HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Abstract Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via CrossRef Citing Articles via Google Scholar Google Scholar Articles by Nedashkovskaya, O. I. Articles by Mikhailov, V. V. Search for Related Content PubMed PubMed Citation Articles by Nedashkovskaya, O. I. Articles by Mikhailov, V. V. Agricola Articles by Nedashkovskaya, O. I. Articles by Mikhailov, V. V.

Echinicola vietnamensis sp. nov., a member of the phylum Bacteroidetes isolated from seawater

¹ Pacific Institute of Bioorganic Chemistry of the Far-Eastern Branch of the Russian Academy of Sciences, Pr. 100 Let Vladivostoku 159, 690022, Vladivostok, Russia
² Department of Microbiology, School of Bioscience and Biotechnology, Chungnam National University, 220 Gung-dong, Yusong, Daejon 305-764, Republic of Korea
³ BCCM/LMG Bacteria Collection, and Laboratory of Microbiology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
⁴ Institute of Marine Biology of the Far-Eastern Branch of the Russian Academy of Sciences, Pal'chevskogo St. 17, 690032, Vladivostok, Russia

Correspondence
Olga I. Nedashkovskaya
olganedashkovska{at}piboc.dvo.ru
or
olganedashkovska{at}yahoo.com

	ABSTRACT

TOP ABSTRACT MAIN TEXT REFERENCES

 
The taxonomic position of a novel marine, heterotrophic, gliding, halotolerant and light-pink-pigmented bacterium, designated strain KMM 6221^T, was examined by using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain KMM 6221^T is affiliated with the genus Echinicola, a member of the phylum Bacteroidetes, with levels of similarity of 94.7–95.0 % to strains of Echinicola pacifica. Growth of strain KMM 6221^T was observed with 0–15 % NaCl and at 6–44 °C. The DNA G+C content of strain KMM 6221^T was 45.9 mol%. On the basis of molecular distinctiveness supported by phenotypic and chemotaxonomic data, strain KMM 6221^T is considered to represent a novel species of the genus Echinicola, for which the name Echinicola vietnamensis sp. nov. is proposed. The type strain is KMM 6221^T (=DSM 17526^T=LMG 23754^T).

	MAIN TEXT

TOP ABSTRACT MAIN TEXT REFERENCES

 
The genus Echinicola was proposed to accommodate heterotrophic, Gram-negative, gliding and pigmented bacteria with menaquinone-7 as the major respiratory quinone belonging to the phylum Bacteroidetes (Nedashkovskaya et al., 2006). Strains of the only species of the genus recognized so far, Echinicola pacifica, were isolated from the sea urchin Strongylocentrotus intermedius, and differed from those of their closest relatives Algoriphagus, Hongiella, Aquiflexum and Belliella by the ability to ferment D-glucose. In this study we report the isolation and identification of a novel marine bacterium that was affiliated with the genus Echinicola on the basis of phylogenetic, phenotypic and chemotaxonomic characteristics.

Strain KMM 6221^T was isolated by direct plating on a medium containing 0.5 % (w/v) Bacto peptone (Difco), 0.2 % (w/v) casein hydrolysate (Merck), 0.2 % (w/v) Bacto yeast extract (Difco), 0.1 % (w/v) glucose, 0.02 % (w/v) KH₂PO₄, 0.005 % (w/v) MgSO₄ and 1.5 % (w/v) Bacto agar (Difco) in 50 % (v/v) natural seawater and 50 % (v/v) distilled water, from seawater collected in a mussel farm located in a lagoon of Nha Trang Bay, South China Sea, Vietnam, in January 2005. After primary isolation and purification on marine agar 2216 (Difco), strains were cultivated on the same medium at 25 °C for 48 h and stored at –80 °C in marine broth (Difco) supplemented with 20 % (v/v) glycerol.

DNA extraction, PCR and 16S rRNA gene sequencing were carried out as described by Vancanneyt et al. (2006). The amplification primers used were MH1 (5'-AGTTTGATCCTGGCTCAG-3') and MH2 (5'-TACCTTGTTACGACTTCACCCCA-3'), respectively hybridizing at positions 10–27 and 1507–1485 according to the Escherichia coli numbering system. Sequence data obtained were aligned with those of representative members of the phylum Bacteroidetes by using PHYDIT version 3.2 (http://plaza.snu.ac.kr/jchun/phydit/). Phylogenetic trees were inferred by using suitable programs of the PHYLIP package (Felsenstein, 1993). Phylogenetic distances were calculated according to the Kimura two-parameter model (Kimura, 1980), and trees were constructed on the basis of the neighbour-joining (Saitou & Nei, 1987), maximum-parsimony (Kluge & Farris, 1969) and maximum-likelihood (Felsenstein, 1993) algorithms. Bootstrap analysis was performed with 1000 resampled data sets by using the SEQBOOT and CONSENSE programs of the PHYLIP package.

Phylogenetic analysis of the almost-complete 16S rRNA gene sequences revealed that strain KMM 6221^T occupied a distinct lineage within the genus Echinicola and possessed sequence similarities of 94.7–95.0 % with strains of Echinicola pacifica (Fig. 1).

View larger version (33K): [in this window] [in a new window]   Fig. 1. Neighbour-joining tree based on 16S rRNA gene sequences of strain KMM 6221T and members of related genera of the phylum Bacteroidetes. The topology of the tree was not changed in trees generated with the least-squares or maximum-likelihood algorithms (not shown; asterisks indicate branches that were also recovered by using the least-squares and maximum-likelihood algorithms). Numbers at nodes indicate bootstrap percentages from 1000 resampled datasets. Bar, 0.01 substitutions per nucleotide position.

Analysis of fatty acid methyl esters was carried out according to the standard protocol of the Sherlock Microbial Identification System (Microbial ID). The predominant cellular fatty acids of strain KMM 6221^T were iso-C_{15 : 0}, C_{16 : 1}5c, iso-C_{17 : 1}9c, C_{17 : 1}6c, iso-C_{15 : 0} 3-OH, iso-C_{17 : 0} 3-OH, summed feature 3 (comprising C_{16 : 1}7c and/or iso-C_{15 : 0} 2-OH) and summed feature 4 (comprising iso-C_{17 : 1} I and/or anteiso-C_{17 : 1} B). Echinicola pacifica strains have a similar fatty acid composition (Nedashkovskaya et al., 2006), including the presence of summed feature 4.

Physiological and biochemical properties of strain KMM 6221^T were examined as described by Nedashkovskaya et al. (2004, 2006).

The new strain displayed many features similar to those of Echinicola pacifica (Table 1). It moved by means of gliding, was positive for oxidase, catalase and alkaline phosphatase activities, and hydrolysed starch, as found previously for strains of Echinicola pacifica. However, KMM 6221^T differed in that it could not ferment D-glucose, produce hydrogen sulfide or hydrolyse agar, gelatin or Tween 40. Production of acid from several carbohydrates and susceptibility to antibiotics could also be used to differentiate between strain KMM 6221^T and Echinicola pacifica (Table 1). KMM 6221^T also differs from its closest relatives by the ability to grow at up to 44 °C and with 15 % NaCl.

Description of Echinicola vietnamensis sp. nov.
Echinicola vietnamensis (vi.et.nam.en'sis. N.L. fem. adj. vietnamensis referring to Vietnam, the country of origin of the type strain).

Has the following characteristics in addition to those given for the genus. Cells are 0.4–0.5x1.1–2.3 µm. On marine agar, colonies are circular, 2–3 mm in diameter, convex, shiny, smooth and light pink. -Galactosidase-positive. Does not require Na⁺ ions or seawater for growth. Growth occurs at 6–44 °C. Optimal temperature for growth is 30–32 °C. Growth occurs with 0–15 % NaCl. No flexirubin-type pigments are formed. Degrades starch, but not agar, casein, gelatin, Tweens 20, 40 or 80, urea, cellulose (carboxymethylcellulose and filter paper) or chitin. Does not produce acid from L-arabinose, D-cellobiose, D-fructose, D-galactose, D-glucose, D-lactose, D-maltose, D-melibiose, L-raffinose, L-rhamnose, L-sorbose, sucrose, DL-xylose, N-acetylglucosamine, glycerol, adonitol, dulcitol, inositol or mannitol. Does not ferment D-glucose. Nitrate is not reduced to nitrite. Indole and hydrogen sulfide are not produced. Susceptible to carbenicillin, chloramphenicol, doxycycline, erythromycin, lincomycin and oleandomycin. Resistant to ampicillin, benzylpenicillin, gentamicin, kanamycin, neomycin, polymyxin B, streptomycin and tetracycline. Fatty acids accounting for 1 % of the total are anteiso-C_{15 : 0} (1.4 %), iso-C_{15 : 0} (20.0 %), C_{15 : 1}6c (1.2 %), C_{15 : 0} (1.5 %), C_{16 : 1}5c (4.9 %), iso-C_{17 : 1}9c (4.4 %), iso-C_{17 : 0} (1.0 %), C_{17 : 1}6c (4.5 %), iso-C_{15 : 0} 3-OH (3.7 %), C_{16 : 0} 3-OH (2.3 %), iso-C_{17 : 0} 3-OH (10.0 %), summed feature 3 (comprising C_{16 : 1}7c and/or iso C_{15 : 0} 2-OH; 34.5 %), and summed feature 4 (comprising iso-C_{17 : 1} I and/or anteiso-C_{7 : 1} B; 5 %). The G+C content of the DNA is 45.9 mol%.

The type strain, KMM 6221^T (=DSM 17526^T=LMG 23754^T), was isolated from seawater collected in a mussel farm located in a lagoon of Nha Trang Bay, South China Sea, Vietnam.

	ACKNOWLEDGEMENTS

 
We are most grateful to Claudine Vereecke, Public Collection Curator of the BCCM/LMG Bacteria Collection, Ghent, Belgium, for her help during preparation of the paper. This research was supported by grants from the Presidium of the Far Eastern Branch of the Russian Academy of Sciences (no. 06-04-96067), State Contract ‘Scientific Schools' from the Federal Agency for Science and Innovations of the Russian Federation and Presidium of the Russian Academy of Sciences ‘Molecular and Cell Biology’. I. A. B. is deeply indebted to Dr Nguyen Tac An, Director of the Institute of Oceanography, Nha Trang, Vietnam.

	REFERENCES

TOP ABSTRACT MAIN TEXT REFERENCES

 
Felsenstein, J. (1993). PHYLIP (phylogeny inference package), version 3.5c. Department of Genome Sciences, University of Washington, Seattle, USA.

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]

Kluge, A. G. & Farris, F. S. (1969). Quantitative phyletics and the evolution of anurans. Syst Zool 18, 1–32.[Abstract/Free Full Text]

Marmur, J. (1961). A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3, 208–218.

Marmur, J. & Doty, P. (1962). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5, 109–118.[Medline]

Nedashkovskaya, O. I., Kim, S. B., Han, S. K., Rhee, M. S., Lysenko, A. M., Falsen, E., Frolova, G. M., Mikhailov, V. V. & Bae, K. S. (2004). Ulvibacter litoralis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the green alga Ulva fenestrata. Int J Syst Evol Microbiol 54, 119–123.[Abstract/Free Full Text]

Nedashkovskaya, O. I., Kim, S. B., Vancanneyt, M., Lysenko, A. M., Shin, D. S., Park, M. S., Lee, K. H., Jung, W. J., Mikhailov, V. & other authors (2006). Echinicola pacifica gen. nov., sp. nov., a novel flexibacterium isolated from the sea urchin Strongylocentrotus intermedius. Int J Syst Evol Microbiol 56, 953–958.[Abstract/Free Full Text]

Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.[Abstract]

Vancanneyt, M., Naser, S. M., Engelbeen, K., De Wachter, M., Van der Meulen, R., Cleenwerck, I., Hoste, B., De Vuyst, L. & Swings, J. (2006). Reclassification of Lactobacillus brevis strains LMG 11494 and LMG 11984 as Lactobacillus parabrevis sp. nov. Int J Syst Evol Microbiol 56, 1553–1557.[Abstract/Free Full Text]

This Article Abstract Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via CrossRef Citing Articles via Google Scholar Google Scholar Articles by Nedashkovskaya, O. I. Articles by Mikhailov, V. V. Search for Related Content PubMed PubMed Citation Articles by Nedashkovskaya, O. I. Articles by Mikhailov, V. V. Agricola Articles by Nedashkovskaya, O. I. Articles by Mikhailov, V. V.