14529181 DOI: 10.1078/072320203322497419] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A new, moderately haloalkaliphilic and restricted-facultatively methylotrophic bacterium (strain Bur2T) with the ribulose monophosphate pathway of carbon assimilation is described. The isolate, which utilizes methanol, methylamine and fructose, is an aerobic, Gram-negative, asporogenous, motile short rod multiplying by binary fission. It is auxotrophic for vitamin B12, and requires NaHCO3 or NaCl for growth in alkaline medium. Cellular fatty acids profile consists primarily of straight-chain saturated C16:0, unsaturated C16:1 and C18:1 acids. The major ubiquinone is Q-8. The dominant phospholipids are phosphatidylethanolamine and phosphatidylglycerol. Diphosphatidylglycerol is also present. Optimal growth conditions are 25-29 degrees C, pH 8.5-9.0 and 2-3% (w/v) NaCl. Cells accumulate ectoine and glutamate as the main osmoprotectants. The G + C content of the DNA is 45.0 mol%. Based on 16S rDNA sequence analysis and DNA-DNA relatedness (25-35%) with type strains of marine and soda lake methylobacteria belonging to the genus Methylophaga, the novel isolate was classified as a new species of this genus and named Methylophaga natronica (VKM B-2288T).
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Affiliation(s)
- Nina Doronina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
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Miroshnichenko ML, Kostrikina NA, Chernyh NA, Pimenov NV, Tourova TP, Antipov AN, Spring S, Stackebrandt E, Bonch-Osmolovskaya EA. Caldithrix abyssi gen. nov., sp. nov., a nitrate-reducing, thermophilic, anaerobic bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent, represents a novel bacterial lineage. Int J Syst Evol Microbiol 2003; 53:323-329. [PMID: 12656191 DOI: 10.1099/ijs.0.02390-0] [Citation(s) in RCA: 107] [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, moderately thermophilic, strictly anaerobic, mixotrophic bacterium, designated strain LF13T, was isolated from a deep-sea hydrothermal chimney sample that was collected at a vent site at 14 degrees 45' N, 44 degrees 59' W on the Mid-Atlantic Ridge. Cells were Gram-negative, thin, non-motile rods of variable length. Strain LF13T grew optimally at pH 6.8-7.0 and 60 degrees C with 2.5% (w/v) NaCl. It grew chemo-organoheterotrophically, fermenting proteinaceous substrates, pyruvate and Casamino acids. The strain was able to grow by respiration, utilizing molecular hydrogen (chemolithoheterotrophically) or acetate as electron donors and nitrate as an electron acceptor. Ammonium was formed in the course of denitrification. One-hundred milligrams of yeast extract per litre were required for growth of the strain. The G + C content of the genomic DNA of strain LF13T was 42.5 mol%. Neither 16S rDNA sequence similarity values nor phylogenetic analysis unambiguously related strain LF13T with members of any recognized bacterial phyla. On the basis of 16S rDNA sequence comparisons, and in combination with physiological and morphological traits, a novel genus, Caldithrix, is proposed, with strain LF13T (= DSM 13497T =VKM B-2286T) representing the type species, Caldithrix abyssi.
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MESH Headings
- Atlantic Ocean
- Base Composition
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/genetics
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/classification
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/genetics
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/isolation & purification
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/metabolism
- Hot Temperature
- Microscopy, Electron
- Molecular Sequence Data
- Nitrates/metabolism
- Oxidation-Reduction
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Seawater/microbiology
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Affiliation(s)
- Margarita L Miroshnichenko
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117811 Moscow, Russia
| | - Nadezhda A Kostrikina
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117811 Moscow, Russia
| | - Nikolai A Chernyh
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117811 Moscow, Russia
| | - Nikolai V Pimenov
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117811 Moscow, Russia
| | - Tatyana P Tourova
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117811 Moscow, Russia
| | - Alexei N Antipov
- AN Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Stefan Spring
- Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ), Mascheroder Weg 1b, D-38124 Braunschweig, Germany
| | - Erko Stackebrandt
- Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ), Mascheroder Weg 1b, D-38124 Braunschweig, Germany
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A novel plant-associated thermotolerant alkaliphilic methylotroph of the genusParacoccus. Microbiology (Reading) 2000. [DOI: 10.1007/bf02756814] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Paracoccus methylutens sp. nov. — a New Aerobic Facultatively Methylotrophic Bacterium Utilizing Dichloromethane. Syst Appl Microbiol 1998. [DOI: 10.1016/s0723-2020(98)80027-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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50
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Boekhout T, Roeijmans H, Spaay F. A new pleomorphic ascomycete, Calyptrozyma arxii gen. et sp. nov., isolated from the human lower oesophagus. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/s0953-7562(09)80285-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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