1
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Characterization of Heumann’s pigmented and non-pigmented strains of [Pseudomonas] Sphingomonas echinoides. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00447-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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2
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Screening, Isolation, and Identification of Zeaxanthin-Producing Bacteria. Methods Mol Biol 2018. [PMID: 30109632 DOI: 10.1007/978-1-4939-8742-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Zeaxanthin is a yellow xanthophyll, dihydroxy-carotenoid, that is naturally found in some of the green, orange, and yellow vegetables and fruits and has a powerful antioxidant activity. Epidemiological evidences suggest that increasing the consumption of zeaxanthin in the diet is associated with a lower risk of age-related macular degeneration (ARMD) and cataracts, two of the leading causes of blindness in the world. Zeaxanthin is a promising nutraceutical/colorant with many applications in feed, food, and pharmaceutical industries. Currently, the commercial production of zeaxanthin is dependent on synthetic routes with limitation in production from biological sources. However, the biotechnological production of natural zeaxanthin is favored due to its safety, potential large-scale production and consumers' preference for natural additives. In this chapter, we describe a rapid screening method based on 16S rRNA gene sequencing and effective HPLC with diode array detector/MS methods for the isolation and identification of zeaxanthin-producing bacteria and their carotenoid analysis.
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3
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A rapid and simple method for identifying bacterial polar lipid components in wet biomass. J Microbiol 2017; 55:635-639. [DOI: 10.1007/s12275-017-7092-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/17/2017] [Accepted: 06/02/2017] [Indexed: 12/16/2022]
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4
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Sohlenkamp C, Geiger O. Bacterial membrane lipids: diversity in structures and pathways. FEMS Microbiol Rev 2015; 40:133-59. [DOI: 10.1093/femsre/fuv008] [Citation(s) in RCA: 571] [Impact Index Per Article: 63.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2015] [Indexed: 12/22/2022] Open
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5
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Kondakova T, Merlet-Machour N, Chapelle M, Preterre D, Dionnet F, Feuilloley M, Orange N, Duclairoir Poc C. A new study of the bacterial lipidome: HPTLC-MALDI-TOF imaging enlightening the presence of phosphatidylcholine in airborne Pseudomonas fluorescens MFAF76a. Res Microbiol 2014; 166:1-8. [PMID: 25478686 DOI: 10.1016/j.resmic.2014.11.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 11/15/2022]
Abstract
Lipids are major functional components of bacterial cells that play fundamental roles in bacterial metabolism and the barrier function between cells and the environment. In an effort to investigate the bacterial lipidome, we adopted a protocol using MALDI-TOF MS imaging coupled to HPTLC to screen a large number of phospholipid classes in a short span of time. With this method, phospholipids of airborne Pseudomonas fluorescens MFAF76a were visualized and identified in sample extracts (measurement accuracy below 0.1 Da, phospholipid identification by means of four characteristic fragment peaks). Via this technique, the P. fluorescens lipidome was shown to comprise three major lipid classes: phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The protocol described herein is simple, rapid and effective for screening of bacterial phospholipid classes. The remarkable presence of a eukaryotic phospholipid, phosphatidylcholine, was observed in P. fluorescens MFAF76a. This lipid is known to play a role in bacteria-host interactions and had not been known to be found in P. fluorescens cells.
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Affiliation(s)
- Tatiana Kondakova
- Laboratory of Microbiology Signals and Microenvironment (LMSM) EA4312, Normandy Univ., Univ. Rouen, 55 rue St Germain, 27000 Evreux, France; Aerothermic and Internal Combustion Engine Technological Research Center (CERTAM), 1 Rue Joseph Fourier, 76800 Saint Etienne du Rouvray, France.
| | - Nadine Merlet-Machour
- Team Modified to Surface and Interface Analysis (SIMA), UMR 6014 COBRA, Normandy Univ., Univ. Rouen, 55 rue St Germain, 27000 Evreux, France.
| | | | - David Preterre
- Aerothermic and Internal Combustion Engine Technological Research Center (CERTAM), 1 Rue Joseph Fourier, 76800 Saint Etienne du Rouvray, France.
| | - Frédéric Dionnet
- Aerothermic and Internal Combustion Engine Technological Research Center (CERTAM), 1 Rue Joseph Fourier, 76800 Saint Etienne du Rouvray, France.
| | - Marc Feuilloley
- Laboratory of Microbiology Signals and Microenvironment (LMSM) EA4312, Normandy Univ., Univ. Rouen, 55 rue St Germain, 27000 Evreux, France.
| | - Nicole Orange
- Laboratory of Microbiology Signals and Microenvironment (LMSM) EA4312, Normandy Univ., Univ. Rouen, 55 rue St Germain, 27000 Evreux, France.
| | - Cécile Duclairoir Poc
- Laboratory of Microbiology Signals and Microenvironment (LMSM) EA4312, Normandy Univ., Univ. Rouen, 55 rue St Germain, 27000 Evreux, France.
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6
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Huang J, Huang Z, Zhang ZD, He LY, Sheng XF. Sphingomonas yantingensis sp. nov., a mineral-weathering bacterium isolated from purplish paddy soil. Int J Syst Evol Microbiol 2014; 64:1030-1034. [DOI: 10.1099/ijs.0.055954-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel type of mineral-weathering bacterium was isolated from purplish soils collected from Yanting (Sichuan, south-western China). Cells of strain 1007T were Gram-stain-negative and rod-shaped, motile and yellow-pigmented. The isolate was strictly aerobic, catalase- and oxidase-positive, and grew optimally at 28-30 °C and pH 6.0-7.0. The genomic DNA G+C content of strain 1007T was 67±0.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 1007T belonged to the genus
Sphingomonas
and was most closely related to
Sphingomonas pruni
IFO 15498T (97.3 %),
Sphingomonas mali
IFO 15500T (97.2 %),
Sphingomonas japonica
KC7T (97.2 %) and
Sphingomonas koreensis
JSS26T (97.0 %). This affiliation of strain 1007T to the genus
Sphingomonas
was confirmed by the presence of Q-10 as the major ubiquinone, sphingoglycolipid, C14 : 0 2-OH and by the absence of 3-hydroxy fatty acids. The major polyamine was homospermidine. The main cellular fatty acids included summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. Based on the low level of DNA–DNA relatedness (ranging from 26.1 % to 58.7 %) to these type strains of species of the genus
Sphingomonas
and unique phenotypic characteristics, strain 1007T represents a novel species of the genus
Sphingomonas
, for which the name Sphingomonas yantingensis sp. nov. is proposed. The type strain is 1007T ( = DSM 27244T = JCM 19201T = CCTCC AB 2013146T).
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Affiliation(s)
- Jing Huang
- Key Laboratory of Agricultural Environment Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zhi Huang
- Key Laboratory of Agricultural Environment Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zhen-Dong Zhang
- Key Laboratory of Agricultural Environment Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Lin-Yan He
- Key Laboratory of Agricultural Environment Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xia-Fang Sheng
- Key Laboratory of Agricultural Environment Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
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7
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Lipids from therapeutic mud bacteria Pseudomonas sp. and Arthrobacter sp. Chem Nat Compd 2013. [DOI: 10.1007/s10600-013-0626-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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8
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Abstract
Sphingomonas is a Gram-negative, yellow-pigmented, chemoheterotrophic, strictly aerobic bacterium. The bacterium is known to be metabolically versatile and can utilize a wide range of natural compounds as well as some types of environmental contaminants, such as creosote, polychlorinated biphenyls, etc. Here, we report the draft genome sequence of Sphingomonas echinoides ATCC 14820, which will provide additional information to enhance our understanding of metabolic versatility of Sphingomonas.
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9
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Asker D, Awad TS, Beppu T, Ueda K. Novel zeaxanthin-producing bacteria isolated from a radioactive hot spring water. Methods Mol Biol 2012; 892:99-131. [PMID: 22623298 DOI: 10.1007/978-1-61779-879-5_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Zeaxanthin is a powerful antioxidant that is widely found in vegetables and fruits. Epidemiological evidences suggest that increasing the consumption of zeaxanthin in the diet is associated with a lower risk of age-related macular degeneration, helps prevent glaucoma and cataracts, and supports normal eye health. Zeaxanthin is a promising nutraceutical with many applications in the feed, food, and pharmaceutical industries. Currently, the commercial production of zeaxanthin is still dependant on synthetic routes with limitation for the biological one. Nevertheless, the biotechnological production of zeaxanthin is emerging due to its safety, potential large-scale production, and consumers' demand and preference for natural additives. Using a rapid screening method based on 16S rRNA gene and effective high-performance liquid chromatography (HPLC)-Diodearray-MS methods for carotenoids' analysis, we isolated effective zeaxanthin-producing bacteria (strain TDMA-5(T) and -16(T)) that belong to the family Sphingobacteriaceae and Sphingomonadaceae, respectively. In this chapter, we provide a detailed description of the HPLC-Diodearray-MS methods used for rapid analysis and identification of the carotenoids produced by both strains. In addition, the polyphasic taxonomic analysis of both novel strains and the description of a novel species and genus are described.
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Affiliation(s)
- Dalal Asker
- Faculty of Agriculture, Food Science and Technology Department, Alexandria University, Alexandria, Egypt.
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10
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Rickettsia prowazekii uses an sn-glycerol-3-phosphate dehydrogenase and a novel dihydroxyacetone phosphate transport system to supply triose phosphate for phospholipid biosynthesis. J Bacteriol 2010; 192:4281-8. [PMID: 20581209 DOI: 10.1128/jb.00443-10] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rickettsia prowazekii is an obligate intracellular pathogen that possesses a small genome and a highly refined repertoire of biochemical pathways compared to those of free-living bacteria. Here we describe a novel biochemical pathway that relies on rickettsial transport of host cytosolic dihydroxyacetone phosphate (DHAP) and its subsequent conversion to sn-glycerol-3-phosphate (G3P) for synthesis of phospholipids. This rickettsial pathway compensates for the evolutionary loss of rickettsial glycolysis/gluconeogenesis, the typical endogenous source of G3P. One of the components of this pathway is R. prowazekii open reading frame RP442, which is annotated GpsA, a G3P dehydrogenase (G3PDH). Purified recombinant rickettsial GpsA was shown to specifically catalyze the conversion of DHAP to G3P in vitro. The products of the GpsA assay were monitored spectrophotometrically, and the identity of the reaction product was verified by paper chromatography. In addition, heterologous expression of the R. prowazekii gpsA gene functioned to complement an Escherichia coli gpsA mutant. Furthermore, gpsA mRNA was detected in R. prowazekii purified from hen egg yolk sacs, and G3PDH activity was assayable in R. prowazekii lysed-cell extracts. Together, these data strongly suggested that R. prowazekii encodes and synthesizes a functional GpsA enzyme, yet R. prowazekii is unable to synthesize DHAP as a substrate for the GpsA enzymatic reaction. On the basis of the fact that intracellular organisms often avail themselves of resources in the host cell cytosol via the activity of novel carrier-mediated transport systems, we reasoned that R. prowazekii transports DHAP to supply substrate for GpsA. In support of this hypothesis, we show that purified R. prowazekii transported and incorporated DHAP into phospholipids, thus implicating a role for GpsA in vivo as part of a novel rickettsial G3P acquisition pathway for phospholipid biosynthesis.
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11
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Romanenko LA, Tanaka N, Frolova GM, Mikhailov VV. Winogradskyella arenosi sp. nov., a member of the family Flavobacteriaceae isolated from marine sediments from the Sea of Japan. Int J Syst Evol Microbiol 2009; 59:1443-6. [DOI: 10.1099/ijs.0.006809-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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12
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Romanenko LA, Tanaka N, Frolova GM, Mikhailov VV. Sphingomonas japonica sp. nov., isolated from the marine crustacean Paralithodes camtschatica. Int J Syst Evol Microbiol 2009; 59:1179-82. [DOI: 10.1099/ijs.0.003285-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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13
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Grajewski RS, Hansen AM, Agarwal RK, Kronenberg M, Sidobre S, Su SB, Silver PB, Tsuji M, Franck RW, Lawton AP, Chan CC, Caspi RR. Activation of invariant NKT cells ameliorates experimental ocular autoimmunity by a mechanism involving innate IFN-gamma production and dampening of the adaptive Th1 and Th17 responses. THE JOURNAL OF IMMUNOLOGY 2008; 181:4791-7. [PMID: 18802082 DOI: 10.4049/jimmunol.181.7.4791] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Invariant NKT cells (iNKT cells) have been reported to play a role not only in innate immunity but also to regulate several models of autoimmunity. Furthermore, iNKT cells are necessary for the generation of the prototypic eye-related immune regulatory phenomenon, anterior chamber associated immune deviation (ACAID). In this study, we explore the role of iNKT cells in regulation of autoimmunity to retina, using a model of experimental autoimmune uveitis (EAU) in mice immunized with a uveitogenic regimen of the retinal Ag, interphotoreceptor retinoid-binding protein. Natural strain-specific variation in iNKT number or induced genetic deficiencies in iNKT did not alter baseline susceptibility to EAU. However, iNKT function seemed to correlate with susceptibility and its pharmacological enhancement in vivo by treatment with iNKT TCR ligands at the time of uveitogenic immunization reproducibly ameliorated disease scores. Use of different iNKT TCR ligands revealed dependence on the elicited cytokine profile. Surprisingly, superior protection against EAU was achieved with alpha-C-GalCer, which induces a strong IFN-gamma but only a weak IL-4 production by iNKT cells, in contrast to the ligands alpha-GalCer (both IFN-gamma and IL-4) and OCH (primarily IL-4). The protective effect of alpha-C-GalCer was associated with a reduction of adaptive Ag-specific IFN-gamma and IL-17 production and was negated by systemic neutralization of IFN-gamma. These data suggest that pharmacological activation of iNKT cells protects from EAU at least in part by a mechanism involving innate production of IFN-gamma and a consequent dampening of the Th1 as well as the Th17 effector responses.
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Affiliation(s)
- Rafael S Grajewski
- Laboratory of Immunology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
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14
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Asker D, Beppu T, Ueda K. Sphingomonas jaspsi sp. nov., a novel carotenoid-producing bacterium isolated from Misasa, Tottori, Japan. Int J Syst Evol Microbiol 2007; 57:1435-1441. [PMID: 17625171 DOI: 10.1099/ijs.0.64828-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A yellow-pigmented, Gram-negative, motile, strictly aerobic, pleomorphic bacterium (strain TDMA-16T) was isolated from a freshwater sample collected at Misasa (Tottori, Japan). Strain TDMA-16T was slightly tolerant to gamma-ray irradiation and produced carotenoids, including zeaxanthin, nostoxanthin and an unknown carotenoid, effectively [1.7 mg (g dry cells)−1]. The DNA G+C content of strain TDMA-16T was 63.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed strain TDMA-16T in a distinct lineage in the family Sphingomonadaceae; sequence data showed that strain TDMA-16T was most closely related to Sphingomonas mali IFO 15500T (95.1 %), Sphingomonas aquatilis JSS7T (95.0 %), Sphingomonas pruni IFO 15498T (94.9 %), Sphingomonas melonis DSM 14444T (94.9 %) and Sphingomonas asaccharolytica IFO 15499T (94.5 %). The major fatty acids of strain TDMA-16T were C17 : 1
ω6c (34.5 %) and C18 : 1
ω7c (29.3 %). The presence of Q-10 as the main ubiquinone, the Sphingomonadaceae-specific sphingoglycolipid in the polar lipid profile and 2-hydroxy fatty acids, plus the absence of 3-hydroxy fatty acids, supported identification of this strain as a member of the genus Sphingomonas sensu stricto. Phylogenetic distinctiveness and unique phenotypic characteristics differentiated strain TDMA-16T from closely related Sphingomonas species. The results of polyphasic taxonomic analyses suggest that strain TDMA-16T represents a novel Sphingomonas species, for which the name Sphingomonas jaspsi sp. nov. is proposed. The type strain is strain TDMA-16T (=NBRC 102120T=DSM 18422T=CCUG 53607T).
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MESH Headings
- Aerobiosis
- Bacterial Typing Techniques
- Base Composition
- Carotenoids/biosynthesis
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Fresh Water/microbiology
- Gamma Rays
- Genes, rRNA
- Glycolipids/analysis
- Japan
- Locomotion
- Molecular Sequence Data
- Phospholipids/analysis
- Phylogeny
- Pigments, Biological/biosynthesis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sphingomonas/chemistry
- Sphingomonas/classification
- Sphingomonas/genetics
- Sphingomonas/isolation & purification
- Ubiquinone/analysis
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Affiliation(s)
- Dalal Asker
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa 252-8510, Japan
| | - Teruhiko Beppu
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa 252-8510, Japan
| | - Kenji Ueda
- Life Science Research Center, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa 252-8510, Japan
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15
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Romanenko LA, Uchino M, Frolova GM, Mikhailov VV. Marixanthomonas ophiurae gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from a deep-sea brittle star. Int J Syst Evol Microbiol 2007; 57:457-462. [PMID: 17329768 DOI: 10.1099/ijs.0.64662-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Gram-negative, non-motile, yellow-pigmented bacterium, strain KMM 3046T, was isolated from a deep-sea brittle star from the Fiji Sea and was subjected to a polyphasic taxonomic analysis. Strain KMM 3046T grew at 5–32 °C and in the presence of 1–12 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone and 3-OH i16 : 0, 3-OH i17 : 0 and 3-OH a17 : 0 as the major fatty acids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KMM 3046T forms a distinct evolutionary lineage within the family Flavobacteriaceae (phylum Bacteroidetes), displaying 92.3–91.9 % sequence similarity with respect to Salegentibacter species. On the basis of the phenotypic and phylogenetic data, strain KMM 3046T represents a novel genus and species of the family Flavobacteriaceae, for which the name Marixanthomonas ophiurae gen. nov., sp. nov. is proposed. The type strain of Marixanthomonas ophiurae is KMM 3046T (=NRIC 0684T=JCM 14121T).
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Affiliation(s)
- Lyudmila A Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Masataka Uchino
- Laboratory of Food Science and Technology, Department of Applied Biology and Chemistry, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Galina M Frolova
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Valery V Mikhailov
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, 690022 Vladivostok, Russia
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16
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Romanenko LA, Uchino M, Frolova GM, Tanaka N, Kalinovskaya NI, Latyshev N, Mikhailov VV. Sphingomonas molluscorum sp. nov., a novel marine isolate with antimicrobial activity. Int J Syst Evol Microbiol 2007; 57:358-363. [PMID: 17267979 DOI: 10.1099/ijs.0.64441-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Gram-negative, yellow-pigmented, non-motile bacterium, designated strain KMM 3882T, was isolated from a marine bivalve (Anadara broughtoni) collected from Peter the Great Bay, Sea of Japan, and was subjected to phenotypic and phylogenetic analyses. Strain KMM 3882T was found to exert a remarkable inhibitory activity against a number of Gram-positive micro-organisms. Phylogenetic analysis based on 16S rRNA gene sequences placed strain KMM 3882T within the genus Sphingomonas, as an independent lineage adjacent to Sphingomonas dokdonensis DS-4T and Sphingomonas panni DSM 15761T. Strain KMM 3882T showed the highest 16S rRNA gene sequence similarity to Sphingomonas dokdonensis DS-4T (97.3 %); similarities of 96.5–96.7 % were obtained with Sphingomonas pituitosa DSM 13101T, Sphingomonas azotifigens NBRC 15497T, Sphingomonas asaccharolytica NBRC 15499T, Sphingomonas trueperi DSM 7225T and Sphingomonas panni DSM 15761T. Chemotaxonomically, strain KMM 3882T contained sphingoglycolipid, C16 : 0 and C18 : 1 as predominant fatty acids and 2-OH C14 : 0 as a major 2-hydroxy fatty acid, confirming the affiliation of strain KMM 3882T with the genus Sphingomonas. On the basis of phylogenetic analysis, DNA–DNA hybridization and physiological and biochemical characterization, strain KMM 3882T should be classified as representing a novel species of the genus Sphingomonas, for which the name Sphingomonas molluscorum sp. nov. is proposed. The type strain is KMM 3882T (=An 18T=NRIC 0685T=JCM 14122T=CIP 109223T).
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MESH Headings
- Aerobiosis
- Animals
- Antibiosis
- Arcidae/microbiology
- Bacterial Typing Techniques
- Carbohydrate Metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Fatty Acids/chemistry
- Genes, rRNA
- Glycosphingolipids/analysis
- Glycosphingolipids/chemistry
- Gram-Positive Bacteria/drug effects
- Japan
- Molecular Sequence Data
- Movement
- Nucleic Acid Hybridization
- Phylogeny
- Pigments, Biological/biosynthesis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sphingomonas/classification
- Sphingomonas/cytology
- Sphingomonas/isolation & purification
- Sphingomonas/physiology
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Affiliation(s)
- Lyudmila A Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Masataka Uchino
- Tokyo University of Agriculture, Department of Applied Biology and Chemistry, Faculty of Applied Bioscience, Laboratory of Food Science and Technology, Sakuragaoka 1-1-1, Setagaya-ku, Tokyo 156-8502, Japan
| | - Galina M Frolova
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Naoto Tanaka
- Department of Medical and Life Science, Faculty of Pharmaceutical Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Natalia I Kalinovskaya
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Nicolai Latyshev
- Institute of Marine Biology, Far-Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Valery V Mikhailov
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, 690022 Vladivostok, Russia
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17
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Zhdanov RI, Shmyrina AS, Zarubina TV, Mulyukin AL, El-Registan GI, Haupt N, Kraus A, Lorenz W. Nature of DNA-bound fatty acids in Pseudomonas aurantiaca. FEMS Microbiol Lett 2006; 265:151-8. [PMID: 16989655 DOI: 10.1111/j.1574-6968.2006.00461.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The existence of Pseudomonas aurantiaca DNA-bound fatty acids and lipids is presented in this work. The isolation of DNA was carried out by two different procedures, namely, phenol and detergent-based phenol isolation in order to prove the presence of DNA-bound lipids. The lipid content of DNA is expressed in terms of fatty acid profile. A high level of 16:0, 18:0 and 18:1 is characteristic for tightly bound DNA lipids. On the other hand, the fatty acids such as 14:1, iso14:0 and iso16:0 are found in trace amounts only in DNA lipid fraction, but these fatty acids are not found in the whole-cell lipids. Absolutely no 3-hydroxy fatty acids were found in DNA lipids. However, both C16 and C18 species represent the main fatty acids of whole-cell and DNA-bound lipids. The presence of DNA-bound lipids even under tough treatment of DNA allows to conclude that these lipids represent a special pool among cellular lipids.
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Affiliation(s)
- Renat I Zhdanov
- Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, Moscow, Russian Federation.
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Sahin N. Isolation and characterization of a diazotrophic, oxalate-oxidizing bacterium from sour grass (Oxalis pes-caprae L.). Res Microbiol 2005; 156:452-6. [PMID: 15808950 DOI: 10.1016/j.resmic.2004.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2004] [Revised: 09/30/2004] [Accepted: 10/11/2004] [Indexed: 11/27/2022]
Abstract
A new type of nitrogen-fixing, oxalate-oxidizing Azospirillum sp. was isolated from the roots of Oxalis pes-caprae. Polyphasic taxonomy was performed, including auxanography using API galleries, physiological tests and 16S rRNA sequence comparison. Optimum growth occurred at 30 degrees C, pH 7.5. Growth was observed at 37 and 42 degrees C with oxalate and in the presence of 3-4% NaCl and 2% potassium oxalate. In liquid culture, the doubling time (t(d)) with oxalate was 9 h. Its closest phylogenetic neighbors, as deduced by 16S rDNA-based analysis, were Azospirillum brasilense, Azospirillum doebereinerae and Azospirillum lipoferum, with 99.5, 98.4 and 96.7% sequence similarity, respectively. The strain differed from A. brasilense by its ability to use N-acetylglucosamine, D-glucose and D-mannitol. It may be a variant strain of A. brasilense. Oxalotrophic, N2-fixing species of the genus Azospirillum may be important contributors to soil formation, soil fertility, and retention and/or cycling of elements necessary for plant growth.
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Affiliation(s)
- Nurettin Sahin
- Mugla University, Egitim Fakultesi, Ortaogretim Fen ve Matematik Alanlar Egitimi Bolumu, Biyoloji Egitimi Anabilim Dali, 48170 Kötekli, Mugla, Turkey.
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Rösch P, Harz M, Schmitt M, Peschke KD, Ronneberger O, Burkhardt H, Motzkus HW, Lankers M, Hofer S, Thiele H, Popp J. Chemotaxonomic identification of single bacteria by micro-Raman spectroscopy: application to clean-room-relevant biological contaminations. Appl Environ Microbiol 2005; 71:1626-37. [PMID: 15746368 PMCID: PMC1065155 DOI: 10.1128/aem.71.3.1626-1637.2005] [Citation(s) in RCA: 216] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2004] [Accepted: 09/29/2004] [Indexed: 11/20/2022] Open
Abstract
Microorganisms, such as bacteria, which might be present as contamination inside an industrial food or pharmaceutical clean room process need to be identified on short time scales in order to minimize possible health hazards as well as production downtimes causing financial deficits. Here we describe the first results of single-particle micro-Raman measurements in combination with a classification method, the so-called support vector machine technique, allowing for a fast, reliable, and nondestructive online identification method for single bacteria.
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Affiliation(s)
- Petra Rösch
- Institut für Physikalische Chemie, Friedrich-Schiller-Universität Jena, Helmholtzweg 4, D-07743 Jena, Germany
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Lee HY, Bahn SC, Shin JS, Hwang I, Back K, Doelling JH, Ryu SB. Multiple forms of secretory phospholipase A2 in plants. Prog Lipid Res 2004; 44:52-67. [PMID: 15748654 DOI: 10.1016/j.plipres.2004.10.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/01/2004] [Accepted: 10/07/2004] [Indexed: 11/26/2022]
Abstract
Multiple secretory phospholipase A2 (sPLA2) genes have been identified in plants and encode isoforms with distinct regulatory and catalytic properties. Elucidation of this genetic and biochemical heterogeneity has provided important clues to the regulation and function of the individual enzymes. An increasing body of evidence shows that their lipid products, lysophospholipids and free fatty acids, mediate a variety of cellular responses, including plant growth, development, and responses to stress and defense. This review discusses the newly-acquired information on plant sPLA2s including the molecular and biochemical characteristics, and signaling functions of each isoform.
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Affiliation(s)
- Hyoung Yool Lee
- Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
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Eguchi M, Ostrowski M, Fegatella F, Bowman J, Nichols D, Nishino T, Cavicchioli R. Sphingomonas alaskensis strain AFO1, an abundant oligotrophic ultramicrobacterium from the North Pacific. Appl Environ Microbiol 2001; 67:4945-54. [PMID: 11679312 PMCID: PMC93257 DOI: 10.1128/aem.67.11.4945-4954.2001] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2001] [Accepted: 08/07/2001] [Indexed: 11/20/2022] Open
Abstract
Numerous studies have established the importance of picoplankton (microorganisms of < or =2 microm in length) in energy flow and nutrient cycling in marine oligotrophic environments, and significant effort has been directed at identifying and isolating heterotrophic picoplankton from the world's oceans. Using a method of diluting natural seawater to extinction followed by monthly subculturing for 12 months, a bacterium was isolated that was able to form colonies on solid medium. The strain was isolated from a 10(5) dilution of seawater where the standing bacterial count was 3.1 x 10(5) cells ml(-1). This indicated that the isolate was representative of the most abundant bacteria at the sampling site, 1.5 km from Cape Muroto, Japan. The bacterium was characterized and found to be ultramicrosized (less than 0.1 microm(3)), and the size varied to only a small degree when the cells were starved or grown in rich media. A detailed molecular (16S rRNA sequence, DNA-DNA hybridization, G+C mol%, genome size), chemotaxonomic (lipid analysis, morphology), and physiological (resistance to hydrogen peroxide, heat, and ethanol) characterization of the bacterium revealed that it was a strain of Sphingomonas alaskensis. The type strain, RB2256, was previously isolated from Resurrection Bay, Alaska, and similar isolates have been obtained from the North Sea. The isolation of this species over an extended period, its high abundance at the time of sampling, and its geographical distribution indicate that it has the capacity to proliferate in ocean waters and is therefore likely to be an important contributor in terms of biomass and nutrient cycling in marine environments.
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MESH Headings
- Base Composition
- Colony Count, Microbial
- DNA, Bacterial/analysis
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/analysis
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Heat-Shock Response
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Pacific Ocean
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Seawater/microbiology
- Sequence Analysis, DNA
- Sphingomonas/classification
- Sphingomonas/genetics
- Sphingomonas/isolation & purification
- Sphingomonas/ultrastructure
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Affiliation(s)
- M Eguchi
- Department of Fisheries, Kinki University, Nara 631-8505, Japan
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