A rapid fingerprinting approach to distinguish between closely related strains of Shewanella

Journal of Microbiological Methods

Volumn 86, Issue 1, 2011, Pages 62-68

  Kan, Jinjun ^a   Flood, Beverly ^a   McCrow, John P ^a   Kim, Ji S ^a   Tan, Lynette ^a   Nealson, Kenneth H ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

Bacterial isolation; ITS DGGE; MFCs; Shewanella

Indexed keywords

INTERNAL TRANSCRIBED SPACER; RIBOSOME RNA; RNA 16S;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; CONTROLLED STUDY; DENATURING GRADIENT GEL ELECTROPHORESIS; ECOTYPE; GENOTYPE; INDEL MUTATION; MICROBIAL FUEL CELL; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; RNA FINGERPRINTING; RNA GENE; RNA SEQUENCE; SHEWANELLA; SLUDGE; UNINDEXED SEQUENCE;

BACTERIAL TYPING TECHNIQUES; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA FINGERPRINTING; DNA, BACTERIAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SHEWANELLA;

BACTERIA (MICROORGANISMS); SHEWANELLA;

EID: 79956259898     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2011.03.017     Document Type: Article

References (45)

1. Amann R.I., Ludwig W., Schleifer K.H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 1995, 59:143-169.
2. Bremer H. Parameters affecting the synthesis of ribosomes and RNA polymerase in bacteria. J. Theor. Biol. 1975, 53:115-124.
3. Bretschger O., Obraztsova A., Sturm C.A., Chang I.S., Gorby Y.A., Reed S.B., Culley D.E., Reardon C.L., Barua S., Romine M.F., Zhou J., Beliaev A.S., Bouhenni R., Saffarini D., Mansfeld F., Kim B.-H., Fredrickson J.K., Nealson K.H. Current production and metal oxide reduction by Shewanella oneidensis MR-1 wild type and mutants. Appl. Environ. Microbiol. 2007, 73:7003-7012.
4. Brown M.V., Schwalbach M.S., Hewson I., Fuhrman J.A. Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series. Environ. Microbiol. 2005, 7:1466-1479.
5. Buchan A., Alber M., Hodson R.E. Strain-specific differentiation of environmental Escherichia coli isolates via denaturing gradient gel electrophoresis (DGGE) analysis of the 16S-23S intergenic spacer region. FEMS Microbiol. Ecol. 2001, 35:313-321.
6. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 2000, 17:540-552.
7. Chun J., Huq A., Colwell R.R. Analysis of 16S-23S rRNA intergenic spacer regions of Vibrio cholerae and Vibrio mimicus. Appl. Environ. Microbiol. 1999, 65:2202-2208.
8. Cornell R.M., Schwertmann U. The Iron Oxides: Structure, Properties, Reactions, Occurrence and Uses 1996, VCH, Weinheim, Germany.
9. de Oliveira V.M., Coutinho H.L.C., Sobral B.W.S., Guimaraes C.T., Van Elsas J.D., Manfio G.P. Discrimination of Rhizobium tropici and R. leguminosarum strains by PCR-specific amplification of 16S-23S rDNA spacer region fragments and denaturing gradient gel electrophoresis (DGGE). Lett. Appl. Microbiol. 1999, 28:137-141.
10. de Oliveira V.M., Manfio G.P., da Costa Coutinho H.L., Keijzer-Wolters A.C., van Elsas J.D. A ribosomal RNA gene intergenic spacer based PCR and DGGE fingerprinting method for the analysis of specific rhizobial communities in soil. J. Microbiol. Methods 2006, 64:366-379.
11. D'Elia T.V., Cooper C.R., Johnston C.G. Source tracking of Escherichia coli by 16S-23S intergenic spacer region denaturing gradient gel electrophoresis (DGGE) of the rrnB ribosomal operon. Can. J. Microbiol. 2007, 53:1174-1184.
12. Dolzani L., Tonin E., Lagatolla C., Monti-Bragodin C. Typing of Staphylococcus aureus by amplification of the 16S-23S rRNA intergenic spacer sequences. FEMS Microbiol. Lett. 1994, 119:167-174.
13. Felsenstein J. PHYLIP (Phylogeny Inference Package) Version 3.6 2005, Distributed by the author, Department of Genome Sciences, University of Washington, Seattle.
14. Ferris M.J., Muyzer G., Ward D.M. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl. Environ. Microbiol. 1996, 62:340-346.
15. Fisher M.M., Triplett E.W. Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl. Environ. Microbiol. 1999, 65:4630-4636.
16. Fredrickson J.K., Romine M.F., Beliaev A.S., Auchtung J.M., Driscoll M.E., Gardner T.S., Nealson K.H., Osterman A.L., Pinchuk G., Reed J.L., Rodionov D.A., Rodrigues J.L., Saffarini D.A., Serres M.H., Spormann A.M., Zhulin I.B., Tiedje J.M. Towards environmental systems biology of Shewanella. Nat. Rev. Microbiol. 2008, 6:592-603.
17. García-Martínez J., Acinas S.G., Antón A.I., Rodríguez-Valera F. Use of the 16S-23S ribosomal genes spacer region in studies of prokaryotic diversity. J. Microbiol. Methods 1999, 36:55-64.
18. Gonzalez-Escalona N., Jaykus L.-A., DePaola A. Typing of Vibrio vulnificus strains by variability in their 16S-23S rRNA intergenic spacer regions. Foodborne Pathog. Dis. 2007, 4:327-337.
19. Gurtler V., Stanisich V.A. New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 1996, 142:3-16.
20. Hau H.H., Gralnick J.A. Ecology and biotechnology of the genus Shewanella. Annu. Rev. Microbiol. 2007, 61:237-258.
21. Heuer H., Krsek M., Baker P., Smalla K., Wellington E.M.H. Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl. Environ. Microbiol. 1997, 63:3233-3241.
22. Janse I., Meima M., Kardinaal W.E., Zwart G. High-resolution differentiation of cyanobacteria by using rRNA-internal transcribed spacer denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 2003, 69:6634-6643.
23. Jensen M.A., Webster J.A., Straus N. Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Appl. Environ. Microbiol. 1993, 59:945-952.
24. Kan J., Wang K., Chen F. Temporal variation and detection limit of an estuarine bacterioplankton community analyzed by denaturing gradient gel electrophoresis (DGGE). Aquat. Microb. Ecol. 2006, 42:7-18.
25. Kan J., Hsu L., Cheung A.C.M., Pirbazari M., Nealson K.H. Current production by bacterial communities in microbial fuel cells enriched from wastewater sludge with different electron donors. Environ. Sci. Technol. 2011, 45:1139-1146.
26. Klappenbach J.A., Dunbar J.M., Schmidt T.M. rRNA operon copy number reflects ecological strategies of bacteria. Appl. Environ. Microbiol. 2000, 66:1328-1333.
27. Lane D.J. 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics 1991, 115-175. Wiley, New York. E. Stackebrandt, M. Goodfellow (Eds.).
28. Maeda T., Takada N., Furushita M., Shiba T. Structural variation in the 16S-23S rRNA intergenic spacers of Vibrio parahaemolyticus. FEMS Microbiol. Lett. 2000, 192:73-77.
29. McCrow J.P. Alignment of phylogenetically unambiguous indels in Shewanella. J. Comp. Biol. 2009, 16:1517-1528.
30. Mendoza M., Meugnier H., Bes M., Etienne J., Freney J. Identification of Staphylococcus species by 16S-23S rDNA intergenic spacer PCR analysis. Int. J. Syst. Bacteriol. 1998, 48:1049-1055.
31. Muyzer G., de Waal E.C., Uitterlinden A.G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 1993, 59:695-700.
32. Myers R.M., Fischer S.G., Lerman L.S., Maniatis T. Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acids Res. 1985, 13:3131-3145.
33. Nour M. 16S-23S and 23S-5S intergenic spacer regions of lactobacilli: nucleotide sequence, secondary structure and comparative analysis. Res. Microbiol. 1998, 149:433-448.
34. Øvreås L., Forney L., Daae F.L., Torsvik V. Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl. Environ. Microbiol. 1997, 63:3367-3373.
35. Park H.S., Kilbane J.J. Rapid detection and high-resolution discrimination of the genus Streptomyces based on 16S-23S rDNA spacer region and denaturing gradient gel electrophoresis. J. Ind. Microbiol. Biotechnol. 2006, 33:289-297.
36. Scäfer H., Muyzer G. Denaturing gradient gel electrophoresis in marine microbial ecology. Methods Microbiol. 2001, 425-468. Academic Press, London. J. Paul (Ed.).
37. Schmidt T.M., DeLong E.F., Pace N.R. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J. Bacteriol. 1991, 173:4371-4378.
38. Seurinck S., Verstraete W., Siciliano S.D. Use of 16S-23S rRNA intergenic spacer region PCR and repetitive extragenic palindromic PCR analyses of Escherichia coli isolates to identify nonpoint fecal sources. Appl. Environ. Microbiol. 2003, 69:4942-4950.
39. Shaver Y.J., Nagpal M.L., Fox K.F., Rudner R., Fox A. Variation in 16S-23S rRNA intergenic spacer regions among Bacillus subtilis 168 isolates. Mol. Microbiol. 2001, 42:101-109.
40. Sheffield V.C., Cox D.R., Lerman L.S., Myers R.M. Attachment of a 40-base-pair G+C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proc. Natl. Acad. Sci. U. S. A. 1989, 86:232-236.
41. Stookey L.L. Ferrozine - a new spectrophotometric reagent for iron. Anal. Chem. 1970, 42:779-781.
42. Suzuki M.T., Preston C.M., Beja O., de la Torre J.R., Steward G.F., DeLong E.F. Phylogenetic screening of ribosomal RNA gene-containing clones in bacterial artificial chromosome (BAC) libraries from different depths in Monterey Bay. Microb. Ecol. 2004, 48:473-488.
43. Swofford D.L. PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods) 1998, Sinauer Associates, Sunderland, MA.
44. Tannock G.W., Tilsala-Timisjarvi A., Rodtong S., Ng J., Munro K., Alatossava T. Identification of Lactobacillus isolates from the gastrointestinal tract, silage, and yoghurt by 16S-23S rRNA gene intergenic spacer region sequence comparisons. Appl. Environ. Microbiol. 1999, 65:4264-4267.
45. Yang C.H., Crowley D.E., Hay A.G., Keen N.T. Strain level identification of pseudomonads using denaturing gradient gel electrophoresis of 16S-23S spacer region rDNA. J. Gen. Plan. Pathol. 2000, 66:225-233.