1887

Abstract

A Gram-stain-negative, rod-shaped, non-motile, non-spore-forming bacterium, designated strain BY-1, was isolated from a soil sample from the city of Qiqihar in Heilongjiang Province, PR China. Strain BY-1 grew optimally at pH 7.0 and 30–35 °C in the presence of 0.5 % (w/v) NaCl. Analysis of 16S rRNA gene sequences revealed that strain BY-1 fell within the radiation of the genus , and showed highest 16S rRNA gene sequence similarities to IAM 13000 (99.5 %) and HR2 (97.3 %); the levels of sequence similarity with respect to other recognized species of the genus were <96.7 %. Strain BY-1 showed low DNA–DNA relatedness values with IAM 13000 (29±3.1 %) and HR2 (21±1.5 %). The GC content of the genomic DNA of strain BY-1 was 55.3 mol%. The major fatty acids were C, C and summed feature 3 (Cω6 and/or Cω7). Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and the major ubiquinone was Q-9. Data obtained in this study indicated that this isolate represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is BY-1 ( = KACC 15471 = ACCC 05688).

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2012-11-01
2020-01-28
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References

  1. Anzai Y. , Kim H. , Park J.-Y. , Wakabayashi H. , Oyaizu H. . ( 2000; ). Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. . Int J Syst Evol Microbiol 50:, 1563–1589. [CrossRef] [PubMed]
    [Google Scholar]
  2. Buck J. D. . ( 1982; ). Nonstaining (KOH) method for determination of gram reactions of marine bacteria. . Appl Environ Microbiol 44:, 992–993.[PubMed]
    [Google Scholar]
  3. Collins M. D. , Pirouz T. , Goodfellow M. , Minnikin D. E. . ( 1977; ). Distribution of menaquinones in actinomycetes and corynebacteria. . J Gen Microbiol 100:, 221–230.[PubMed] [CrossRef]
    [Google Scholar]
  4. Cowan S. T. , Steel K. J. . ( 1965; ). Manual for the Identification of Medical Bacteria. London:: Cambridge University Press;.
    [Google Scholar]
  5. Eck R. V. , Dayhoff M. O. . ( 1966; ). Atlas of Protein Sequence and Structure. Silver Springs, MD:: National Biomedical Research Foundation;.
    [Google Scholar]
  6. 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:, 224–229. [CrossRef]
    [Google Scholar]
  7. Felsenstein J. . ( 1981; ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17:, 368–376. [CrossRef] [PubMed]
    [Google Scholar]
  8. Felsenstein J. . ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39:, 783–791. [CrossRef]
    [Google Scholar]
  9. Fitch W. M. . ( 1971; ). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20:, 406–416. [CrossRef]
    [Google Scholar]
  10. He L. , Li W. , Huang Y. , Wang L. , Liu Z. H. , Lanoot B. , Vancanneyt M. , Swings J. . ( 2005; ). Streptomyces jietaisiensis sp. nov., isolated from soil in northern China. . Int J Syst Evol Microbiol 55:, 1939–1944. [CrossRef] [PubMed]
    [Google Scholar]
  11. Kim O. S. , Cho Y. J. , Lee K. , Yooh S. H. , Kim M. , Na H. , Park S. C. , Joen Y. S. , Lee J. H. , Yi H. , Won S. , Chun J. . ( 2012; ). Introducing EzTaxon‐e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species.. Int J Syst Evol Microbiol 62:, 716–721. [CrossRef]
    [Google Scholar]
  12. 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] [PubMed]
    [Google Scholar]
  13. King E. O. , Ward W. K. , Raney D. E. . ( 1954; ). Two simple media for the demonstration of pyocyanin and fluorescein. . J Lab Clin Med 44:, 301–307.
    [Google Scholar]
  14. Kodama K. , Kimura N. , Komagata K. . ( 1985; ). Two new species of Pseudomonas: P. oryzihabitans isolated from rice paddy and clinical specimens and P. luteola isolated from clinical specimens. . Int J Syst Evol Microbiol 35:, 467–474.
    [Google Scholar]
  15. Liu R. , Liu H. , Feng H. , Wang X. , Zhang C. X. , Zhang K. Y. , Lai R. . ( 2008; ). Pseudomonas duriflava sp. nov., isolated from a desert soil. . Int J Syst Evol Microbiol 58:, 1404–1408. [CrossRef] [PubMed]
    [Google Scholar]
  16. Mandel M. , Marmur J. . ( 1968; ). Use of ultraviolet absorbance-temperature profile for determining the guanine plus cytosine content of DNA. . Methods Enzymol 12B:, 195–206. [CrossRef]
    [Google Scholar]
  17. Minnikin D. E. , Collins M. D. , Goodfellow M. . ( 1979; ). Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. . J Appl Microbiol 47:, 87–95. [CrossRef]
    [Google Scholar]
  18. Ohta H. , Hattori T. . ( 1983; ). Agromonas oligotrophica gen. nov., sp. nov., a nitrogen-fixing oligotrophic bacterium. . Antonie van Leeuwenhoek 49:, 429–446.[PubMed]
    [Google Scholar]
  19. Oyaizu H. , Komagata K. . ( 1983; ). Grouping of Pseudomonas species on the basis of cellular fatty acid composition and the quinone system with special reference to the existence of 3-hydroxy fatty acids. . J Gen Appl Microbiol 29:, 17–40. [CrossRef]
    [Google Scholar]
  20. Palleroni N. J. . ( 1984; ). Genus I. Pseudomonas Migula 1894. . In Bergey’s Manual of Systematic Bacteriology, vol. 1, pp. 141–199. Edited by Krieg N. R. , Holt J. G. . . Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  21. Rzhetsky A. , Nei M. . ( 1992; ). A simple method for estimating and testing minimum evolution trees. . Mol Biol Evol 9:, 945–967.
    [Google Scholar]
  22. Saitou N. , Nei M. . ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4:, 406–425.[PubMed]
    [Google Scholar]
  23. Sambrook J. , Russell D. W. . ( 2001; ). Molecular cloning: a Laboratory Manual, 3rd ed. Cold Spring Harbor, NY:: Cold Spring Harbor Laboratory;.
    [Google Scholar]
  24. Sasser M. . ( 1990; ). Identification of bacteria by gas chromatography of cellular fatty acids. . USFCC Newsl 20:, 16.
    [Google Scholar]
  25. Smibert R. M. , Krieg N. R. . ( 1994; ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by Gerhardt P. , Murray R. G. E. , Wood W. A. , Krieg N. R. . . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  26. Sneath P. H. A. , Stevens M. , Sackin M. J. . ( 1981; ). Numerical taxonomy of Pseudomonas based on published records of substrate utilization. . Antonie van Leeuwenhoek 47:, 423–448. [CrossRef] [PubMed]
    [Google Scholar]
  27. 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:, 1639–1652. [CrossRef] [PubMed]
    [Google Scholar]
  28. Tamaoka J. , Katayama-Fujimura Y. , Kuraishi H. . ( 1983; ). Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. . J Appl Bacteriol 54:, 31–36. [CrossRef]
    [Google Scholar]
  29. Tamura K. , Peterson D. , Peterson N. , Stecher G. , Nei M. , Kumar S. . ( 2011; ). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28:, 2731–2739. [CrossRef] [PubMed]
    [Google Scholar]
  30. Tindall B. J. , Rosselló-Móra R. , Busse H.-J. , Ludwig W. , Kämpfer P. . ( 2010; ). Notes on the characterization of prokaryote strains for taxonomic purposes. . Int J Syst Evol Microbiol 60:, 249–266. [CrossRef] [PubMed]
    [Google Scholar]
  31. Vancanneyt M. , Witt S. , Abraham W.-R. , Kersters K. , Fredrickson H. L. . ( 1996; ). Fatty acid content in whole-cell hydrolysates and phospholipid fractions of pseudomonads: a taxonomic evaluation. . Syst Appl Microbiol 19:, 528–540. [CrossRef]
    [Google Scholar]
  32. Wang B. Z. , Guo P. , Zheng J. W. , Hang B. J. , Li L. , He J. , Li S. P. . ( 2011; ). Sphingobium wenxiniae sp. nov., a synthetic pyrethroid (SP)-degrading bacterium isolated from activated sludge in an SP-manufacturing wastewater treatment facility. . Int J Syst Evol Microbiol 61:, 1776–1780. [CrossRef] [PubMed]
    [Google Scholar]
  33. Wayne L. G. , Brenner D. J. , Colwell R. R. et al. ( 1987; ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37:, 463–464.[CrossRef]
    [Google Scholar]
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