1887

Abstract

Employing a modified cultivation method, we studied two bacterial strains, UC10 and UC38, found on the Kyonggi University campus, Suwon in Gyeonggi-Do province, South Korea. These strains were non-spore-forming, Gram-stain-negative, motile and rod-shaped. Growth occurred in the presence of 0–2 % (w/v) NaCl, at pH 4–9 and a temperature range of 4–35 °C. On an R2A agar plate incubated for 5 days at 28 °C, irregular, raised and pale-yellowish colonies were observed. Comparative analysis of nearly full-length 16S rRNA gene sequences indicated that these strains were closely related to GXGD002, with 98.6 % similarity. Strains UC10 and UC38were 98.0 % similar to GH9-3; 97.8 % to DS-43; 97.3–97.7 % to Gsoil 3165; 97.7–98.0 % to IAM 12373; 97.4–97.6 % to 2C1-b; and 97.3–97.4 % to BAM-48. The predominant ubiquinone was Q-8. The primary polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were C, summed feature 3 (Cω7 and/or Cω6), summed feature 8 (Cω7 and/or Cω6) and Ccyclo. DNA–DNA hybridization assays indicated 89.2–91.4 % genomic DNA similarity between strains UC10 and UC38. Moreover, genomic DNA similarity between these novel strains and reference strains of the genus was less than the 70 %. Based on these results, strain UC38 was designated a representative of a novel species of the genus , with the proposed name sp. nov. The type strain is UC38(=KACC 18501=NBRC 111520).

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2016-07-01
2020-09-26
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References

  1. Belimov A. A., Hontzeas N., Safronova V. I., Demchinskaya S. V., Piluzza G., Bullitta S., Glick B. R.. 2005; Cadmium-tolerant plant growth-promoting bacteria associated with the roots of Indian mustard (Brassica juncea L.Czern.). Soil Biol Biochem37:241–250[CrossRef]
    [Google Scholar]
  2. Belimov A. A., Dodd I. C., Hontzeas N., Theobald J. C., Safronova V. I., Davies W. J.. 2009; Rhizosphere bacteria containing 1-aminocyclopropane-1-carboxylate deaminase increase yield of plants grown in drying soil via both local and systemic hormone signalling. New Phytol181:413–423 [CrossRef][PubMed]
    [Google Scholar]
  3. Blümel S., Busse H. J., Stolz A., Kämpfer P.. 2001; Xenophilus azovorans gen. nov., sp. nov., a soil bacterium that is able to degrade azo dyes of the Orange II type. Int J Syst Evol Microbiol51:1831–1837 [CrossRef][PubMed]
    [Google Scholar]
  4. Bruland N., Bathe S., Willems A., Steinbüchel A.. 2009; Pseudorhodoferax soli gen. nov., sp. nov. and Pseudorhodoferax caeni sp. nov., two members of the class Betaproteobacteria belonging to the family Comamonadaceae . Int J Syst Evol Microbiol59:2702–2707 [CrossRef][PubMed]
    [Google Scholar]
  5. Collins M. D., Goodfellow M.. 1979; Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol41:81–95
    [Google Scholar]
  6. Da Costa M. S., Albuquerque L., Nobre M. F., Wait R.. 2011; The extraction and identification of respiratory lipoquinones of Prokaryotes and their use in taxonomy. In Methods in Microbiology, 1st edn.vol. 38 pp197–206 Edited by Rainey. F., Oren A.. Elsevier: Academic Press;
    [Google Scholar]
  7. Davis D. H., Doudoroff M., Stanier R. Y., Mandel M.. 1969; Proposal to reject the genus Hydrogenomonas: taxonomic implications. Int J Syst Bacteriol19:375–390[CrossRef]
    [Google Scholar]
  8. Ding L., Yokota A.. 2004; Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov. Int J Syst Evol Microbiol54:2223–2230 [CrossRef][PubMed]
    [Google Scholar]
  9. 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 Bacteriol39:224–229[CrossRef]
    [Google Scholar]
  10. Felsenstein J.. 1985; Confidence limits on Phylogenies: an approach using the bootstrap. Evolution (N Y)39:783–791 [CrossRef]
    [Google Scholar]
  11. Fisher P. R., Appleton J., Pemberton J. M.. 1978; Isolation and characterization of the pesticide-degrading plasmid pJP1 from Alcaligenes paradoxus . J Bacteriol135:798–804[PubMed]
    [Google Scholar]
  12. Frank J. A., Reich C. I., Sharma S., Weisbaum J. S., Wilson B. A., Olsen G. J.. 2008; Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol74:2461–2470 [CrossRef][PubMed]
    [Google Scholar]
  13. Gao J. L., Yuan M., Wang X. M., Qiu T. L., Li J. W., Liu H. C., Li X. A., Chen J., Sun J. G.. 2015; Variovorax guangxiensis sp. nov., an aerobic, 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from banana rhizosphere. Antonie Van Leeuwenhoek107:65–72 [CrossRef][PubMed]
    [Google Scholar]
  14. Im W. T., Liu Q. M., Lee K. J., Kim S. Y., Lee S. T., Yi T. H.. 2010; Variovorax ginsengisoli sp. nov., a denitrifying bacterium isolated from soil of a ginseng field. Int J Syst Evol Microbiol60:1565–1569 [CrossRef][PubMed]
    [Google Scholar]
  15. Jacin H., Mishkin A. R.. 1965; Separation of carbohydrates on borate-impregnated silica gel G plates. J Chromatogr18:170–173 [CrossRef][PubMed]
    [Google Scholar]
  16. Jin L., Kim K. K., Ahn C. Y., Oh H. M.. 2012; Variovorax defluvii sp. nov., isolated from sewage. Int J Syst Evol Microbiol62:1779–1783 [CrossRef][PubMed]
    [Google Scholar]
  17. Kim B. Y., Weon H. Y., Yoo S. H., Lee S. Y., Kwon S. W., Go S. J., Stackebrandt E.. 2006; Variovorax soli sp. nov., isolated from greenhouse soil. Int J Syst Evol Microbiol56:2899–2901 [CrossRef][PubMed]
    [Google Scholar]
  18. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al. 2012; Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  19. Kim S. J., Kim Y. S., Weon H. Y., Anandham R., Noh H. J., Kwon S. W.. 2010; Xenophilus aerolatus sp. nov., isolated from air. Int J Syst Evol Microbiol60:327–330 [CrossRef][PubMed]
    [Google Scholar]
  20. Kimura M.. 1983; The Neutral Theory of Molecular Evolution Cambridge, UK: Cambridge University Press;[CrossRef]
    [Google Scholar]
  21. Krieg N. R., Padgett P. J.. 2011; Phenotypic and physiological characterization methods. In Methods in Microbiology, 1st edn.vol. 38 pp15–60 Edited by Rainey. F., Oren A.. Elsevier: Academic Press;
    [Google Scholar]
  22. Li Q. F., Sun L. N., Kwon S. W., Chen Q., He J., Li S. P., Zhang J.. 2014; Xenophilus arseniciresistens sp. nov., an arsenite-resistant bacterium isolated from soil. Int J Syst Evol Microbiol64:1926–1931 [CrossRef][PubMed]
    [Google Scholar]
  23. Mergaert J., Webb A., Anderson C., Wouters A., Swings J.. 1993; Microbial degradation of poly(3-hydroxybutyrate) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) in soils. Appl Environ Microbiol59:3233–3238[PubMed]
    [Google Scholar]
  24. Mergaert J., Ruffieux K., Bourban C., Storms V., Wagemans W., Wintermantel E., Swings J.. 2000; In vitro biodegradation of polyester-based plastic materials by selected bacterial cultures. J Polym Environ8:17–27[CrossRef]
    [Google Scholar]
  25. Mesbah M., Premachandran U., Whitman W. B.. 1989; Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol39:159–167[CrossRef]
    [Google Scholar]
  26. 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 Methods2:233–241[CrossRef]
    [Google Scholar]
  27. Miwa H., Ahmed I., Yoon J., Yokota A., Fujiwara T.. 2008; Variovorax boronicumulans sp. nov., a boron-accumulating bacterium isolated from soil. Int J Syst Evol Microbiol58:286–289 [CrossRef][PubMed]
    [Google Scholar]
  28. Otsu Y., Matsuda Y., Shimizu H., Ueki H., Mori H., Fujiwara K., Nakajima T., Miwa A., Nonomura T. et al. 2003; Biological control of phytophagous ladybird beetles Epilachna vigintioctopunctata (Col., Coccinellidae) by chitinolyticphylloplane bacteria Alcaligenes paradoxus entrapped in alginate beads. J Appl Ent 127:441–446[CrossRef]
    [Google Scholar]
  29. Pitcher D. G., Saunders N. A., Owen R. J.. 1989; Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol8:151–156 [CrossRef]
    [Google Scholar]
  30. Rohde M.. 2011; Microscopy. In Methods in Microbiology, 1st edn.vol. 3861–100Edited by Rainey. F., Oren A.. Elsevier: Academic Press;
    [Google Scholar]
  31. Ryu S. H., Lee D. S., Park M., Wang Q., Jang H. H., Park W., Jeon C. O.. 2008; Caenimonas koreensis gen. nov., sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol58:1064–1068 [CrossRef][PubMed]
    [Google Scholar]
  32. Sasser M.. 1990; Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. MIDI Technical Note 101 Newark, DE: MIDI Inc;
    [Google Scholar]
  33. Sierra G.. 1957; A simple method for the detection of lipolytic activity of micro-organisms and some observations on the influence of the contact between cells and fatty substrates. Antonie Van Leeuwenhoek23:15–22 [CrossRef][PubMed]
    [Google Scholar]
  34. Sun J ., Matsumoto K ., Nduko J. M., Ooi T., Taguchi S.. 2014; Enzymatic characterization of a depolymerase from the isolated bacterium Variovorax sp. C34 that degrades poly (enriched lactate-co-3-hydroxybutyrate). Polym Degrad Stab 110:44–49[CrossRef]
    [Google Scholar]
  35. Talia P., Sede S. M., Campos E., Rorig M., Principi D., Tosto D., Hopp H. E., Grasso D., Cataldi A.. 2012; Biodiversity characterization of cellulolytic bacteria present on native Chaco soil by comparison of ribosomal RNA genes. Res Microbiol163:221–232 [CrossRef][PubMed]
    [Google Scholar]
  36. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S.. 2013; MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  37. 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 Res25:4876–4882 [CrossRef][PubMed]
    [Google Scholar]
  38. Tschech A., Pfennig N.. 1984; Growth yield increase linked to caffeate reduction in Acetobacteriumwoodii . Arch Microbiol137:163–167[CrossRef]
    [Google Scholar]
  39. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moor L. H., Moore W. E. C., Murray R. G. E. et al. 1987; Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol37:463–464[CrossRef]
    [Google Scholar]
  40. Wheater D. M.. 1955; The characteristics of Lactobacillus acidophilus and Lactobacillus bulgaricus . J Gen Microbiol12:123–132 [CrossRef][PubMed]
    [Google Scholar]
  41. Widdel F., Kohring G.-W., Mayer F.. 1983; Studies on Dissimilatory Sulfate-reducing bacteria that decompose fatty acids III. characterization of the Filamentous gliding Desulfonema limicola gen. nov. sp. nov., and Desulfonema magnum sp. nov. Arch Microbiol 134:286–294[CrossRef]
    [Google Scholar]
  42. Willems A., Ley J. D., Gillis M., Kersters K.. 1991; NOTES: Comamonadaceae, a new family encompassing the acidovorans rRNA complex, including Variovorax paradoxus gen. nov., comb. nov., for Alcaligenes paradoxus (Davis 1969). Int J Syst Evol Microbiol41:445–450
    [Google Scholar]
  43. Willems A., Mergaert J., Swings J.. 2005; Genus X. Variovorax Willems, De Ley, Gillis and Kersters 1991a, 446VP . In Bergey's Manual of Systematic Bacteriologyvol. 2, 2nd edn. Part C pp732–735 Edited by Brenner D. J., Krieg. N. R., Staley. J. T.. Springer;[CrossRef]
    [Google Scholar]
  44. Yoon J. H., Kang S. J., Oh T. K.. 2006; Variovorax dokdonensis sp. nov., isolated from soil. Int J Syst Evol Microbiol56:811–814 [CrossRef][PubMed]
    [Google Scholar]
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