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

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