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Int J Syst Evol Microbiol 57 (2007), 233-237; DOI  10.1099/ijs.0.64669-0
© 2007 International Union of Microbiological Societies

Flavobacterium defluvii sp. nov., isolated from activated sludge

Minjeong Park1, Seung Hyun Ryu1, Thu-Huong Thi Vu1, Hyeon-Su Ro2, Pil-Yong Yun3 and Che Ok Jeon1

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


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A Gram-negative bacterium, designated strain EMB117T, was isolated from a municipal wastewater treatment plant and characterized by polyphasic taxonomy. The cells were non-spore-forming rods that showed gliding motility. Optimal growth occurred at 25–30 °C and pH 7.0–8.0. Strain EMB117T contained phosphatidylethanolamine as the predominant polar lipid, and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and summed feature 3 (C16 : 1{omega}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 DNA–DNA 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).


The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain EMB117T is DQ372986.

A transmission electron micrograph of cells of strain EMB117T is available as a supplementary figure in IJSEM Online.


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Since the description of the genus Flavobacterium was emended by Bernardet et al. (1996)Go, many additional Flavobacterium species have been described from diverse environmental habitats, such as microbial mats from Antarctic lakes, freshwater, seawater, sea ice, soil, the gut of an earthworm, sediments and wastewater treatment plants (McCammon & Bowman, 2000Go; Van Trappen et al., 2002Go; Zhu et al., 2003Go; Horn et al., 2005Go; Kim et al., 2006Go; Yi & Chun, 2006Go). Their physiological characteristics are also very diverse: they can be psychrophilic, psychrotolerant or mesophilic, they can be halotolerant, halophilic or sensitive to salts and they produce a variety of enzymes (Humphry et al., 2001Go; Tamaki et al., 2003Go; Aslam et al., 2005Go). Hence, the genus Flavobacterium may have diverse environmental functions. Recently, a novel Gram-negative bacterium, designated strain EMB117T, was isolated from activated sludge from a domestic wastewater treatment plant. On the basis of phenotypic and phylogenetic investigations, EMB117T represents a novel species in the genus Flavobacterium.

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, 1991Go). 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., 1994Go). Phylogenetic trees were constructed using the neighbour-joining, maximum-likelihood and maximum-parsimony algorithms available in PHYLIP software, version 3.6 (Felsenstein, 2002Go). 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., 2003Go). A bootstrap analysis was performed according to the Kimura two-parameter model (Kimura, 1980Go) 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. 1Go). 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 %.


Figure 1
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Fig. 1. Neighbour-joining phylogenetic tree, based on 16S rRNA gene sequences, showing the phylogenetic relationships of strain EMB117T and related taxa. Bootstrap values are shown as percentages of 1000 replicates, when greater than 50 %. Capnocytophaga ochracea ATCC 33596T was used as an outgroup. Bar, 0.01 changes per nucleotide position.

 
DNA–DNA hybridization was carried out to evaluate the genomic DNA relatedness between strain EMB117T and F. johnsoniae ATCC 17061T. Extracted genomic DNAs were fragmented with HaeIII for slot hybridization (Lim et al., 2005Go). Digested DNAs were diluted serially and loaded into slots, with three replications, and each DNA was used individually as a labelled DNA probe for cross-hybridization. Random primed DNA labelling with digoxigenin–dUTP and hybridization (hybridization at 40 °C; washing at 60 °C) were performed using the DIG High Prime DNA labelling kit (Roche Applied Science) according to the manufacturer's instructions and standard procedures (Sambrook & Russell, 2001Go; Lim et al., 2005Go). Signals from the series of dilutions were quantified using GelDoc scanning software (Bio-Rad). The signals produced by self-hybridization were inferred as representing 100 %, and relatedness values (percentages) were calculated from triplicate samples. The DNA–DNA relatedness between strain EMB117T and F. johnsoniae ATCC 17061T was about 18 %, clearly below the 70 % threshold generally accepted for species delineation (Stackebrandt et al., 2002Go).

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)Go, 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)Go. 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{omega}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., 2002Go; Van Trappen et al., 2004Go, 2005Go; Aslam et al., 2005Go; Wang et al., 2006Go; Yoon et al., 2006Go).

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., 2002Go; Jeon et al., 2005Go). 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, 1955Go). Salt tolerance was tested using R2A broth supplemented with 0–3 % (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., 2002Go). 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, 1987Go; Gerhardt et al., 1994Go). Nitrate reduction was determined according to the method of Lanyi (1987)Go, and acid production from carbohydrates was tested as described by Leifson (1963)Go. 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., 2005Go) and some F. johnsoniae strains (Stanier, 1947Go). Consequently, strain EMB117T probably grew anaerobically by fermenting carbohydrates, as reported for Flavobacterium hydatis (Strohl & Tait, 1978Go) and Flavobacterium succinicans (Anderson & Ordal, 1961Go).

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., 2002Go) but could be differentiated from related Flavobacterium species by means of a number of traits, which are listed in Table 1Go. 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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Table 1. Differential characteristics of strain EMB117T and related Flavobacterium species

Taxa: 1, strain EMB117T; 2, F. johnsoniae (data from Bernardet etal., 1996Go); 3, F. denitrificans (Horn et al., 2005Go); 4, F. soli (Yoon et al., 2006Go); 5, F. daejeonense (Kim et al., 2006Go); 6, F. aquatile (Bernardet et al., 1996Go). Symbols: +, positive; –, negative; d, variable among strains; V, variable among references according to Bernardet et al. (1996)Go; (+), weakly positive; NA, no data available.

 
Description of Flavobacterium defluvii sp. nov.
Flavobacterium defluvii (de.flu'vi.i. L. gen. n. defluvii of sewage).

Cells are Gram-negative, non-spore-forming rods, 0.4–0.5 µm wide and 2.3–6.5 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 10–40 °C (optimum, 25–30 °C) and at pH 5.0–10.0 (optimum, pH 7.0–8.0). 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, Luria–Bertani 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, {alpha}-glucosidase, beta-glucosidase and N-acetyl-beta-glucosaminidase in API ZYM kits, but does not produce esterase (C4), lipase (C14), cystine arylamidase, {alpha}-chymotrypsin, {alpha}-galactosidase, beta-glucuronidase, {alpha}-mannosidase or {alpha}-fucosidase. Weak enzymic activities are observed for esterase lipase (C8), trypsin, acid phosphatase and beta-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{omega}6c (2.4 %), iso-C16 : 0 (2.3 %), iso-C17 : 0{omega}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{omega}7c and/or iso-C15 : 0 2-OH, 10.1 %) and traces (<1 %) of C15 : 1{omega}6c, iso-C14 : 0 and C17 : 1{omega}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
 
This work was supported by grants from MOST/KOSEF to the Environmental Biotechnology National Core Research Center (grant R15-2003-012-02002-0) and to the 21C Frontier Microbial Genomics and Application Center Program (grant MG05-0104-4-0), Ministry of Science and Technology, Korea. The first three authors were supported by scholarships from the BK21 program of the Ministry of Education and Human Resources Development in Korea.


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S. Lu, J. R. Lee, S. H. Ryu, B. S. Chung, W.-S. Choe, and C. O. Jeon
Runella defluvii sp. nov., isolated from a domestic wastewater treatment plant
Int J Syst Evol Microbiol, November 1, 2007; 57(11): 2600 - 2603.
[Abstract] [Full Text] [PDF]


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Int. J. Syst. Evol. Microbiol.Home page
S. H. Ryu, M. Park, Y. Jeon, J. R. Lee, W. Park, and C. O. Jeon
Flavobacterium filum sp. nov., isolated from a wastewater treatment plant in Korea
Int J Syst Evol Microbiol, September 1, 2007; 57(9): 2026 - 2030.
[Abstract] [Full Text] [PDF]


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