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Pelagibius litoralis gen. nov., sp. nov., a marine
bacterium in the family Rhodospirillaceae isolated
from coastal seawater
Dong Han Choi,1Chung Yeon Hwang2and Byung Cheol Cho2
Byung Cheol Cho
1Open and Tropical Ocean Research Division, Korea Ocean Research and Development Institute,
Ansan 426-744, Republic of Korea
2School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul
National University, Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea
A Gram-negative, strictly aerobic, slightly curved rod-shaped bacterial strain, designated CL-
UU02T, was isolated from coastal seawater off the east coast of Korea. 16S rRNA gene sequence
analysis revealed a clear affiliation of this novel strain with the family Rhodospirillaceae. Strain CL-
UU02Tformed a robust cluster with the type strains of species of the genus Rhodovibrio at 16S
rRNA gene sequence similarity levels of 89.9–90.4%. Strain CL-UU02Tshared no more than
89% 16S rRNA gene sequence similarity with the type strains of other species in the family
Rhodospirillaceae. Strain CL-UU02Twas able to grow in the presence of 2–6% sea salts, and
grew optimally at 28–30 6C and pH 7–8. The DNA G+C content of strain CL-UU02Twas
66.3 mol%. On the basis of phylogenetic analyses and chemotaxonomic and physiological data,
strain CL-UU02Tis considered to represent a novel species of a new genus in the family
Rhodospirillaceae, for which the name Pelagibius litoralis gen. nov., sp. nov. is proposed. The type
strain of Pelagibius litoralis is CL-UU02T(5KCCM 42323T5JCM 15426T).
The order Rhodospirillales currently comprises two fam-
ilies, Rhodospirillaceae and Acetobacteraceae, in the class
Alphaproteobacteria (Garrity et al., 2005). At the time of
writing, the family Rhodospirillaceae comprises 16 genera,
namely Azospirillum, Caenispirillum, Defluviicoccus, Inquili-
nus, Magnetospirillum, Phaeospirillum, Rhodocista, Rhodo-
spira, Rhodospirillum, Rhodovibrio, Roseospira, Skermanella,
Tistrella (see http://www.bacterio.cict.fr).
Among 40 recognized species in the family Rhodospirillaceae,
only seven species affiliated with the genera Rhodovibrio
(Mack et al., 1993), Rhodospira (Pfennig et al., 1997),
Thalassospira (Lo ´pez-Lo ´pez et al., 2002; Liu et al., 2007;
Kodama et al., 2008) and Thalassobaculum (Zhang et al.,
2008) have been recovered from marine environments. Other
speciesinthefamilyRhodospirillaceae havebeenisolated from
various non-marine habitats, such as freshwater, activated
sludge biomass, air, soiland roots of plants, and cystic fibrosis
patients (Coenye et al., 2002; Garrity et al., 2005; Weon
et al., 2007; Yoon et al., 2007). In the present study, a novel
bacterial strain, designated CL-UU02T, affiliated with the
family Rhodospirillaceae was isolated from urea-enriched
seawater and was subjected to a polyphasic taxonomic
In February 2005, coastal seawater taken from the east
coast of Korea was brought back to the laboratory for
analysis. One hundred microlitres of seawater was
inoculated in autoclaved seawater (500 ml) supplemented
with urea (final concentration of 100 mM) and incubated
at 20 uC in the dark. After about 8 months, 100 ml of the
sample was taken and spread on a marine agar 2216 (MA;
Difco) plate, which was then incubated aerobically at 30 uC
for 2 weeks. Strain CL-UU02Twas isolated and subse-
quently streaked onto fresh MA plates at 30 uC under
aerobic conditions. Thepurification
repeated four times. Strain CL-UU02Twas maintained
both on MA at 30 uC and in marine broth 2216 (MB;
Difco) supplemented with 30% (v/v) glycerol at 280 uC.
For 16S rRNA gene amplification by PCR, DNA was
extracted from a single colony based on a boiling method
(Englen & Kelley, 2000). The crude extracts served as the
DNA template for PCRs, which included Taq DNA
polymerase (Bioneer) and primers 27F and 1492R (Lane,
1991). The PCR product was purified by using an
AccuPrep PCR purification kit (Bioneer) and was cloned
by using pGEM T-Easy vector (Promega). Sequencing of
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene
sequence of strain CL-UU02Tis DQ401091.
An extended neighbour-joining tree based on 16S rRNA gene sequences
showing the position of strain CL-UU02Tamong members of the family
Rhodospirillaceae is available as supplementary material with the online
version of this paper.
International Journal of Systematic and Evolutionary Microbiology (2009), 59, 818–823
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Gram-negative coccus/coccobacillus in the ‘Alphaproteobacteria’ from
activated sludge. Int J Syst Evol Microbiol 55, 2105–2111.
Minnikin, D. E., O’Donnell, A. G., Goodfellow, M., Alderson, G.,
Athalye, M., Schaal, A. & Parlett, J. H. (1984). An integrated
procedure for the extraction of bacterial isoprenoid quinones and
polar lipids. J Microbiol Methods 2, 233–241.
Nissen, H. & Dundas, I. D. (1984). Rhodospirillum salinarum sp. nov.,
a halophilic photosynthetic bacterium isolated from a Portuguese
saltern. Arch Microbiol 138, 251–256.
Ostle, A. G. & Holt, J. G. (1982). Nile blue A as fluorescent stain for
poly-b-hydroxybutyrate. Appl Environ Microbiol 44, 238–241.
Pfennig, N., Lu ¨nsdorf, H., Su ¨ling, J. & Imhoff, J. F. (1997). Rhodospira
trueperi gen. nov., spec. nov., a new phototrophic Proteobacterium of
the alpha group. Arch Microbiol 168, 39–45.
Posada, D. & Crandall, K. A. (1998). MODELTEST: testing the model of
DNA substitution. Bioinformatics 14, 817–818.
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new
method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–
Shi, B. H., Arunpairojana, V., Palakawong, S. & Yokota, A. (2002).
Tistrella mobilis gen. nov., sp. nov., a novel polyhydroxyalkanoate-
producing bacterium belonging to a-Proteobacteria. J Gen Appl
Microbiol 48, 335–343.
Smibert, R. M. & Krieg, N. R. (1994). Phenotypic characterization. In
Methods for General and Molecular Bacteriology, pp. 607–654. Edited
by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg.
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,
Swofford, D. L. (1998). PAUP: phylogenetic analysis using parsimony
(and other methods), version 4. Sunderland, MA: Sinauer Associates.
Tamaoka, J. & Komagata, K. (1984). Determination of DNA base
composition by reversed-phase high-performance liquid chromato-
graphy. FEMS Microbiol Lett 25, 125–128.
Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007). MEGA4: molecular
evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol
Evol 24, 1596–1599.
Weon, H.-Y., Kim, B.-Y., Hong, S.-B., Joa, J.-H., Nam, S.-S., Lee, K. H.
& Kwon, S.-W. (2007). Skermanella aerolata sp. nov., isolated from air,
and emended description of the genus Skermanella. Int J Syst Evol
Microbiol 57, 1539–1542.
Yi, H. & Chun, J. (2004). Nocardioides ganghwensis sp. nov., isolated
from tidal flat sediment. Int J Syst Evol Microbiol 54, 1295–1299.
Yoon, J.-H., Lee, M.-H. & Oh, T.-K. (2004). Porphyrobacter donghaensis
sp. nov., isolated from sea water of the East Sea in Korea. Int J Syst
Evol Microbiol 54, 2231–2235.
Yoon, J.-H., Kang, S.-J., Park, S. & Oh, T.-K. (2007). Caenispirillum
bisanense gen. nov., sp. nov., isolated from sludge of a dye works. Int J
Syst Evol Microbiol 57, 1217–1221.
Zhang, G. I., Hwang, C. Y. & Cho, B. C. (2008). Thalassobaculum
litoreumgen. nov.,sp. nov.,
Rhodospirillaceae isolated from coastal seawater. Int J Syst Evol
Microbiol 58, 479–485.
a memberofthe family
Pelagibius litoralis gen. nov., sp. nov.