|
|
||||||||
1 Division of Applied Life Science, EB-NCRC, PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
2 Division of Environmental Science and Ecological Engineering, Korea University, Seoul 136-701, Republic of Korea
Correspondence
Che Ok Jeon
cojeon{at}gnu.ac.kr
| ABSTRACT |
|---|
|
|
|---|
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain EMB34T is DQ372981.
A transmission electron micrograph showing cells of strain EMB34T linked by extracellular fibrils is available as a supplementary figure with the online version of this paper.
| MAIN TEXT |
|---|
|
|
|---|
Strain EMB34T was isolated from a wastewater treatment plant in Korea that performed enhanced biological phosphorus removal. The sludge sample was serially diluted with 1 % (w/v) saline solution, spread on R2A agar (Difco) and incubated at 20 °C for 5 days. The strain was grown routinely aerobically on R2A agar at 30 °C for 3 days.
Sequencing of the 16S rRNA gene of strain EMB34T was carried out as described previously by Lane (1991
). The resulting 16S rRNA gene sequence (1436 nucleotides) was compared with available 16S rRNA gene sequences from GenBank using the BLAST program (http://www.ncbi.nlm.nih.gov/BLAST/) to determine an approximate phylogenetic affiliation, and gene sequences were aligned with those of closely related species by using CLUSTAL W software (Thompson et al., 1994
). Phylogenetic trees were constructed by using three different algorithms, neighbour-joining (NJ), maximum-likelihood (ML) and maximum-parsimony (MP), available in the PHYLIP software, version 3.6 (Felsenstein, 2002
). Sequence similarity values between the novel strain and related organisms were computed using the program FASTA3 in EBI (http://www.ebi.ac.uk/fasta33/nucleotide.html). Bootstrap analysis was performed according to the Kimura two-parameter model (Kimura, 1980
) of the NJ method in the PHYLIP package. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain EMB34T formed a distinct phyletic lineage within the genus Flavobacterium (Fig. 1
). The overall topologies of the ML and MP trees were essentially the same as that of the NJ tree (data not shown). Comparative 16S rRNA gene sequence analyses showed that strain EMB34T was most closely related to Flavobacterium flevense ATCC 27944T, Flavobacterium aquatile ATCC 11947T and Flavobacterium omnivorum JCM 11313T, with similarities of 94.4, 94.1 and 93.9 %, respectively. Sequence similarities with other Flavobacterium species were less than 93.5 %.
|
Transmission electron micrographs showed that the cells were surrounded and linked with what appeared to be extracellular fibrils (see Supplementary Fig. S1 in IJSEM Online). Phenotypic characteristics of strain EMB34T are presented in Table 1
and in the description of the novel species. Some of the characteristics are in accordance with those of members of the genus Flavobacterium, whereas others allow the differentiation of strain EMB34T from closely related Flavobacterium species (Table 1
).
|
Description of Flavobacterium filum sp. nov.
Flavobacterium filum [fi'lum. L. neut. n. filum (nominative in apposition), a thread, a Flavobacterium species called the thread].
Cells are Gram-negative straight rods, 0.4–0.7 µm in width and 1.3–1.8 µm in length, linked by extracellular fibrils and devoid of flagellar and gliding motility. Colonies on R2A agar are pale-yellow, glistening, translucent, sticky, slightly raised and circular with entire margins. Growth occurs at 10–40 °C (optimum, 25–35 °C) and at pH 6.0–9.5 (optimum, 7.5–8.0). Nitrate is reduced to nitrite and nitrogen is produced. Oxidase-negative and catalase-positive. Grows at 30 °C on R2A agar, Luria–Bertani agar and trypticase soy agar (Difco), but not on nutrient agar (Difco) at 30 °C. Grows optimally on R2A agar without addition of NaCl; growth is severely inhibited on R2A agar containing more than 2.0 % (w/v) NaCl. No anaerobic growth after 7 days on R2A agar, but weak growth occurs after 16 days, suggesting that growth may occur by anaerobic respiration using nitrate or nitrite as an electron acceptor. Casein is hydrolysed. Gelatin, Tween 80, Tween 20, aesculin, urea, tyrosine, starch and carboxymethylcellulose are not hydrolysed. Congo red is not absorbed by colonies and flexirubin-type pigments are not produced. Indole, H2S and acetoin are not produced and citrate is not utilized (API 20E kit). Acid is produced from raffinose, D-glucose, myo-inositol, lactose and melibiose, but not from D-fructose, D-galactose, D-mannose, D-mannitol, L-arabinose, arbutin or salicin. In API ZYM kits, leucine arylamidase is produced, but esterase (C4), lipase (C14), cystine arylamidase,
-chymotrypsin,
-galactosidase,
-galactosidase,
-glucuronidase,
-glucosidase,
-glucosidase, N-acetyl-
-glucosaminidase,
-mannosidase,
-fucosidase, acid phosphatase, tryptophan deaminase, arginine dihydrolase, lysine decarboxylase, ornithine decarboxylase and urease are not produced. Weak enzymic activities are observed for alkaline phosphatase, esterase lipase (C8), valine arylamidase, trypsin and naphthol-AS-BI-phosphohydrolase. Resistant to polymyxin B, oleandomycin and neomycin, but sensitive to ampicillin, streptomycin, penicillin G, chloramphenicol, tetracycline, lincomycin, carbenicillin, novobiocin, gentamicin and kanamycin. Contains a large amount of phosphatidylethanolamine and a small amount of phosphatidylinositol as the polar lipids. The major isoprenoid quinone is MK-6. The cellular fatty acids are iso-C15 : 0 (19.7 %), C15 : 0 (17.2 %), iso-C15 : 1 G (16.8 %), iso-C16 : 0 3-OH (9.7 %), iso-C15 : 0 3-OH (9.2 %), iso-C16 : 0 (5.8 %), anteiso-C15 : 0 (3.7 %), iso-C14 : 0 (3.5 %), iso-C17 : 0 3-OH (3.5 %), C15 : 0 3-OH (1.9 %), C15 : 1
6c (1.8 %), iso-C16 : 1 H (1.5 %), iso-C14 : 0 3-OH (1.5 %), C16 : 0 (1.5 %), C16 : 0 3-OH (1.2 %), C14 : 0 (1.0 %) and iso-C13 : 0 (0.7 %). The G+C content of the DNA of the type strain is 34.2 mol% (HPLC).
The type strain is EMB34T (=KCTC 12610T=DSM 17961T), which was isolated in Korea from a wastewater treatment plant that performed enhanced biological phosphorus removal.
| ACKNOWLEDGEMENTS |
|---|
| REFERENCES |
|---|
|
|
|---|
Bergey, D. H., Harrison, F. C., Breed, R. S., Hammer, B. W. & Huntoon, F. M. (1923). Bergey's Manual of Determinative Bacteriology, 1st edn. Baltimore, MD: Williams & Wilkins.
Bernardet, J.-F., Segers, P., Vancanneyt, M., Berthe, F., Kersters, K. & Vandamme, P. (1996). Cutting a Gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 46, 128–148.
Bernardet, J. F., Nakagawa, Y. & Holmes, B. (2002). Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52, 1049–1070.[Abstract]
Cousin, S., Pauker, O. & Stackebrandt, E. (2007). Flavobacterium aquidurense sp. nov. and Flavobacterium hercynium sp. nov., from a hard-water creek. Int J Syst Evol Microbiol 57, 243–249.
Felsenstein, J. (2002). PHYLIP (phylogeny inference package), version 3.6a. Department of Genome Sciences, University of Washington, Seattle, USA.
Gerhardt, P., Murray, R. G. M., Wood, W. A. & Krieg, N. R. (1994). Phenotypic characterization. In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by P. Gerhardt. Washington DC: American Society for Microbiology.
Gomori, G. (1955). Preparation of buffers for use in enzyme studies. Methods Enzymol 1, 138–146.[CrossRef]
Humphry, D. R., George, A., Black, G. W. & Cummings, S. P. (2001). Flavobacterium frigidarium sp. nov., an aerobic, psychrophilic, xylanolytic and laminarinolytic bacterium from Antarctica. Int J Syst Evol Microbiol 51, 1235–1243.[Abstract]
Jeon, C. O., Lim, J. M., Lee, J. M., Xu, L. H., Jiang, C. L. & Kim, C. J. (2005). Reclassification of Bacillus haloalkaliphilus Fritze 1996 as Alkalibacillus haloalkaliphilus gen. nov., comb. nov. and the description of Alkalibacillus salilacus sp. nov., a novel halophilic bacterium isolated from a salt lake in China. Int J Syst Evol Microbiol 55, 1891–1896.
Kämpfer, P., Young, C. C., Sridhar, K. R., Arun, A. B., Lai, W. A., Shen, F. T. & Rekha, P. D. (2006). Transfer of [Flexibacter] sancti, [Flexibacter] filiformis, [Flexibacter] japonensis and [Cytophaga] arvensicola to the genus Chitinophaga and description of Chitinophaga skermanii sp. nov. Int J Syst Evol Microbiol 56, 2223–2228.
Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111–120.[CrossRef][Medline]
Komagata, K. & Suzuki, K. (1987). Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19, 161–207.
Lane, D. J. (1991). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. Edited by E. Stackebrandt & M. Goodfellow. Chichester, UK: John Wiley and Sons.
Lanyi, B. (1987). Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19, 1–67.
Leifson, E. (1963). Determination of carbohydrate metabolism of marine bacteria. J Bacteriol 85, 1183–1184.
McCammon, S. A. & Bowman, J. P. (2000). Taxonomy of Antarctic Flavobacterium species: description of Flavobacterium gillisiae sp. nov., Flavobacterium tegetincola sp. nov., and Flavobacterium xanthum sp. nov., nom. rev. and reclassification of [Flavobacterium] salegens as Salegentibacter salegens gen. nov., comb. nov. Int J Syst Evol Microbiol 50, 1055–1063.[Abstract]
Park, M., Lu, S., Ryu, S. H., Chung, B. S., Park, W., Kim, C. J. & Jeon, C. O. (2006). Flavobacterium croceum sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 56, 2443–2447.
Park, M., Ryu, S. H., Vu, T. H., Ro, H. S., Yun, P. Y. & Jeon, C. O. (2007). Flavobacterium defluvii sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 57, 233–237.
Tamaki, H., Hanada, S., Kamagata, Y., Nakamura, K., Nomura, N., Nakano, K. & Matsumura, M. (2003). Flavobacterium limicola sp. nov., a psychrophilic, organic-polymer-degrading bacterium isolated from freshwater sediments. Int J Syst Evol Microbiol 53, 519–526.
Tamaoka, J. & Komagata, K. (1984). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25, 125–128.[CrossRef]
Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.
Van Trappen, S., Vandecandelaere, I., Mergaert, J. & Swings, J. (2004). Flavobacterium degerlachei sp. nov., Flavobacterium frigoris sp. nov. and Flavobacterium micromati sp. nov., novel psychrophilic bacteria isolated from microbial mats in Antarctic lakes. Int J Syst Evol Microbiol 54, 85–92.
Van Trappen, S., Vandecandelaere, I., Mergaert, J. & Swings, J. (2005). Flavobacterium fryxellicola sp. nov. and Flavobacterium psychrolimnae sp. nov., novel psychrophilic bacteria isolated from microbial mats in Antarctic lakes. Int J Syst Evol Microbiol 55, 769–772.
Wang, Z.-W., Liu, Y.-H., Dai, X., Wang, B.-J., Jiang, C.-Y. & Liu, S.-J. (2006). Flavobacterium saliperosum sp. nov., isolated from freshwater lake sediment. Int J Syst Evol Microbiol 56, 439–442.
Yoon, J.-H., Kang, S.-J. & Oh, T.-K. (2006). Flavobacterium soli sp. nov., isolated from soil. Int J Syst Evol Microbiol 56, 997–1000.
Zhang, D. C., Wang, H. X., Liu, H. C., Dong, X. Z. & Zhou, P. J. (2006). Flavobacterium glaciei sp. nov., a novel psychrophilic bacterium isolated from the China No.1 glacier. Int J Syst Evol Microbiol 56, 2921–2925.
Zhu, F., Wang, S. & Zhou, P. (2003). Flavobacterium xinjiangense sp. nov. and Flavobacterium omnivorum sp. nov., novel psychrophiles from the China No. 1 glacier. Int J Syst Evol Microbiol 53, 853–857.
This article has been cited by other articles:
![]() |
H. S. Yoon, Z. Aslam, G. C. Song, S. W. Kim, C. O. Jeon, T. S. Chon, and Y. R. Chung Flavobacterium sasangense sp. nov., isolated from a wastewater stream polluted with heavy metals Int J Syst Evol Microbiol, May 1, 2009; 59(5): 1162 - 1166. [Abstract] [Full Text] [PDF] |
||||
![]() |
Y. Shao, B. S. Chung, S. S. Lee, W. Park, S.-S. Lee, and C. O. Jeon Zoogloea caeni sp. nov., a floc-forming bacterium isolated from activated sludge Int J Syst Evol Microbiol, March 1, 2009; 59(3): 526 - 530. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. H. Ryu, J. H. Park, J. C. Moon, Y. Sung, S.-S. Lee, and C. O. Jeon Flavobacterium resistens sp. nov., isolated from stream sediment Int J Syst Evol Microbiol, October 1, 2008; 58(10): 2266 - 2270. [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 | |