The hierarchical system of the 'Alphaproteobacteria': Description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov

International Journal of Systematic and Evolutionary Microbiology

Volumn 55, Issue 5, 2005, Pages 1907-1919

  Lee, Kyung Bum ^a   Liu, Chi Te ^a   Anzai, Yojiro ^b   Kim, Hongik ^a   Aono, Toshihiro ^a   Oyaizu, Hiroshi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b TOHO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; RNA 16S; SMALL SUBUNIT RIBOSOMAL RNA;

ALPHAPROTEOBACTERIA; ANCYLOBACTER; ARTICLE; AZORHIZOBIUM; BACTERIAL STRAIN; CAULOBACTERALES; CLUSTER ANALYSIS; ERYTHROBACTER; ERYTHROBACTERACEAE; ERYTHROMICROBIUM; GENE SEQUENCE; HIRSCHIA; HYPHOMONADACEAE; HYPOMONAS; LABRYS; MARICAULIS; MAXIMUM LIKELIHOOD METHOD; NEW GENUS; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; OCEANICAULIS; PARVULARCULALES; PHYLOGENETIC TREE; PORPHYROBACTER; PRIORITY JOURNAL; RHIZOBIALES; RHODOSPIRILLALES; RICKETTSIA; RNA SEQUENCE; SEQUENCE ANALYSIS; SPECIES DIVERSITY; SPHINGOMONADALES; STARKEYA; STRAIN DIFFERENCE; TAXONOMIC RANK; UNINDEXED SEQUENCE; XANTHOBACTER; XANTHOBACTERACEAE;

ALPHAPROTEOBACTERIA; BACTERIAL TYPING TECHNIQUES; BASE SEQUENCE; DNA, BACTERIAL; DNA, RIBOSOMAL; GENES, RRNA; PHYLOGENY; RNA, RIBOSOMAL, 16S;

ALPHAPROTEOBACTERIA; ANCYLOBACTER; AZORHIZOBIUM; BACTERIA (MICROORGANISMS); ERYTHROBACTER; ERYTHROMICROBIUM; HIRSCHIA; HYPHOMONAS; LABRYS; MARICAULIS; OCEANICAULIS; PORPHYROBACTER; STARKEYA; XANTHOBACTER;

EID: 26444500123     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.63663-0     Document Type: Article

References (76)

1. Abraham, W.-R., Strömpl, C., Meyer, H. & 8 other authors (1999). Phylogeny and polyphasic taxonomy of Caulobacter species. Proposal of Maricaulis gen. nov. with Maricaulis maris (Poindexter) comb. nov. as the type species, and emended description of the genera Brevundimonas and Caulobacter. Int J Syst Bacteriol 49, 1053-1073.
2. Abraham, W.-R., Strömpl, C., Vancanneyt, M., Lünsdorf, H. & Moore, E. R. (2001). Determination of the systematic position of the genus Asticcacaulis Poindexter by a polyphasic analysis. Int J Syst Evol Microbiol 51, 27-34.
3. Adachi, J. & Hasegawa, M. (1996). MOLPHY: Programs for Molecular Phylogenetics, version 2.3. Tokyo: Institute of Statistical Mathematics.
4. Alarico, S., Rainey, F. A., Empadinhas, N., Schumann, P., Nobre, M. F. & da Costa, M. S. (2002). Rubritepida flocculans gen. nov., sp. nov., a new slightly thermophilic member of the α-1 subclass of the Proteobacteria. Syst Appl Microbiol 25, 198-206.
5. 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.
6. Auling, G., Busse, H.-J., Egli, T., El-Banna, T. & Stackebrandt, E. (1993). Description of the gram-negative, obligately aerobic, nitrilotriacetate (NTA)-utilizing bacteria as Chelatobacter heintzii, gen. nov., sp. nov., and Chelatococcus asaccharovorans, gen. nov., sp. nov. Syst Appl Microbiol 16, 104-112.
7. Birtles, R. J., Rowbotham, T. J., Michel, R., Pitcher, D. G., Lascola, B., Alexiou-Daniel, S. & Raoult, D. (2000). 'Candidatus Odyssella thessalonicensis' gen. nov., sp. nov., an obligate intracellular parasite of Acanthamoeba species. Int J Syst Evol Microbiol 50, 63-72.
8. Borsodi, A. K., Micsinai, A., Kovács, G., Tóth, E., Schumann, P., Kóvacs, A. L., Böddi, B. & Márialigeti, K. (2003). Pannonibacter phragmitetus gen. nov., sp. nov., a novel alkalitolerant bacterium isolated from decomposing reed rhizomes in a Hungarian soda lake. Int J Syst Evol Microbiol 53, 555-561.
9. Breed, R. S., Murray, E. G. D. & Smith, N. R. (editors) (1957). Bergey's Manual of Determinative Bacteriology, 7th edn. Baltimore: Williams & Wilkins.
10. Brenner, D. J., Hollis, D. G., Moss, C. W. & 25 other authors (1991). Proposal of Afipia gen. nov., with Afipia felis sp. nov. (formerly the cat scratch disease bacillus), Afipia clevelandensis sp. nov. (formerly the Cleveland Clinic Foundation strain), Afipia broomeae sp. nov., and three unnamed genospecies. J Clin Microbiol 29, 2450-2460.
11. Chen, W. X., Yan, G. H. & Li, J. L. (1988). Numerical taxonomic study of fast-growing soybean rhizobia and a proposal that Rhizobium fredii be assigned to Sinorhizobium gen. nov. Int J Syst Bacteriol 38, 392-397.
12. Cho, J.-C. & Giovannoni, S. J. (2003a). Parvularcula bermudensis gen. nov., sp. nov., a marine bacterium that forms a deep branch in the α-Proteobacteria. Int J Syst Evol Microbiol 53, 1031-1036.
13. Cho, J.-C. & Giovannoni, S. J. (2003b). 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.
14. Das, S. K., Mishra, A. K., Tindall, B. J., Rainey, F. A. & Stackebrandt, E. (1996). Oxidation of thiosulfate by a new bacterium, Bosea thiooxidans (strain BI-42) gen. nov., sp. nov.: analysis of phylogeny based on chemotaxonomy and 16S ribosomal DNA sequencing. Int J Syst Bacteriol 46, 981-987.
15. Danner, E. B. M., Vybiral, D., Kobližek, M., Kämpfer, P., Busse, H.-J. & Velimirov, B. (2002). Erythrobacter citreus sp. nov., a yellow-pigmented bacterium that lacks bacteriochlorophyll a, isolated from the western Mediterranean Sea. Int J Syst Evol Microbiol 52, 1655-1661.
16. Danner, 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.
17. De Rijk, P., Van de Peer, Y., Van den Broeck, I. & De Wachter, R. (1995). Evolution according to large ribosomal subunit RNA. J Mol Evol 41, 366-375.
18. Dreyfus, B., Garcia, J. L. & Gillis, M. (1988). Characterization of Azorhizobium caulinodans gen. nov., sp. nov., a stem-nodulating nitrogen-fixing bacterium isolated from Sesbania rostrata. Int J Syst Bacteriol 38, 89-98.
19. Dumler, J. S., Barbet, A. F., Bakker, C. P. J., Desch, G. A., Palmer, G. H., Ray, S. C., Rikihisa, Y. & Rurangirwa, F. R. (2001). Reorganization of genera in the families Rickettsiaceae and Anaplasmataceae inthe order Rickettsiales: unification of some species of Ehrlichia with Anaplasma, Cowdria with Ehrlichia and Ehrlichia with Neorickettsia, descriptions of six new species combinations and designation of Ehrlichia equi and 'HGE agent' as subjective synonyms of Ehrlichia phagocytophila. Int J Syst Evol Microbiol 51, 2145-2165.
20. Eisen, J. A. (1995). The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. J Mol Evol 41, 1105-1123.
21. Fox, G. E., Stackebrandt, E., Hespell, R. B. & 16 other authors (1980). The phylogeny of prokaryotes. Science 209, 457-463.
22. Friedman, C. S., Andrea, K. B., Beauchamp, K. A., Moore, J. D., Robbins, T. T., Shields, J. D. & Hedrick, R. P. (2000). 'Candidatus Xenohaliotis californiensis', a newly described pathogen of abalone, Haliotis spp., along the west coast of North America. Int J Syst Evol Microbiol 50, 847-855.
23. Fritz, I., Strömpl, C. & Abraham, W.-R. (2004). Phylogenetic relationships of the genera Stella, Labrys and Angulomicrobium within the 'Alphaproteobacteria' and description of Angulomicrobium amanitiforme sp. nov. Int J Syst Evol Microbiol 54, 651-657.
24. Fuerst, J. A., Hawkins, J. A., Holmes, A., Sly, L. I., Moore, C. J. & Stackebrandt E. (1993). Porphyrobacter neustonensis gen. nov., sp. nov., an aerobic bacteriochlorophyll-synthesizing budding bacterium from fresh water. Int J Syst Bacteriol 43, 125-134.
25. Garrity, G. M. & Holt, J. G. (2001). The road map to the Manual. In Bergey's Manual of Systematic Bacteriology, 2nd edn, pp. 119-166. Edited by D. R. Boone, R. W. Castenholz & G. M. Garrity. New York: Springer.
26. 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
27. Gebers, R. & Beese, M. (1988). Pedomicrobium americanum sp. nov. and Pedomicrobium australicum sp. nov. from aquatic habitats, Pedomicrobium gen. emend., and Pedomicrobium ferrugineum sp. emend. Int J Syst Bacteriol 38, 303-315.
28. Gillis, M. & De Ley, J. (1980). Intra- and intergeneric similarities of the ribosomal ribonucleic acid cistrons of Acetobacter and Gluconobacter. Int J Syst Bacteriol 30, 7-27.
29. Gupta, R. S. (1998). Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev 62, 1435-1491.
30. Hasegawa, M. & Kishino, H. (1994). Accuracies of the simple methods for estimating the bootstrap probability of a maximum-likelihood tree. Mol Biol Evol 11, 142-145.
31. Hasegawa, M., Kishino, H. & Yano, T. (1985). Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22, 160-174.
32. Hiraishi, A. (1997). Transfer of the bacteriochlorophyll b-containing phototrophic bacteria Rhodopseudomonas viridis and Rhodopseudomonas sulfoviridis to the genus Blastochloris gen. nov. Int J Syst Bacteriol 47, 217-219.
33. 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.
34. Hirsch, P. & Müller, M. (1985). Blastobacter aggregatus sp. nov., Blastobacter capsulatus sp. nov., and Blastobacter denitrificans sp. nov., new budding bacteria from freshwater habitats. Syst Appl Microbiol 6, 281-286.
35. Holmes, B., Popoff, M., Kiredjlan, M. & Kersters, K. (1988). Ochrobactrum anthropi gen. nov., sp. nov. from human clinical specimens and previously known as group Vd. Int J Syst Bacteriol 38, 406-416.
36. Imhoff, J. F. (2001). Transfer of Rhodopseudomonas acidophila to the new genus Rhodoblastus as Rhodoblastus acidophilus gen. nov., comb. nov. Int J Syst Evol Microbiol 51, 1863-1866.
37. Imhoff, J. F., Petri, R. & Süling, J. (1998). Reclassication of species of the spiral-shaped phototrophic purple non-sulfur bacteria of the α-Proteobacteria: description of the new genera Phaeospirillum gen. nov., Rhodovibrio, gen. nov., Rhodothalassium gen. nov. and Roseospira gen. nov. as well as transfer of Rhodospirillum fulvum to Phaeospirillum fulvum comb. nov., of Rhodospirillum molischianum to Phaeospirillum molischianum comb. nov., of Rhodospirillum salinarum to Rhodovibrio salinarum comb. nov., of Rhodospirillum sodomense to Rhodovibrio sodomensis comb. nov.
38. Karlin, S., Weinstock, G. M. & Brendel, V. (1995). Bacterial classifications derived from RecA protein sequence comparisons. J Bacteriol 177, 6881-6893.
39. Kämpfer, P., Andersson, M. A., Jäckel, U. & Salkinoja-Salonen, M. (2003). Teichococcus ludipueritiae gen. nov. sp. nov., and Muricoccus roseus gen. nov. sp. nov. representing two new genera of the α-1 subclass of the Proteobacteria. Syst Appl Microbiol 26, 23-29.
40. 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.
41. Kersters, K., Ludwig, W., Vancanneyt, M., De Vos, P., Gillis, M. & Schleifer, K.-H. (1996). Recent changes in the classification of the pseudomonads: an overview. Syst Appl Microbiol 19, 465-477.
42. Kishino, H., Miyata, T. & Hasegawa, M. (1990). Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J Mol Evol 31, 151-160.
43. Klenk, H.-P. & Zillig, W. (1994). DNA-dependent RNA polymerase subunit B as a tool for phylogenetic reconstructions: branching topology of the archaeal domain. J Mol Evol 38, 420-432.
44. Kosako, Y., Yabuuchi, E., Naka, T., Fujiwara, N. & Kobayashi, K. (2000). Proposal of Sphingomonadaceae fam. nov., consisting of Sphingomonas Yabuuchi et al. 1990, Erythrobacter Shiba and Shimidu 1982, Erythromicrobium Yurkov et al. 1994, Porphyrobacter Fuerst et al. 1993, Zymomonas Kluyver and van Niel 1936, and Sandaracinobacter Yurkov et al. 1997, with the type genus Sphingomonas Yabuuchi et al. 1990. Microbiol Immunol 44, 563-575.
45. Ludwig, W. & Klenk, H.-P. (2001). Overview: a phylogenetic backbone and taxonomic framework for procaryotic systematics. In Bergey's Manual of Systematic Bacteriology, 2nd edn, pp. 49-65. Edited by D. R. Boone, R. W. Castenholz & G. M. Garrity. New York: Springer.
46. Ludwig, W. & Schleifer, K. H. (1994). Bacterial phylogeny based on 16S and 23S rRNA sequence analysis. FEMS Microbiol Rev 15, 155-173.
47. Ludwig, W., Neumaier, J., Klugbauer, N. & 9 other authors (1993). Phylogenetic relationships of Bacteria based on comparative sequence analysis of elongation factor Tu and ATP-synthase β-subunit genes. Antonie van Leeuwenhoek 64, 285-305.
48. Ludwig, W., Strunk O., Klugbauer, S., Klugbauer, N., Weizenegger, M., Neumaier, J., Bachleitner, M. & Schleifer, K. H. (1998). Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19, 554-568.
49. Meyer, O., Lalucat J. & Schlegel, H. G. (1980). Pseudomonas carboxydohydrogena (Sanjieva and Zarvarzin) comb. nov., a monotrichous, nonbudding, strictly aerobic, carbon monoxide-utilizing hydrogen bacterium previously assigned to Seliberia. Int J Syst Bacteriol 30, 189-195.
50. Moore, R. L., Weiner, R. M. & Gebers, R. (1984). Genus Hyphomonas Pongratz 1957 nom. rev. emend., Hyphomonas polymorpha Pongratz 1957 nom. rev. emend., and Hyphomonas neptunium (Leifson 1964) comb. nov. emend. (Hyphomicrobium neptunium). Int J Syst Bacteriol 34, 71-73.
51. Nakagawa, Y., Sakane, T. & Yokota, A. (1996). Transfer of "Pseudomonas riboflavina" (Foster 1944), a gram-negative, motile rod with long-chain 3-hydroxy fatty acids, to Devosia riboflavina gen. nov., sp. nov., nom. rev. Int J Syst Bacteriol 46, 16-22.
52. Olsen, G. J., Woese, C. R. & Overbeek, R. (1994). The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol 176, 1-6.
53. Patt, T. E., Cole, G. C. & Hanson, R. S. (1976). Methylobacterium, a new genus of facultatively methylotrophic bacteria. Int J Syst Bacteriol 26, 226-229.
54. Pfennig, N. & Trüper, H. G. (1971). Higher taxa of the phototrophic bacteria. Int J Syst Bacteriol 21, 17-18.
55. Rainey, F. A., Ward-Rainey, N., Gliesche, C. G. & Stackebrandt, E. (1998). Phylogenetic analysis and intrageneric structure of the genus Hyphomicrobium and the related genus Filomicrobium. Int J Syst Bacteriol 48, 635-639.
56. Raj, H. D. (1983). Proposal of Ancylobacter gen. nov. as a substitute for the bacterial genus Microcyclus Ørskov 1928. Int J Syst Bacteriol 33, 397-398.
57. Saitoh, S., Suzuki, T. & Nishimura, Y. (1998). Proposal of Craurococcus, roseus gen. nov., sp. nov. and Paracraurococcus ruber gen. nov., sp. nov., novel aerobic bacteriochlorophyll a-containing bacteria from soil. Int J Syst Bacteriol 48, 1043-1047.
58. Schlesner, H. (1987). Filomicrobium fusiforme gen. nov., sp. nov., a slender budding, hyphal bacterium from brackish water. Syst Appl Microbiol 10, 63-67.
59. Schlesner, H., Bartels, C., Sittig, M., Dorsch, M. & Stackebrandt, E. (1990). Taxonomic and phylogenetic studies on a new taxon of budding, hyphal Proteobacteria, Hirschia baltica gen. nov., sp. nov. Int J Syst Bacteriol 40, 443-451.
60. Shiba, T. & Simidu, U. (1982). Erythrobacter longus, gen. nov., sp. nov., an aerobic bacterium which contains bacteriochlorophyll a. Int J Syst Bacteriol 32, 211-217.
61. Sly, L. I., Cox, T. L. & Beckenham, T. B. (1999). The phylogenetic relationships of Caulobacter, Asticcacaulis and Brevundimonas species and their taxonomic implications. Int J Syst Bacteriol 49, 483-488.
62. Stackebrandt, E., Murray, R. G. E. & Trüper, H. G. (1988). Proteobacteria classis nov., a name for the phylogenetic taxon that includes the "purple bacteria and their relatives". Int J Syst Bacteriol 38, 321-325.
63. Staley, J. T. (1968). Prosthecomicrobium and Ancalomicrobium: new prosthecate freshwater bacteria. J Bacteriol 95, 1921-1942.
64. Strömpl, C., Hold, G. L., Lünsdorf, H., Graham, J., Gallacher, S., Abraham, W.-R., Moore, E. R. B. & Timmis, K. N. (2003). Oceanicaulis alexandrii gen. nov., sp. nov., a novel stalked bacterium isolated from a culture of the dinoflagellate Alexandrium tamarense (Lebour) Balech. Int J Syst Evol Microbiol 53, 1901-1906.
65. Suzuki, T., Muroga, Y., Takahama, M. & Nishimura, Y. (2000). Roseibium denhamense gen. nov., sp. nov. and Roseibium hamelinense sp. nov., aerobic bacteriochlorophyll-containing bacteria isolated from the east and west coasts of Australia. Int J Syst Evol Microbiol 50, 2151-2156.
66. Takeuchi, M., Sawada, H., Oyaizu, H. & Yokota, A. (1994). Phylogenetic evidence for Sphingomonas and Rhizomonas as nonphotosynthetic members of the alpha-4 subclass of the Proteobacteria. Int J Syst Bacteriol 44, 308-314.
67. Takeuchi, M., Hamana, K. & Hiraishi, A. (2001). Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 51, 1405-1417.
68. Trust, T. J., Logan, S. M., Gustafson, C. E., Romaniuk, P. J., Kim, N. W., Chan, V. L., Ragan, M. A., Guerry, P. & Gutell, R. R. (1994). Phylogenetic and molecular characterization of a 23S rRNA gene positions the genus Campylobacter in the epsilon subdivision of the Proteobacteria and shows that the presence of transcribed spacers is common in Campylobacter spp. J Bacteriol 176, 4597-4609.
69. Uchino, Y., Hirata, A., Yokota, A. & Sugiyama, J. (1998). Reclassification of marine Agrobacterium species: proposals of Stappia stellulata gen. nov., comb. nov., Stappia aggregata sp. nov., nom. rev., Ruegeria atlantica gen. nov., comb. nov., Ruegeria gelatinovora comb. nov., Ruegeria algicola comb. nov., and Ahrensia kieliense gen. nov., sp. nov., nom. rev. J Gen Appl Microbiol 44, 201-210.
70. Viale, A. M., Arakaki, A., Soncini, F. C. & Ferreyra, R. G. (1994). Evolutionary relationships among eubacterial groups as inferred from GroEL (chaperonin) sequence comparisons. Int J Syst Bacteriol 44, 527-533.
71. Wetmur, J. G., Wong, D. M., Ortiz, B., Tong, J., Reichert, F. & Gelfand, D. H. (1994). Cloning, sequencing, and expression of RecA proteins from three distantly related thermophilic eubacteria. J Biol Chem 269, 25928-25935.
72. Woese, C. R. (1987). Bacterial evolution. Microbiol Rev 51, 221-271.
73. Woese, C. R., Sogin, M. L., Bonen, L. & Stahl, D. (1975). Sequence studies on 16S ribosomal RNA from a blue-green alga. J Mol Evol 4, 307-315.
74. Woese, C. R., Magrum, L. J. & Fox, G. E. (1978). Archaebacteria. J Mol Evol 11, 245-251.
75. Yurkov, V., Stackebrandt, E., Holmes, A. & 7 other authors (1994). Phylogenetic positions of novel aerobic, bacteriochlorophyll a-containing bacteria and description of Roseococcus thiosulfatophilus gen. nov., sp. nov., Erythromicrobium ramosum gen. nov., sp. nov., and Erythrobacter litoralis sp. nov. Int J Syst Bacteriol 44, 427-434.
76. Zablen, L. & Woese, C. R. (1975). Procaryote phylogeny IV: concerning the phylogenetic status of a photosynthetic bacterium. J Mol Evol 5, 25-34.