- 1) Maier, R. M., Pepper, I. L., and Gerba, C. P., “Environmental Microbiology,” Academic Press, San Diego, California (2000).
- 2) Tran, Q. H., and Unden, G., Changes in the proton potential and the cellular energetics of Escherichia coli during growth by aerobic and anaerobic respiration or by fermentation. Eur. J. Biochem., 251, 538–543 (1998).
- 3) Snaidr, J., Amann, R., Huber, I., Ludwig, W., and Schleifer, K. H., Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl. Environ. Microbiol., 63, 2884–2896 (1997).
- 4) Amann, R. I., Ludwig, W., and Schleifer, K. H., Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev., 59, 143–169 (1995).
- 5) Hugenholtz, P., Goebel, B. M., and Pace, N. R., Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol., 180, 4765–4774 (1998).
- 6) Woese, C. R., Bacterial evolution. Microbiol. Rev., 51, 221–271 (1987).
- 7) Sambrook, J., Fritsch, E. F., and Maniatis, T., “Molecular Cloning, a Laboratory Manual” 2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor (1989).
- 8) Ohshima, H., Matsuoka, S., Asai, K., and Sadaie, Y., Molecular organization of intrinsic restriction and modification genes BsuM of Bacillus subtilis Marburg. J. Bacteriol., 184, 381–389 (2002).
- 9) Cole, J. R., Chai, B., Farris, R. J., Wang, Q., Kulam, S. A., McGarrell, D. M., Garrity, G. M., and Tiedje, J. M., The ribosomal database project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res., 33, D294–D296 (2005).
- 10) Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and Higgins, D. G., The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res., 24, 4876–4882 (1997).
- 11) Kumar, S., Tamura, K., and Nei, M., MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform., 5, 150–163 (2004).
- 12) Page, R. D. M., TREEVIEW: an application to display phylogenetic trees on personal computers. Comp. Appl. Biosci., 12, 357–358 (1996).
- 13) Bjornsson, L., Hugenholtz, P., Tyson, G. W., and Blackall, L. L., Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiol., 148, 2309–2318 (2002).
- 14) Sekiguchi, Y., Takahashi, H., Kamagata, Y., Ohashi, A., and Harada, H., In situ detection, isolation, and physiological properties of a thin filamentous microorganism abundant in methanogenic granular sludges: a novel isolate affiliated with a clone cluster, the green non-sulfur bacteria, subdivision I. Appl. Environ. Microbiol., 67, 5740–5749 (2001).
- 15) Khan, S. T., Horiba, Y., Yamamoto, M., and Hiraishi, A., Members of the family comamonadaceae as primary poly(3-hydroxybutyrate-co-3-hydroxyvalerate)-degrading denitrifiers in activated sludge as revealed by polyphasic approach. Appl. Environ. Microbiol., 68, 3206–3214 (2002).
- 16) Naimuddin, M., and Nishigaki, K., Genome analysis technologies: towards species identification by genotype. Brief. Funct. Genomic. Proteomic., 1, 356–371 (2003).
Bioscience, Biotechnology, and Biochemistry
Volume 71, 2007 - Issue 3