|
|
||||||||
Biological Resource Center (NBRC), Department of Biotechnology, National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
Correspondence
Yasuyoshi Nakagawa
nakagawa{at}nbrc.nite.go.jp
| ABSTRACT |
|---|
|
|
|---|
Tables detailing the sources of the isolates, their cellular fatty acid contents and variable phenotypic characteristics between isolates are available as supplementary material in IJSEM Online.
| MAIN TEXT |
|---|
|
|
|---|
During a survey of microbial communities within subtropical zones of Japan (Nakagawa, 2004
), five strains, IR25-3T, IR27-3, IR28-1, IS22-1 and IS26-1, were isolated from seaweeds, coastal sands and dead leaves. These samples were collected along the seashores of Iriomote and Ishigaki Islands in October 2001 (see Supplementary Table S1 in IJSEM Online). These islands are located at 24° 20' N 123° 45' E and 24° 20' N 124° 9' E, respectively and belong to the Yaeyama Island group. In this paper, we describe taxonomic studies on the five novel strains and M. arenaria NBRC 15982.
Genomic DNA extraction and 16S rRNA gene sequencing were conducted according to previously published procedures (Nakagawa et al., 2002
). Sequence data obtained were aligned with those of representative members of the phylum Bacteroidetes by using CLUSTAL_X (Thompson et al., 1997
) and then manually aligned following the 16S rRNA secondary structure of Escherichia coli (Gutell et al., 1994
) by using the Se-Al v2.0 alignment editor (available at http://evolve.zoo.ox.ac.uk/). A phylogenetic tree was constructed on the basis of the neighbour-joining method (Saitou & Nei, 1987
) and Knuc values (Kimura, 1980
) (Fig. 1)
. The topology of the tree was evaluated by bootstrap analysis (Felsenstein, 1985
) using 1000 replicates. The almost-complete 16S rRNA gene sequences, ranging from E. coli equivalent positions (Brosius et al., 1978
) 28 to 1494, were determined for the five novel isolates and for F. aprica NBRC 15941T. All of the novel isolates showed identical 16S rRNA gene sequences. Phylogenetic analysis of strain IR25-3T and M. arenaria NBRC 15982 revealed that they were closely related to the genus Flammeovirga. 16S rRNA gene sequence similarities between F. aprica NBRC 15941T and strain IR25-3T and M. arenaria NBRC 15982 were 95.2 and 98.1 %, respectively. Gene sequence similarity between strain IR25-3T and M. arenaria NBRC 15982 was 95.9 %.
|
The G+C content of DNA was determined according to Mesbah et al. (1989)
. The DNA G+C contents of the novel isolates were 33.435.7 mol%. The value for M. arenaria NBRC 15982 was 31.8 mol%. These values were similar to the value of 34.2 mol% obtained in this study for F. aprica NBRC 15941T. To determine whole-cell fatty acid content, all strains were grown on Bacto marine agar 2216 (Difco) at 25 °C for 24 h. Fatty acid methyl esters were prepared and analysed according to the standard protocol of the Microbial Identification System (Microbial ID). F. aprica NBRC 15941T, M. arenaria NBRC 15982 and the novel isolates had similar fatty acid contents in which the dominant fatty acids were iso-C15 : 0, C20 : 4
6,9,12,15c and C16 : 0 3-OH (see Supplementary Table S2 in IJSEM Online). The presence of arachidonic acid (C20 : 4
6,9,12,15c) was confirmed by using a GC-MS (5973 Network MSD; Agilent) with commercially available standards. Respiratory quinones were extracted according to Nakagawa & Yamasato (1993)
and determined by using a LC-MS (8000
; Shimadzu). MK-7 was found to be the major respiratory quinone in all strains. Using the bathochromic shift test with 20 % (w/v) KOH (Fautz & Reichenbach, 1980
), no flexirubin-type pigments were detected in any of the strains. Carotenoids were extracted as described by Schmidt et al. (1994)
and their light absorption spectra were investigated by using a UV-visible spectrophotometer (UV-1650PC; Shimadzu). It has been previously reported that F. aprica NBRC 15941T and M. arenaria NBRC 15982 contained saproxanthin (Reichenbach, 1989a
, b
). In this study, the carotenoids of the novel isolates were identified as saproxanthin as they showed identical spectra to those of F. aprica NBRC 15941T and M. arenaria NBRC 15982. Cellular polyamines were prepared and analysed according to Hamana et al. (1995)
. In addition to cadaverine, spermidine and agmatine were detected for the novel isolates when they were cultivated on Bacto marine agar. It has been previously reported that putrescine, cadaverine, spermidine and agmatine are present in M. arenaria NBRC 15982 (Hosoya & Hamana, 2003
).
Gliding motility was determined as described by Perry (1973)
. Anaerobic growth was examined by using the Anaeropack system (Mitsubishi Gas Chemical). The ability of strains to degrade agar, alginic acid, casein, cellulose, carboxymethylcellulose, chitin, DNA, inulin, aesculin, gelatin, starch, Tween 80, tyrosine and urea was investigated according to the methods of Lewin & Lounsbery (1969)
, Smibert & Krieg (1981)
and Barrow & Feltham (1993)
with media prepared with Daigo's artificial seawater SP (Wako Pure Chemicals). Production of indole, H2S and the activities of oxidase, urease and nitrate reductase were also examined as described by Smibert & Krieg (1981)
. Oxidation or fermentation of glucose (OF test; Hugh & Leifson, 1953
) was investigated by using OF basal media (Eiken Kizai) prepared with artificial seawater. For growth responses at different temperatures (545 °C) and pH (311), one-fifth strength LBM medium was used (Suzuki et al., 2001
) for cultivation. The potential of the strains to metabolize 95 different carbon sources was examined by using GN2 Microplates (Biolog) with the method modified for marine bacteria as described by Rüger & Krambeck (1994)
. Acid production from various carbon sources was determined by using the API 50CH test (bioMérieux) with cells grown on a medium composed of 50 % CHB/E medium with artificial seawater (Lau et al., 2005
). The phenotypic characteristics of F. aprica NBRC 15941T, M. arenaria NBRC 15982 and the novel isolates are given in the genus and species descriptions and in Table 1
(see also Supplementary Table S3 in IJSEM Online).
|
Emended description of the genus Flammeovirga
Flammeovirga (Flam.me.o.vir'ga. L. adj. flammeus fire-coloured; L. fem. n. virga rod; L. fem. n. Flammeovirga fire-coloured rod).
Cells are Gram-negative, aerobic, chemo-organotrophic, asporogenic, long rods that are 0.40.9 µm wide and 1.796 µm long or longer. Motile by gliding. Cell mass is orange to reddish orange. Oxidase and catalase activities are variable. Major respiratory quinone is MK-7. Saproxanthin is present as the major carotenoid pigment. Flexirubin-type pigments are absent. Predominant cellular fatty acids are iso-C15 : 0, C20 : 4
6,9,12,15c and C16 : 0 3-OH. Members of the genus are marine organisms that require NaCl or seawater for growth. Growth is supported by NaCl alone. Nitrate is reduced. Agar, alginic acid, aesculin and starch are degraded. The G+C content of DNA is 3136 mol%. The type species of the genus is Flammeovirga aprica.
Emended description of Flammeovirga aprica
Flammeovirga aprica (a'pri.ca. L. fem. adj. aprica sunlit, sun-loving).
Displays the following properties in addition to those given in the genus description. Cells are long rods, 0.50.9 µm wide and 1.796 µm long or longer. Colonies spread and produce large gelase fields and deep craters in agar plates. Growth is detected at 1530 °C, with the optimum growth yield at 25 °C. The pH range for growth is 68 with the optimum growth yield at pH 7. Growth occurs at 15 % NaCl with the optimum growth yield at 3 %. Oxidase and catalase activities are positive. Urease activity is negative. Agar, alginic acid, carboxymethylcellulose, DNA, aesculin and starch are degraded, but cellulose, chitin, inulin, gelatin, Tween 80 and tyrosine are not degraded. Casein is weakly degraded. H2S is produced, but indole is not. OF test of glucose is fermentative. Utilization (Biolog GN2 microplate data) is observed for
-cyclodextrin, dextrin, L-fucose, glycogen, D-galactose, gentiobiose,
-D-glucose, DL-lactic acid,
-D-lactose, D-trehalose, lactulose, maltose, glucose 1-phosphate, cellobiose, D-mannose, monomethyl succinate, glycyl L-glutamic acid and glucose 6-phosphate, but not for D-melibiose, urocanic acid, L-ornithine, L-rhamnose, L-alanyl glycine, N-acetyl-D-glucosamine or L-threonine. Acid production (API 50CH data) is positive for D-xylose, galactose, N-acetylglucosamine, amygdalin, aesculin, salicin, cellobiose, maltose, lactose, starch, glycogen and gentiobiose and weakly positive for ribose, glucose, mannose and L-fucose. Acid is not produced from rhamnose, mannitol, sorbitol, methyl
-D-glucoside, arbutin, melibiose, melezitose, raffinose or xylitol. The major cellular fatty acids are iso-C15 : 0, C20 : 4
6,9,12,15c, C16 : 0 3-OH and C14 : 0. The DNA G+C content of the type strain is 34.2 mol%.
The type strain is NBRC 15941T (=ATCC 23126T=CIP 104807T).
Description of Flammeovirga arenaria nom. rev., comb. nov.
Synonym: Microscilla arenaria Lewin 1969
Flammeovirga arenaria (a.re.na'ria. L. fem. adj. arenarius pertaining to sand, referring to the source of the organism).
Displays the following properties in addition to those given in the genus description. Cells are long rods, 0.50.9 µm wide and 2.040 µm long or longer. Cell mass is orange. Colonies spread and produce large gelase fields and deep craters in agar plates. Growth is detected at 1030 °C with the optimum growth yield at 25 °C. The pH range for growth is 68 with the optimum growth yield at pH 7. Growth occurs at 15 % NaCl with the optimum growth yield at 3 %. Oxidase, catalase and urease activities are negative. Agar, alginic acid, aesculin and starch are degraded, but carboxymethylcellulose, cellulose, chitin, DNA, inulin, gelatin, Tween 80 and tyrosine are not degraded. Casein is weakly degraded. H2S is produced, but indole is not. OF test of glucose is oxidative. Utilization (Biolog GN2 microplate data) is observed for D-melibiose,
-cyclodextrin, dextrin, L-fucose, glycogen, D-galactose, gentiobiose,
-D-glucose, N-acetyl-D-glucosamine,
-D-lactose, lactulose, maltose, L-glutamic acid, glycyl L-aspartic acid, glucose 1-phosphate, cellobiose, D-mannose, glycyl L-glutamic acid and glucose 6-phosphate. Weakly positive for utilization of alaninamide, L-ornithine, DL-lactic acid, L-alanine, L-alanyl glycine, L-aspartic acid and L-threonine, but negative for urocanic acid, L-rhamnose and monomethyl succinate. Acid production (API 50CH data) is positive for galactose, glucose, mannose, N-acetylglucosamine, amygdalin, arbutin, aesculin, cellobiose, maltose, lactose, melibiose, trehalose, starch, glycogen, gentiobiose and L-fucose and weakly positive for ribose, fructose, mannitol, sorbitol, methyl
-D-mannoside, methyl
-D-glucoside, salicin, sucrose, melezitose, raffinose, xylitol and 5-ketogluconate. Acid is not produced from D-xylose or rhamnose. The major cellular fatty acids are iso-C15 : 0, C14 : 0, C16 : 0 3-OH, C20 : 4
6,9,12,15c, C16 : 1
5c and iso-C15 : 0 3-OH. The DNA G+C content of the type strain is 31.8 mol%.
The type strain is NBRC 15982T (=CIP 109101T).
Description of Flammeovirga yaeyamensis sp. nov.
Flammeovirga yaeyamensis (ya.e.ya.men'sis. N.L. fem. adj. yaeyamensis referring to the Yaeyama Islands, from where the organisms were isolated).
Displays the following properties in addition to those given in the genus description. Cells are long rods, 0.40.9 µm wide and 1.790 µm long or longer. Cell mass is orange. Colonies spread and produce large gelase fields and deep craters in agar plates. Growth is detected at 1535 °C with the optimum growth yield at 30 °C. The pH range for growth is 610 with the optimum growth yield at pH 7. Growth occurs at 15 % NaCl with the optimum growth yield at 3 %. Oxidase activity is positive. Catalase activity is variable. Urease activity is negative. Agar, alginic acid, carboxymethylcellulose, DNA, aesculin, inulin, gelatin, starch and Tween 80 are degraded, but casein, cellulose, chitin and tyrosine are not degraded. H2S is produced, but indole is not. OF test of glucose is fermentative. Utilization (Biolog GN2 microplate data) is observed for D-melibiose, urocanic acid, D-galactose, gentiobiose, L-rhamnose, N-acetyl-D-glucosamine, cellobiose and glycyl L-glutamic acid. Positive or weakly positive for L-ornithine,
-D-glucose, L-alanyl glycine, maltose and L-threonine, but negative for glucose 1-phosphate, monomethyl succinate and glucose 6-phosphate. Acid production (API 50CH data) is positive for D-xylose, galactose, glucose, mannose, rhamnose, N-acetylglucosamine, amygdalin, arbutin, aesculin, salicin, cellobiose, maltose, lactose, melibiose, starch, glycogen and gentiobiose. Positive or weakly positive for methyl
-D-glucoside, raffinose, xylitol and L-fucose. Acid is not produced from ribose, mannitol, sorbitol or melezitose. The major cellular fatty acids are iso-C15 : 0, C20 : 4
6,9,12,15c, C16 : 0 3-OH, iso-C15 : 0 3-OH, C16 : 0 and C14 : 0. The G+C content of DNA is 33.435.7 mol%.
The type strain is IR25-3T (=NBRC 100898T=CIP 109099T). Four other strains, IR27-3 (=NBRC 100899), IR28-1 (=NBRC 100900), IS22-1 (=NBRC 100901) and IS26-1 (=NBRC 100902), are available as reference strains.
| ACKNOWLEDGEMENTS |
|---|
| REFERENCES |
|---|
|
|
|---|
Brosius, J., Palmer, M. L., Kennedy, P. J. & Noller, H. F. (1978). Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A 75, 48014805.
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, 224229.
Fautz, E. & Reichenbach, H. (1980). A simple test for flexirubin-type pigments. FEMS Microbiol Lett 8, 8791.
Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783791.[CrossRef]
Gutell, R. R., Larsen, N. & Woese, C. R. (1994). Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev 58, 1026.
Hamana, K., Nakagawa, Y. & Yamasato, K. (1995). Chemotaxonomic significance of polyamine distribution patterns in the Flavobacterium-Cytophaga complex and related genera. Microbios 81, 135145.
Hosoya, R. & Hamana, K. (2003). Absence of cellular triamines in four novel flavobacteria located in FlavobacteriumFlexibacterCytophaga complex. Ann Gunma Health Sci 24, 1316.
Hugh, R. & Leifson, E. (1953). The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various Gram negative bacteria. J Bacteriol 66, 2426.
Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111120.[CrossRef][Medline]
Lau, K. W. K., Ng, C. Y. M., Ren, J., Lau, S. C. L., Qian, P.-Y., Wong, P.-K., Lau, T. C. & Wu, M. (2005). Owenweeksia hongkongensis gen. nov., sp. nov., a novel marine bacterium of the phylum Bacteroidetes. Int J Syst Evol Microbiol 55, 10511057.
Lewin, R. A. (1969). A classification of flexibacteria. J Gen Microbiol 58, 189206.[Medline]
Lewin, R. A. & Lounsbery, D. M. (1969). Isolation, cultivation and characterization of flexibacteria. J Gen Microbiol 58, 145170.[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, 159167.
Nakagawa, Y. (2004). Taxonomic studies of Cytophaga-like bacteria. Microbiol Cult Coll 20, 4151.
Nakagawa, Y. & Yamasato, K. (1993). Phylogenetic diversity of the genus Cytophaga revealed by 16S rRNA sequencing and menaquinone analysis. J Gen Microbiol 139, 11551161.
Nakagawa, Y., Hamana, K., Sakane, T. & Yamasato, K. (1997). Reclassification of Cytophaga aprica (Lewin 1969
) Reichenbach 1989 in Flammeovirga gen. nov. as Flammeovirga aprica comb. nov. and of Cytophaga diffluens (ex Stanier 1940; emend. Lewin 1969
) Reichenbach 1989 in Persicobacter gen. nov. as Persicobacter diffluens comb. nov. Int J Syst Bacteriol 47, 220223.
Nakagawa, Y., Sakane, T., Suzuki, M. & Hatano, K. (2002). Phylogenetic structure of the genera Flexibacter, Flexithrix, and Microscilla deduced from 16S rRNA sequence analysis. J Gen Appl Microbiol 48, 155165.
Perry, L. B. (1973). Gliding motility in some non-spreading flexibacteria. J Appl Microbiol 36, 227232.
Reichenbach, H. (1989a). Genus I Cytophaga Winogradsky 1929, 577AL, emend. In Bergey's Manual of Systematic Bacteriology, vol. 3, pp. 20152050. Edited by J. T. Staley, M. P. Bryant, N. Pfennig & J. G. Holt. Baltimore: Williams & Wilkins.
Reichenbach, H. (1989b). Genus Microscilla Pringsheim 1951, 140, emend. Lewin 1969
, 194AL. In Bergey's Manual of Systematic Bacteriology, vol. 3, pp. 20712073. Edited by J. T. Staley, M. P. Bryant, N. Pfennig & J. G. Holt. Baltimore: Williams & Wilkins.
Rüger, H.-J. & Krambeck, H.-J. (1994). Evaluation of the BIOLOG substrate metabolism system for classification of marine bacteria. Syst Appl Microbiol 17, 281288.
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406425.[Abstract]
Schmidt, K., Connor, A. & Britton, G. (1994). Analysis of pigments: carotenoids and related polyenes. In Chemical Methods in Prokaryotic Systematics, pp. 403461. Edited by M. Goodfellow & A. G. O'Donnell. West Sussex: Wiley.
Smibert, R. M. & Krieg, N. R. (1981). General characterization. In Manual of Methods for General Bacteriology, pp. 409443. Edited by P. Gerhardt, R. G. E. Murray, R. N. Costilow, E. W. Nester, W. A. Wood, N. R. Krieg & G. B. Phillips. Washington, DC: American Society for Microbiology.
Suzuki, M., Nakagawa, Y., Harayama, S. & Yamamoto, S. (2001). Phylogenetic analysis and taxonomic study of marine Cytophaga-like bacteria: proposal for Tenacibaculum gen. nov. with Tenacibaculum maritimum comb. nov. and Tenacibaculum ovolyticum comb. nov., and description of Tenacibaculum mesophilum sp. nov. and Tenacibaculum amylolyticum sp. nov. Int J Syst Evol Microbiol 51, 16391652.[Abstract]
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, 48764882.
This article has been cited by other articles:
![]() |
J. Yoon, Y. Matsuo, H. Kasai, and A. Yokota Limibacter armeniacum gen. nov., sp. nov., a novel representative of the family 'Flammeovirgaceae' isolated from marine sediment Int J Syst Evol Microbiol, April 1, 2008; 58(4): 982 - 986. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Hosoya, V. Arunpairojana, C. Suwannachart, A. Kanjana-Opas, and A. Yokota Aureispira maritima sp. nov., isolated from marine barnacle debris Int J Syst Evol Microbiol, September 1, 2007; 57(9): 1948 - 1951. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. T. Khan, Y. Nakagawa, and S. Harayama Sediminitomix flava gen. nov., sp. nov., of the phylum Bacteroidetes, isolated from marine sediment Int J Syst Evol Microbiol, August 1, 2007; 57(8): 1689 - 1693. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Hosoya and A. Yokota Flammeovirga kamogawensis sp. nov., isolated from coastal seawater in Japan Int J Syst Evol Microbiol, June 1, 2007; 57(6): 1327 - 1330. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. Yoon, S. Ishikawa, H. Kasai, and A. Yokota Perexilibacter aurantiacus gen. nov., sp. nov., a novel member of the family 'Flammeovirgaceae' isolated from sediment Int J Syst Evol Microbiol, May 1, 2007; 57(5): 964 - 968. [Abstract] [Full Text] [PDF] |
||||
![]() |
O. I. Nedashkovskaya, S. B. Kim, D. S. Shin, I. A. Beleneva, and V. V. Mikhailov Fulvivirga kasyanovii gen. nov., sp. nov., a novel member of the phylum Bacteroidetes isolated from seawater in a mussel farm Int J Syst Evol Microbiol, May 1, 2007; 57(5): 1046 - 1049. [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 | |