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1 State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Zhong-Guan-Cun, Haidian, Beijing 100080, China
2 State Key Laboratory for Marine Environmental Sciences, Xiamen University, Xiamen, 361005, China
Correspondence
Shuang-Jiang Liu
shuangjiang{at}hotmail.com
| ABSTRACT |
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Published online ahead of print on 28 October 2005 as DOI 10.1099/ijs.0.64013-0.
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of Yangia pacifica DX5-10T is AJ877265.
| MAIN TEXT |
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During an ecological survey of microbial diversity of coastal sediments, an aerobic, Gram-negative bacterium, strain DX5-10T, was obtained that is phylogenetically related to members of the genera Roseobacter, Loktanella, Roseisalinus, Roseivivax, Salipiger, Silicibacter and Sulfitobacter. This bacterial strain, together with some uncharacterized marine isolates (Teske et al., 2000
; Buchan et al., 2001
), formed a distinct lineage within the Roseobacter clade. In this note, we describe the characterization and classification of strain DX5-10T.
Strain DX5-10T was isolated from coastal sediment of the East China Sea located in Fujian Province. The sample (from 46 cm beneath the surface) was diluted with 9 ml sterile saline solution and 0·1 ml 103 and 104 dilutions were plated onto artificial sea water basal medium with 1 % peptone and 0·5 % yeast extract (Eguchi et al., 1996
). Routine cultivation of strain DX5-10T was done at 30 °C in marine broth 2216 (MB; Difco). Methods for observation of morphology, physiological and biochemical tests, including catalase and oxidase reactions, nitrate reduction, requirement for NaCl, ranges of temperature and pH for growth, decomposition of gelatin and casein and hydrolysis of starch were described and cited in a previous report (Dai et al., 2005
).
Biomass for chemotaxonomic analysis was harvested from MB cultures on a rotary shaker (100 r.p.m., 30 °C). Quinones were extracted and purified according to Collins (1985)
and were analysed by HPLC equipped with a Hewlett Packard 1050 system and a Zorbax ODS column (Agilent Technologies) operating at 40 °C, with Ruegeria gelatinovorans DSM 5887T as reference strain. The mobile phase was a mixture of acetonitrile/2-propanol (2 : 1·2) with a flow rate of 1 ml min1. The UV detection wavelength was set at 270 nm. The fatty-acid profile of whole cells was analysed by gas chromatography by using a model HP6890GC equipped with a hydrogen-ionization detector. Peaks were identified with pre-installed software, HPCHEM-STATION (version A5.01).
Genomic DNA of strain DX5-10T was extracted according to Marmur (1961)
and G+C content was determined by thermal denaturation. The 16S rRNA gene of strain DX5-10T was amplified and sequenced as described previously (Zhang et al., 2003
). Alignments of 16S rRNA gene sequences of strain DX5-10T and species of the Roseobacter clade (Fig. 1
) were carried out with CLUSTAL X program (version 1.8; Thompson et al., 1997
). Phylogenetic trees were constructed using the neighbour-joining method (Saitou & Nei, 1987
) with the Kimura two-parameter model (Kimura, 1980
) by using the programs of TREECON (Van de Peer & De Wachter, 1994
).
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=362 nm) as described by Koblí
ek et al. (2003)
Strain DX5-10T formed faint-yellowish colonies on MB agar. Cells of strain DX5-10T were motile, Gram-negative rods (0·8x1·01·5 µm in size). The catalase reaction was positive and oxidase reaction was weakly positive. Growth occurred at temperatures of 2240 °C and at pH 5·010·0, with optima at 37 °C and pH 7·5. NaCl was required but concentrations greater than 13 % were inhibitory to growth. Maximal growth was observed at 5 % NaCl. Bchl a was not detected either in vivo or in vitro. Additional phenotypic properties are given in the following genus and species description. The cells of strain DX5-10T contained ubiquinone 10 (Q-10). The fatty-acid profile of strain DX5-10T grown in MB is detailed in the species description and in Table 1
. The genomic DNA G+C content was 63·3 mol%. A list of properties that differentiate strain DX5-10T from some related members of the Roseobacter clade is provided in Tables 1 and 2![]()
. In brief, strain DX5-10T was different from members of the genera Roseivivax and Salipiger in that Bchl a was not detected either in vivo or in vitro (Table 2
). Furthermore, strain DX5-10T contained 17 : 1
8c (3·93 %) and 17 : 0 (1·44 %), which were not detected in any other genera as listed in Table 1
, and the fatty acid methyl ester 11-methyl 18 : 1
7c and cyclo-substituted fatty acid 19 : 0 cyclo
8c that were present in Salipiger mucosus A3T were not detected in strain DX5-10T.
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Combining the phenotypic and phylogenetic studies, we propose that strain DX5-10T represents a novel species of a novel genus, Yangia pacifica gen. nov., sp. nov.
Description of Yangia gen. nov.
Yangia (Yan'gi.a. N.L. fem. n. Yangia after the Chinese microbiologist H.-F. Yang, who founded the research of environmental microbiology in the early 1960s in China).
Gram-negative rods, motile. Aerobic heterotroph. When grown on marine agar 2216 plates, small, wettish, shiny, faint-yellowish colonies develop within 35 days. Cells do not form spores. Growth requires NaCl. Catalase reaction is positive and oxidase reaction is weakly positive. The predominant respiratory quinone is Q-10. Major fatty acids are 18 : 1 and 16 : 0. Cells also contain 3-hydroxylated 12 : 0. The type species is Yangia pacifica.
Description of Yangia pacifica sp. nov.
Yangia pacifica (pa.ci'fi.ca N.L. fem. adj. pacifica pertaining to the Pacific Ocean, the origin of the type strain).
In addition to the properties described above for the genus, the following properties are observed. Cells are 0·8x1·01·5 µm in size and tend to aggregate after cell division. Strictly aerobic; does not grow under anaerobic conditions. Cells grow at 2240 °C and at pH 5·010·0, with optima at 37 °C and pH 7·5. NaCl is required and the species grows in the NaCl concentration range of 110 % (optimal growth occurs at 5 % NaCl). Bchl a is not detected either in vivo or in vitro. Nitrate reduction, hydrolysis of starch, gelatin liquefaction and indole formation are negative. Accumulates poly-(3-hydroxybutyric) acids. Urease formation is positive. Citric acid is not assimilated. Tests for methyl red and VogesProskauer are negative. Maltose, lactate, malate, arginine and glutamate support growth as sole carbon sources. Glucose, lactose, mannitol, sorbitol, inositol, arabinose, fructose, sucrose, L-lysine, L-leucine and L-phenylalanine do not support growth. The cellular fatty-acid profile is outlined in Table 1
. DNA G+C content is 63·3 mol%.
The type strain, DX5-10T (=CGMCC 1.3455T=JCM 12573T), was isolated from a sample of coastal sediment from the East China Sea of the Pacific Ocean.
| ACKNOWLEDGEMENTS |
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