Capillary electrophoresis single-strand conformation polymorphism analysis for monitoring soil bacteria

Journal of Microbiological Methods

Volumn 60, Issue 1, 2005, Pages 83-92

  King, Stephanie ^a   McCord, Bruce R ^a   Riefler, R Guy ^b  

^a OHIO UNIVERSITY   (United States)

^b Ohio University   (United States)

Author keywords

Capillary electrophoresis; PCR; Single strand conformation polymorphism; Soil bacteria

Indexed keywords

ARTICLE; BACTERIAL FLORA; CAPILLARY ELECTROPHORESIS; COMPUTER PROGRAM; CONTROLLED STUDY; GENE AMPLIFICATION; GENETIC ANALYSIS; NONHUMAN; PRIORITY JOURNAL; SOIL MICROFLORA;

DNA, BACTERIAL; ELECTROPHORESIS, CAPILLARY; GRAM-NEGATIVE BACTERIA; GRAM-POSITIVE BACTERIA; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE-STRANDED CONFORMATIONAL; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS);

EID: 9644295617     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2004.08.014     Document Type: Article

References (31)

1. P.S. Anderson, C. Jespersgaard, J. Vuust, M. Christiansen, and L.A. Larsen Capillary electrophoresis-based single strand DNA conformation analysis in high-throughput mutation screening Human Mutat. 21 2003 455 465
2. V.A. Castro, A.N. Thrasher, M. Healy, C.M. Ott, and D.L. Pierson Microbial characterization during the early habitation of the international space station Microb. Ecol. 47 2004 119 126
3. F. Duthoit, J. Godon, and M. Montel Bacterial community dynamics during production of registered designation of origin salers cheese as evaluated by 16S rRNA gene single-strand conformation polymorphism analysis Appl. Environ. Microbiol. 69 2003 3840 3848
4. C.A. Eichner, R.W. Erb, K.N. Timmis, and I. Wagner-Döbler Thermal gradient gel electrophoresis analysis of bioprotection from pollutant shocks in the activated microbial community Appl. Environ. Microbiol. 65 1999 102 109
5. A. Gelsomino, A.C. Keijzer-Wolters, G. Cacco, and J.D. van Elsas Assessment of bacterial community structure in soil by polymerase chain reaction and denaturing gradient gel electrophoresis J. Microbiol. Methods 38 1999 1 15
6. R. Ghozzi, P. Morand, A. Ferroni, J. Beretti, E. Bingen, C. Segonds, M. Husson, D. Izard, P. Berche, and J. Gaillard Capillary electrophoresis-single strand conformation polymorphism analysis for rapid identification of Pseudomonas aeruginosa and other gram-negative nonfermenting bacilii recovered from patients with cystic fibrosis J. Clin. Microbiol. 37 1999 3374 3379
7. L.M. Gillman, J. Gunton, C.Y. Turenne, J. Wolfe, and A.M. Kabani Identification of Mycobacterium species by multiple-fluorescence PCR-single strand conformation polymorphism analysis of the 16S rRNA gene J. Clin. Microbiol. 39 2001 3085 3091
8. K. Hayashi Recent enhancements in SSCP Genet. Anal.: Biomol. Eng. 14 1999 193 196
9. H. Junca, and D.H. Pieper Functional gene diversity analysis in BTEX contaminated soils by means of PCR-SSCP DNA fingerprinting: comparative diversity assessment against bacterial isolates and PCR-DNA clone libraries Environ. Microbiol. 6 2004 95 110
10. J.L. Kirk, L.A. Beaudette, M. Hart, P. Moutoglis, J.N. Klironomos, H. Lee, and J.T. Trevors Methods of studying soil microbial diversity J. Microbiol. Methods 58 2004 169 188
11. I.V. Kourkine, C.N. Hestekin, and A.E. Barron Technical challenges in applying capillary electrophoresis-single strand conformation polymorphism for routine genetic analysis Electrophoresis 23 2002 1375 1385
12. J. Kozdrój, and J.D. van Elsas Application of polymerase chain reaction-denaturing gradient gel electrophoresis for comparison of direct and indirect extraction methods of soil DNA used for microbial community fingerprinting Biol. Fertil. Soils 31 2000 372 378
13. D. Lee, Y. Zo, and S. Kim Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism Appl. Environ. Microbiol. 62 1996 3112 3120
14. R. Miethling, G. Wieland, H. Backhaus, and C.C. Tebbe Variation of microbial rhizosphere communities in response to crop species, soil origin, and inoculation with Sinorhizobium meliloti L33 Microb. Ecol. 41 2000 43 56
15. G. Muyzer, and K. Smalla Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology Antonie van Leeuwenhoek 73 1998 127 141
16. J.A. Nicklas, and E. Buel Quantification of DNA in forensic samples Anal. Bioanal. Chem. 376 2003 1160 1167
17. R.M. Niemi, I. Heiskanen, K. Wallenius, and K. Lindström Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia J. Microbiol. Methods 45 2001 155 165
18. M. Orita, H. Iwahana, H. Kanazawa, K. Hayashi, and T. Sekyia Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms Proc. Natl. Acad. Sci. U. S. A. 86 1989 2766 2770
19. M. Orita, Y. Suzuki, T. Sekiya, and K. Hayashi Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction Genomics 5 1989 874 879
20. J. Ren High-throughput single-strand conformation polymorphism analysis by capillary electrophoresis J. Chromatogr., B, Biomed. Sci. Appl. 741 2000 115 128
21. A. Schmalenberger, and C.C. Tebbe Bacterial diversity in maize rhizospheres: conclusions on the use of genetic profiles based on PCR-amplified partial small subunit rRNA genes in ecological studies Mol. Ecol. 12 2003 251 262
22. A. Schmalenberger, F. Schweiger, and C.C. Tebbe Effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling Appl. Environ. Microbiol. 67 2001 3557 3563
23. S.D. Siciliano, and C.W. Greer Plant-bacterial combinations to phytoremediate soil contaminated with high concentrations of 2,4,6-trinitrotoluene J. Environ. Qual. 29 2000 311 316
24. S.D. Siciliano, J.J. Germida, K. Banks, and C.W. Greer Changes in microbial community composition and function during a polyaromatic hydrocarbon phytoremediation trial Appl. Environ. Microbiol. 69 2003 483 489
25. S. Susarla, V.F. Medina, and S.C. McCutcheon Phytoremediation: an ecological solution to organic chemical contamination Ecol. Eng. 18 2002 647 658
26. C.C. Tebbe, A. Schmalenberger, S. Peters, and F. Schweiger Single-strand conformation polymorphism (SSCP) for microbial community analysis P.A. Rochelle Environmental Molecular Microbiology: Protocols and Applications 2001 Horizon Scientific Press Wymondham, UK 161 175
27. C.Y. Turenne, E. Witwicki, D.J. Hoban, J.A. Karlowsky, and A.M. Kabani Rapid identification of bacteria from positive blood cultures by fluorescence-based PCR-single-strand conformation polymorphism analysis of the 16S rRNA gene J. Clin. Microbiol. 38 2000 513 520
28. B. Van Aken, J. Moon Yoon, and J.L. Schnoor Biodegradation of nitro-substituted explosives 2,4,6-trinitrotoluene, hexahydro-1,3,5-trinitro-1, 3,5-triazine, and octahydro-1,3,5,7-tetranitro-1,3,5-tetrazocine by a phytosymbiotic Methylobacterium sp. associated with poplar tissues (Populus deltoids X nigra DN34) Appl. Environ. Microbiol. 70 2004 508 517
29. K. Watanabe, Y. Kodama, and S. Harayama Design and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting J. Microbiol. Methods 44 2001 253 262
30. M.N. Widjojoatmodjo, A.C. Fluit, and J. Verhoef Rapid identification of bacteria by PCR-single-strand conformation polymorphism J. Clin. Microbiol. 32 1994 3002 3007
31. M.N. Widjojoatmodjo, A.C. Fluit, and J. Verhoef Molecular identification of bacteria by fluorescence-based PCR-single-strand conformation polymorphism analysis of the 16S rRNA gene J. Clin. Microbiol. 33 1995 2601 2606