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Sphingomonas Zeae Sp. Nov., Isolated from the Stem of Zea Mays

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International Journal of Systematic and Evolutionary Microbiology (2015), 65, 2542–2548 DOI 10.1099/ijs.0.000298 Sphingomonas zeae sp. nov., isolated from the stem of Zea mays Peter Ka¨mpfer,1 Hans-Ju¨rgen Busse,2 John A. McInroy3 and Stefanie P. Glaeser1 Correspondence 1Institut fu¨r Angewandte Mikrobiologie, Universita¨t Giessen, Giessen, Germany Peter Ka¨mpfer 2Institut fu¨r Mikrobiologie, Veterina¨rmedizinische Universita¨t, A-1210 Wien, Austria peter.kaempfer@agrar. 3 uni-giessen.de Department of Entomology and Plant Pathology, Auburn University, Alabama, USA A yellow-pigmented bacterial isolate (strain JM-791T) obtained from the healthy internal stem tissue of 1-month-old corn (Zea mays, cultivar ‘Sweet Belle’) grown at the Plant Breeding Unit of the E.V. Smith Research Center in Tallassee (Elmore county), Alabama, USA, was taxonomically characterized. The study employing a polyphasic approach, including 16S RNA gene sequence analysis, physiological characterization, estimation of the ubiquinone and polar lipid patterns, and fatty acid composition, revealed that strain JM-791T shared 16S rRNA gene sequence similarities with type strains of Sphingomonas paucimobilis (98.3 %), Sphingomonas pseudosanguinis (97.5 %) and Sphingomonas yabuuchiae (97.4 %), but also showed pronounced differences, both genotypically and phenotypically. On the basis of these results, a novel species of the genus Sphingomonas is described, for which we propose the name Sphingomonas zeae sp. nov. with the type strain JM-791T (5LMG 28739T5CCM 8596T). The genus Sphingomonas, proposed by Yabuuchi et al. Strain JM-791T was originally grown on Tryptic Soy Agar (1990) encompassed Gram-negative, non-fermentative (TSA; Oxoid), and was further studied and sub-cultivated rods, which can be chemotaxonomically characterized by on nutrient agar (NA; Oxoid) at 28 8C for 48 h and sub- the presence of ubiquinone Q-10, sym-homospermidine sequently analysed for its 16S rRNA gene sequence, fatty as the key polyamine, a lipid pattern consisting of phospha- acid methyl ester composition of the whole-cell hydroly- sate, further phenotypic features, and DNA–DNA related- tidylethanolamine (exception: Sphingomonas echinoides T ness to those species most closely related on the basis of DSM 1805 ; Denner et al., 1999), phosphatidylglycerol, 16S rRNA gene sequence similarities. diphosphatidylglycerol, sphingoglycolipid and phospha- 8 tidylcholine as major lipids, and the presence of 2-hydroxy- On NA at 28 C the strain showed a yellow pigmentation. Cells of strain JM-791T stained as Gram-negative with the myristic acid (C 2-OH) and the absence of 3-hydroxy 14 : 0 modified Hucker method after Gerhardt et al. (1994). fatty acids in their fatty acid profiles (Busse et al., 1999; Cell morphology was observed under a Zeiss light micro- Takeuchi et al., 2001; Zhang et al., 2005; Yoon et al., 2006). scope at 61000 magnification, with cells grown for 24 h Members of the genus have been isolated from roots or rhi- at 28 8C on medium NA. Good growth occurred on NA, zosphere soil (Xie & Yokoto, 2006; Takeuchi et al., 1995; as well as on brain heart infusion agar, R2A agar and Chung et al., 2011), the phyllosphere (Tala` et al., 2013; TSA, but no growth was observed on MacConkey agar Rivas et al., 2004) and also from endophytic compartments (Oxoid). Very reduced growth was observed at 4 8C and of plants (Huang et al., 2012) suggesting an important role 45 8C. The best growth was recorded at temperatures 8 8 T of the genus for plant–microbe interaction. between 25 C and 30 C. Strain JM-791 grew in TSB at 28 8C in the presence of 1 %, but not 2 % (w/v) NaCl In this study employing a polyphasic characterization, we and above, and in TSB adjusted to pH 5.5–9.5 but not at describe a novel species of the genus Sphingomonas, which pH 4.5 or pH 10.5. was isolated from the healthy internal stem tissue of 1- Detailed physiological characterization and biochemical month-old corn (Zea mays, cultivar ‘Sweet Belle’) grown at tests were performed to assess the carbon source utilization the Plant Breeding Unit of the E.V. Smith Research Center pattern, acid formation from different sugars and/or sugar- in Tallassee (Elmore county), Alabama, USA. related compounds, and hydrolysis of chromogenic sub- strates as described by Ka¨mpfer et al. (1991). In addition, The GenBank/EMBL/DDBJ accession number for the 16S rRNA other biochemical tests were performed, such as pro- gene sequence of strain JM-791T is KP999966. duction of hydrogen sulphide, indole reaction with Downloaded from www.sgmjournals.org by 2542 000298 G 2015 IUMS Printed in Great Britain IP: 131.204.246.172 On: Tue, 01 Sep 2015 13:41:07 Sphingomonas zeae sp. nov. Ehrlich’s and Kovacs’ reagents, the activity of arginine and tyrosine were performed according to Smibert & dihydrolase, lysine decarboxylase, ornithine decarboxylase, Krieg (1994). Isolate JM-791T utilized many carbon b-galactosidase (ONPG), and urease on Christensen’s urea sources, similar to all species of the genus Sphingomonas, agar (all performed with the Micronaut E kit; Ka¨mpfer, and was able to produce acid from D-glucose, lactose 1990). Hydrolysis of casein, gelatin (plate method), starch (weak), sucrose, L-arabinose (weak), maltose, D-xylose, Table 1. Differentiating characteristics of strain JM-791T, and related sym-homospermidine-containing species of the genus Sphingomonas 1, JM-791T;2,S. pseudosanguinis G1-2T;3,S. yabuuchiae DSM 14562T;4,S. sanguinis NBRC 13937T;5,S. pituitosa EDIVT;6,S. trueperi ATCC 12417T;7,S. paucimobilis ATCC 29837T;8,S. parapaucimobilis JCM 7510T;9,S. roseiflava IAM 14823T. Data for taxa 1 from this study; data for taxa 2–9 from Ka¨mpfer et al. (2007), obtained under exactly the same conditions. All data were obtained with the same method (Ka¨mpfer et al., 1991).+, Positive; (+), weakly positive; 2, negative. Characteristic 1 2 3 4 5 6 7 8 9 Acid production from: Glucose + 2 (+) 2 (+) 22 2 2 D-Mannitol 2222222 2 2 Salicin 222222+ 22 Sorbitol 22222+ 222 Rhamnose 2222222(+) 2 Maltose + 222(+) 2 (+)(+) 2 D-Xylose + 222(+) 2 + (+) 2 Trehalose + 222222 2 2 Cellobiose 22 2 2(+) 2 (+)(+) 2 Methyl D-glucoside 222222+ 22 Melibiose + 22222(+)(+) 2 D-Mannose + 22222(+)(+) 2 Hydrolysis of: Aesculin ++ + 2 + 2 (+)(+) + pNP-b-D-glucuronide 22(+) +++2 + 2 pNP-phosphoryl-choline ++ 2 +++2 + 2 L-Alanine-pNA +++++2 +++ L-Proline-pNA ++ + 2222 ++ Assimilation of: | D-Fructose ++++ 2 + 22+ Gluconate 22 + 2| 222 ++ a-Melibiose + 2 ++++2 + 2 L-Rhamnose 2222222(+) 2 Salicin + 2 ++++2 + 2 Maltitol 22 ++2 + 222 Acetate + 2 ++++2 + 2 Propionate 22 2 + 2 + 2 + 2 cis-Aconitate 22 + 222+++ trans-Aconitate 22 + 222+ 2 + Citrate ++ + 2222 + 2 Fumarate +++++++ 2 + Glutarate ++ + 22+ 2 + 2 DL-3-Hydroxybutyrate 2 +++++2 ++ DL-Lactate + 2 ++2 + 2 + 2 Oxoglutarate ++ + + 22+++ L-Alanine 2 +++++2 + (+) L-Asparate 22 2 + 2 + 222 L-Leucine 2 + 2 + 2 + 2 + (+) L-Ornithine 22 2 + 222 2 2 L-Proline 2 ++++22 2 + L-Serine 22222+ 222 4-Hydroxybenzoate 22222+ 222 Downloaded from www.sgmjournals.org by http://ijs.sgmjournals.org 2543 IP: 131.204.246.172 On: Tue, 01 Sep 2015 13:41:07 P. Ka¨mpfer and others 0.10 Sphingomonas zeae JM–791T (KP999966) Sphingomonas paucimobilis ATCC 29837T (U37337) 92 Sphingomonas sanguinis NBRC 13937T (D84529) Sphingomonas roseiflava MK341T (D84520) Sphingomonas yabuuchiae GTC 868T (AB071955) Sphingomonas parapaucimobilis NBRC 15100T (D13724) Sphingomonas pseudosanguinis G1−2T (AM412238) 100 Sphingomonas phyllosphaerae FA2T (AY453855) Sphingomonas endophytica YIM 65583T (HM629444) Sphingomonas yunnanensis YIM 003T (AY894691) Sphingomonas ginsenosidimutans Gsoil 1429T (HM204925) Sphingomonas polyaromaticivorans B2−7T (EF467848) 100 Sphingomonas oligoaromativorans SY-6T (FJ434127) Sphingomonas desiccabilis CP1DT (AJ871435) 73 Sphingomonas molluscorum An 18T (B248285) Sphingomonas pituitosa EDIVT (AJ243751) 94 Sphingomonas trueperi LMG 2142T (X97776) Sphingomonas azotifigens NBRC 15497T (AB03397) Sphingomonas guangdongensis 9NM−8T (JQ608326) Sphingomonas aerophila 5413J−26T (KC735148) 100 Sphingomonas ginsengisoli DCY58T (JN852951) Sphingomonas gei ZFGT−11T (KF551181) 79 Sphingomonas naasensis KIS18−15T (KC735149) Sphingomonas leidyi ATCC 15260T (AJ227812) Sphingomonas kyeonggiensis THG−DT81T (KC252615) Sphingomonas sanxanigenens NX02T (DQ789172) Stakelama sediminis CJ70T (EU099873) 88 Sphingomonas dokdonensis DS−4T (DQ178975) Sphingomonas mucosissima CP173−2T (AM229669) Sphingomonas xinjiangensis 10−1−84T (FJ754464) Sphingomonas japonica KC7T (AB428568) Sphingomonas yantingensis 1007T (JX566547) 100 Sphingomonas aestuarii K4T (EF660755) 'Sphingomonas hunanensis' JSM 083058T (FJ527417) Sphingomonas soli T5−04T (AB166883) Sphingomonas pruni NBRC 15498T (Y09637) Sphingomonas mali NBRC 15500T (Y09638) Sphingomonas asaccharolytica NBRC 15499T (Y09639) Sphingomonas koreensis JSS26T (AF131296) 86 T Sphingomonas panni C52 (AJ575818) Sphingomonas hankookensis ODN7T (FJ194436) Sphingomonas cynarae SPC−1T (HQ439186) Sphingomonas jinjuensis YC6723T (EU707561) Sphingomonas rubra BH3T (FJ834325) 77 Sphingomonas aquatilis JSS−7T (AF131295) Sphingomonas melonis PG−224T (AB055863) Sphingomonas kyungheensis THG-B283T (JN196137) Sphingomonas insulae DS−28 T (EF363714) Sphingomonas aerolata NW12T (AJ429240) 76 Sphingomonas aurantiaca MA101bT (AJ429236) 96 Sphingomonas faeni MA−olkiT (AJ429239) 'Sphingomonas ginsenosidivorax' KHI67 (HM204924) Sphingomonas abaci C42T (AJ575817) Sphingomonas echinoides ATCC 14820T (AB021370) Sphingomonas glacialis C16yT (GQ253122) Sphingomonas oligophenolica
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    University of Plymouth PEARL https://pearl.plymouth.ac.uk Faculty of Health: Medicine, Dentistry and Human Sciences School of Biomedical Sciences 2016-04-01 Domestic shower hose biofilms contain fungal species capable of causing opportunistic infection Moat, J http://hdl.handle.net/10026.1/11067 10.2166/wh.2016.297 Journal of Water and Health All content in PEARL is protected by copyright law. Author manuscripts are made available in accordance with publisher policies. Please cite only the published version using the details provided on the item record or document. In the absence of an open licence (e.g. Creative Commons), permissions for further reuse of content should be sought from the publisher or author. Pre-review submitted version archived under RoMEO Yellow policy Accepted article available at – DOI:10.2166/wh.2016.297 Domestic shower hose biofilms contain fungal species capable of causing opportunistic infection John Moat1*, Athanasios Rizoulis2, Graeme Fox1 & Mathew Upton1,3# 1Faculty of Medical and Human Sciences and 2School of Earth, Atmospheric and Environmental Sciences, The University of Manchester, Manchester, M13 9WL, UK. 3Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth, PL4 8AA, UK. #Author for correspondence Dr Mathew Upton School of Biomedical and Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Portland Square, Drake Circus, Plymouth, PL4 8AA Tel: +44 1752 5884466 Email: [email protected] *Current Address – AV Hill Building, University of Manchester, Rumford Street, Manchester. M13 9PT Key words: Exophiala, Fusarium, Malassezia, opportunistic pathogen, pyrosequencing, shower hose biofilm 1 Pre-review submitted version archived under RoMEO Yellow policy Accepted article available at – DOI:10.2166/wh.2016.297 Abstract The domestic environment can be a source of pathogenic bacteria.
  • Functions, Transmission and Emission of the Canopy Microbiota Tania Fort

    Functions, Transmission and Emission of the Canopy Microbiota Tania Fort

    Functions, transmission and emission of the canopy microbiota Tania Fort To cite this version: Tania Fort. Functions, transmission and emission of the canopy microbiota. Vegetal Biology. Univer- sité de Bordeaux, 2019. English. NNT : 2019BORD0338. tel-02869590 HAL Id: tel-02869590 https://tel.archives-ouvertes.fr/tel-02869590 Submitted on 16 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE PRESENTÉE POUR OBTENIR LE GRADE DE DOCTEUR DE L’UNIVERSITE DE BORDEAUX ECOLE DOCTORALE SCIENCES ET ENVIRONNEMENTS ECOLOGIE ÉVOLUTIVE, FONCTIONNELLE, ET DES COMMUNAUTÉS Par Tania Fort Fonctions, transmission et émission du microbiote de la canopée Sous la direction de Corinne Vacher Soutenue le 10 décembre 2019 Membres du jury : Mme. Anne-Marie DELORT Directrice de recherche Institut de Chimie de Clermont-Ferrand Rapporteuse M. Stéphane Uroz Directeur de recherche INRA Nancy Rapporteur Mme. Patricia Luis Maître de conférence Université de Lyon 1 Rapporteuse Mme. Annabel Porté Directrice de recherche INRA Bordeaux Présidente Mme. Corinne Vacher Directrice de recherche INRA Bordeaux Directrice Fonctions, transmission et émission du microbiote de la canopée. Les arbres interagissent avec des communautés microbiennes diversifiées qui influencent leur fitness et le fonctionnement des écosystèmes terrestres.
  • ORIGIN and FATE of ODOROUS METABOLITES, 2-METHYLISOBORNEOL and GEOSMIN, in a EUTROPHIC RESERVOIR Nicolas André Clercin Submit

    ORIGIN and FATE of ODOROUS METABOLITES, 2-METHYLISOBORNEOL and GEOSMIN, in a EUTROPHIC RESERVOIR Nicolas André Clercin Submit

    ORIGIN AND FATE OF ODOROUS METABOLITES, 2-METHYLISOBORNEOL AND GEOSMIN, IN A EUTROPHIC RESERVOIR Nicolas André Clercin Submitted to the faculty of the University Graduate School in partial fulfillment of the requirements for the degree Doctor of Philosophy in the Department of Earth Sciences, Indiana University June 2019 Accepted by the Graduate Faculty of Indiana University, in partial fulfillment of the requirements for the degree of Doctor of Philosophy. Doctoral Committee ______________________________________ Gregory K. Druschel, PhD, Chair ______________________________________ Pierre-André Jacinthe, PhD November 13, 2018 ______________________________________ Gabriel Filippelli, PhD ______________________________________ Max Jacobo Moreno-Madriñán, PhD ______________________________________ Sarath Chandra Janga, PhD ii © 2019 Nicolas André Clercin iii DEDICATION I would like to dedicate this work to my family, my wife Angélique and our three sons Pierre-Adrien, Aurélien and Marceau. I am aware that the writing of this manuscript has been an intrusion into our daily life and its achievement now closes the decade-long ‘Indiana’ chapter of our family. Another dedication to my parents and my young brother who have always been supportive and respectful of my choices even if they never fully understood the content of my research. A special thought to my dad (†2005) who loved so much sciences and technologies but never got the chance to study as a kid. Him who idolized his own father, a WWII resistant but became head of the family upon his father’s death when he was only 8. Him who had to work to support his widowed mother and his two younger brothers. Him who decided to join the French navy at the age of 16 as a seaman recruit in order to finally reach his personal goal and study, learn diesel engine mechanics, a skill that served him later in the civilian life.