| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
Correspondence
I. Cleenwerck
Ilse.Cleenwerck{at}ugent.be
 |
ABSTRACT |
|---|
 TOP ABSTRACT MAIN TEXTREFERENCES |
|---|
The EMBL/GenBank/DDBJ accession number for the 16S rDNA sequence of strain LMG 4329T is AJ487013.
|
MAIN TEXT |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
for two aerobic freshwater spirilla with a G+C content of 63–65 mol% and the ability to reduce nitrate beyond the level of nitrite. Later studies on intra- and intergeneric relationships and chemotaxonomic characteristics of various species of Aquaspirillum showed that A. dispar should be removed from the genus Aquaspirillum and that a new genus should be created for organisms belonging to this species (Pot et al., 1992; Hamana et al., 1994; Sakane & Yokota, 1994). In this study, we determined the 16S rDNA sequence of [A.] dispar LMG 4329T, compared it with all accessible 16S rDNA sequences in the EMBL database and found a high level of similarity (99·4 %) to the sequence of Microvirgula aerodenitrificans SGLY2T (=LMG 18919T). M. aerodenitrificans was created by Patureau et al. (1998) for an aerobic, denitrifying Gram-negative bacterium that could not be assigned at that time to any recognized genus on the basis of its 16S rDNA sequence. In the present note, we report on a polyphasic taxonomic study that demonstrates that [A.] dispar and M. aerodenitrificans belong in the same species.
[A.] dispar strains LMG 4329T and LMG 4330 and M. aerodenitrificans LMG 18919T were grown on medium M8 (Janssens et al., 1998) or trypticase soy agar (TSA; BBL) and incubated at 28 °C. DNA for 16S rDNA sequence analysis was prepared by alkali extraction as described by Niemann et al. (1997). DNA for determination of the DNA base composition and hybridization analysis was prepared by the method of Pitcher et al. (1989). To obtain DNA solutions free of RNA, an RNase treatment was performed, followed by a chloroform extraction. The 16S rDNA sequence of [A.] dispar LMG 4329T was determined as described by Cleenwerck et al. (2002). The sequencing primers used were Gamma, *Gamma, PD, *PD, 3, *3 and *O (Coenye et al., 1999). The 16S rDNA sequence of LMG 4329T was compared with all accessible 16S rDNA sequences in the EMBL database and aligned with the 16S rDNA sequences of the phylogenetically closest species using the GeneCompar 2.1 software package (Applied Maths). Unknown bases were discarded from the calculations. The G+C content of the DNA was determined by HPLC according to the method of Mesbah et al. (1989) using a Waters Symmetry Shield RP8 column thermostatted at 37 °C. DNA–DNA hybridizations were performed using a modification of the microplate method described by Ezaki et al. (1989) (Goris et al., 1998; Cleenwerck et al., 2002). The hybridization temperature was 45 °C. Gram staining and oxidase and catalase activity were determined as described by Cleenwerck et al. (2002). API 20 NE (bioMérieux) and Biolog GN2 analyses were performed according to the manufacturers' instructions. Cellular fatty acid methyl ester extraction and analyses from cells grown on TSA (BBL) for 24 h at 28 °C were performed according to the recommendations of the MIDI system (Microbial Identification System).
The 16S rDNA sequence of [A.] dispar LMG 4329T (1490 bases) was 99·4 % similar to the 16S rDNA sequence of M. aerodenitrificans SGLY2T (accession no. U89333). Sequence similarities to other published taxa belonging to the 
-Proteobacteria were below 95 %. The closest taxa were Laribacter hongkongensis (accession no. AF389085; 94·3 %), Vogesella indigofera (accession no. AB021385; 91·8 %), Zoogloea ramigera (accession no. X74913; 90·4 %) and Chromobacterium violaceum (accession no. AJ247211; 86·3 %). The DNA G+C contents of [A.] dispar LMG 4329T and M. aerodenitrificans LMG 18919T were respectively 64·3 and 64·5 mol%. The DNA–DNA binding value between LMG 4329T and LMG 18919T was 84 %, showing that the two strains belong to the same species. In addition, the target site of a specific probe developed by Patureau et al. (1998) for M. aerodenitrificans LMG 18919T, within the V4 variable region of the 16S rRNA (positions 636–653; Escherichia coli numbering), was also present in the 16S rDNA sequence of [A.] dispar LMG 4329T.
Comparison of the morphological, physiological and biochemical characteristics of M. aerodenitrificans LMG 18919T and [A.] dispar strains LMG 4329T and LMG 4330 (the latter two strains showing 100 % DNA–DNA relatedness; Aragno et al., 1978) showed that these strains were phenotypically highly similar. Cells were Gram-negative, motile, curved to rod-shaped, occurring singly or in pairs. All three strains were oxidase- and catalase-positive. In API 20 NE tests, the three strains gave identical reactions. They were able to denitrify, assimilate caprate and malate and hydrolyse arginine. According to the API 20 NE identification system, the strains are phenotypically highly similar to Comamonas testosteroni and Pseudomonas alcaligenes, with only arginine dehydrolase as a differentiating feature. The three strains shared nearly identical carbon source oxidation patterns, as determined by the Biolog identification system. All strains were able to oxidize a large spectrum of carbon sources, except sugars. Some minor quantitative differences were found in the oxidation of glycogen, alaninamide, the organic acids cis-aconitic acid and 
-ketovaleric acid and the amino acids hydroxy-L-proline, D-serine and L-threonine. For M. aerodenitrificans LMG 18919T, the Biolog results were similar to those obtained by Patureau et al. (1998) except that -ketoglutaric acid, malonic acid, D-alanine and L-threonine were oxidized, while sebacic acid, L-leucine and glycerol were not. The cellular fatty acid profiles of LMG 4329T and LMG 18919T were very similar, with summed feature 3, 16 : 0 and 18 : 1 as the major non-polar fatty acid compounds and 12 : 0 3-OH as the only 3-hydroxy fatty acid (Table 1). Analogous results were obtained by Sakane & Yokota (1994) for [A.] dispar and, in their study, it was shown that this profile was not found in other Aquaspirillum species. Phenotypic characteristics that enable the differentiation of LMG 4329T, LMG 4330 and LMG 18919T from the phylogenetically and phenotypically most related species are given in Table 2.
|
|
), the name Microvirgula aerodenitrificans must be retained for the unified taxon, since it is the type of the genus Microvirgula.
Emended description of Microvirgula aerodenitrificans Patureau et al. 1998
The description of the species is that given by Patureau et al. (1998), emended by the additional features described in the current paper. The species includes strains previously classified as Aquaspirillum dispar. The type strain is strain SGLY2T (=DSM 15089T=LMG 18919T).
|
ACKNOWLEDGEMENTS |
|---|
|
REFERENCES |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
Cleenwerck, I., Vandemeulebroecke, K., Janssens, D. & Swings, J. (2002). Re-examination of the genus Acetobacter, with descriptions of Acetobacter cerevisiae sp. nov. and Acetobacter malorum sp. nov. Int J Syst Evol Microbiol 52, 1551–1558.[Abstract]
Coenye, T., Falsen, E., Vancanneyt, M., Hoste, B., Govan, J. R. W., Kersters, K. & Vandamme, P. (1999). Classification of Alcaligenes faecalis-like isolates from the environment and human clinical samples as Ralstonia gilardii sp. nov. Int J Syst Bacteriol 49, 405–413.
Ezaki, T., Hashimoto, Y. & Yabuuchi, E. (1989). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39, 224–229.
Goris, J., Suzuki, K., De Vos, P., Nakase, T. & Kersters, K. (1998). Evaluation of a microplate DNA-DNA hybridization method compared with the initial renaturation method. Can J Microbiol 44, 1148–1153.[CrossRef]
Hamana, K., Sakane, T. & Yokota, A. (1994). Polyamine analysis of the genera Aquaspirillum, Magnetospirillum, Oceanospirillum and Spirillum. J Gen Appl Microbiol 40, 75–82.[CrossRef]
Hylemon, P. B., Wells, J. S., Jr, Krieg, N. R. & Jannasch, H. W. (1973). The genus Spirillum: a taxonomic study. Int J Syst Bacteriol 23, 340–380.
Janssens, D., Vereecke, C., Vanhonacker, K. & 7 other editors (1998). BCCMTM/LMG Catalogue of Cultures 1998. http://www.belspo.be/bccm/lmg.htm
Lapage, S. P., Sneath, P. H. A., Lessel, E. F., Skerman, V. B. D., Seeliger, H. P. R. & Clark, W. A. (editors) (1992). International Code of Nomenclature of Bacteria (1990 Revision). Bacteriological Code. Washington, DC: American Society for Microbiology.
Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39, 159–167.
Niemann, S., Pühler, A., Tichy, H.-V., Simon, R. & Selbitschka, W. (1997). Evaluation of the resolving power of three different DNA fingerprinting methods to discriminate among isolates of a natural Rhizobium meliloti population. J Appl Microbiol 82, 477–484.[CrossRef][Medline]
Patureau, D., Godon, J.-J., Dabert, P., Bouchez, T., Bernet, N., Delgenes, J. P. & Moletta, R. (1998). Microvirgula aerodenitrificans gen. nov., sp. nov., a new Gram-negative bacterium exhibiting co-respiration of oxygen and nitrogen oxides up to oxygen-saturated conditions. Int J Syst Bacteriol 48, 775–782.
Pitcher, D. G., Saunders, N. A. & Owen, R. J. (1989). Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8, 109–114.
Pot, B., Willems, A., Gillis, M. & De Ley, J. (1992). Intra- and intergeneric relationships of the genus Aquaspirillum: Prolinoborus, a new genus for Aquaspirillum fasciculus, with the species Prolinoborus fasciculus comb. nov. Int J Syst Bacteriol 42, 44–57.
Sakane, T. & Yokota, A. (1994). Chemotaxonomic investigation of heterotrophic, aerobic and microaerophilic spirilla, the genera Aquaspirillum, Magnetospirillum and Oceanospirillum. Syst Appl Microbiol 17, 128–134.
Willems, A., Pot, B., Falsen, E., Vandamme, P., Gillis, M., Kersters, K. & De Ley, J. (1991). Polyphasic taxonomic study of the emended genus Comamonas: relationship to Aquaspirillum aquaticum, E. Falsen group 10, and other clinical isolates. Int J Syst Bacteriol 41, 427–444.
Yuen, K.-Y., Woo, P. C. Y., Teng, J. L. L., Leung, K.-W., Wong, M. K. M. & Lau, S. K. P. (2001). Laribacter hongkongensis gen. nov., sp. nov., a novel Gram-negative bacterium isolated from a cirrhotic patient with bacteremia and empyema. J Clin Microbiol 39, 4227–4232.
Yumoto, I., Yamazaki, K., Hishinuma, M., Nodasaka, Y., Suemori, A., Nakajima, K., Inoue, N. & Kawasaki, K. (2001). Pseudomonas alcaliphila sp. nov., a novel facultatively psychrophilic alkaliphile isolated from seawater. Int J Syst Evol Microbiol 51, 349–355.[Abstract]
This article has been cited by other articles:
|
|
 |
|
  B. J. Tindall Rule 15 of the International Code of Nomenclature of Bacteria: a current source of confusion Int J Syst Evol Microbiol, July 1, 2008; 58(7): 1775 - 1778. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-H. Yoon, S.-J. Kang, S. Park, S.-Y. Lee, and T.-K. Oh Reclassification of Aquaspirillum itersonii and Aquaspirillum peregrinum as Novispirillum itersonii gen. nov., comb. nov. and Insolitispirillum peregrinum gen. nov., comb. nov. Int J Syst Evol Microbiol, December 1, 2007; 57(12): 2830 - 2835. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-M. Lim, C. O. Jeon, G. S. Lee, D.-J. Park, U.-G. Kang, C.-Y. Park, and C.-J. Kim Leeia oryzae gen. nov., sp. nov., isolated from a rice field in Korea Int J Syst Evol Microbiol, June 1, 2007; 57(6): 1204 - 1208. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Grabovich, E. Gavrish, J. Kuever, A. M. Lysenko, D. Podkopaeva, and G. Dubinina Proposal of Giesbergeria voronezhensis gen. nov., sp. nov. and G. kuznetsovii sp. nov. and reclassification of [Aquaspirillum] anulus, [A.] sinuosum and [A.] giesbergeri as Giesbergeria anulus comb. nov., G. sinuosa comb. nov. and G. giesbergeri comb. nov., and [Aquaspirillum] metamorphum and [A.] psychrophilum as Simplicispira metamorpha gen. nov., comb. nov. and S. psychrophila comb. nov. Int J Syst Evol Microbiol, March 1, 2006; 56(Pt 3): 569 - 576. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| INT J SYST EVOL MICROBIOL | MICROBIOLOGY | J GEN VIROL |
| J MED MICROBIOL | ALL SGM JOURNALS | |
