1887

Abstract

Two novel Gram-negative bacterial strains, designated CL-GR15 and CL-GR35, were isolated from coastal seawater of the east coast of Korea. Identical 16S rRNA gene sequences were found in the two strains, and it was found that the strains represented a distinct and deep evolutionary lineage of descent in the order , and clustered with yet-uncultured marine bacteria. This lineage could not be associated with any of 12 known families in the order . The most closely related established genus was (90.7–92.5 % sequence similarity) in the family . Cells of the strains were facultatively anaerobic, weakly motile rods which occasionally exhibited cohesion with each other. The strains were catalase-, oxidase- and gelatinase-positive, and accumulated intracellular poly--hydroxybutyrate granules. Ubiquinone 10 was the major quinone. The major polar lipids comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, an unidentified aminolipid and an unidentified glycolipid. The cellular fatty acids mainly consisted of C 7, summed feature 3 (C iso 2-OH and/or C 7) and C 7. The DNA G+C content was 52.8–53.0 mol%. DNA–DNA hybridization experiments revealed high values (>97 %) for relatedness between strains CL-GR15 and CL-GR35 and suggested that these two strains constituted a single species. The distinct phylogenetic position and combinations of genotypic, phenotypic and chemotaxonomic characteristics support the proposal of gen. nov., with the type species sp. nov. (type strain, CL-GR15=KCCM 42319=DSM 18289). fam. nov. is also proposed.

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2008-01-01
2019-10-22
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References

  1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. ( 1990; ). Basic local alignment search tool. J Mol Biol 215, 403–410.[CrossRef]
    [Google Scholar]
  2. Aslam, Z., Lee, C. S., Kim, K.-H., Im, W.-T., Ten, L. N. & Lee, S.-T. ( 2007; ). Methylobacterium jeotgali sp. nov., a non-pigmented, facultatively methylotrophic bacterium isolated from jeotgal, a traditional Korean fermented seafood. Int J Syst Evol Microbiol 57, 566–571.[CrossRef]
    [Google Scholar]
  3. Balkwill, D. L. ( 2005; ). Genus VI. Ensifer Casida 1982, 343VP. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 354–358. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  4. Bambauer, A., Rainey, F. A., Stackebrandt, E. & Winter, J. ( 1998; ). Characterization of Aquamicrobium defluvii gen. nov. sp. nov., a thiophene-2-carboxylate-metabolizing bacterium from activated sludge. Arch Microbiol 169, 293–302.[CrossRef]
    [Google Scholar]
  5. Bauer, A. W., Kirby, W. M. M., Sherris, J. C. & Turck, M. ( 1966; ). Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 45, 493–496.
    [Google Scholar]
  6. Baumann, P. & Baumann, L. ( 1981; ). The marine Gram-negative eubacteria: genera Photobacterium, Beneckea, Alteromonas, Pseudomonas, and Alcaligenes. In The Prokaryotes, pp. 1302–1331. Edited by M. P. Starr, H. Stolp, H. G. Trüper, A. Balows & H. G. Schlegel. Berlin: Springer-Verlag.
  7. Bermond, D., Heller, R., Barrat, F., Delacour, G., Dehio, C., Alliot, A., Monteil, H., Chomel, B., Boulouis, H.-J. & Piémont, Y. ( 2000; ). Bartonella birtlesii sp. nov., isolated from small mammals (Apodemus spp.). Int J Syst Evol Microbiol 50, 1973–1979.[CrossRef]
    [Google Scholar]
  8. Bermond, D., Boulouis, H.-J., Heller, R., Van Laere, G., Monteil, H., Chomel, B. B., Sander, A., Dehio, C. & Piémont, Y. ( 2002; ). Bartonella bovis Bermond et al. sp. nov. and Bartonella capreoli sp. nov., isolated from European ruminants. Int J Syst Evol Microbiol 52, 383–390.
    [Google Scholar]
  9. Bowman, J. P. ( 2005a; ). Genus I. Methylocystis (ex Romanovskaya, Malashenko and Bogachenko 1978) Bowman, Sly, Nichols and Hayward 1993c, 751VP. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 413–416. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  10. Bowman, J. P. ( 2005b; ). Genus III. Methylosinus (ex Romanovskaya, Malashenko and Bogachenko 1978) Bowman, Sly, Nichols and Hayward 1993c, 751VP. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 417–420. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  11. Chen, W. X., Wang, E. T. & Kuykendall, L. D. ( 2005; ). Genus VI. Mesorhizobium Jarvis, van Berkum, Chen, Nour, Fernandez, Cleyet-Marel and Gillis 1997, 897VP. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 403–408. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  12. Cho, J.-C. & Giovannoni, S. J. ( 2003; ). Fulvimarina pelagi gen. nov., sp. nov., a marine bacterium that forms a deep evolutionary lineage of descent in the order ‘Rhizobiales’. Int J Syst Evol Microbiol 53, 1853–1859.[CrossRef]
    [Google Scholar]
  13. Choi, D. H., Kim, Y.-G., Hwang, C. Y., Yi, H., Chun, J. & Cho, B. C. ( 2006; ). Tenacibaculum litoreum sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 56, 635–640.[CrossRef]
    [Google Scholar]
  14. Cole, J. R., Chai, B., Marsh, T. L., Farris, R. J., Wang, Q., Kulam, S. A., Chandra, S., McGarrell, D. M., Schmidt, T. M. & other authors ( 2003; ). The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31, 442–443.[CrossRef]
    [Google Scholar]
  15. Collins, M. D. ( 1985; ). Isoprenoid quinone analysis in classification and identification. In Chemical Methods in Bacterial Systematics, pp. 267–287. Edited by M. Goodfellow & D. E. Minnikin. London: Academic Press.
  16. Collins, M. D. & Jones, D. ( 1981; ). Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol Rev 45, 316–354.
    [Google Scholar]
  17. Coloe, P. J., Sinclair, A. J., Slattery, J. F. & Burke, D. ( 1984; ). Differentiation of Brucella ovis from Brucella abortus by gas-liquid chromatographic analysis of cellular fatty acids. J Clin Microbiol 19, 896–898.
    [Google Scholar]
  18. Corbel, M. J. & Banai, M. ( 2005; ). Genus I. Brucella Meyer and Shaw 1920, 173AL. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 370–386. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  19. Das, S. K. ( 2005; ). Genus V. Bosea Das, Mishra, Tindall, Rainey and Stackebrandt 1996, 985VP. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 459–461. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  20. Dedysh, S. N., Liesack, W., Khmelenina, V. N., Suzina, N. E., Trotsenko, Y. A., Semrau, J. D., Bares, A. M., Panikov, N. S. & Tiedje, J. M. ( 2000; ). Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs. Int J Syst Evol Microbiol 50, 955–969.[CrossRef]
    [Google Scholar]
  21. Dedysh, S. N., Khmelenina, V. N., Suzina, N. E., Trotsenko, Y. A., Semrau, J. D., Liesack, W. & Tiedje, J. M. ( 2002; ). Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog. Int J Syst Evol Microbiol 52, 251–261.
    [Google Scholar]
  22. Dees, S. B., Hollis, D. G., Weaver, R. E. & Moss, C. W. ( 1981; ). Cellular fatty acids of Brucella canis and Brucella suis. J Clin Microbiol 14, 111–112.
    [Google Scholar]
  23. Dehio, C., Lanz, C., Pohl, R., Behrens, P., Bermond, D., Piémont, Y., Pelz, K. & Sander, A. ( 2001; ). Bartonella schoenbuchii sp. nov., isolated from the blood of wild roe deer. Int J Syst Evol Microbiol 51, 1557–1565.
    [Google Scholar]
  24. Denner, E. B. M., Smith, G. W., Busse, H.-J., Schumann, P., Narzt, T., Polson, S. W., Lubitz, W. & Richardson, L. L. ( 2003; ). Aurantimonas coralicida gen. nov., sp. nov., the causative agent of white plague type II on Caribbean scleractinian corals. Int J Syst Evol Microbiol 53, 1115–1122.[CrossRef]
    [Google Scholar]
  25. Doronina, N. V. & Trotsenko, Y. A. ( 2005a; ). Genus Incertae Sedis IV. Methylopila Doronina, Trotsenko, Krausova, Boulygina and Tourova 1998a, 1319VP. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 420–422. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  26. Doronina, N. V. & Trotsenko, Y. A. ( 2005b; ). Genus XIII. Methylorhabdus Doronina, Braus-Stromeyer, Leisinger and Trotsenko 1996a, 362VP (Effective publication: Doronina, Braus-Stromeyer, Leisinger and Trotsenko 1995, 97). In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 525–527. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  27. Doronina, N. V., Trotsenko, Y. A., Krausova, V. I., Boulygina, E. S. & Tourova, T. P. ( 1998; ). Methylopila capsulata gen. nov., sp. nov., a novel non-pigmented aerobic facultatively methylotrophic bacterium. Int J Syst Evol Microbiol 48, 1313–1321.
    [Google Scholar]
  28. Doronina, N. V., Trotsenko, Y. A., Tourova, T. P., Kuznetsov, B. B. & Leisinger, T. ( 2001; ). Albibacter methylovorans gen. nov., sp. nov., a novel aerobic, facultatively autotrophic and methylotrophic bacterium that utilizes dichloromethane. Int J Syst Evol Microbiol 51, 1051–1058.[CrossRef]
    [Google Scholar]
  29. Dunfield, P. F., Khmelenina, V. N., Suzina, N. E., Trotsenko, Y. A. & Dedysh, S. N. ( 2003; ). Methylocella silvestris sp. nov., a novel methanotroph isolated from an acidic forest cambisol. Int J Syst Evol Microbiol 53, 1231–1239.[CrossRef]
    [Google Scholar]
  30. Egli, T. W. & Auling, G. ( 2005; ). Genus II. Chelatococcus Auling, Busse, Egli, El-Banna and Stackebrandt 1993b, 624VP (Effective publication: Auling, Busse, Egli, El-Banna and Stackebrandt 1993a, 109). In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 433–437. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  31. Ewalt, D. R., Payeur, J. B., Martin, B. M., Cummins, D. R. & Miller, W. G. ( 1994; ). Characteristics of a Brucella species from a bottlenose dolphin (Tursiops truncatus). J Vet Diagn Invest 6, 448–452.[CrossRef]
    [Google Scholar]
  32. 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]
  33. Gao, J.-L., Turner, S. L., Kan, F. L., Wang, E. T., Tan, Z. Y., Qiu, Y. H., Gu, J., Terefework, Z., Young, J. P. W. & other authors ( 2004; ). Mesorhizobium septentrionale sp. nov. and Mesorhizobium temperatum sp. nov., isolated from Astragalus adsurgens growing in the northern regions of China. Int J Syst Evol Microbiol 54, 2003–2012.[CrossRef]
    [Google Scholar]
  34. Garrity, G. M., Bell, J. A. & Lilburn, T. G. ( 2004; ). Taxonomic Outline of the Prokaryotes. Bergey's Manual of Systematic Bacteriology, 2nd edn. Release 5.0. New York: Springer. http://dx.doi.org/10.1007/bergeysoutline
  35. Garrity, G. M., Bell, J. A. & Liburn, T. ( 2005; ). Class I. Alphaproteobacteria class. nov. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, p. 1. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  36. Gliesche, C., Fesefeldt, A. & Hirsch, P. ( 2005; ). Genus I. Hyphomicrobium Stutzer and Hartleb 1898, 76AL. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 476–494. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  37. Green, P. N. ( 2005; ). Genus I. Methylobacterium Patt, Cole and Hanson 1976, 228AL emend. Green and Bousfield 1983, 876. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 567–571. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  38. Hiraishi, A. & Imhoff, J. F. ( 2005; ). Genus XVII. Rhodoplanes Hiraishi and Ueda 1994b, 671VP. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 545–549. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  39. Hiraishi, A., Urata, K. & Satoh, T. ( 1995; ). A new genus of marine budding phototrophic bacteria, Rhodobium gen. nov., which includes Rhodobium orientis sp. nov. and Rhodobium marinum comb. nov. Int J Syst Bacteriol 45, 226–234.[CrossRef]
    [Google Scholar]
  40. Hirsch, P. & Gebers, R. ( 2005; ). Genus XIV. Pedomicrobium Aristovskaya 1961, 957VP emend. Gebers and Beese 1988, 305. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 527–538. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  41. Holmes, B. ( 2005; ). Genus III. Ochrobactrum Holmes, Popoff, Kiredjian and Kersters 1988, 412VP. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 389–392. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  42. Hougardy, A., Tindall, B. J. & Klemme, J.-H. ( 2000; ). Rhodopseudomonas rhenobacensis sp. nov., a new nitrate-reducing purple non-sulfur bacterium. Int J Syst Evol Microbiol 50, 985–992.[CrossRef]
    [Google Scholar]
  43. Im, W.-T., Yokota, A., Kim, M.-K. & Lee, S.-T. ( 2004; ). Kaistia adipata gen. nov., sp. nov., a novel α-proteobacterium. J Gen Appl Microbiol 50, 249–254.[CrossRef]
    [Google Scholar]
  44. Imhoff, J. F. ( 2005a; ). Genus VIII. Rhodoblastus Imhoff 2001, 1865VP. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 471–473. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  45. Imhoff, J. F. ( 2005b; ). Genus IX. Rhodopseudomonas Czurda and Maresch 1937, 119AL emend. Imhoff, Trüper and Pfennig 1984, 341. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 473–476. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  46. Imhoff, J. F. ( 2005c; ). Genus VII. Blastochloris Hiraishi 1997, 218VP. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 506–509. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  47. Imhoff, J. F. ( 2005d; ). Genus XVI. Rhodomicrobium Duchow and Douglas 1949, 415AL emend. Imhoff, Trüper and Pfennig 1984, 341. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 543–545. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  48. Imhoff, J. F. & Hiraishi, A. ( 2005; ). Genus I. Rhodobium Hiraishi, Urata and Satoh 1995d, 230VP. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 571–574. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  49. Imhoff, J. F. & Thiemann, B. ( 1991; ). Influence of salt concentration and temperature on the fatty acid compositions of Ectothiorhodospira and other halophilic phototrophic purple bacteria. Arch Microbiol 156, 370–375.[CrossRef]
    [Google Scholar]
  50. Ivanova, E. P., Flavier, S. & Christen, R. ( 2004; ). Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov. Int J Syst Evol Microbiol 54, 1773–1788.[CrossRef]
    [Google Scholar]
  51. Jenkins, C., Stanley, P. M. & Staley, J. T. ( 2005a; ). Genus II. Ancalomicrobium Staley 1968, 1940AL. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 494–497. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  52. Jenkins, C., Rainey, F. A., Ward, N. L. & Staley, J. T. ( 2005b; ). Genus XV. Prosthecomicrobium Staley 1968, 1940AL emend. Staley 1984, 304. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 538–543. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  53. Jeon, Y.-S., Chung, H., Park, S., Hur, I., Lee, J.-H. & Chun, J. ( 2005; ). jphydit: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences. Bioinformatics 21, 3171–3173.[CrossRef]
    [Google Scholar]
  54. Jiang, C.-Y., Dai, X., Wang, B.-J., Zhou, Y.-G. & Liu, S.-J. ( 2006; ). Roseomonas lacus sp. nov., isolated from freshwater lake sediment. Int J Syst Evol Microbiol 56, 25–28.[CrossRef]
    [Google Scholar]
  55. Jukes, T. H. & Cantor, C. R. ( 1969; ). Evolution of protein molecules. In Mammalian Protein Metabolism, vol. 3, pp. 21–132. Edited by H. N. Munro. New York: Academic Press.
  56. Jurado, V., Laiz, L., Gonzalez, J. M., Hernandez-Marine, M., Valens, M. & Saiz-Jimenez, C. ( 2005; ). Phyllobacterium catacumbae sp. nov., a member of the order ‘Rhizobiales’ isolated from Roman catacombs. Int J Syst Evol Microbiol 55, 1487–1490.[CrossRef]
    [Google Scholar]
  57. Jurado, V., Gonzalez, J. M., Laiz, L. & Saiz-Jimenez, C. ( 2006; ). Aurantimonas altamirensis sp. nov., a member of the order Rhizobiales isolated from Altamira Cave. Int J Syst Evol Microbiol 56, 2583–2585.[CrossRef]
    [Google Scholar]
  58. Kämpfer, P. ( 2005; ). Genus VII. Pseudaminobacter Kämpfer, Müller, Mau, Neef, Auling, Busse, Osborn and Stolz 1999, 894VP. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 409–410. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  59. Kämpfer, P., Neef, A., Salkinoja-Salonen, M. S. & Busse, H.-J. ( 2002; ). Chelatobacter heintzii (Auling et al. 1993) is a later subjective synonym of Aminobacter aminovorans (Urakami et al. 1992). Int J Syst Evol Microbiol 52, 835–839.[CrossRef]
    [Google Scholar]
  60. Kämpfer, P., Buczolits, S., Albrecht, A., Busse, H.-J. & Stackebrandt, E. ( 2003; ). Towards a standardized format for the description of a novel species (of an established genus): Ochrobactrum gallinifaecis sp. nov. Int J Syst Evol Microbiol 53, 893–896.[CrossRef]
    [Google Scholar]
  61. Kämpfer, P., Rosselló-Mora, R., Scholz, H. C., Welinder-Olsson, C., Falsen, E. & Busse, H.-J. ( 2006; ). Description of Pseudochrobactrum gen. nov., with two species Pseudochrobactrum asaccharolyticum sp. nov. and Pseudochrobactrum saccharolyticum sp. nov. Int J Syst Evol Microbiol 56, 1823–1829.[CrossRef]
    [Google Scholar]
  62. Kanso, S. & Patel, B. K. C. ( 2003; ). Microvirga subterranea gen. nov., sp. nov., a moderate thermophile from a deep subsurface Australian thermal aquifer. Int J Syst Evol Microbiol 53, 401–406.[CrossRef]
    [Google Scholar]
  63. Kelly, D. P., McDonald, I. R. & Wood, A. P. ( 2000; ). Proposal for the reclassification of Thiobacillus novellus as Starkeya novella gen. nov., comb. nov., in the α-subclass of the Proteobacteria. Int J Syst Evol Microbiol 50, 1797–1802.
    [Google Scholar]
  64. Kennedy, C. ( 2005a; ). Genus I. Beijerinckia Derx 1950a, 145AL. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 423–432. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  65. Kennedy, C. ( 2005b; ). Genus III. Agromonas Ohta and Hattori 1985, 223VP (Effective publication: Ohta and Hattori 1983, 43). In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 448–452. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  66. Komagata, K. & Suzuki, K. ( 1987; ). Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 19, 161–207.
    [Google Scholar]
  67. Kumar, S., Tamura, K. & Nei, M. ( 2004; ). mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef]
    [Google Scholar]
  68. Kuykendall, L. D. ( 2005a; ). Order VI. Rhizobiales ord. nov. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, p. 324. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  69. Kuykendall, L. D. ( 2005b; ). Genus I. Bradyrhizobium Jordan 1982, 137VP. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 438–443. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  70. Kuykendall, L. D. ( 2005c; ). Genus VI. Azorhizobium Dreyfus, Garcia and Gillis 1988, 89VP. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 505–506. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  71. Kuykendall, L. D., Hashem, F. M. & Wang, E. T. ( 2005; ). Genus VII. Sinorhizobium Chen, Yan and Li 1988b, 396VP emend. de Lajudie, Willems, Pot, Dewettinck, Maestrojuan, Neyra, Collins, Dreyfus, Kersters and Gillis 1994, 732. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 358–361. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  72. La Scola, B., Mallet, M.-N., Grimont, P. A. D. & Raoult, D. ( 2002; ). Description of Afipia birgiae sp. nov. and Afipia massiliensis sp. nov. and recognition of Afipia felis genospecies A. Int J Syst Evol Microbiol 52, 1773–1782.[CrossRef]
    [Google Scholar]
  73. La Scola, B., Mallet, M.-N., Grimont, P. A. D. & Raoult, D. ( 2003; ). Bosea eneae sp. nov., Bosea massiliensis sp. nov. and Bosea vestrisii sp. nov., isolated from hospital water supplies, and emendation of the genus Bosea (Das et al. 1996). Int J Syst Evol Microbiol 53, 15–20.[CrossRef]
    [Google Scholar]
  74. Labbé, N., Parent, S. & Villemur, R. ( 2004; ). Nitratireductor aquibiodomus gen. nov., sp. nov., a novel α-proteobacterium from the marine denitrification system of the Montreal Biodôme (Canada). Int J Syst Evol Microbiol 54, 269–273.[CrossRef]
    [Google Scholar]
  75. Lane, D. J. ( 1991; ). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. Edited by E. Stackebrandt & M. Goodfellow. Chichester: Wiley.
  76. Lee, K.-B., Liu, C.-T., Anzai, Y., Kim, H., Aono, T. & Oyaizu, H. ( 2005; ). The hierarchical system of the ‘Alphaproteobacteria’: description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov. Int J Syst Evol Microbiol 55, 1907–1919.[CrossRef]
    [Google Scholar]
  77. Manaia, C. M., Nogales, B. & Nunes, O. C. ( 2003; ). Tepidiphilus margaritifer gen. nov., sp. nov., isolated from a thermophilic aerobic digester. Int J Syst Evol Microbiol 53, 1405–1410.[CrossRef]
    [Google Scholar]
  78. Mantelin, S., Saux, M. F.-L., Zakhia, F., Béna, G., Bonneau, S., Jeder, H., de Lajudie, P. & Cleyet-Marel, J.-C. ( 2006; ). Emended description of the genus Phyllobacterium and description of four novel species associated with plant roots: Phyllobacterium bourgognense sp. nov., Phyllobacterium ifriqiyense sp. nov., Phyllobacterium leguminum sp. nov. and Phyllobacterium brassicacearum sp. nov. Int J Syst Evol Microbiol 56, 827–839.[CrossRef]
    [Google Scholar]
  79. Marmur, J. ( 1961; ). A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3, 208–218.[CrossRef]
    [Google Scholar]
  80. Mergaert, J. & Swings, J. ( 2005; ). Genus I. Phyllobacterium (ex Knösel 1962) Knösel 1984b, 356VP (Effective publication: Knösel 1984a, 254). In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 394–396. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  81. Mergaert, J., Cnockaert, M. C. & Swings, J. ( 2002; ). Phyllobacterium myrsinacearum (subjective synonym Phyllobacterium rubiacearum) emend. Int J Syst Evol Microbiol 52, 1821–1823.[CrossRef]
    [Google Scholar]
  82. 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 Bacteriol 39, 159–167.[CrossRef]
    [Google Scholar]
  83. Meyer, O. O. ( 2005; ). Genus VII. Oligotropha Meyer, Stackebrandt and Auling 1994, 182VP (Effective publication: Meyer, Stackebrandt and Auling 1993, 391). In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 468–471. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  84. Miller, J. A., Kalyuzhnaya, M. G., Noyes, E., Lara, J. C., Lidstrom, M. E. & Chistoserdova, L. ( 2005; ). Labrys methylaminiphilus sp. nov., a novel facultatively methylotrophic bacterium from a freshwater lake sediment. Int J Syst Evol Microbiol 55, 1247–1253.[CrossRef]
    [Google Scholar]
  85. Minnikin, D. E., O'Donnell, A. G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, K. & Parlett, J. H. ( 1984; ). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233–241.[CrossRef]
    [Google Scholar]
  86. Nakagawa, Y., Sakane, T. & Yokota, A. ( 2005; ). Genus VIII. Devosia Nakagawa, Sakane and Yokota 1996, 20VP. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 509–512. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  87. Ostle, A. G. & Holt, J. G. ( 1982; ). Nile blue A as fluorescent stain for poly-β-hydroxybutyrate. Appl Environ Microbiol 44, 238–241.
    [Google Scholar]
  88. Peix, A., Rivas, R., Trujillo, M. E., Vancanneyt, M., Velázquez, E. & Willems, A. ( 2005; ). Reclassification of Agrobacterium ferrugineum LMG 128 as Hoeflea marina gen. nov., sp. nov. Int J Syst Evol Microbiol 55, 1163–1166.[CrossRef]
    [Google Scholar]
  89. Rihs, J. D., Brenner, D. J., Weaver, R. E., Steigerwalt, A. G., Hollis, D. G. & Yu, V. L. ( 1993; ). Roseomonas, a new genus associated with bacteremia and other human infections. J Clin Microbiol 31, 3275–3283.
    [Google Scholar]
  90. Rivas, R., Sánchez, M., Trujillo, M. E., Zurdo-Piñeiro, J. L., Mateos, P. F., Martínez-Molina, E. & Velázquez, E. ( 2003; ). Xylanimonas cellulosilytica gen. nov., sp. nov., a xylanolytic bacterium isolated from a decayed tree (Ulmus nigra). Int J Syst Evol Microbiol 53, 99–103.[CrossRef]
    [Google Scholar]
  91. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  92. Schleheck, D., Tindall, B. J., Rosselló-Mora, R. & Cook, A. M. ( 2004; ). Parvibaculum lavamentivorans gen. nov., sp. nov., a novel heterotroph that initiates catabolism of linear alkylbenzenesulfonate. Int J Syst Evol Microbiol 54, 1489–1497.[CrossRef]
    [Google Scholar]
  93. Schlesner, H. ( 2005; ). Genus X. Filomicrobium Schlesner 1988, 220VP (Effective publication: Schlesner 1987, 65). In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 518–520. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  94. Sekar, R., Mills, D. K., Remily, E. R., Voss, J. D. & Richardson, L. L. ( 2006; ). Microbial communities in the surface mucopolysaccharide layer and the black band microbial mat of black band-diseased Siderastrea siderea. Appl Environ Microbiol 72, 5963–5973.[CrossRef]
    [Google Scholar]
  95. Sly, L. I. & Hugenholtz, P. ( 2005; ). Genus IV. Blastobacter Zavarzin 1961, 962AL emend. Sly 1985, 44. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 452–459. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  96. 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.
  97. Spieck, E. & Bock, E. ( 2005; ). Genus VI. Nitrobacter Winogradsky 1892, 127AL Nom. Cons. Opin. 23 Jud. Comm. 1958, 169. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 461–468. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  98. Staley, J. T., Boone, D. R., Brenner, D. J., De Vos, P., Garrity, G. M., Goodfellow, M., Krieg, N. R., Rainey, F. A. & Schleifer, K.-H. ( 2005a; ). Genus III. Aquamicrobium Bambauer, Rainey, Stackebrandt and Winter 1998b, 631VP (Effective publication: Bambauer, Rainey, Stackebrandt and Winter 1998a, 300). In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 399–400. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  99. Staley, J. T., Boone, D. R., Brenner, D. J., De Vos, P., Garrity, G. M., Goodfellow, M., Krieg, N. R., Rainey, F. A. & Schleifer, K.-H. ( 2005b; ). Genus IV. Defluvibacter Fritsche, Auling, Andreesen and Lechner 1999b, 1325VP (Effective publication: Fritsche, Auling, Andreesen and Lechner 1999a, 202). In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, p. 400. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  100. Staley, J. T., Boone, D. R., Brenner, D. J., De Vos, P., Garrity, G. M., Goodfellow, M., Krieg, N. R., Rainey, F. A. & Schleifer, K.-H. ( 2005c; ). Genus III. Methylocella Dedysh, Liesack, Khmelenina, Suzina, Trotsenko, Semrau, Bares, Panikov and Tiedje 2000, 967VP. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, p. 437. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  101. Teyssier, C., Marchandin, H., Jean-Pierre, H., Masnou, A., Dusart, G. & Jumas-Bilak, E. ( 2007; ). Ochrobactrum pseudintermedium sp. nov., a novel member of the family Brucellaceae, isolated from human clinical samples. Int J Syst Evol Microbiol 57, 1007–1013.[CrossRef]
    [Google Scholar]
  102. Thompson, E. A., Kaufman, A. E., Johnston, N. C. & Goldfine, H. ( 1983; ). Phospholipids of Rhizobium meliloti and Agrobacterium tumefaciens: lack of effect of Ti plasmid. Lipids 18, 602–606.[CrossRef]
    [Google Scholar]
  103. Tighe, S. W., de Lajudie, P., Dipietro, K., Lindström, K., Nick, G. & Jarvis, B. D. W. ( 2000; ). Analysis of cellular fatty acids and phenotypic relationships of Agrobacterium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium species using the Sherlock Microbial Identification System. Int J Syst Evol Microbiol 50, 787–801.[CrossRef]
    [Google Scholar]
  104. Tripathi, A. K., Verma, S. C., Chowdhury, S. P., Lebuhn, M., Gattinger, A. & Schloter, M. ( 2006; ). Ochrobactrum oryzae sp. nov., an endophytic bacterial species isolated from deep-water rice in India. Int J Syst Evol Microbiol 56, 1677–1680.[CrossRef]
    [Google Scholar]
  105. Trujillo, M. E., Willems, A., Abril, A., Planchuelo, A.-M., Rivas, R., Ludeña, D., Mateos, P. F., Martínez-Molina, E. & Velázquez, E. ( 2005; ). Nodulation of Lupinus albus by strains of Ochrobactrum lupini sp. nov. Appl Environ Microbiol 71, 1318–1327.[CrossRef]
    [Google Scholar]
  106. Urakami, T. ( 2005; ). Genus II. Aminobacter Urakami, Araki, Oyanagi, Suzuki and Komagata 1992, 90VP. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 397–399. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  107. Urakami, T. & Segers, P. ( 2005; ). Genus II. Mycoplana Gray and Thornton 1928, 82AL emend. Urakami, Oyanagi, Araki, Suzuki and Komagata 1990d, 439. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 386–389. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  108. Valverde, A., Velázquez, E., Fernández-Santos, F., Vizcaíno, N., Rivas, R., Mateos, P. F., Martínez-Molina, E., Igual, J. M. & Willems, A. ( 2005; ). Phyllobacterium trifolii sp. nov., nodulating Trifolium and Lupinus in Spanish soils. Int J Syst Evol Microbiol 55, 1985–1989.[CrossRef]
    [Google Scholar]
  109. Vandamme, P., Pot, B., Gillis, M., De Vos, P., Kersters, K. & Swings, J. ( 1996; ). Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60, 407–438.
    [Google Scholar]
  110. Vasilyeva, L. V. ( 2005a; ). Genus IV. Angulomicrobium Vasilyeva, Lafitskaya and Namsaraev 1986, 354VP (Effective publication: Vasilyeva, Lafitskaya and Namsaraev 1979, 1037). In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 501–504. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  111. Vasilyeva, L. V. ( 2005b; ). Genus XII. Labrys Vasilyeva and Semenov 1985, 375VP (Effective publication: Vasilyeva and Semenov 1984, 92). In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 523–525. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  112. Wang, E. T., Tan, Z. Y., Willems, A., Fernández-López, M., Reinhold-Hurek, B. & Martínez-Romero, E. ( 2002; ). Sinorhizobium morelense sp. nov., a Leucaena leucocephala-associated bacterium that is highly resistant to multiple antibiotics. Int J Syst Evol Microbiol 52, 1687–1693.[CrossRef]
    [Google Scholar]
  113. Welch, D. F. ( 2005; ). Genus I. Bartonella Strong, Tyzzer and Sellards 1915, 808VP emend. Birtles, Harrison, Saunders and Molyneux 1995, 7. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 362–370. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  114. Welch, D. F., Pickett, D. A., Slater, L. N., Steigerwalt, A. G. & Brenner, D. J. ( 1992; ). Rochalimaea henselae sp. nov., a cause of septicemia, bacillary angiomatosis, and parenchymal bacillary peliosis. J Clin Microbiol 30, 275–280.
    [Google Scholar]
  115. Weyant, R. S. & Whitney, A. M. ( 2005; ). Genus II. Afipia Brenner, Hollis, Moss, English, Hall, Vincent, Radosevic, Birkness, Bibb and other authors 1992, 327VP (Effective publication: Brenner, Hollis, Moss, English, Hall, Vincent, Radosevic, Birkness, Bibb and other authors, 1991, 2457). In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 443–448. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  116. Weyland, H. ( 1969; ). Actinomycetes in North Sea and Atlantic Ocean sediments. Nature 223, 858
    [Google Scholar]
  117. Wiegel, J. K. W. ( 2005; ). Genus XX. Xanthobacter Wiegel, Wilke, Baumgarten, Opitz and Schlegel 1978, 573AL. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 555–566. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  118. Woese, C. R., Stackebrandt, E., Weisburg, W. G., Paster, B. J., Madigan, M. T., Fowler, V. J., Hahn, C. M., Blanz, P., Gupta, R. & other authors ( 1984; ). The phylogeny of purple bacteria: the alpha subdivision. Syst Appl Microbiol 5, 315–326.[CrossRef]
    [Google Scholar]
  119. Xin, Y. H., Zhou, Y. G., Zhou, H. L. & Chen, W. X. ( 2004; ). Ancylobacter rudongensis sp. nov., isolated from roots of Spartina anglica. Int J Syst Evol Microbiol 54, 385–388.[CrossRef]
    [Google Scholar]
  120. Yoo, S.-H., Weon, H.-Y., Kim, B.-Y., Hong, S.-B., Kwon, S.-W., Cho, Y.-H., Go, S.-J. & Stackebrandt, E. ( 2006; ). Devosia soli sp. nov., isolated from greenhouse soil in Korea. Int J Syst Evol Microbiol 56, 2689–2692.[CrossRef]
    [Google Scholar]
  121. Yoon, J.-H., Kang, S.-J., Park, S. & Oh, T.-K. ( 2007; ). Devosia insulae sp. nov., isolated from soil, and emended description of the genus Devosia. Int J Syst Evol Microbiol 57, 1310–1314.[CrossRef]
    [Google Scholar]
  122. Young, J. M., Kerr, A. & Sawada, H. ( 2005; ). Genus II. Agrobacterium Conn 1942, 359AL. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 340–345. Edited by D. J. Brenner, N. R. Krieg, J. T. Staley & G. M. Garrity. New York: Springer.
  123. Zhang, D., Yang, H., Huang, Z., Zhang, W. & Liu, S.-J. ( 2002; ). Rhodopseudomonas faecalis sp. nov., a phototrophic bacterium isolated from an anaerobic reactor that digests chicken faeces. Int J Syst Evol Microbiol 52, 2055–2060.[CrossRef]
    [Google Scholar]
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vol. , part 1, pp. 267–277

Neighbour-joining tree showing relationship between the strains studied and most validly published species of related families in the order .

Transmission electron micrograph of negatively stained cells of strain CL-GR15 and strain CL-GR35.

Two-dimensional thin-layer chromatograms of the polar lipids of strain CL-GR15 .



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