DOCSLIB.ORG

Phylogenetic Evidence for Sphingomonas and Rhizomonas As Nonphotosynthetic Members of the Alpha-4 Subclass of the Proteobacteria

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Phylogenetic Evidence for Sphingomonas and Rhizomonas As Nonphotosynthetic Members of the Alpha-4 Subclass of the Proteobacteria INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Apr. 1994, p. 308-314 Vol. 44, No. 2 0020-7713/94/$04.00 +0 Copyright 0 1994, International Union of Microbiological Societies Phylogenetic Evidence for Sphingomonas and Rhizomonas as Nonphotosynthetic Members of the Alpha-4 Subclass of the Proteobacteria MARIKO TAKEUCHI,' * HIROYUKI SAWADA,2t HIROSHI OYAIZU,3 AND AURA YOKOTA' Institute for Fermentation, Osaka, Yodogawa-ku, Osaka 532, Akitsu Branch, Fruit Tree Research Station, Ministq of Agriculture, Forestry and Fisheries, Akitsu, Hiroshima 729-24, and Faculty of Agriculture, The University of Tokyo, Bunkyo-ku, Tokyo 113,3 Japan To clarify the taxonomic relationships of the genera Rhizomonas and Sphingomonas, the 16s rFWA sequence of Rhizornonas suberifaciens IF0 15211T (T = type strain) was determined. A phylogenetic analysis of aligned 16s rRNA gene sequences revealed that eight species of the genus Sphingomonas and R. suberifaciens are closely related to Erythrobacter longus and Porphyrobucter neustonensis and, therefore, belong in the alpha-4 subclass of the Proteobacteria. Within this subclass, Sphingomonus species and R. suberifaciens are phylogenetically interrelated and comprise several subgroups.-- Our findings show that the genus and species definitions of these organisms are in need of revision. The genus Sphingomonas, whose type species, Sphingomonas of these organisms are similar to those reported for Sphin- paucimobilis, was previously named Pseudomonas paucimobilis gomonas paucimobilis (33, 42). Neither Rhizomonas suberifa- Holmes et al. (6), was proposed by Yabuuchi et al. (42) for ciens nor Sphingomonas paucimobilis produces acid on pep- yellow-pigmented, motile rods with single polar flagella and tone-glucose medium, but both organisms produce acid on nonmotile, nonfermentative, gram-negative rods. Sphingomo- ammonium or nitrate-glucose medium (6). Strains of these two nus paucimobilis contains large amounts of a unique sphingo- species have the same isoprenoid quinone (ubiquinone 10) and glycolipid with the long-chain base dihydrosphingosin, 2-hy- similar fatty acid compositions (8, 17, 33), and the results of droxymyristic acid (41,43), and isoprenoid quinone Q-10. Five grouping based on these two characteristics have been shown species, Sphingomonas paucimobilis, Sphingomonas parapauci- to coincide with the results of grouping based on rRNA-DNA mobilis, Sphingomonas yanoikuyae, Sphingomonas adhaesiva, homology data (33). and Sphingomonas capsulata, were described by Yabuuchi et On the basis of these findings, we suggested previously that al. (42). Recently, we described three new species of the genus species belonging to the genera Sphingomonas and Rhizomo- Sphingomonas, Sphingomonas sanguis, Sphingomonas macro- nus are closely related to each other (29). goltabidus, and Sphingomonas terrae (29). Sphingomonas sun- Recently, on the basis of sequencing data for 270 bases of guis is the new species name proposed for Sphingomonas 16s rRNA genes from eight strains of Rhizomonas species and genospecies 1 of Yabuuchi et al. (42). Sphingomonas macro- eight strains of Sphingomonas species, van Bruggen et al. (33) goltabidus and Sphingomonas terrae are polyethylene glycol- reported that Sphingomonas yanoikuyae is more closely related utilizing bacteria (11, 12) which were previously classified as to Rhizomonas suberifaciens than to other Sphingomonas spe- Flavobacterium species. Polyethylene glycol 4000 is utilized by cies and should be transferred to the genus Rhizomonas and a single bacterium, Sphingomonas terrae, but polyethylene that Sphingomonas capsulata should be removed from the glycol 6000 is utilized by symbiotic mixed cultures of two genus Sphingomonas and placed in a separate genus. strains (13), and the dominant bacterium in the mixed cultures In order to investigate the phylogenetic interrelationships of is Sphingomonas macrogoltabidus. these organisms, we determined the 16s rRNA gene sequence Recently, we compared the 16s rRNA sequences of the and chemotaxonomic characteristics of Rhizomonas suberifa- eight previously described and newly proposed species of the ciens and compared the resulting data with data for Sphin- genus Sphingomonas with the 16s rRNA sequences of 15 gomonas species, Erythrobacter longus, and other members of representative species belonging to the alpha subclass of the the alpha subclass of the Proteobacteria. Proteobacteria (29), and we found that the eight Sphingomonas In this paper we describe the 16s rRNA sequence of species form a large and heterogeneous cluster which is clearly Rhizomonas suberifaciens and phylogenetic evidence which separate from all other representatives of the alpha subclass of indicates that the genera Sphingomonas and Rhizomonas are the Proteobacteria (26,38) except Erythrobacter longus (23,24). nonphotosynthetic members of the alpha-4 subclass of the On the other hand, the genus Rhizomonas and the single Proteo bacteria. species Rhizomonas suberifaciens were proposed by van Brug- gen et al. (32) for the gram-negative, motile, rod-shaped bacteria that cause corky root of lettuce. Most strains of MATERIALS AND METHODS Rhizomonas suberifaciens are oligotrophic (31), but the mor- Cultures. Rhizomonas suberifaciens IF0 15211T (= ATCC phological, physiological, and chemotaxonomic characteristics 493ST = NCPPB 3629T) (T = type strain) and IF0 15212 (= ATCC 49382 = NCPPB 3631) were cultured at 28°C in shake * Corresponding author. Mailing address: Institute for Fermenta- flasks containing (per liter) 5.0 g of peptone, 2.5 g of glucose, tion, Osaka, 17-85, Juso-honmachi 2-chome7 Yodogawa-ku, Osaka 1.3 g of K,HPO,, 0.5 g of MgSO, * 7H,O, 0.5 g of KNO,, and 532, Japan. Phone: 06-300-6555. Fax: 06-300-6814. 0.06 g of Ca(N03),*4H,0 (pH 7.2) (PG medium). Eryth- ? Present address: National Institute of Agro-Environmental Sci- robacter longus IF0 14126* (= ATCC 33941T) was cultivated ences, 3-14, Kannondai, Tsukuba, Ibaraki 305, Japan. in seawater medium containing (per liter) 4.0 g of peptone, 2.0 308 VOL. 44, 1994 PHYLOGENETIC ANALYSIS OF RHZZOMONAS AND SPHINGOMONAS 309 TABLE 1. Comparison of morphological, physiological, and biochemical characteristics of the genera Sphingomonas and Rhizomonas Characteristic Sphirigomonas" Rhizomonas Plant pathogenicity - h +' Oligotroph - v' Morphological characteristics Cell shape Rods Rods Color of colonies Yellow or whitish yellow Yellow or whitish yellow Motility V V Flagellum Single, polar Single, lateral, subpolar, or polar Physiological characteristics Oxidase + + Catalase + + Acid produced from glucose + + Arginine dihydrolase - - Nitrate reduction V + Bacteriochlorophyll a - - Chemical characteristics lsoprenoid quinone Q-10 Q- 10 Major cellular fatty acids Nonpolar fatty acid 18:1 18:l 2-Hydroxy fatty acids 14:0, 159, 16:O 14:0, 15:O 3-Hydroxy fatty acid - - Sphingolipids + (d-18:0, d-19:1, d-20:1, d-2111) + (d-18:0, d-20:l d-21~1) LPS - - d G+C content (mol%) 61.6-67.8 5 8.0-63.0 " Data from references 29 and 42. '' +, all strains are positive; -, all strains are ncgative; v, variable from strain to strain. ' Data from reference 33. All strains are positive according to van Bruggen et al. (33). g of yeast extract, 10 mg of FeSO, * 7H,O, 750 ml of seawater, and analyzed as trimethylsilyl ethers by gas chromatography- and enough distilled water to bring the volume up to 1,000 ml mass spectrometry. (23, 24). Analysis of bacteriochlorophyll. Bacteriochlorophyll was Cellular lipids and fatty acid analysis. Cells were harvested extracted from dried cells with methanol by the method of Stal after they were cultured for 24 h in PG medium and freeze- et al. (28). Samples were extracted twice for 2 h, and the two dried, and then 50 mg of dried cells was mixed with 2 ml of 5% extracts were pooled in the dark at room temperature and HCl in methanol and the preparation was heated at 100°C for purified by thin-layer chromatography by using a petroleum 3 h. Fatty acid methyl esters were extracted with n-hexane and ether-acetone-methanol (82: 16:2, vol/vol) solvent system. were separated by thin-layer chromatography by using an In vitro amplification of rRNA genes. DNA was used for in n-hexane-diethyl ether (1 :1, vol/vol) solvent system. Nonpolar vitro amplification of the rRNA gene by the PCR technique acids and 2-hydroxy and 3-hydroxy fatty acids, visualized by (19) in combination with a 16s rRNA gene-specific primer spraying plates 0.02% dichlorofluorescein in ethanol, were pair, 5'-AGTTTGATCCTGGCTC OH-3' (identical to se- extracted with diethyl ether and analyzed by gas-liquid chro- quence positions 10 to 25 in the Escherichia coli numbering matography as described previously (29). The long-chain bases system [1]) and 5'-AAGGAGGTGATCCAGCC OH-3' (com- of the cellular sphingolipids were obtained from acid hydroly- plementary to positions 1541 to 1525), as described previously sates of dried cells as described by Yano et al. (44). The bases (29). Amplification was carried out by using a Taq polymerase were then subjected to thin-layer chromatography by using a of kit (Cetus Inc.). The PCR cycle parameters were as follows: chloroform-methanol-water (65:25:4, vol/vol) solvent system preheating for 2.5 min at 95"C, denaturation for 1 min at 94"C, 1 101 201 301 401 501 601 701 801 901 1001 1101 1201 1301 1401 FIG. 1. Partial 16s rRNA sequence of Rhizomonus suberifaciens. The first and last nucleotides are analogous to positions 10 and 1483 of the Escherichia coli sequence (1). w 0CI ? t, a- 2 VOL.44, 1994 PHYLOGENETIC ANALYSIS OF
Load more

Recommended publications
  • Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas Sp
    microorganisms Article Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas sp. AAP5 Karel Kopejtka 1 , Yonghui Zeng 1,2, David Kaftan 1,3 , Vadim Selyanin 1, Zdenko Gardian 3,4 , Jürgen Tomasch 5,† , Ruben Sommaruga 6 and Michal Koblížek 1,* 1 Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 379 81 Tˇreboˇn,Czech Republic; [email protected] (K.K.); [email protected] (Y.Z.); [email protected] (D.K.); [email protected] (V.S.) 2 Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark 3 Faculty of Science, University of South Bohemia, 370 05 Ceskˇ é Budˇejovice,Czech Republic; [email protected] 4 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 Ceskˇ é Budˇejovice,Czech Republic 5 Research Group Microbial Communication, Technical University of Braunschweig, 38106 Braunschweig, Germany; [email protected] 6 Laboratory of Aquatic Photobiology and Plankton Ecology, Department of Ecology, University of Innsbruck, 6020 Innsbruck, Austria; [email protected] * Correspondence: [email protected] † Present Address: Department of Molecular Bacteriology, Helmholtz-Centre for Infection Research, 38106 Braunschweig, Germany. Abstract: An aerobic, yellow-pigmented, bacteriochlorophyll a-producing strain, designated AAP5 Citation: Kopejtka, K.; Zeng, Y.; (=DSM 111157=CCUG 74776), was isolated from the alpine lake Gossenköllesee located in the Ty- Kaftan, D.; Selyanin, V.; Gardian, Z.; rolean Alps, Austria. Here, we report its description and polyphasic characterization. Phylogenetic Tomasch, J.; Sommaruga, R.; Koblížek, analysis of the 16S rRNA gene showed that strain AAP5 belongs to the bacterial genus Sphingomonas M. Characterization of the Aerobic and has the highest pairwise 16S rRNA gene sequence similarity with Sphingomonas glacialis (98.3%), Anoxygenic Phototrophic Bacterium Sphingomonas psychrolutea (96.8%), and Sphingomonas melonis (96.5%).
    [Show full text]
  • Proposal of Sphingomonadaceae Fam. Nov., Consisting of Sphingomonas Yabuuchi Et Al. 1990, Erythrobacter Shiba and Shimidu 1982, Erythromicrobium Yurkov Et Al
    Microbiol. Immunol., 44(7), 563-575, 2000 Proposal of Sphingomonadaceae Fam. Nov., Consisting of Sphingomonas Yabuuchi et al. 1990, Erythrobacter Shiba and Shimidu 1982, Erythromicrobium Yurkov et al. 1994, Porphyrobacter Fuerst et al. 1993, Zymomonas Kluyver and van Niel 1936, and Sandaracinobacter Yurkov et al. 1997, with the Type Genus Sphingomonas Yabuuchi et al. 1990 Yoshimasa Kosako*°', Eiko Yabuuchi2, Takashi Naka3,4, Nagatoshi Fujiwara3, and Kazuo Kobayashi3 'JapanCollection of Microorganis ms,RIKEN (Institute of Physical and ChemicalResearch), Wako, Saitama 351-0198, Japan, 2Departmentof Microbiologyand Immunology , AichiMedical University, Aichi 480-1101, Japan, 'Departmentof Host Defense,Osaka City University, Graduate School of Medicine,Osaka, Osaka 545-8585, Japan, and Instituteof SkinSciences, ClubCosmetics Co., Ltd., Osaka,Osaka 550-0005, Japan ReceivedJanuary 25, 2000; in revisedform, April 11, 2000. Accepted April 14, 2000 Abstract:Based on the results of phylogeneticanalysis of the 16SrDNA sequences and the presence of N- 2'-hydroxymyristoyldihydrosphingosine 1-glucuronic acid (SGL-1)and 2-hydroxymyristicacid (non- hydroxymyristicacid in Zymomonas)in cellular lipids,a new family,Sphingomonadaceae, for Group 4 of the alpha-subclassof the classProteobacteria is hereinproposed and a descriptionof the familyis given.The familyconsists of six genera, Sphingomonas,Erythrobacter, Erythromicrobium, Porphyrobacter, Sandara- cinobacterand Zymomonas.Thus, all the validlypublished and currently known genera in Group 4 of the alpha-subclassof
    [Show full text]
  • Sequencing and Functional Analysis of a Multi-Component Dioxygenase from PAH-Degrading Sphingomonas Paucimobilis EPA505" (2010)
    Clemson University TigerPrints All Dissertations Dissertations 12-2010 Sequencing and functional analysis of a multi- component dioxygenase from PAH-degrading Sphingomonas paucimobilis EPA505 Renuka Miller Clemson University, [email protected] Follow this and additional works at: https://tigerprints.clemson.edu/all_dissertations Part of the Microbiology Commons Recommended Citation Miller, Renuka, "Sequencing and functional analysis of a multi-component dioxygenase from PAH-degrading Sphingomonas paucimobilis EPA505" (2010). All Dissertations. 678. https://tigerprints.clemson.edu/all_dissertations/678 This Dissertation is brought to you for free and open access by the Dissertations at TigerPrints. It has been accepted for inclusion in All Dissertations by an authorized administrator of TigerPrints. For more information, please contact [email protected]. SEQUENCING AND FUNCTIONAL ANALYSIS OF A MULTI-COMPONENT DIOXYGENASE FROM PAH-DEGRADING SPHINGOMONAS PAUCIMOBILIS EPA505 A Dissertation Presented to the Graduate School of Clemson University In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy Microbiology by Renuka Persad Miller December 2010 Accepted by: Thomas A. Hughes, Committee Chair Steven Hayasaka Jeremy Tzeng Annel Greene i ABSTRACT Polycyclic aromatic hydrocarbons (PAHs) are hydrophobic organic compounds consisting of two or more fused benzene rings. PAHs derive from many different sources including petroleum refining, wood treatment, and coal coking industries. Because of their structural stability and water insolubility, PAHs are extremely resistant to degradation. These compounds are also believed to have mutagenic, carcinogenic, and teratogenic effects. Therefore, there are currently 16 PAH compounds on the EPA’s list of priority pollutants. Many species of bacteria have the ability to breakdown these persistent pollutants. However, bioremediation strategies using these organisms have many unresolved issues.
    [Show full text]
  • Benzo[A]Pyrene Co-Metabolism in the Presence of Plant Root Extracts and Exudates: Implications for Phytoremediation
    Environmental Pollution 136 (2005) 477e484 www.elsevier.com/locate/envpol Benzo[a]pyrene co-metabolism in the presence of plant root extracts and exudates: Implications for phytoremediation Jeremy A. Rentza, Pedro J.J. Alvarezb, Jerald L. Schnoora,* aCivil and Environmental Engineering, University of Iowa, Iowa City, IA 52242, USA bCivil and Environmental Engineering, Rice University, Houston, TX 77251, USA Received 29 July 2004; accepted 28 December 2004 Bacterial benzo[a]pyrene cometabolism, a plant-microbe interaction affecting polycyclic aromatic hydrocarbon phytoremediation was demonstrated with Sphingomonas yanoikuyae JAR02 that utilized plant root extracts and exudates as primary substrates. Abstract Benzo[a]pyrene, a high molecular weight (HMW) polycyclic aromatic hydrocarbon (PAH) was removed from solution by Sphingomonas yanoikuyae JAR02 while growing on root products as a primary carbon and energy source. Plant root extracts of osage orange (Maclura pomifera), hybrid willow (Salix alba!matsudana), or kou (Cordia subcordata), or plant root exudates of white mulberry (Morus alba) supported 15e20% benzo[a]pyrene removal over 24 h that was similar to a succinate grown culture and an unfed acetonitrile control. No differences were observed between the different root products tested. Mineralization of 14C-7- 14 benzo[a]pyrene by S. yanoikuyae JAR02 yielded 0.2 to 0.3% CO2 when grown with plant root products. Collectively, these observations were consistent with field observations of enhanced phytoremediation of HMW PAH and corroborated the hypothesis that co-metabolism may be a plant/microbe interaction important to rhizoremediation. However, degradation and mineralization was much less for root product-exposed cultures than salicylate-induced cultures, and suggested the rhizosphere may not be an optimal environment for HMW PAH degradation by Sphingomonas yanoikuyae JAR02.
    [Show full text]
  • Sphingomonas Solaris Sp. Nov., Isolated from a Solar Panel in Boston, Massachusetts
    TAXONOMIC DESCRIPTION Tanner et al., Int. J. Syst. Evol. Microbiol. 2020;70:1814–1821 DOI 10.1099/ijsem.0.003977 Sphingomonas solaris sp. nov., isolated from a solar panel in Boston, Massachusetts Kristie Tanner1,2,3,4, Christopher P. Mancuso5,6, Juli Peretó1,4,7, Ahmad S. Khalil3,5,6, Cristina Vilanova1 and Javier Pascual1,* Abstract Solar panel surfaces, although subjected to a range of extreme environmental conditions, are inhabited by a diverse microbial community adapted to solar radiation, desiccation and temperature fluctuations. This is the first time a new bacterial species has been isolated from this environment. Strain R4DWNT belongs to the genus Sphingomonas and was isolated from a solar panel surface in Boston, MA, USA. Strain R4DWNT is a Gram- negative, non-motile and rod- shaped bacteria that tested posi- tive for oxidase and catalase and forms round-shaped, shiny and orange- coloured colonies. It is mesophilic, neutrophilic and non- halophilic, and presents a more stenotrophic metabolism than its closest neighbours. The major fatty acids in this strain are C18:1ω7c/C18:1ω6c, C16:1ω7c/C16:1ω6c, C14:0 2OH and C16:0. Comparison of 16S rRNA gene sequences revealed that the closest type strains to R4DWNT are Sphingomonas fennica, Sphingomonas formosensis, Sphingomonas prati, Sphingomonas montana and Sphingomonas oleivorans with 96.3, 96.1, 96.0, 95.9 and 95.7 % pairwise similarity, respectively. The genomic G+C content of R4DWNT is 67.9 mol%. Based on these characteristics, strain R4DWNT represents a novel species of the genus Sphingomonas for which the name Sphingomonas solaris sp. nov. is proposed with the type strain R4DWNT (=CECT 9811T=LMG 31344T).
    [Show full text]
  • Sphingobium Bisphenolivorans Sp
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Institutional Repository of Yantai Institute of Coastal Zone Research, CAS TAXONOMIC DESCRIPTION Qin et al., Int. J. Syst. Evol. Microbiol. 2020;70:1822–1829 DOI 10.1099/ijsem.0.003978 Sphingobium estronivorans sp. nov. and Sphingobium bisphenolivorans sp. nov., isolated from a wastewater treatment plant Dan Qin1,2, Cong Ma3, Min Lv4 and Chang- Ping Yu1,5,* ABSTRACT Two Gram- stain- negative, aerobic, motile and rod- shaped bacteria, one designated as strain AXBT, capable of degrading estro- gens, and another, YL23T, capable of degrading estrogen and bisphenol A, were isolated from activated sludge in Xiamen City, PR China. The optimum temperature and pH of both strains were 25–35 °C and pH 7.0–8.0. While strain AXBT could tolerate 3 % (w/v) NaCl, YL23T could only grow between 0–1 % (w/v) NaCl. They contained ubiquinone-10 as the major quinone, spermidine as the major polyamine, summed feature 8 (comprising C18:1ω6c and/or C18:1ω7c) as the major fatty acids and diphosphatidyl- glycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and sphin- goglycolipid as the major polar lipids. The DNA G+C contents of strains AXBT and YL23T were 63.6 and 63.7 mol%, respectively. Based on the results of 16S rRNA gene sequence analysis, strains AXBT and YL23T belonged to the genus Sphingobium. Strain AXBT was most closely related to Sphingobium chlorophenolicum NBRC 16172T (97.5 %) and Sphingobium chungbukense DJ77T (97.2 %), and strain YL23T was most closely related to S.
    [Show full text]
  • Sphingomonas Paucimobilis: an Uncommon Cause of Meningitis Sphingomonas Paucimobilis: Az Rastlanan Bir Menenjit Etkeni
    Case Report / Olgu Sunumu DOI: 10.5578/ced.201734 • J Pediatr Inf 2017; 11(3): e124-e128 Sphingomonas paucimobilis: An Uncommon Cause of Meningitis Sphingomonas paucimobilis: Az Rastlanan Bir Menenjit Etkeni Nazlı Deveci1, Nazlı Gürkan2, Nurşen Belet1, Serpil Uğur Baysal1 1 Department of Pediatrics, Dokuz Eylul University School of Medicine, Izmir, Turkey 2 Department of Medical Microbiology, Dokuz Eylul University School of Medicine, Izmir, Turkey Abstract Özet Sphingomonas paucimobilis is a gram-negative bacillus. It is widespread in Sphingomonas paucimobilis, gram-negatif bir çomaktır. Doğada ve nature and in hospital environments; but it hardly causes life-threatening hastane ortamında yaygın olarak bulunur; pek az olguda hayatı teh- infections. In this report, a case of community- onset bacterial meningitis dit eden enfeksiyonlara yol açmaktadır. Bu bildiride, S. paucimobilis’in in an adolescent patient was presented. A previously healthy, 14-year etken olduğu, bakteriyel menenjit gelişen bir adolesan olgu sunul- old boy attended to our hospital with fever of two days, headache and muştur. Daha önce sağlıklı, 14 yaşında erkek lise öğrencisi, iki gündür vomiting. Based on the patient’s history, physical examination signs süren ateş, baş ağrısı ve kusma yakınmaları ile hastanemize başvurdu. and laboratory results, he was hospitalized with the diagnosis of acute Öykü, fizik muayene ve laboratuvar bulguları temelinde akut bakteri- bacterial meningitis. The aerobic bacterial culture of the CSF yielded yel menenjit tanısı ile servise yatırıldı. Beyin omurilik sıvısı (BOS) ör- yellow pigmented, slow growing, oxidase and catalase positive colonies neğinin aerop kültürü, Columbia koyun kanlı agar plağında 48 saatlik after 48 hours of incubation on Columbia sheep blood agar plates.
    [Show full text]
  • Polycyclic Aromatic Hydrocarbon Degradation by Novel Bacteria Isolated from Burrow Sediments of Marine Benthic Macrofauna Wai Ki Chung
    The University of Maine DigitalCommons@UMaine Electronic Theses and Dissertations Fogler Library 12-2001 Polycyclic aromatic hydrocarbon degradation by novel bacteria isolated from burrow sediments of marine benthic macrofauna Wai Ki Chung Follow this and additional works at: http://digitalcommons.library.umaine.edu/etd Part of the Bacteria Commons, and the Environmental Microbiology and Microbial Ecology Commons Recommended Citation Chung, Wai Ki, "Polycyclic aromatic hydrocarbon degradation by novel bacteria isolated from burrow sediments of marine benthic macrofauna" (2001). Electronic Theses and Dissertations. 521. http://digitalcommons.library.umaine.edu/etd/521 This Open-Access Dissertation is brought to you for free and open access by DigitalCommons@UMaine. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of DigitalCommons@UMaine. POLYCYCLIC AROMATIC HYDROCARBON DEGRADATION BY NOVEL BACTERIA ISOLATED FROM BURROW SEDIMENTS OF MARINE BENTHIC MACROFAUNA BY Wai Ki Chung B.Sc. The Chinese University of Hong Kong, 1990 M.Phi1. The Chinese University of Hong Kong, 1992 A THESIS Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy (in Microbiology) The Graduate School The University of Maine December, 2001 Advisory Committee: Gary King, Clare S. Darling Professor of Oceanography and Professor of Microbiology and Marine Studies, Advisor Katherine Boettcher, Assistant Professor of Microbiology Daniel Distel, Associate Professor of Biochemistry, Microbiology & Molecular Biology Jean MacRae, Assistant Professor of Civil & Environmental Engineering John Singer, Professor of Microbiology and Chair of Department of Biochemistry, Microbiology & Molecular Biology POLYCYCLIC AROMATIC HYDROCARBON DEGRADATION BY NOVEL BACTERIA ISOLATED FROM BURROW SEDIMENTS OF MARINE BENTHIC MACROFAUNA By Wai Ki Chung Thesis Advisor: Dr.
    [Show full text]
  • Sphingomonas from Petroleum-Contaminated Soils In
    b r a z i l i a n j o u r n a l o f m i c r o b i o l o g y 4 7 (2 0 1 6) 271–278 ht tp://www.bjmicrobiol.com.br/ Environmental Microbiology Sphingomonas from petroleum-contaminated soils in Shenfu, China and their PAHs degradation abilities a a,b,∗ a a a Lisha Zhou , Hui Li , Ying Zhang , Siqin Han , Hui Xu a Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China b State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China a r t i c l e i n f o a b s t r a c t Article history: Members of the Sphingomonas genus are often isolated from petroleum-contaminated soils Received 22 October 2012 due to their unique abilities to degrade polycyclic aromatic hydrocarbons (PAHs), which Accepted 17 August 2015 are important for in situ bioremediation. In this study, a combined phenotypic and geno- Available online 2 March 2016 typic approach using streptomycin-containing medium and Sphingomonas-specific PCR was developed to isolate and identify culturable Sphingomonas strains present in petroleum- Associate Editor: Rodrigo Costa contaminated soils in the Shenfu wastewater irrigation zone. Of the 15 soil samples examined, 12 soils yielded yellow streptomycin-resistant colonies. The largest number of Keywords: 5 −1 yellow colony-forming units (CFUs) could reach 10 CFUs g soil. The number of yellow CFUs Sphingomonas had a significant positive correlation (p < 0.05) with the ratio of PAHs to total petroleum Polycyclic aromatic hydrocarbons hydrocarbons (TPH), indicating that Sphingomonas may play a key role in degrading the PAH (PAHs) fraction of the petroleum contaminants at this site.
    [Show full text]
  • And Polychlorinated Biphenyls-Degrading Bacterium Without Dead-End Intermediates Accumulation
    RESEARCH ARTICLE Sphingobium fuliginis HC3: A Novel and Robust Isolated Biphenyl- and Polychlorinated Biphenyls-Degrading Bacterium without Dead-End Intermediates Accumulation Jinxing Hu1, Mingrong Qian2, Qian Zhang1, Jinglan Cui1, Chunna Yu3, Xiaomei Su1, Chaofeng Shen1*, Muhammad Z. Hashmi1, Jiyan Shi1 1 Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China, 2 Institute of Quality and Standard on Agricultural Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China, 3 College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China * [email protected] OPEN ACCESS Citation: Hu J, Qian M, Zhang Q, Cui J, Yu C, Su X, et al. (2015) Sphingobium fuliginis HC3: A Novel and Abstract Robust Isolated Biphenyl- and Polychlorinated Biphenyls-Degrading Bacterium without Dead-End Biphenyl and polychlorinated biphenyls (PCBs) are typical environmental pollutants. Howev- Intermediates Accumulation. PLoS ONE 10(4): er, these pollutants are hard to be totally mineralized by environmental microorganisms. One e0122740. doi:10.1371/journal.pone.0122740 reason for this is the accumulation of dead-end intermediates during biphenyl and PCBs bio- Academic Editor: Hans-Joachim Lehmler, The degradation, especially benzoate and chlorobenzoates (CBAs). Until now, only a few micro- University of Iowa, UNITED STATES organisms have been reported to have the ability to completely mineralize biphenyl and Received: November 11, 2014 PCBs. In this research, a novel bacterium HC3, which could degrade biphenyl and PCBs Accepted: February 12, 2015 without dead-end intermediates accumulation, was isolated from PCBs-contaminated soil Published: April 13, 2015 and identified as Sphingobium fuliginis. Benzoate and 3-chlorobenzoate (3-CBA) trans- Copyright: © 2015 Hu et al.
    [Show full text]
  • Antimicrobial, Anti-Protease and Immunomodulatory Activities of Secondary Metabolites from Caribbean Sponges and Their Associated Bacteria
    Antimicrobial, anti-protease and immunomodulatory activities of secondary metabolites from Caribbean sponges and their associated bacteria Sekundärmetabolite mit antimikrobiellen, Protease-hemmenden und immunmodulatorischen Aktivitäten aus karibischen Schwämmen und assoziierten Bakterien Dissertation towards a Doctoral Degree at the Graduate School of Life Sciences Julius-Maximilians-University Würzburg Section: Infection and Immunity Submitted by Paula Tabares from Pereira, Colombia Würzburg, 2011 Submitted on: Members of the thesis committee: Chairperson: ………………………………………………………………....... Primary Supervisor: Ute Hentschel Humeida Supervisor (Second): Thomas Hünig Supervisor (Third): Tanja Schirmeister Date of Public Defense: …………………………………………….………… Date of Receipt of Certificates: ………………………………………………. ii AFFIDAVIT I hereby declare that my thesis entitled “Antimicrobial, anti-protease and immunomodulatory activities of secondary metabolites from Caribbean sponges and their associated bacteria” is the result of my own work. I did not receive help or support from commercial consultants. All sources and/or materials applied are listed and specified in the thesis. Furthermore, I verify that this thesis has not yet been submitted as part of another examination process neither in identical nor in similar form. Place, date Signature iii AKNOWLEDGMENTS I am deeply grateful to the following for making this dissertation possible: Ute Hentschel Humeida, Thomas Hünig and Tanja Schirmeister, whose encouragement, guidance and insightful criticism made it possible to accomplish the goals of this thesis, as well as giving me the opportunity to conduct an interdisciplinary project involving three different scientific disciplines thus providing me with the proper academic environment to improve my skills and enhance my knowledge. My special thanks go to Prof. Hünig for bringing me to Germany and giving me his full and unconditional support.
    [Show full text]
  • Isolation and Characterization of a Novel Sphingobium Yanoikuyae
    F1000Research 2020, 9:767 Last updated: 07 SEP 2020 RESEARCH ARTICLE Isolation and characterization of a novel Sphingobium yanoikuyae strain variant that uses biohazardous saturated hydrocarbons and aromatic compounds as sole carbon sources [version 1; peer review: 2 approved] Mautusi Mitra 1, Kevin Manoap-Anh-Khoa Nguyen1,2, Taylor Wayland Box1, Jesse Scott Gilpin1, Seth Ryan Hamby1, Taylor Lynne Berry3,4, Erin Harper Duckett1 1Biology Department, University of West Georgia, Carrollton, GA, 30118, USA 2Department of Mechanical Engineering, Kennesaw State University, Marietta, GA, 30060, USA 3Carrollton High School, Carrollton, GA, 30117, USA 4Department of Chemistry and Biochemistry, University of North Georgia, Dahlonega, GA, 30597, USA v1 First published: 24 Jul 2020, 9:767 Open Peer Review https://doi.org/10.12688/f1000research.25284.1 Latest published: 24 Jul 2020, 9:767 https://doi.org/10.12688/f1000research.25284.1 Reviewer Status Abstract Invited Reviewers Background: Green micro-alga, Chlamydomonas reinhardtii (a Chlorophyte), can be cultured in the laboratory heterotrophically or 1 2 photo-heterotrophically in Tris-Phosphate-Acetate (TAP) medium, which contains acetate as the carbon source. Chlamydomonas can version 1 convert acetate in the TAP medium to glucose via the glyoxylate cycle, 24 Jul 2020 report report a pathway present in many microbes and higher plants. A novel bacterial strain, CC4533, was isolated from a contaminated TAP agar 1. David Dewez, University of Quebec at medium culture plate of a Chlamydomonas wild type strain. In this article, we present our research on the isolation, and biochemical and Montreal, Montreal, Canada molecular characterizations of CC4533. 2. Arun Karnwal , Lovely Professional Methods: We conducted several microbiological tests and spectrophotometric analyses to biochemically characterize CC4533.
    [Show full text]