Exploring the diversity of myxobacteria in a soil niche by myxobacteria-specific primers and probes

Environmental Microbiology

Volumn 7, Issue 10, 2005, Pages 1602-1610

  Wu, Zhi Hong ^a   Jiang, De Ming ^a   Li, Peng ^a   Li, Yue Zhong ^a  

^a SHANDONG UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; PRIMER DNA; RIBOSOME DNA; RNA 16S;

ARTICLE; CLASSIFICATION; CULTURE MEDIUM; DNA SEQUENCE; ECOSYSTEM; GENE LIBRARY; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; MYXOCOCCALES; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA GENE; SPECIES DIFFERENCE;

CULTURE MEDIA; DNA PRIMERS; DNA, BACTERIAL; DNA, RIBOSOMAL; ECOSYSTEM; GENE LIBRARY; GENES, RRNA; MOLECULAR SEQUENCE DATA; MYXOCOCCALES; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; SPECIES SPECIFICITY;

BACTERIA (MICROORGANISMS); CORALLOCOCCUS; CYSTOBACTER; CYSTOBACTERINEAE; MYXOCOCCALES; MYXOCOCCUS; NANNOCYSTIS; SORANGINEAE;

EID: 25144521051     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2005.00852.x     Document Type: Article

References (32)

1. Acinas, S.G., Klepac-Ceraj, V., Hunt, D.E., Pharino, C., Ceraj, I., Distel, D.L., and Polz, M.F. (2004) Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430: 551-554.
2. Brosius, J., Palmer, M.L., Kennedy, P.J., and Noller, H.F. (1978) Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci USA 75: 4801-4805.
3. Dawid, W. (2000) Biology and global distribution of myxobacteria in soils. FEMS Microbiol Rev 24: 403-427.
4. Dawid, W., Gallikowski, C.A., and Hirsch, P. (1988) Psychrophilic myxobacteria from Antarctic soils. Polarforschung 58: 271-278.
5. Dworkin, M. (1996) Recent advances in the social and developmental biology of the myxobacteria. Microbiol Rev 60: 70-102.
6. Dworkin, M., and Kaiser, D. (1993) Myxobacteria II. Washington, DC, USA: American Society for Microbiology.
7. Felsenstein, J. (2001) phylip (Phylogeny Inference Package) 3.61. Seattle, WA, USA: Department of Genetics, University of Washington.
8. Fudou, R., Jojima, Y., Iizuka, T., and Yamanaka, S. (2002) Haliangium ochraceum gen. nov., sp. nov. and Haliangium tepidum sp. nov. novel moderately halophilic myxobacteria isolated from coastal saline environments. J Gen Appl Microbiol 48: 109-116.
9. Iizuka, T., Jojima, Y., Fudou, R., Hiraishi, A., Ahn, J.W., and Yamanaka, S. (2003a) Plesiocystis pacifica gen. nov., sp. nov., a marine myxobacterium that contains dihydrogenated menaquinone, isolated from the Pacific coasts of Japan. Int J Syst Evol Microbiol 53: 189-195.
10. Iizuka, T., Jojima, Y., Fudou, R., Tokura, M., Hiraishi, A., and Yamanaka, S. (2003b) Enhygromyxa salina gen. nov., sp. nov., a slightly halophilic myxobacterium isolated from the coastal areas of Japan. Syst Appl Microbiol 26: 189-196.
11. Kaiser, D. (2004) Signaling in myxobacteria. Annu Rev Microbiol 58: 75-98.
12. Klappenbach, J.A., Dunbar, J.M., and Schmidt, T.M. (2000) rRNA operon copy number reflects ecological strategies of bacteria. Appl Environ Microbiol 66: 1328-1333.
13. Li, Y.-Z., Li, J., Zhou, L., Zhang, Y., Hu, W., and Chen, Q. (2000) Isolation and identification of myxobacterial sources in China. Acta Microbiol Sinica (in Chinese) 40: 652-656.
14. Li, Y.Z., Hu, W., Zhang, Y.Q., Qiu, Z., Zhang, Y., and Wu, B.H. (2002) A simple method to isolate salt-tolerant myxobacteria from marine samples. J Microbiol Methods 50: 205-209.
15. Ludwig, W., Schleifer, K.H., Reichenbach, H., and Stackebrandt, E. (1983) A phylogenetic analysis of the myxobacteria Myxococcus fulvus, Stigmatella aurantiaca, Cystobacter fuscus, Sorangium cellulosum and Nannocystis exedens. Arch Microbiol 135: 58-62.
16. McCurdy, H.D. (1989) Bergey's Manual of Systematic Bacteriology. Baltimore, MD, USA: Williams & Wilkins.
17. Miller, D.N., Bryant, J.E., Madsen, E.L., and Ghiorse, W.C. (1999) Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol 65: 4715-4724.
18. Oyaizu, H., and Woese, C.R. (1985) Phylogenetic relationships among the sulfate respiring bacteria, myxobacteria and purple bacteria. Syst Appl Microbiol 6: 257-263.
19. Rappe, M.S., and Giovannoni, S.J. (2003) The uncultured microbial majority. Annu Rev Microbiol 57: 369-394.
20. Reichenbach, H. (1993) Myxobacteria II. Washington, DC, USA: American Society for Microbiology.
21. Reichenbach, H. (1999) The ecology of the myxobacteria. Environ Microbiol 1: 15-21.
22. Reichenbach, H., and Dworkin, M. (1992) The Prokaryotes. New York, USA: Springer-Verlag.
23. Rosenberg, E. (1984) Myxobacteria: Development and Cell Interactions. New York, USA: Springer-Verlag.
24. Sambrook, J., and Russell, D.W. (2001) Molecular Cloning: A Laboratory Manual, 3rd edn. Cold Spring Harbor, NY, USA: Cold Spring Harbor Laboratory Press.
25. Sanford, R.A., Cole, J.R., and Tiedje, J.M. (2002) Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic myxobacterium. Appl Environ Microbiol 68: 893-900.
26. Shimkets, L.J. (1990) Social and developmental biology of the myxobacteria. Microbiol Rev 54: 473-501.
27. Shimkets, L., and Woese, C.R. (1992) A phylogenetic analysis of the myxobacteria: basis for their classification. Proc Natl Acad Sci USA 89: 9459-9463.
28. Spröer, C., Reichenbach, H., and Stackebrandt, E. (1999) The correlation between morphogenetic classification of myxobacteria. Int J Syst Bacteriol 49: 1255-1262.
29. Stackebrandt, E., Murray, R.G.E., and Trüper, H.G. (1988) Proteo-bacteria classis nov., a name for the phylogenetic taxon that includes the purple bacteria and their relatives. Int J Syst Bacteriol 38: 321-325.
30. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
31. Yan, Z.C., Wang, B., Li, Y.Z., Gong, X., Zhang, H.Q., and Gao, P.J. (2003) Morphologies and phylogenetic classification of cellulolytic myxobacteria. Syst Appl Microbiol 26: 104-109.
32. Zhang, J., Liu, Z., Wang, S., and Jiang, P. (2002) Characterization of a bioflocculant produced by the marine myxobacterium Nannocystis sp. NU-2. Appl Microbiol Biotechnol 59: 517-522.