Isolation and phylogenetic analysis of aerobic copiotrophic ultramicrobacteria from urban soil

Journal of General and Applied Microbiology

Volumn 44, Issue 1, 1998, Pages 75-84

  Iizuka, Takashi ^a   Yamanaka, Shigeru ^a   Nishiyama, Tohru ^a   Hiraishi, Akira ^a,b  

^a AJINOMOTO CO INC   (Japan)

^b TOYOHASHI UNIVERSITY OF TECHNOLOGY   (Japan)

Author keywords

16S rDNA; Phylogeny; Soil bacteria; Ultramicrobacteria

Indexed keywords

BACTERIAL DNA; RIBOSOME DNA; RNA 16S;

ACTINOBACTERIA; ARTICLE; BACTERIAL CELL WALL; BACTERIAL GROWTH; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; CELL VOLUME; DNA SEQUENCE; FLUORESCENCE MICROSCOPY; GROWTH CURVE; IMAGE ANALYSIS; MEMBRANE FILTER; NONHUMAN; PHYLOGENY; SCANNING ELECTRON MICROSCOPY; SOIL MICROFLORA; TRANSMISSION ELECTRON MICROSCOPY;

ACTINOBACTERIA; GAMMAPROTEOBACTERIA; NEGIBACTERIA; POSIBACTERIA; PROTEOBACTERIA;

EID: 0031789346     PISSN: 00221260     EISSN: None     Source Type: Journal    
DOI: 10.2323/jgam.44.75     Document Type: Article

References (47)

1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Amako, K. and Takeda, A. (1985) The fine structure of Bacillus subtilis revealed by the rapid-freezing and substitution-fixation method. J. Electron Microsc., 34, 13-17.
3. Bradbury, J. F. (1984) Genus II. Xanthomonas. In Bergey's Manual of Systematic Bacteriology, Vol. 1, ed. by Krieg, N. R. and Holt, J. G., Williams & Wilkins, Baltimore, pp. 199-220.
4. Brosius, J., Palmer, J. L., Kennedy, J. P., and Noller, H. F. (1978) Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc. Natl. Acad. Sci. U.S.A., 75, 4801-4805.
5. Collins, M. D. and Bradbury, J. F. (1986) Plant pathogenic species of Corynebacterium. In Bergey's Manual of Systematic Bacteriology, Vol. 2, ed. by Sneath, P. H. A., Mair, N. A., Sharpe, M. E., and Holt, J. G., Williams & Wilkins, Baltimore, pp. 1276-1283.
6. Collins, M. D. and Bradbury, J. F. (1992) The genera Agromyces, Aureobacterium, Clavibacter, Curtobacterium, and Microbacterium. In The Prokaryotes, 2nd ed., ed. by Balows, A., Trüper, H. G., Dworkin, M., Harder, W., and Schleifer, K.-H., Springer-Verlag, Berlin, pp. 1355-1368.
7. Cusack, F., Singh, S., McCarthy, C., Grieco, J., De Rocco, M., Nguyen, D., Lappin-Scott, H., and Costerton, J. W. (1992) Enhanced oil recovery - three dimensional sandpack simulation of ultramicrobacteria resuscitation in reservoir formation. J. Gen. Microbiol., 138, 647-655.
8. Doudroff, M. and Palleroni, N. J. (1974) Genus Pseudomonas. In Bergey's Manual of Determinative Bacteriology, 8th ed., ed. by Buchanan, R. E. and Gibbons, N. E., Williams & Wilkins, Baltimore, pp. 217-243.
9. Eguchi, M., Nishikawa, T., MacDonald, K., Cavicehioli, R., Gottschal, J. C., and Kjelleberg, S. (1996) Responses to stress and nutrient availability by the marine ultramicrobacterium Sphingomonas sp. strain RB2256. Appl. Environ. Microbiol., 62, 1287-1294.
10. AL. In Bergey's Manual of Systematic Bacteriology, Vol. 1, ed. by Krieg, N. R. and Holt, J. G., Williams & Wilkins, Baltimore, pp. 394-399.
11. Felsenstein, J. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39, 783-791.
12. Fry, J. C. and Davies, A. R. (1985) An assessment of methods for measuring volumes of planktonic bacteria, with particular reference to television image analysis. J. Appl. Bacteriol., 58, 113-115.
13. Fuhrman, J. A. (1981) Influence of method on the apparent size distribution of bacterioplankton cells: Epifluorescence microscopy compared to scanning electron microscopy. Mar. Ecol. Prog. Ser., 5, 103-106.
14. Hiraishi, A., Hoshino, Y., and Kitamura, H. (1984) Isoprenoid quinone composition in the classification of Rhodospirillaceae. J. Gen. Appl. Microbiol., 30, 197-210.
15. Hiraishi, A., Kamagata, Y., and Nakamura, K. (1995) Polymerase chain reaction amplification and restriction fragment length polymorphism analysis of 16S rRNA genes from methanogens. J. Ferment. Bioeng., 79, 523-529.
16. Hiraishi, A. and Komagata, K. (1989) Effects of the growth medium composition on menaquinone homolog formation in Micrococcus luteus. J. Gen. Appl. Microbiol., 35, 311-318.
17. Hiraishi, A., Shin, Y. K., and Sugiyama, J. (1997) Proposal to reclassify Zoogloea ramigera IAM 12670 (P. R. Dugan 115) as Duganella zoogloeoides gen. nov., sp. nov. Int. J. Syst. Bacteriol., 47, 1249-1252.
18. Hiraishi A., Shin, Y. K., Ueda, Y., and Sugiyama, J. (1994) Automated sequencing of PCR-amplified 16S rDNA on "Hydrolink" gels. J. Microbiol. Methods, 19, 145-154.
19. Hiraishi, A. and Ueda, Y. (1994) Rhodoplanes gen. nov., a new genus of phototrophic bacteria including Rhodopseudomonas rosea as Rhodoplanes roseus comb. nov. and Rhodoplanes elegans sp. nov. Int. J. Syst. Bacteriol., 44, 665-673.
20. Hobbie, J. E., Daley, R. J., and Jasper, S. (1977) Use of nucleopore filters for counting bacteria by fluorescense microscopy. Appl. Environ. Microbiol., 33, 1225-1228.
21. Hood, M. A. and MacDonell, M. T. (1987) Distribution of ultramicrobacteria in a gulf coast estuary and induction of ultramicrobacteria. Microb. Ecol., 14, 113-127.
22. Janssen, P. H., Schuhmann, A., Mörehel, E., and Rainey, F. A. (1997) Novel anaerobic ultramicrobacteria belonging to the Verrucomicrobiales lineage of bacterial descent isolated by dilution culture from anoxic rice paddy soil. Appl. Environ. Microbiol., 63, 1382-1388.
23. Juhnke, M. E., Mathre, D. E., and Sands, D. C. (1987) Identification of rhizosphere-competent bacteria of wheat. Appl. Environ. Microbiol., 55, 747-750.
24. Kato, K. (1996) Image analysis of bacterial cell size and diversity. In Microbial Diversity in Time and Space, ed. by Colwell, R. R., Plenum Press, New York, pp. 141-147.
25. Kimura, M. (1980) A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences. J. Mol. Evol., 16, 111-120.
26. Koch, A. L. (1996) What size should a bacterium be? A question of scale. Annu. Rev. Microbiol., 50, 317-348.
27. Krawiec, S. and Riley, M. (1990) Organization of the bacterial chromosome. Microbiol. Rev., 54, 502-539.
28. Lane, D. J. (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, ed. by Stackebrandt, E. and Goodfellow, M., John Wiley & Sons, Chichester, pp. 115-175.
29. Lappin-Scott, H. M. and Costerton, J. W. (1992) Ultramicrobacteria and their biotechnological applications. Curr. Opin. Biotechnol., 3, 282-285.
30. Leifson, E. (1962) The bacterial flora of distilled and stored water. III. New species of the genera Corynebacterium, Flavobacterium, Spirillum, and Pseudomonas. Int. Bull. Bacteriol. Nomencl. Taxon., 12, 161-170.
31. MacDonell, M. T. and Hood, M. A. (1982) Isolation and characterization of ultramicrobacteria from a Gulf Coast estuary. Appl. Environ. Microbiol., 43, 556-571.
32. MacLeod, F. A., Lappin-Scott, H. M., and Costerton, J. W. (1988) Plugging of a model rock system by using starved bacteria. Appl. Environ. Microbiol., 54, 1365-1372.
33. VP, (Effective publication: Pohl 1979, 81). In Bergey's Manual of Systematic Bacteriology, Vol. 1, ed. by Krieg, N. R. and Holt, J. G., Williams & Wilkins, Baltimore, pp. 550-552.
34. Mergaert, J., Schirmer, A., Hauben, L., Mau, M., Hoste, B., Kersters, K., Jendrossek, D., and Swings, J. (1996) Isolation and identification of poly(3-hydroxyvalerate)-degrading strains of Pseudomonas lemoignei. Int. J. Syst. Bacteriol., 46, 769-773.
35. AL. In Bergey's Manual of Systematic Bacteriology, Vol. 1, ed. by Krieg, N. R. and Holt, J. G., Williams & Wilkins, Baltimore, pp. 729-738.
36. Razin, S. (1992) The genera Mycoplasma, Ureaplasma, Acholeplasma, Anaeroplasma, and Asteroleplasma. In The Prokaryotes, 2nd ed., ed. by Balows, A., Trüper, H. G., Dworkin, M., Harder, W., and Schleifer, K.-H., Springer-Verlag, Berlin, pp. 1937-1959.
37. AL. In Bergey's Manual of Systematic Bacteriology, Vol. 1, ed. by Krieg, N. R. and Holt, J. G., Williams & Wilkins, Baltimore, pp. 681-683.
38. Ruby, E. D. (1992) The genus Bdellovibrio. In The Prokaryotes, 2nd ed., ed. by Balows, A., Trüper, H. G., Dworkin, M., Harder, W., and Schleifer, K.-H., Springer-Verlag, Berlin, pp. 3400-3415.
39. Saitou, N. and Nei, M. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
40. Schut, F., DeVries, E. J., Gottschal, J. C., Robertson, B. R., Harder, W., Prins, R. A., and Button, D. K. (1993) Isolation of typical marine bacteria by dilution culture: Growth, maintenance, and characteristics of isolates under laboratory conditions. Appl. Environ. Microbiol., 59, 2150-2160.
41. Schut, F., Jansen, M., Gomes, T. M. P., Gottschal, J. C., Harder, W., and Prins, R. A. (1995) Substrate uptake and utilization by a marine ultramicrobacterium. Microbiology, 141, 351-361.
42. Suzuki, S., Horinouchi, S., and Beppu, T. (1988) Growth of a tryptophanase-producing thermophile, Symbiobacterium thermophilum gen. nov., sp. nov., is dependent on co-culture with a Bacillus sp. J. Gen. Microbiol., 134, 2353-2362.
43. Tamaoka, J., Katayama, Y., and Kuraishi, H. (1983) Analysis of bacterial menaquinones by reverse-phase high-performance liquid chromatography. J. Appl. Microbiol., 54, 31-36.
44. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
45. Torrella, F. and Morita, R. Y. (1981) Microcultural study of bacterial size changes and microcolony and ultramicrocolony formation by heterotrophic bacteria in seawater. Appl. Environ. Microbiol., 41, 518-527.
46. AL. In Bergey's Manual of Systematic Bacteriology, Vol. 1, ed. by Krieg, N. R. and Hold, J. G., Williams & Wilkins, Baltimore, pp. 687-704.
47. Zgurskaya, H. I., Evtushenko, L. I., Akimov, V. N., and Kalakoutskii, L. V. (1993) Rathayibacter gen. nov., including the species Rathayibacter rathyi com. nov., Rathayibacter tritici comb. nov., Rathayibacter iranicus comb. nov., and six strains from annual grasses. Int. J. Syst. Bacteriol., 43, 143-149.