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1 Division of Applied Life Science, EB-NCRC, PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
2 Department of Microbiology and Research Institute of Life Science, Gyeongsang National University, Jinju 660-701, Republic of Korea
3 Jeju Hi-Tech Industry Development Institute, 4-8 Ara-1 dong, Jeju 690-121, Republic of Korea
Correspondence
Che Ok Jeon
cojeon{at}gnu.ac.kr
| ABSTRACT |
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7c and/or iso-C15 : 0 2-OH). The G+C content of the genomic DNA was 33.5 mol% and the major isoprenoid quinone was MK-6. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain EMB117T belonged to the genus Flavobacterium and was most closely related to Flavobacterium johnsoniae DSM 425T (97.8 % sequence similarity). The DNADNA relatedness between strain EMB117T and F. johnsoniae ATCC 17061T was about 18 %. On the basis of the phenotypic, chemotaxonomic and molecular data, strain EMB117T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium defluvii sp. nov. is proposed. The type strain is EMB117T (=KCTC 12612T=DSM 17963T).
A transmission electron micrograph of cells of strain EMB117T is available as a supplementary figure in IJSEM Online.
| MAIN TEXT |
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Strain EMB117T was isolated from activated sludge from a domestic wastewater treatment plant in Pohang, Korea. The sludge sample was diluted serially with 1 % (w/v) saline solution and spread on R2A (Difco) agar at 20 °C for 2 days. Subculturing was done using R2A agar at 30 °C for 1 day.
Sequencing of the 16S rRNA gene was carried out as described previously (Lane, 1991
). The resulting 16S rRNA gene sequence (1436 nt) of strain EMB117T was compared with 16S available rRNA gene sequences (from GenBank), using the BLAST program (http://www.ncbi.nlm.nih.gov/blast/) to determine an approximate phylogenetic affiliation; gene sequences were aligned with those of closely related species using CLUSTAL W software (Thompson et al., 1994
). Phylogenetic trees were constructed using the neighbour-joining, maximum-likelihood and maximum-parsimony algorithms available in PHYLIP software, version 3.6 (Felsenstein, 2002
). The values for sequence similarity between the novel strain and related members of the genus Flavobacterium were computed using SIMILARITY MATRIX, version 1.1 (Ribosomal Database Project II; http://35.8.164.52/html/; Cole et al., 2003
). A bootstrap analysis was performed according to the Kimura two-parameter model (Kimura, 1980
) of the neighbour-joining method in the PHYLIP package. The phylogenetic analysis based on 16S rRNA gene sequences indicated that strain EMB117T formed a phyletic lineage with Flavobacterium johnsoniae DSM 425T with a relatively low bootstrap value (62.0 %) (Fig. 1
). The overall tree topology of the neighbour-joining tree was supported by the maximum-likelihood and maximum-parsimony trees (data not shown). Comparative 16S rRNA gene sequence analyses showed that the isolate was most closely related to F. johnsoniae DSM 425T, with a 16S rRNA gene sequence similarity of 97.8 %; the sequence similarities with respect to other Flavobacterium species were less than 97.0 %.
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The DNA G+C content of strain EMB117T, determined using HPLC apparatus fitted with a reversed-phase column (GROM-SIL 100 ODS-2FE; Grom) according to the method of Tamaoka & Komagata (1984)
, was found to be 33.5 mol%.
Analysis of the fatty acid methyl esters was performed according to the instructions of the Microbial Identification System (MIDI; Microbial ID). Analyses of polar lipids and isoprenoid quinones were carried out using the methods described by Komagata & Suzuki (1987)
. The cellular membrane contained iso-C15 : 0 (19.8 %), iso-C17 : 0 3-OH (13.1 %), iso-C15 : 0 3-OH (11.2 %), iso-C15 : 1 G (7.6 %), C15 : 0 (6.4 %) and summed feature 3 (C16 : 1
7c and/or iso-C15 : 0 2-OH, 10.1 %) as the major fatty acids. The polar lipid composition was dominated by phosphatidylethanolamine. The major respiratory lipoquinone of strain EMB117T was MK-6. The fatty acid composition, the major lipoquinone and polar lipid and the DNA G+C content of strain EMB117T are in accordance with those of members of the genus Flavobacterium (Bernardet et al., 2002
; Van Trappen et al., 2004
, 2005
; Aslam et al., 2005
; Wang et al., 2006
; Yoon et al., 2006
).
Gram staining was performed using a bioMérieux Gram-stain kit according to the manufacturer's instructions. Cell morphology, flagellation and gliding motility were studied using phase-contrast microscopy and transmission electron microscopy (JEM-1010; JEOL) as described previously (Bernardet et al., 2002
; Jeon et al., 2005
). The physiological characteristics of strain EMB117T were examined by growing the isolate in R2A broth at various temperatures and pH values. R2A media with different pH values were prepared as described previously (Gomori, 1955
). Salt tolerance was tested using R2A broth supplemented with 03 % (w/v) NaCl for 5 days at 30 °C. Duplicate antibiotic tests were performed using the diffusion method on R2A agar at 30 °C with filter-paper discs (8 mm diameter) containing the following antibiotics: ampicillin (10 µg), polymyxin B (100 U), streptomycin (50 µg), penicillin G (10 IU), chloramphenicol (100 µg), gentamicin (30 µg), tetracycline (30 µg), kanamycin (30 µg), lincomycin (15 µg), oleandomycin (15 µg), neomycin (30 µg), carbenicillin (100 µg) and novobiocin (50 µg). The diameters of inhibition zones were measured after 2 days. Oxidase activity was tested by determining the oxidation of 1 % (w/v) tetramethyl-p-phenylenediamine (Merck) and catalase activity was evaluated by determining the production of oxygen bubbles in a 3 % (v/v) aqueous hydrogen peroxide solution. The production of flexirubin-type pigments and extracellular glycans was investigated using the KOH and the Congo red tests, respectively, according to the minimal standards for the description of novel taxa in the family Flavobacteriaceae (Bernardet et al., 2002
). The hydrolysis of casein, gelatin, Tweens 80 and 20, aesculin, urea, tyrosine, starch and carboxylmethylcellulose was investigated on R2A agar after 7 days incubation, according to methods described previously (Lanyi, 1987
; Gerhardt et al., 1994
). Nitrate reduction was determined according to the method of Lanyi (1987)
, and acid production from carbohydrates was tested as described by Leifson (1963)
. Additional enzymic activities and biochemical features were determined using API ZYM and API 20E kits (bioMérieux) at 30 °C. Growth under anaerobic conditions was determined in an anaerobic chamber (H2/CO2/N2, 5 : 10 : 85) at 30 °C on R2A agar.
Anaerobic growth was not observed after 7 days at 30 °C on R2A agar, but the strain showed weak growth after 16 days. As strain EMB117T did not reduce nitrate to nitrite, it was unable to grow by anaerobic respiration using nitrate or nitrite as an electron acceptor, as reported for Flavobacterium denitrificans (Horn et al., 2005
) and some F. johnsoniae strains (Stanier, 1947
). Consequently, strain EMB117T probably grew anaerobically by fermenting carbohydrates, as reported for Flavobacterium hydatis (Strohl & Tait, 1978
) and Flavobacterium succinicans (Anderson & Ordal, 1961
).
The phenotypic features of strain EMB117T are presented in the species description. Strain EMB117T showed the characteristics typical of members of the genus Flavobacterium (Bernardet et al., 2002
) but could be differentiated from related Flavobacterium species by means of a number of traits, which are listed in Table 1
. The physiological, biochemical and phylogenetic data support the description of strain EMB117T as the type strain of a novel species within the genus Flavobacterium, for which the name Flavobacterium defluvii sp. nov. is proposed.
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Cells are Gram-negative, non-spore-forming rods, 0.40.5 µm wide and 2.36.5 µm long. Some cells show a knar (see Supplementary Fig. S1 available in IJSEM Online). Cells are devoid of flagella, but gliding motility is observed. Colonies on R2A agar are pale yellow, glistening, translucent, slightly sticky, irregular, slightly raised and have curled margins. Grows at 1040 °C (optimum, 2530 °C) and at pH 5.010.0 (optimum, pH 7.08.0). Grows optimally in plain R2A broth (no added NaCl) and in R2A broth to which 1 % (w/v) NaCl has been added. Growth in R2A broth is severely inhibited by the addition of more than 2 % (w/v) NaCl. Grows at 30 °C on R2A agar, LuriaBertani agar, tryptic soy agar (Difco) and nutrient agar (Difco). Grows well under aerobic conditions. Growth is weak and delayed under anaerobic conditions. Catalase-positive and oxidase-negative. Nitrate is not reduced to nitrite. Casein, Tween 20, urea, aesculin, gelatin and carboxylmethylcellulose are hydrolysed. Tween 80, tyrosine and starch are not hydrolysed. Congo red is not adsorbed by colonies, and flexirubin-type pigments are produced. Negative for indole, H2S and acetoin production and for citrate utilization (API 20E). Produces acid from raffinose, D-glucose, myo-inositol, lactose, L-arabinose, melibiose, D-fructose, D-galactose, D-mannose, D-mannitol and arbutin, but not from salicin. Produces alkaline phosphatase, leucine arylamidase, valine arylamidase, naphthol-AS-BI-phosphohydrolase,
-glucosidase,
-glucosidase and N-acetyl-
-glucosaminidase in API ZYM kits, but does not produce esterase (C4), lipase (C14), cystine arylamidase,
-chymotrypsin,
-galactosidase,
-glucuronidase,
-mannosidase or
-fucosidase. Weak enzymic activities are observed for esterase lipase (C8), trypsin, acid phosphatase and
-galactosidase. Resistant to polymyxin B, ampicillin, gentamicin, kanamycin, lincomycin, oleandomycin, neomycin, carbenicillin and novobiocin. Sensitive to streptomycin, penicillin G, chloramphenicol and tetracycline. Phosphatidylethanolamine is the predominant polar lipid. The major isoprenoid quinone is MK-6. The cellular fatty acids are iso-C15 : 0 (19.8 %), iso-C17 : 0 3-OH (13.1 %), iso-C15 : 0 3-OH (11.2 %), iso-C15 : 1 G (7.6 %), C15 : 0 (6.4 %), iso-C16 : 0 3-OH (5.6 %), C16 : 0 3-OH (4.5 %), anteiso-C15 : 0 (4.4 %), C17 : 1
6c (2.4 %), iso-C16 : 0 (2.3 %), iso-C17 : 0
9c (2.3 %), C15 : 0 3-OH (1.9 %), C16 : 0 (1.9 %), C17 : 0 3-OH (1.0 %), summed feature 2 (iso-C16 : 1 I and/or C14 : 0 3-OH, 1.2 %), summed feature 3 (C16 : 1
7c and/or iso-C15 : 0 2-OH, 10.1 %) and traces (<1 %) of C15 : 1
6c, iso-C14 : 0 and C17 : 1
8c. The DNA G+C content is 33.5 mol% (HPLC).
The type strain, EMB117T (=KCTC 12612T=DSM 17963T), was isolated from sludge that performed enhanced biological phosphorus removal in a laboratory-scale sequencing batch reactor.
| ACKNOWLEDGEMENTS |
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