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1 Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Life Sciences College of Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
2 Biotoxin Department of Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, People's Republic of China
3 Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology and Yunnan University, Kunming, Yunnan 650091, People's Republic of China
4 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, People's Republic of China
Correspondence
Ren Lai
rlai72{at}njau.edu.cn
Wen-Jun Li
wjli{at}ynu.edu.cn
| ABSTRACT |
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These authors contributed equally to this work. ![]()
| MAIN TEXT |
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Strain AKS 1T was isolated from a desert soil sample collected from Akesu, XinJiang Province, north-west China, by using the traditional dilution plating method. LB agar (Sambrook & Russell, 2002
) was used for selective isolation and cultures were incubated at 30 °C for 1 week. The novel strain was maintained on LB agar slants at 4 °C and as glycerol suspensions (20 %, v/v) at 80 °C. Biomass for molecular systematic and chemotaxonomic studies was obtained after incubation in LB at 30 °C for 2 days in shake flasks (about 150 r.p.m.), with the pH adjusted to pH 7.8 using NaOH.
Cell morphology of the novel isolate was observed by light microscopy (BH2; Olympus) and by transmission electron microscopy (H-7650; Hitachi) after 24 h growth on LB medium. Acid production from carbohydrates was tested using the media and methods described by Gordon et al. (1974)
. Sole carbon and sole carbon/nitrogen source utilization was investigated using the Biolog GN2 Microplate system (Nedashkovskaya et al., 2005b
) according to the manufacturers' instructions. Growth was tested at 4, 10, 27, 30, 36, 37, 40 and 45 °C on LB medium. Requirement for and tolerance of NaCl (1, 4, 7, and 10 %) and pH (3.0, 6.0, 7.0, 7.8, 8.0, 10.0, 11.0, 12.0) were tested using modified LB medium. Susceptibility to antibiotics was examined as described by Nedashkovskaya et al. (2003
, 2005b)
with results recorded after incubation at 30 °C for up to 3 days. Gram-staining and other phenotypic characteristics were determined according to the method described by Gerhardt et al. (1994)
.
Menaquinones were extracted from lyophilized cells and determined using the procedures reported by Akagawa-Matsushita et al. (1992)
and Hu et al. (2001)
. Biomass for the quantitative fatty acid analysis was prepared by collecting growth from shake flasks of LB medium that had been incubated for 2 days at 30 °C. Fatty acids were extracted, methylated and analysed using the standard MIDI (Microbial Identification) system as described by Sasser (1990)
.
For the determination of G+C composition, genomic DNA was prepared according to the method of Marmur (1961)
. The DNA G+C content of strain AKS 1T was determined using the thermal denaturation method (Mandel & Marmur, 1968
).
PCR amplification of the 16S rRNA gene was performed as described by Xu et al. (2003)
. Phylogenetic analysis was performed using the PHYLIP (Felsenstein, 1993
) and MEGA version 3.1 (Kumar et al., 2001
) software packages after multiple alignment of data by using CLUSTAL_X (Thompson et al., 1997
). Distances (distance options according to the Kimura two-parameter model; Kimura, 1980
, 1983
) and clustering were based on the neighbour-joining (Saitou & Nei, 1987
) and maximum-likelihood (Felsenstein, 1981
) methods. Bootstrap analysis was used to evaluate the tree topology of the neighbour-joining data by performing 1500 resamplings (Felsenstein, 1985
).
Cells of strain AKS 1T were collected for morphological observations after being cultured on LB agar for 24 h. Cells were prepared for transmission electron microscopy as described by Nedashkovskaya et al. (2005b)
. Cells of strain AKS 1T ranged from 0.7 to 0.75 µm in width and from 1.5 to 1.6 µm in length and an unknown ropy substance was observed around the cells (Fig. 1
).
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In conclusion, genotypic, chemotaxonomic and phenotypic data demonstrate that strain AKS 1T represents a novel species of the genus Pontibacter, for which we propose the name Pontibacter akesuensis sp. nov.
Description of Pontibacter akesuensis sp. nov.
Pontibacter akesuensis (a.ke.su.en'sis. N.L. masc. adj. akesuensis pertaining to Akesu, a city of XinJiang Province in the north-west of China from where the type strain was isolated).
Cells range from 0.7 to 0.75 µm in width and from 1.5 to 1.6 µm in length. Colonies are circular, 12 mm in diameter, convex, shiny, pink and smooth on nutrient agar plates. Gram-negative. Cells are non-motile, non-spore-forming, aerobic and chemoorganotrophic. A ropy substance is observed around cells. Grows well in very dry environmental conditions, does not require Na+ or other special substances for growth. Growth occurs at between 4 and 36 °C, with an optimum at 2830 °C. Growth occurs at pH 711, with optimal growth at pH 7.68.0. Growth occurs at 04 % NaCl. Pigment can be extracted with organic solvents. Gelatin, DNA and starch are decomposed, but casein, Tweens 20, 40 and 80, cellulose and chitin are not hydrolysed. Forms acid from aesculin, D-fructose, D-sucrose, inositol, L-raffinose, D-maltose, N-acetylglucosamine, L-fucose and D-glucose, but not from D-cellobiose, D-galactose, D-lactose, D-melibiose, L-rhamnose, L-sorbose or DL-xylose. In Biolog GN tests, the type strain utilizes
-cyclodextrin, dextrin, glycogen, N-acetyl-D-galactosamine, L-arabinose, D-arabitol, N-acetyl-D-glucosamine, D-cellobiose, D-fructose, L-fucose, L-alanine, D-galactose, gentiobiose,
-D-glucose, myo-inositol, maltose, D-mannitol, D-melibiose, methyl
-D-glucoside, D-psicose, D-raffinose, L-rhamnose, D-sorbitol, sucrose, D-trehalose, turanose, lactulose, xylitol, methyl pyruvate, monomethyl succinate, acetic acid, D-galactonic acid lactone, cis-aconitic acid, D-galacturonic acid, D-gluconic acid, D-glucuronic acid, D-glucosaminic acid,
-hydroxybutyric acid,
-hydroxybutyric acid,
-hydroxybutyric acid, itaconic acid,
-ketobutyric acid,
-ketoglutaric acid,
-ketovaleric acid, DL-lactic acid, propionic acid, quinic acid, D-saccharic acid, succinic acid, bromosuccinic acid, succinamic acid, L-alaninamide, L-alanyl glycine, L-asparagine, L-aspartic acid, L-glutamic acid, glycyl L-aspartic acid, glycyl L-glutamic acid, L-histidine, hydroxy-L-proline, L-leucine, L-ornithine, L-phenylalanine, L-proline, L-pyroglutamic acid, L-serine, L-threonine, DL-carnitine,
-aminobutyric acid, inosine, thymidine, putrescine, 2,3-butanediol and glucose 6-phosphate. However, it does not utilize Tweens 20, 40, or 80, adonitol, i-erythritol, uridine, urocanic acid,
-D-lactose, D-mannose, citric acid, formic acid, p-hydroxyphenylacetic acid, malonic acid, sebacic acid, glucuronamide, D-alanine, D-serine, phenylethylamine, 2-aminoethanol, DL-
-glycerol phosphate or glucose 1-phosphate. Nitrate is not reduced. Indole and H2S (triple sugar iron reaction) are negative. Susceptible to the following antibiotics: ampicillin, benzylpenicillin, chloramphenicol, neomycin, gentamicin, erythromycin, carbenicillin, lincomycin and tetracycline. Resistant to kanamycin, polymyxin B and streptomycin. The predominant menaquinone is MK-7. The fatty acid profile contains i-C15 : 0 (25.08 %), ai-C17 : 1 B/i-C17 : 1 I (19.97 %), i-C17 : 0 3-OH (11.46 %), i-C17 : 1
9c (7.69 %), i-C17 : 0 (6.06 %), i-C15 : 0 3-OH (3.33 %), C17 : 1
6c (2.87 %), i-C15 : 1 F (1.97 %), i-C15 : 0 2-OH/C16 : 1
7c/C16 : 1
7t (1.94 %), C15 : 0 (1.77 %), i-C15 : 1 I/C13 : 0 3-OH (1.72 %), C18 : 0 (1.71 %), C16 : 0 (1.68 %), and i-C16 : 0 (1.46 %). The DNA G+C content is 51.4 mol%.
The type strain, AKS 1T (=KCTC 12758T=CCTCC AB 206086T), was isolated from the surface layer of a desert soil from Akesu, XinJiang Province, China.
| ACKNOWLEDGEMENTS |
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| REFERENCES |
|---|
|
|
|---|
Bowman, J. P., Nichols, C. M. & Gibson, J. A. E. (2003). Algoriphagus ratkowskyi gen. nov., sp. nov., Brumimicrobium glaciale gen. nov., sp. nov., Cryomorpha ignava gen. nov., sp. nov. and Crocinitomix catalasitica gen. nov., sp. nov., novel flavobacteria isolated from various polar habitats. Int J Syst Evol Microbiol 53, 13431355.
Brettar, I., Christen, R. & Höfle, M. G. (2004a). Belliella baltica gen. nov., sp. nov., a novel marine bacterium of the CytophagaFlavobacteriumBacteroides group isolated from surface water of the central Baltic Sea. Int J Syst Evol Microbiol 54, 6570.
Brettar, I., Christen, R. & Höfle, M. G. (2004b). Aquiflexum balticum gen. nov., sp. nov., a novel marine bacterium of the CytophagaFlavobacteriumBacteroides group isolated from surface water of the central Baltic Sea. Int J Syst Evol Microbiol 54, 23352341.
Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368376.[CrossRef][Medline]
Felsenstein, J. (1985). Conference limits on phylogenies: an approach using the bootstrap. Evolution 39, 783791.[CrossRef]
Felsenstein, J. (1993). PHYLIP (phylogeny inference package), version 3.5c. Department of Genome Sciences, University of Washington, Seattle, USA.
Gerhardt, P., Murray, R. G. E., Wood, W. A. & Krieg, N. R. (editors) (1994). Methods for General and Molecular Bacteriology. Washington, DC: American Society for Microbiology.
Gordon, R. E., Barnett, D. A., Handerhan, J. E. & Pang, C. H. N. (1974). Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 24, 5463.
Hu, H. Y., Lim, B. R., Goto, N. & Fujie, K. (2001). Analytical precision and repeatability of respiratory quinones for quantitative study of microbial community structure in environmental samples. J Microbiol Methods 47, 1724.[Medline]
Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequence. J Mol Evol 16, 111120.[CrossRef][Medline]
Kimura, M. (1983). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
Kumar, S., Tamura, K., Jakobsen, I. B. & Nei, M. (2001). MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17, 12441245.
Mandel, M. & Marmur, J. (1968). Use of ultraviolet absorbance-temperature profile for determining the guanine plus cytosine content of DNA. Methods Enzymol 12B, 195206.[CrossRef]
Marmur, J. (1961). A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3, 208218.
Nedashkovskaya, O. I., Suzuki, M., Vysotskii, M. V. & Mikhailov, V. V. (2003). Reichenbachia agariperforans gen. nov., sp. nov., a novel marine bacterium in the phylum CytophagaFlavobacteriumBacteroides. Int J Syst Evol Microbiol 53, 8185.
Nedashkovskaya, O. I., Vancanneyt, M., Van Trappen, S., Vandemeulebroecke, K., Lysenko, A. M., Rohde, M., Falsen, E., Frolova, G. M., Mikhailov, V. V. & Swings, J. (2004). Description of Algoriphagus aquimarinus sp. nov., Algoriphagus chordae sp. nov. and Algoriphagus winogradskyi sp. nov., from sea water and algae, transfer of Hongiella halophila Yi and Chun 2004
to the genus Algoriphagus as Algoriphagus halophilus comb. nov. and emended descriptions of the genera Algoriphagus Bowman et al. 2003
and Hongiella Yi and Chun 2004
. Int J Syst Evol Microbiol 54, 17571764.
Nedashkovskaya, O. I., Kim, S. B., Lee, D. H., Lysenko, A. M., Shevchenko, L. S., Frolova, G. M., Mikhailov, V. V., Lee, K. H. & Bae, K. S. (2005a). Roseivirga ehrenbergii gen. nov., sp. nov., a novel marine bacterium of the phylum Bacteroidetes, isolated from the green alga Ulva fenestrata. Int J Syst Evol Microbiol 55, 231234.
Nedashkovskaya, O. I., Kim, S. B., Suzuki, M., Shevchenko, L. S., Lee, M. S., Lee, K. H., Park, M. S., Frolova, G. M., Oh, H. W. & other authors (2005b). Pontibacter actiniarum gen. nov., sp. nov., a novel member of the phylum Bacteroidetes, and proposal of Reichenbachiella gen. nov. as a replacement for the illegitimate prokaryotic generic name Reichenbachia Nedashkovskaya et al. (2003)
. Int J Syst Evol Microbiol 55, 25832588.
Raj, H. D. & Maloy, S. R. (1990). Proposal of Cyclobacterium marinus gen. nov., comb. nov. for a marine bacterium previously assigned to the genus Flectobacillus. Int J Syst Bacteriol 40, 337347.
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406425.[Abstract]
Sambrook, J. & Russell, D. W. (2002). Molecular Cloning: a Laboratory Manual, pp. 15951596, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20, 16.
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 24, 48764882.
Van Trappen, S., Vandecandelaere, I., Mergaert, J. & Swings, J. (2004). Algoriphagus antarcticus sp. nov., a novel psychrophile from microbial mats in Antarctic lakes. Int J Syst Evol Microbiol 54, 19691973.
Xu, P., Li, W. J., Xu, L. H. & Jiang, C. L. (2003). A microwave-based method for genomic DNA extraction from Actinomycetes. Microbiology (Beijing) 30, 8284 (in Chinese).
Yi, H. & Chun, J. (2004). Hongiella mannitolivorans gen. nov., sp. nov., Hongiella halophila sp. nov. and Hongiella ornithinivorans sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 54, 157162.
Yoon, J.-H., Yeo, S.-H. & Oh, T.-K. (2004). Hongiella marincola sp. nov., isolated from sea water of the East Sea in Korea. Int J Syst Evol Microbiol 54, 18451848.
Yoon, J.-H., Kang, S.-J., Lee, C.-H. & Oh, T.-K. (2005a). Marinicola seohaensis gen. nov., sp. nov., isolated from sea water of the Yellow Sea, Korea. Int J Syst Evol Microbiol 55, 859863.
Yoon, J.-H., Kang, S.-J., Jung, S.-Y., Lee, C.-H. & Oh, T.-K. (2005b). Algoriphagus yeomjeoni sp. nov., isolated from a marine solar saltern in the Yellow Sea, Korea. Int J Syst Evol Microbiol 55, 865870.
Yoon, J.-H., Kang, S.-J. & Oh, T.-K. (2005c). Algoriphagus locisalis sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 55, 16351639.
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