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1 Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
2 CIFA Las Torres, Alcalá del Río, Sevilla, Spain
3 Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain
Correspondence
Encarna Velázquez
evp{at}usal.es
| ABSTRACT |
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7c and C18 : 1 2-OH. Strains ESC1T and ESC5 were strictly aerobic and were able to reduce nitrate and to hydrolyse aesculin. They produced
-galactosidase and
-glucosidase and did not produce urease after 48 h incubation. The G+C content of strain ESC1T was 56.4 mol%. Both strains ESC1T and ESC5 contained nodD and nifH genes on megaplasmids that were related phylogenetically to those of rhizobial strains nodulating Phaseolus, Leucaena, Trifolium and Lupinus. From the results of this work, we propose that the strains isolated in this study be included in a novel species named Ochrobactrum cytisi sp. nov. The type strain is ESC1T (=LMG 22713T=CECT 7172T).
The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA, nifH and nodD gene sequences of strain ESC1T are AY776289AY776291, respectively.
TP-RAPD profiles, nifH- and nodD-based neighbour-joining trees, photos of nodules induced by strain ESC1T and R. etli CFN42T, fatty acid profiles and differentiating characters for all species of Ochrobactrum are available as supplementary material in IJSEM Online.
Present address: Laboratorium voor Microbiologie, Vakgroep Biochemie, Fysiologie en Microbiologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium. ![]()
| MAIN TEXT |
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Strains ESC1T and ESC5 were isolated from root nodules of Cytisus scoparius according to Vincent (1970)
using yeast mannitol agar (YMA; Bergersen, 1961
). The cultures used in further phenotypic and molecular studies were purified from a single colony after 2 days incubation at 28 °C on YMA. The colonies were white, mucoid, translucent and convex on this medium.
Sequencing of the nearly complete 16S rRNA gene was performed as described previously (Rivas et al., 2002b
). The 16S23S rRNA intergenic spacer (ITS) region was amplified and sequenced as described by Lebuhn et al. (2006)
. Sequence comparison and alignment were performed by using the BLASTN program (Altschul et al., 1990
) and CLUSTAL W software (Thompson et al., 1997
), respectively. Distances were calculated according to Kimura's two-parameter model (Kimura, 1980
). Phylogenetic trees were inferred using the neighbour-joining method (Saitou & Nei, 1987
). Bootstrap analysis was based on 1000 resamplings. The MEGA2 package (Kumar et al., 2001
) was used for all analyses.
The 16S rRNA gene (rrn) sequences obtained (1476 nucleotides) were identical in strains ESC1T and ESC5 and showed 100, 99.9 and 99.7 % similarity, respectively, to sequences from O. anthropi LMG 3331T, O. lupini LUP21T and O. tritici LMG 18957T. Phylogenetic analysis of 16S rRNA gene sequences of the strains from this study showed clearly that they form a separate group within the genus Ochrobactrum together with O. anthropi, O. lupini and O. tritici, being most closely related to the first two of these species (Fig. 1
).
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The G+C content of strain ESC1T was 56.4 mol%, as determined by HPLC (Rivas et al., 2003
). DNADNA hybridization analyses were performed at the DSMZ. DNA was isolated by chromatography on hydroxyapatite by the procedure of Cashion et al. (1977)
, which was carried out as described by De Ley et al. (1970)
with the modifications described by Huß et al. (1983)
and Escara & Hutton (1980)
. Renaturation rates were computed with the TRANSFER.BAS program (Jahnke, 1992
) and DNADNA relatedness was tested at 68 °C in 2x SSC plus 10 % (v/v) DMSO. The resulting values between strain ESC1T and strains O. lupini LUP21T, O. anthropi DSM 6882T and O. tritici DSM 13340T were 70.4 % (individual values 69.8 and 71.0 %), 65.8 % (68.9 and 62.6 %) and 54.5 % (55.3 and 53.7 %), respectively (means of duplicates). The values obtained between O. lupini LUP21T and O. anthropi DSM 6882T and O. tritici DSM 13340T were 69 and 63 %, respectively (means of duplicates). These values were nearly identical to those obtained in a previous work for O. lupini LUP21T and O. anthropi LMG 3331T using a different method for DNADNA hybridization (Trujillo et al., 2005
).
Fatty acids were extracted and analysed at the LMG as described previously (Trujillo et al., 2005
). The fatty acid pattern of strain ESC1T (Supplementary Table S1) confirmed that it is a member of the genus Ochrobactrum, because it contains a major amount of C18 : 1
7c and moderate amounts (110 %) of C16 : 0, C17 : 0, C18 : 0, C19 : 0 cyclo
8c and summed feature 3 (C16 : 1
7c and/or C15 : 0 iso 2-OH). Like other Ochrobactrum species, strain ESC1T contains C18 : 1 2-OH, but the amounts detected in strains ESC1T (20.4 %) and ESC5 (14.2 %) were higher than in their closest relatives O. anthropi and O. lupini. The novel strains also differ from O. anthropi in the amount of C19 : 0 cyclo
8c. Several fatty acids present in small amounts in some closely related species were not detected in the strains from this study (see Supplementary Table S1).
Cells were stained according to the classical Gram procedure as described by Doetsch (1981)
and motility was checked by phase-contrast microscopy. Catalase and oxidase activities were tested as described previously (Rivas et al., 2003
). Physiological studies were done using API 20NE and API 20E systems following the manufacturer's instructions (bioMérieux). API 50CH strips were inoculated with suspensions of the strains in a basal medium containing YNB (yeast nitrogen base; Difco) adjusted to pH 7. For API ZYM strips, suspensions of cells growing for 24 h on TSA plates were used for inoculation as recommended by the manufacturer. Susceptibility to various antibiotics was examined as described previously (Valverde et al., 2005
) using discs (Becton Dickinson) containing (per disc) penicillin (10 U), ampicillin (2 µg), oxytetracycline (30 µg), neomycin (5 µg), cloxacillin (1 µg), erythromycin (2 µg), cefuroxime (30 µg), ciprofloxacin (5 µg), polymyxin B (300 IU) and gentamicin (10 µg) and antibiotic agar 11 (Oxoid) as the basal medium. O. lupini strains LUP21T and LUP23, O. tritici LMG 18957T and O. anthropi LMG 3331T were used as references in phenotypic characterization studies.
Cells of strains ESC1T and ESC5 were Gram-negative, rod-shaped, non-sporulating, motile by means of a polar flagellum and commonly observed as single cells. Strains ESC1T and ESC5 differ in the production of
-galactosidase in API ZYM (Table 1
and Supplementary Table S2). They differ from O. lupini in nitrate reduction, urease production after 48 h incubation and gluconate, D-arabinose, D-turanose and L-lyxose assimilation and from O. anthropi in aesculin hydrolysis, urease production after 48 h incubation, production of
-galactosidase in API ZYM, citrate (24 h) and gluconate assimilation and resistance to polymyxin B. The two strains differ from O. tritici in aesculin hydrolysis, urease production after 24 h incubation, production of
-galactosidase,
-glucosidase and lipase C14 in API ZYM and citrate, D-mannose and L-arabinose assimilation and in resistance to polymyxin B.
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In summary, on the basis of 16S rRNA gene and 16S23S rRNA ITS sequences, strains ESC1T and ESC5 belong to the genus Ochrobactrum, being closely related to O. anthropi, O. lupini and O. tritici. Nevertheless, DNADNA hybridization values and chemotaxonomic and phenotypic data indicate that they represent a taxon that merits species status within the genus Ochrobactrum, for which the name Ochrobactrum cytisi sp. nov. is proposed.
Description of Ochrobactrum cytisi sp. nov.
Ochrobactrum cytisi (cy.ti'si. N.L. masc. n. Cytisus botanical genus name of the legume Cytisus scoparius; N.L. gen. n. cytisi of Cytisus, referring to the isolation source of the first strains, nodules of C. scoparius).
Cells are motile, non-spore-forming, Gram-negative rods. Good growth occurs on YMA and nutrient agar at 2530 °C. Colonies on these media are white to beige, mucoid with entire edges and 23 mm in diameter within 24 h. Oxidase- and catalase-positive. The fatty acid profile is composed mainly of C18 : 1
7c, C18 : 1 2-OH, C19 : 0 cyclo
8c and C16 : 0. The following fatty acids are detected in small amounts: summed features 2 and 3, C18 : 0, C17 : 0, C18 : 0 2-OH and an unknown fatty acid at ECL 11.799. The following tests were done by using API 20E and API 20NE systems. Nitrate is reduced to nitrite. VogesProskauer reaction, indole production and aesculin hydrolysis are positive. Production of
-galactosidase is variable. Production of urease (after 48 h incubation), arginine dihydrolase, lysine decarboxylase, ornithine decarboxylase and gelatinase is negative. Carbon sources utilized include D-glucose, L-arabinose, D-mannose, mannitol, N-acetylglucosamine, maltose, citrate, erythritol, D-arabinose, ribose, adonitol, dulcitol, L-rhamnose, arbutin, maltose, sucrose, turanose, L-lyxose, tagatose, D-fucose, L-fucose, arabitol, 2-ketogluconate and 5-ketogluconate. Assimilation of D-xylose, L-xylose, galactose, D-fructose, lactose, melibiose, cellobiose, trehalose, dulcitol, glycerol, inositol, methyl
-D-glucoside and gluconate is weak. Caprate, adipate, methyl
-D-xyloside, L-sorbose, sorbitol, methyl
-D-mannoside, amygdalin, salicin, inulin, melezitose, D-raffinose, starch, glycogen, xylitol,
-gentiobiose and L-arabitol are not assimilated. The following enzymes are detected by using API ZYM strips: alkaline and acid phosphatases, esterase C4, lipase C8, lipase C14, leucine aminopeptidase, valine aminopeptidase, cystine aminopeptidase, trypsin, chymotrypsin, phosphoamidase,
-galactosidase and
-glucosidase. Production of N-acetyl-
-glucosaminidase,
-galactosidase,
-glucuronidase,
-glucosidase,
-mannosidase and
-fucosidase is negative. Resistant to ampicillin, penicillin, cefuroxime, cloxacillin, oxytetracycline, polymyxin B, erythromycin, neomycin and chloramphenicol. Sensitive to ciprofloxacin and weakly sensitive to gentamicin. The G+C content of the type strain is 56.4 mol%.
The type strain, ESC1T (=LMG 22713T=CECT 7172T), and strain ESC5 (=LMG 23703) were isolated from nodules of Cytisus scoparius.
| ACKNOWLEDGEMENTS |
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| REFERENCES |
|---|
|
|
|---|
Bergersen, F. J. (1961). The growth of Rhizobium in synthetic media. Aust J Biol 14, 349360.
Cashion, P., Holder-Franklin, M. A., McCully, J. & Franklin, M. (1977). A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81, 461466.[CrossRef][Medline]
De Ley, J., Cattoir, H. & Reynaerts, A. (1970). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12, 133142.[Medline]
Doetsch, R. N. (1981). Determinative methods of light microscopy. In Manual of Methods for General Bacteriology, pp. 2133. Edited by P. Gerhardt, R. G. E. Murray, R. N. Costilow, E. W. Nester, W. A. Wood, N. R. Krieg & G. H. Phillips. Washington, DC: American Society for Microbiology.
Escara, J. F. & Hutton, J. R. (1980). Thermal stability and renaturation of DNA in dimethyl sulfoxide solutions: acceleration of the renaturation rate. Biopolymers 19, 13151327.[CrossRef][Medline]
Herrera-Cervera, J. A., Caballero-Mellado, J., Laguerre, G., Tichy, H.-V., Requena, N., Amarger, N., Martínez-Romero, E., Olivares, J., & Sanjuán, J. (1999). At least five rhizobial species nodulate Phaseolus vulgaris in a Spanish soil. FEMS Microbiol Ecol 30, 8797.[CrossRef]
Holmes, B., Popoff, M., Kiredjian, M. & Kersters, K. (1988). Ochrobactrum anthropi gen. nov., sp. nov. from human clinic specimens and previously known as group Vd. Int J Syst Bacteriol 38, 406416.
Huß, V. A. R., Festl, H. & Schleifer, K. H. (1983). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4, 184192.
Jahnke, K. D. (1992). BASIC computer program for evaluation of spectroscopic DNA renaturation data from Gilford System 2600 spectrophotometer on a PC/XT/AT type personal computer. J Microbiol Methods 15, 6173.[CrossRef]
Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111120.[CrossRef][Medline]
Kumar, S., Tamura, K., Jakobsen, I.-B. & Nei, M. (2001). Molecular evolutionary genetics analysis software. Tempe, AZ: Arizona State University.
Lebuhn, M., Achouak, W., Schloter, M., Berge, O., Meier, H., Barakat, M., Hartmann, A. & Heulin, T. (2000). Taxonomic characterization of Ochrobactrum sp. isolates from soil samples and wheat roots and description of Ochrobactrum tritici sp. nov. and Ochrobactrum grignonense sp. nov. Int J Syst Evol Microbiol 50, 22072223.[Abstract]
Lebuhn, M., Bathe, S., Achouak, W., Hartmann, A., Heulin, T. & Schloter, M. (2006). Comparative sequence analysis of the internal transcribed spacer 1 of Ochrobactrum species. Syst Appl Microbiol 29, 265275.[CrossRef][Medline]
Rivas, R., Velázquez, E., Valverde, A., Mateos, P. F. & Martínez-Molina, E. (2001). A two primers random amplified polymorphic DNA procedure to obtain polymerase chain reaction fingerprints of bacterial species. Electrophoresis 22, 10861089.[CrossRef][Medline]
Rivas, R., Velázquez, E., Palomo, J.-L., Mateos, P. F., García-Benavides, P. & Martínez-Molina, E. (2002a). Rapid identification of Clavibacter michiganensis subspecies sepedonicus using two primers random amplified polymorphic DNA (TP-RAPD) fingerprints. Eur J Plant Pathol 108, 179184.[CrossRef][Medline]
Rivas, R., Velázquez, E., Willems, A., Vizcaíno, N., Subba-Rao, N. S., Mateos, P. F., Gillis, M., Dazzo, F. B. & Martínez-Molina, E. (2002b). A new species of Devosia that forms a nitrogen-fixing root-nodule symbiosis with the aquatic legume Neptunia natans (L. f.) Druce. Appl Environ Microbiol 68, 52175222.
Rivas, R., Willems, A., Subba-Rao, N. S., Mateos, P. F., Dazzo, F. B., Martínez-Molina, E., Gillis, M. & Velázquez, E. (2003). Description of Devosia neptuniae sp. nov. that nodulates and fixes nitrogen in symbiosis with Neptunia natans, an aquatic legume from India. Syst Appl Microbiol 26, 4753.[CrossRef][Medline]
Rivas, R., Abril, A., Trujillo, M. E. & Velázquez, E. (2004). Sphingomonas phyllosphaerae sp. nov., from the phyllosphere of Acacia caven in Argentina. Int J Syst Evol Microbiol 54, 21472150.
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406425.[Abstract]
Sy, A., Giraud, E., Jourand, P., García, N., Willems, A., de Lajudie, A. P., Prin, Y., Neyra, M., Gillis, M. & other authors (2001). Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes. J Bacteriol 183, 214220.
Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 48764882.
Trujillo, M. E., Willems, A., Abril, A., Planchuelo, A. M., Rivas, R., Ludeña, D., Mateos, P. F., Martínez-Molina, E. & Velázquez, E. (2005). Nodulation of Lupinus by strains of the new species Ochrobactrum lupini sp. nov. Appl Environ Microbiol 71, 13181327.
Trujillo, M. E., Willems, A., Abril, A., Planchuelo, A. M., Rivas, R., Ludeña, D., Mateos, P. F., Martínez-Molina, E. & Velázquez, E. (2006). Ochrobactrum lupini sp. nov. In List of New Names and New Combinations Previously Effectively, but not Validly, Published, List no. 110. Int J Syst Evol Microbiol 56, 14591460.
Valverde, A., Velázquez, E., Fernández-Santos, F., Vizcaino, N., Rivas, R., Mateos, P. F., Martinez-Molina, E., Igual, J. M. & Willems, A. (2005). Phyllobacterium trifolii sp. nov., nodulating Trifolium and Lupinus in Spanish soils. Int J Syst Evol Microbiol 55, 19851989.
van Berkum, P. & Eardly, B. (2002). The aquatic budding bacterium Blastobacter denitrificans is a nitrogen fixing symbiont of Aeschynomene indica. Appl Environ Microbiol 68, 11321136.
van Rhijn, P., Luyten, E., Vlassak, K. & Vanderleyden, J. (1996). Isolation and characterization of a pSym locus of Rhizobium sp. BR816 that extends nodulation ability of narrow host range Phaseolus vulgaris symbionts to Leucaena leucocephala. Mol Plant Microbe Interact 9, 7477.[Medline]
Velázquez, E., Peix, A., Zurdo-Piñeiro, J. L., Palomo, J. L., Mateos, P. F., Rivas, R., Muñoz-Adelantado, E., Toro, N., García-Benavides, P. & other authors (2005). The coexistence of symbiosis and pathogenicity-determining genes in Rhizobium rhizogenes strains enables them to induce nodules and tumours or hairy roots in plants. Mol Plant Microbe Interact 18, 13251332.[Medline]
Vincent, J. M. (1970). The cultivation, isolation and maintenance of rhizobia. In A Manual for the Practical Study of the Root-Nodule Bacteria, pp. 113. Oxford: Blackwell Scientific.
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