Application of peptide nucleic acid (PNA)-PCR clamping technique to investigate the community structures of rhizobacteria associated with plant roots

Journal of Microbiological Methods

Volumn 92, Issue 3, 2013, Pages 281-288

  Sakai, Masao ^a   Ikenaga, Makoto ^a  

^a KAGOSHIMA UNIVERSITY   (Japan)

Author keywords

Bacteria; Plant organelle; PNA PCR clamping; SSU rRNA gene; T RFLP

Indexed keywords

PEPTIDE NUCLEIC ACID; SMALL SUBUNIT RIBOSOMAL RNA;

ARTICLE; BACTERIUM; BACTERIUM IDENTIFICATION; BINDING AFFINITY; BINDING SITE; COMMUNITY STRUCTURE; CONTROLLED STUDY; CUCUMBER; GENE IDENTIFICATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT ROOT; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RHIZOBACTERIA; RNA BINDING; RNA SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SPINACH;

BACTERIA; BIOTA; DNA PRIMERS; DNA, BACTERIAL; DNA, PLANT; DNA, RIBOSOMAL; MICROBIOLOGICAL TECHNIQUES; PEPTIDE NUCLEIC ACIDS; PLANT ROOTS; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY;

EID: 84873709544     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2012.09.036     Document Type: Article

References (48)

1. Ashelford K.E., Weightman A.J., Fry J.C. PROMEROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA olugonucleotide probes and primers in conjunction with the RDP-II database. Nucleic Acids Res. 2002, 30:3481-3489.
2. 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.
3. Campbell R., Greaves M.P. Anatomy and community structures of the rhizosphere. The Rhizosphere 1990, 11-34. Wiley, Essex, UK. J.M. Lynch (Ed.).
4. Chandler D.P., Stults J.R., Cebula S., Schuch B.L., Weaver D.W., Anderson K.K., Egholm M. Affinity purification of DNA and RNA from environmental samples with peptide nucleic acid clamps. Appl. Environ. Microbiol. 2000, 66:3438-3445.
5. Chelius M., Triplett E.W. The diversity of archaea and bacteria in association with the roots of Zea mays L. Microb. Ecol. 2001, 41:252-263.
6. Danovaro R., Luna G.M., Dell'Anno A., Pietrangeli B. Comparison of two fingerprinting techniques, terminal restriction fragment length polymorphism and automated ribosomal intergenic spacer analysis, for determination of bacterial diversity in aquatic environments. Appl. Environ. Microbiol. 2006, 72:5982-5989.
7. Garbeva P., Overbeek L.S., Vuurde J.W., Elsas J.D. Analysis of endophytic bacterial communities of potato by plating and denaturing gradient gel electrophoresis (DGGE) of 16S rDNA based PCR fragments. Microb. Ecol. 2001, 41:369-383.
8. Hiltner L. Uber neuere erfahrungen und problem auf dem gebeit der bodenbakteriologie und unter besonderer berucksichtigung dergrundungung und brache. Arb. Dtsch. Landwirtsch. Ges. 1904, 98:59-78.
9. Hutter G., Schlagenhauf U., Valenza G., Horn M., Burgemeister S., Claus H., Vogel U. Molecular analysis of bacteria in periodontitis: evaluation of clone libraries, novel phylotypes and putative pathogens. Microbiology 2003, 149:67-75.
10. Idris R., Trifonova R., Puschenreiter M., Wenzel W.W., Sessitsch A. Bacterial communities associated with flowering plant of the Ni hyperaccumulator Thaspi goesingense. Appl. Environ. Microbiol. 2004, 70:2667-2677.
11. Ikeda K., Toyota K., Kimura M. Effects of soil compaction on the microbial populations of melon and maize rhizoplane. Plant Soil 1997, 189:91-96.
12. Ikenaga M., Muraoka Y., Toyota K., Kimura M. Community structure of the microbiota associated with nodal roots of rice plants along with the growth stages: estimation by PCR-RFLP analysis. Biol. Fertil. Soils 2002, 36:397-404.
13. Ikenaga M., Asakawa S., Muraoka Y., Kimura M. Bacterial communities associated with nodal roots of rice plants along with the growth stages: estimation by PCR-DGGE and sequence analyses. Soil Sci. Plant Nutr. 2003, 49:591-602.
14. Ikenaga M., Guevara R., Dean A.L., Pisani C., Boyer J.N. Changes in community structure of sediment bacteria along the Florida coastal Everglades marsh-mangrove-seagrass salinity gradient. Microb. Ecol. 2010, 59:284-295.
15. Ishii K., Fukui M., Takii S. Microbial succession during a composting process as evaluated by denaturing gradient gel electrophoresis analysis. J. Appl. Microbiol. 2000, 89:769-777.
16. Kimura M., Wada H., Takai Y. Effects of direct sowing cultivation on the rhizosphere of lowland rice. Soil Sci. Plant Nutr. 1982, 28:173-182.
17. Liu W.T., Marsh T.L., Cheng H., Fomey L.J. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol. 1997, 63:4516-4522.
18. Lüdemann H., Arth I., Liesack W. Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores. Appl. Environ. Microbiol. 2000, 66:754-762.
19. Lynch D.J. Introduction: some consequences of microbial rhizosphere competence for plant and soil. The Rhizosphere 1990, 1-10. Wiley, Essex, UK. J.M. Lynch (Ed.).
20. Marilley L., Aragno M. Phylogenetic diversity of bacterial communities differing in degree of proximity of Lolium perenne and Trifolium repens roots. Appl. Soil Ecol. 1999, 13:127-136.
21. Marsh T.L. Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products. Curr. Opin. Microbiol. 1999, 2:323-327.
22. Martin J.K. Comparison of agar media for counts of viable soil bacteria. Soil Biol. Biochem. 1975, 7:401-402.
23. Matsuyama T., Nakajima Y., Matsuya K., Ikenaga M., Asakawa S., Kimura M. Bacterial community in plant residues in a Japanese paddy field estimated by RFLP and DGGE analyses. Soil Biol. Biochem. 2007, 39:463-472.
24. Metting F.B. Soil Microbial Ecology: Applications in Agricultural and Environmental Management 1992, Marcel Dekker, New York.
25. Moeseneder M.M., Arrieta J.M., Muyzer G., Winter C., Herndl G.J. Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 1999, 65:3518-3525.
26. Muyzer G., De Waal E.C., Uitterlinden A.G. Profiling of complex microbial populations by denaturing gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 1993, 59:695-700.
27. Nehl D.B., Allen S.J., Brown J.F. Deleterious rhizosphere bacteria: an integrating perspective. Appl. Soil Ecol. 1997, 5:1-20.
28. Newman E.I., Watson A. Microbial abundance in the rhizosphere: a computer model. Plant Soil 1977, 48:17-56.
29. Nielsen P.E. Peptide nucleic acid: a versatile tool in genetic diagnostics and molecular biology. Anal. Biotechnol. 2001, 12:16-20.
30. Normandar B., Prosser J.I. Bacterial origin and community composition in the barley rhizosphere as a function of habitat and presowing conditions. Appl. Environ. Microbiol. 2000, 66:4372-4377.
31. Nübel U., Engelen B., Felske A., Snaidr J., Wieshuber A., Amann R., Ludwig W., Backhaus H. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymixa detected by temperature gradient gel electrophoresis. J. Bacteriol. 1996, 178:5636-5643.
32. Nunan N., Daniell T.J., Singh B.K., Papert A., McNicol J.W., Prosser J.I. Links between plant and rhizoplane bacterial communities in grassland soils, characterized using molecular techniques. Appl. Environ. Microbiol. 2005, 71:6784-6792.
33. Ørum H., Nielsen P.E., Egholm M., Berg R.H., Buchardt O., Stanley C. Single base pair mutation analysis by PNA directed PCR clamping. Nucleic Acids Res. 1993, 21:5332-5336.
34. Polz M.F., Harbison C., Cavanaugh C.M. Diversity and heterogeneity of epibiotic bacterial communities on the marine nematode Eubostrichus dianase. Appl. Environ. Microbiol. 1999, 65:231-240.
35. Reiter B., Sessitsch A. Bacterial endophytes of the wildflower Crocus albiflorus analyzed by characterization of isolates and by a cultivation-independent approach. Can. J. Microbiol. 2006, 52:140-149.
36. Sakai M., Matuska A., Komura T., Kanazawa S. Application of a new PCR primer for terminal restriction fragment length polymorphism analysis of the bacterial communities in plant roots. J. Microbiol. Methods 2004, 59:81-89.
37. Schütte U.M.E., Abdo Z., Bent S.J., Shyu C., Williams C.J., Pierson J.D., Forney L.J. Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities. Appl. Microbiol. Biotechnol. 2008, 80:365-380.
38. Sessitsch A., Reiter B., Pfeifer U., Wilhelm E. Cultivation-independent population analysis of bacterial endophytes in three potato varieties based on eubacterial and Actinomycetes specific PCR of 16S rRNA genes. FEMS Microbiol. Ecol. 2002, 39:23-32.
39. Smalla K., Oros-Sichler M., Milling A., Heuer H., Baumgarte S., Becker R., Neuber G., Kropf S., Ulrich A., Tebbe C. Bacterial diversity of soil assessed by DGGE, T-RFLP and SSCP fingerprints of PCR-amplified 16S rRNA fragments: do the different methods provide similar results?. J. Microbiol. Methods 2007, 69:470-479.
40. Suzuki M.T., Giovannoni S.J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 1996, 62:625-630.
41. + revertants of Salmonella typhimurium TA98 in ames test by peptide nucleic acid (PNA)-mediated PCR clamping. J. Biosci. Bioeng. 2003, 96:588-590.
42. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22:4673-4680.
43. Torsvik V., Goksoyr J., Daae F.L. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 1990, 56:782-787.
44. Tun C.C., Ikenaga M., Asakawa S., Kimura M. Community structure of bacteria and fungi responsible for rice straw decomposition in a paddy field estimated by PCR-RFLP analysis. Soil Sci. Plant Nutr. 2002, 48:805-813.
45. Urakawa H., Yoshida T., Nishimura M., Ohwada K. Characterization of depth-related population variation in microbial communities of a coastal marine sediment using 16S rDNA-based approaches and quinone profiling. Environ. Microbiol. 2000, 2:542-554.
46. von Wintzingerode F., Landt O., Ehrlich A., Göbel U.B. Peptide nucleic acid-mediated PCR clamping as a useful supplement in the determination of microbial diversity. Appl. Environ. Microbiol. 2000, 66:549-557.
47. Weidner S., Arnold W., Puhler A. Diversity of uncultured microorganisms associated with seagrass Halophila stipulacea estimated by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Appl. Environ. Microbiol. 1996, 62:766-771.
48. Yang C.H., Crowley D.E. Rhizosphere microbial community structure in relation to root location and plant iron nutritional status. Appl. Environ. Microbiol. 2000, 66:345-351.