| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
1 Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, People's Republic of China
2 Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
Correspondence
Sung-Taik Lee
e_stlee{at}kaist.ac.kr
 |
ABSTRACT |
|---|
 TOP ABSTRACT MAIN TEXTREFERENCES |
|---|
The API ZYM profiles of strain N4T and other Chryseobacterium species are available as supplementary material in IJSEM Online.
|
MAIN TEXT |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
to accommodate six species formerly classified within the genus Flavobacterium. At present, the genus Chryseobacterium comprises 17 species: Chryseobacterium gleum (type species), C. balustinum, C. indologenes, C. indoltheticum and C. scophthalmum (Vandamme et al., 1994) and the recently described species C. defluvii (Kämpfer et al., 2003), C. joostei (Hugo et al., 2003), C. daecheongense (Kim et al., 2005a), C. formosense (Young et al., 2005), C. shigense (Shimomura et al., 2005), C. taichungense (Shen et al., 2005), C. vrystaatense (de Beer et al., 2005), C. hispanicum (Gallego et al., 2006), C. piscium (de Beer et al., 2006), C. soldanellicola (Park et al., 2006), C. taeanense (Park et al., 2006) and C. wanjuense (Weon et al., 2006). ‘Chryseobacterium proteolyticum’ was described by Yamaguchi & Yokoe (2000), but this name has not yet been validly published. Two former Chryseobacterium species, C. meningosepticum (Vandamme et al., 1994) and C. miricola (Li et al., 2003), have been transferred to the novel genus Elizabethkingia (Kim et al., 2005b).
During a study of bacterial communities associated with the sludge of metal-complexed cyanide treatment bioreactors (Quan et al., 2006), conducted using a culture-dependent approach, a number of bacterial strains were isolated. Strain N4T was isolated from a nickel-complexed cyanide treatment bioreactor. A comparative analysis of 16S rRNA gene sequences indicated that strain N4T was a member of the clade representing the genus Chryseobacterium. In order to determine the precise taxonomic position of strain N4T, a polyphasic taxonomic study was carried out.
Strain N4T was cultivated on R2A agar (Difco) at 28 °C for 48 h. Cell biomass for quinone analysis and for DNA extraction was obtained directly from agar plates. For fatty acid methyl ester analysis, strain N4T was cultivated on tryptic soy agar (Difco) at 28 °C for 24 h for direct comparison with reference strains. Cell morphology was examined under a phase-contrast microscope (1000x magnification; Nikon). A Gram reaction was performed as described by Gerhardt et al. (1994). Flexirubin-type pigments were detected according to the method of Fautz & Reichenbach (1980). Catalase activity was determined by means of bubble production in a 3 % (v/v) hydrogen peroxide solution. Oxidase activity was determined from the oxidation of 1 % p-aminodimethylaniline oxalate. The hydrolysis of starch was tested on starch agar (Difco). Additional enzyme activities, acid production from carbohydrates and the utilization of various substrates as sole carbon sources were determined by using API ZYM, API 20E, API 20NE and API 32GN galleries according to the manufacturer's instructions (bioMérieux). The effects of NaCl concentration (0–5 %), pH (5–10) and temperature (5–42 °C) on growth were determined on R2A agar.
Respiratory quinones were analysed as described by Komagata & Suzuki (1987), using reversed-phase HPLC. For quantitative analysis of the cellular fatty acid composition, a loop of cell mass was harvested and the fatty acids were then saponified, methylated and extracted according to the protocol of the Sherlock Microbial Identification System (MIDI). Fatty acids were analysed by a gas chromatograph (model 6890; Hewlett Packard) and identified by using the Microbial Identification software package (Sasser, 1990). Chromosomal DNA was isolated and purified using a Cell Culture DNA Midi kit (Qiagen) according to the manufacturer's protocol. For the determination of G+C content, DNA was degraded enzymically into nucleotides and analysed by reversed-phase HPLC as described by Mesbah et al. (1989). Non-methylated 
-phage DNA (Sigma) was used as a calibration reference.
The 16S rRNA gene was amplified by a PCR using two universal primers (Quan et al., 2005). The PCR product was purified using a QIAquick PCR purification kit (Qiagen). The 16S rRNA gene sequence was determined directly using the PCR-amplified DNA as a sequencing template. A sequencing PCR was performed with forward and reverse primers (Quan et al., 2005) using a DNA Analyzer (3730X1; Applied Biosystems). The 16S rRNA gene sequences of related taxa were obtained from GenBank. Multiple alignments were performed using the CLUSTAL_X program (Thompson et al., 1997) and gaps were edited in the BioEdit program (Hall, 1999). Phylogenetic trees were constructed on the basis of three tree-making algorithms: neighbour-joining (Saitou & Nei, 1987), minimum-evolution (Rzhetsky & Nei, 1992) and maximum-parsimony (Swofford, 1993) by using the MEGA3 program (Kumar et al., 2004), with bootstrap values based on 1000 replications (Felsenstein, 1985). Evolutionary distances were calculated using the method of Jukes & Cantor (1969).
Details of the cultural, physiological and biochemical characteristics of strain N4T are given in the species description and in Table 1. The results from the API ZYM galleries are available in Supplementary Table S1 in IJSEM Online. The cellular fatty acid profile of strain N4T was characterized by the predominance of summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1
7c/t), iso-C15 : 0 and C16 : 0, and was similar to those of other Chryseobacterium species. However, N4T differed from other Chryseobacterium species (except C. hispanicum) in containing a very large amount of summed feature 4 and lacking iso-C17 : 19c (Table 2). The predominant respiratory quinone was menaquinone MK-6. The DNA G+C content was 38.2 mol%.
|
|
). Similar tree topologies were also found in the trees generated with the maximum-parsimony and minimum-evolution algorithms (data not shown).
|
). The strain could also be distinguished from other Chryseobacterium species by means of some important phenotypic characteristics (summarized in Table 1
): growth conditions, enzyme activities, acid production from carbohydrates, fatty acid profile (Table 2) and API ZYM profile (see Supplementary Table S1 in IJSEM Online). On the basis of the results obtained, strain N4T is sufficiently distinct from all known Chryseobacterium species to be recognized as representing a novel species of the genus Chryseobacterium, for which the name Chryseobacterium caeni sp. nov. is proposed.
Description of Chryseobacterium caeni sp. nov.
Chryseobacterium caeni (ca.e'ni. L. gen. n. caeni of sludge).
Cells are aerobic, non-spore-forming, non-motile rods. Gram-negative, oxidase- and catalase-positive. Good growth is observed on R2A, tryptic soy and nutrient agars, but not on MacConkey agar. Colonies are translucent and shiny with entire edges, becoming mucoid after 3 days incubation. Bright yellow flexirubin-type pigments are produced. Growth occurs at 5–37 °C, but not at 42 °C; the optimum temperature for growth is between 28 and 30 °C. The pH range for growth is 6.0–10.0, with an optimum at between pH 6.5 and 8.0. Cells grow in the presence of 0–3 % NaCl, but not with 5 % NaCl. The major fatty acids are summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 17c/t), iso-C15 : 0 and C16 : 0. Menaquinone MK-6 is the predominant respiratory quinone. The G+C content of the genomic DNA is 38.2 mol%. Acid is not produced from amygdalin, L-arabinose, D-fructose, D-glucose, glycerol, inositol, lactose, D-melibiose, D-maltose, D-mannitol, L-rhamnose, D-sorbitol, D-sucrose, trehalose or D-xylose. The following substrates are utilized as sole carbon sources: D-glucose, L-arabinose, D-sucrose, D-maltose and glycogen. The following substrates are not utilized as sole carbon sources: D-mannitol, D-melibiose, L-fucose, D-sorbitol, propionate, caprate, valerate, citrate, histidine, 2-ketogluconate, 3-hydroxybutyrate, 4-hydroxybenzoate, L-proline, L-rhamnose, N-acetylglucosamine, D-ribose, inositol, itaconate, suberate, malonate, acetate, DL-lactate, L-alanine, 5-ketogluconate, 3-hydroxybenzoate, L-serine, D-mannose, gluconate, caprate, adipate, malate or phenyl acetate. Positive for urease and 
-glucosidase activities, but negative for indole production. Nitrate and nitrite are not reduced. Results from the API ZYM test are given in Supplementary Table S1 in IJSEM Online.
The type strain, N4T (=KCTC 12506T=CCBAU 10201T=DSM 17710T), was isolated from the sludge of a nickel-complexed cyanide treatment bioreactor.
|
ACKNOWLEDGEMENTS |
|---|
|
REFERENCES |
|---|
|
TOPABSTRACTMAIN TEXTREFERENCES |
|---|
de Beer, H., Hugo, C. J., Jooste, P. J., Vancanneyt, M., Coenye, T. & Vandamme, P. (2006). Chryseobacterium piscium sp. nov., isolated from fish of the South Atlantic Ocean off South Africa. Int J Syst Evol Microbiol 56, 1317–1322.
Fautz, E. & Reichenbach, H. (1980). A simple test for flexirubin-type pigments. FEMS Microbiol Lett 8, 87–91.[Medline]
Felsenstein, J. (1985). Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
Gallego, V., García, M. T. & Ventosa, A. (2006). Chryseobacterium hispanicum sp. nov., isolated from the drinking water distribution system of Sevilla, Spain. Int J Syst Evol Microbiol 56, 1589–1592.
Gerhardt, P., Murray, R. G. E., Wood, W. A. & Krieg, N. R. (editors) (1994). Methods for General and Molecular Bacteriology. Washington, DC: American Society for Microbiology.
Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95–98.
Hugo, C. J., Jooste, P. J., Segers, P., Vancanneyt, M. & Kersters, L. (1999). A polyphasic taxonomic study of Chryseobacterium strains isolated from dairy sources. Syst Appl Microbiol 22, 586–595.[Medline]
Hugo, C., Segers, P., Hoste, B., Vancanneyt, M. & Kersters, K. (2003). Chryseobacterium joostei sp. nov., isolated from the dairy environment. Int J Syst Evol Microbiol 53, 771–777.
Jukes, T. H. & Cantor, C. R. (1969). Evolution of protein molecules. In Mammalian Protein Metabolism, vol. 3, pp. 21–132. Edited by H. N. Munro. New York: Academic Press.
Kämpfer, P., Dreyer, U., Neef, A., Dott, W. & Busse, H. J. (2003). Chryseobacterium defluvii sp. nov., isolated from wastewater. Int J Syst Evol Microbiol 53, 93–97.
Kim, K. K., Bae, H. S., Schumann, P. & Lee, S. T. (2005a). Chryseobacterium daecheongense sp. nov., isolated from freshwater lake sediment. Int J Syst Evol Microbiol 55, 133–138.
Kim, K. K., Kim, M. K., Lim, J. H., Park, H. Y. & Lee, S. T. (2005b). Transfer of Chryseobacterium meningosepticum and Chryseobacterium miricola to Elizabethkingia gen. nov. as Elizabethkingia meningoseptica comb. nov. and Elizabethkingia miricola comb. nov. Int J Syst Evol Microbiol 55, 1287–1293.
Komagata, K. & Suzuki, K. I. (1987). Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 19, 161–203.
Kumar, S., Tamura, K. & Nei, M. (2004). MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.
Li, Y., Kawamura, K., Fujiwara, N., Naka, T., Liu, H., Huang, X., Kobayashi, K. & Ezaki, T. (2003). Chryseobacterium miricola sp. nov., a novel species isolated from condensation water of space station Mir. Syst Appl Microbiol 26, 523–528.[CrossRef][Medline]
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.
Mudarris, M., Austin, B., Segers, P., Vancanneyt, M., Hoste, B. & Bernardet, J. F. (1994). Flavobacterium scophthalmum sp. nov., a pathogen of turbot (Scophthalmus maximus L.). Int J Syst Bacteriol 44, 447–453.
Quan, Z. X., Bae, H. S., Baek, J. H., Chen, W. F., Im, W. T. & Lee, S. T. (2005). Rhizobium daejeonense sp. nov. isolated from a cyanide treatment bioreactor. Int J Syst Evol Microbiol 55, 2543–2549.
Quan, Z. X., Rhee, S. K., Bae, J. W., Baek, J. H., Park, Y. H. & Lee, S. T. (2006). Bacterial community structure in activated sludge reactors treating free or metal-complexed cyanides. J Microbiol Biotechnol 16, 232–249.
Rzhetsky, A. & Nei, M. (1992). A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 9, 945–967.
Saitou, N. & Nei, M. (1987). The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.[Abstract]
Sasser, M. (1990). Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI.
Shen, F. O., Kämpfer, P., Young, C. C., Lai, W. A. & Arun, A. B. (2005). Chryseobacterium taichungense sp. nov., isolated from contaminated soil. Int J Syst Evol Microbiol 55, 1301–1304.
Shimomura, K., Kaji, S. & Hiraishi, A. (2005). Chryseobacterium shigense sp. nov., a yellow-pigmented aerobic bacterium isolated from a lactic acid beverage. Int J Syst Evol Microbiol 55, 1903–1906.
Stackebrandt, E. & Goebel, B. M. (1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rDNA sequence analysis in the present species identification in bacteriology. Int J Syst Bacteriol 44, 846–849.
Swofford, D. L. (1993). PAUP. Phylogenetic Analysis Using Parsimony, version 3.1.1. Champaign, IL: Illinois Natural History Survey.
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, 4876–4882.
Vandamme, P., Bernardet, J. F., Segers, P., Kersters, K. & Holmes, B. (1994). New perspectives in the classification of the flavobacteria: description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev. Int J Syst Bacteriol 44, 827–831.
Weon, H. Y., Kim, B. Y., Yoo, S. H., Kwon, S. W., Cho, Y. H., Go, S. J. & Stackebrandt, E. (2006). Chryseobacterium wanjuense sp. nov., isolated from greenhouse soil in Korea. Int J Syst Evol Microbiol 56, 1501–1504.
Yamaguchi, S. & Yokoe, M. (2000). A novel protein-deamidating enzyme from Chryseobacterium proteolyticum sp. nov., a newly isolated bacterium from soil. Appl Environ Microbiol 66, 3337–3343.
Young, C. C., Kämpfer, P., Shen, E. T., Lai, W. A. & Arun, A. B. (2005). Chryseobacterium formosense sp. nov., isolated from the rhizosphere of Lactuca sativa L. (garden lettuce). Int J Syst Evol Microbiol 55, 423–426.
This article has been cited by other articles:
|
|
 |
|
  P. Kampfer, M. Vaneechoutte, N. Lodders, T. De Baere, V. Avesani, M. Janssens, H.-J. Busse, and G. Wauters Description of Chryseobacterium anthropi sp. nov. to accommodate clinical isolates biochemically similar to Kaistella koreensis and Chryseobacterium haifense, proposal to reclassify Kaistella koreensis as Chryseobacterium koreense comb. nov. and emended description of the genus Chryseobacterium Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2421 - 2428. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Kampfer, N. Lodders, M. Vaneechoutte, and G. Wauters Transfer of Sejongia antarctica, Sejongia jeonii and Sejongia marina to the genus Chryseobacterium as Chryseobacterium antarcticum comb. nov., Chryseobacterium jeonii comb. nov. and Chryseobacterium marinum comb. nov. Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2238 - 2240. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Peng, M. Liu, L. Zhang, J. Dai, X. Luo, H. An, and C. Fang Planobacterium taklimakanense gen. nov., sp. nov., a member of the family Flavobacteriaceae that exhibits swimming motility, isolated from desert soil Int J Syst Evol Microbiol, July 1, 2009; 59(7): 1672 - 1678. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Szoboszlay, B. Atzel, J. Kukolya, E. M. Toth, K. Marialigeti, P. Schumann, and B. Kriszt Chryseobacterium hungaricum sp. nov., isolated from hydrocarbon-contaminated soil Int J Syst Evol Microbiol, December 1, 2008; 58(12): 2748 - 2754. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Hantsis-Zacharov, T. Shaked, Y. Senderovich, and M. Halpern Chryseobacterium oranimense sp. nov., a psychrotolerant, proteolytic and lipolytic bacterium isolated from raw cow's milk Int J Syst Evol Microbiol, November 1, 2008; 58(11): 2635 - 2639. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
U. Behrendt, A. Ulrich, and P. Schumann Chryseobacterium gregarium sp. nov., isolated from decaying plant material Int J Syst Evol Microbiol, May 1, 2008; 58(5): 1069 - 1074. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Hantsis-Zacharov, Y. Senderovich, and M. Halpern Chryseobacterium bovis sp. nov., isolated from raw cow's milk Int J Syst Evol Microbiol, April 1, 2008; 58(4): 1024 - 1028. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. C. Park, M. S. Kim, K. S. Baik, E. M. Kim, M. S. Rhee, and C. N. Seong Chryseobacterium aquifrigidense sp. nov., isolated from a water-cooling system Int J Syst Evol Microbiol, March 1, 2008; 58(3): 607 - 611. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Herzog, I. Winkler, D. Wolking, P. Kampfer, and A. Lipski Chryseobacterium ureilyticum sp. nov., Chryseobacterium gambrini sp. nov., Chryseobacterium pallidum sp. nov. and Chryseobacterium molle sp. nov., isolated from beer-bottling plants Int J Syst Evol Microbiol, January 1, 2008; 58(1): 26 - 33. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Vaneechoutte, P. Kampfer, T. De Baere, V. Avesani, M. Janssens, and G. Wauters Chryseobacterium hominis sp. nov., to accommodate clinical isolates biochemically similar to CDC groups II-h and II-c Int J Syst Evol Microbiol, November 1, 2007; 57(11): 2623 - 2628. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Hantsis-Zacharov and M. Halpern Chryseobacterium haifense sp. nov., a psychrotolerant bacterium isolated from raw milk Int J Syst Evol Microbiol, October 1, 2007; 57(10): 2344 - 2348. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Zhou, J. Dong, X. Wang, X. Huang, K.-Y. Zhang, Y.-Q. Zhang, Y.-F. Guo, R. Lai, and W.-J. Li Chryseobacterium flavum sp. nov., isolated from polluted soil Int J Syst Evol Microbiol, August 1, 2007; 57(8): 1765 - 1769. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
U. Behrendt, A. Ulrich, C. Sproer, and P. Schumann Chryseobacterium luteum sp. nov., associated with the phyllosphere of grasses Int J Syst Evol Microbiol, August 1, 2007; 57(8): 1881 - 1885. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-H. Yoon, S.-J. Kang, and T.-K. Oh Chryseobacterium daeguense sp. nov., isolated from wastewater of a textile dye works Int J Syst Evol Microbiol, June 1, 2007; 57(6): 1355 - 1359. [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 | |
