Molecular profiling of microbial communities associated with seeds of Beta vulgaris subsp. Vulgaris (sugar beet)

Journal of Microbiological Methods

Volumn 56, Issue 1, 2004, Pages 17-26

  Dent, Katherine C ^a   Stephen, John R ^a,b   Finch Savage, William E ^a  

^a UNIVERSITY OF WARWICK   (United Kingdom)

^b UNIVERSITY OF ADELAIDE   (Australia)

Author keywords

Microflora; PCR DGGE; Seed vigour

Indexed keywords

PRIMER DNA; PROTEIN SUBUNIT; SMALL SUBUNIT RIBOSOMAL RNA;

AMPLICON; ARTICLE; BACTERIAL FLORA; BACTERIUM DETECTION; BACTERIUM IDENTIFICATION; BEET; CELL FRACTIONATION; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA EXTRACTION; DNA TEMPLATE; EUBACTERIUM; EUKARYOTE; FUNGUS IDENTIFICATION; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENE INSERTION; GENE SEGREGATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PERICARP; PLANT SEED; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; TARGET CELL;

BACTERIA (MICROORGANISMS); BETA VULGARIS; BETA VULGARIS SUBSP. VULGARIS; EUKARYOTA; FUNGI;

EID: 0347360167     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2003.09.001     Document Type: Article

References (24)

1. Bloemberg G.V., Lugtenberg B.J. Molecular basis of plant growth promotion and biocontrol by rhizobacteria. Curr. Opin. Plant Biol. 44:2001;343-350.
2. Brüggemann J., Stephen J.R., Chang Y.-J., Macnaughton S.J., Kowalchuk G.A., Kline E., White D.C. Competitive PCR-DGGE analysis of bacterial mixtures: an internal standard and an appraisal of template enumeration accuracy. J. Microbiol. Methods. 40:2000;111-123.
3. Chelius M.K., Triplett E.W. The diversity of Archaea and Bacteria in association with the roots of Zea mays L. Microb. Ecol. 41:2001;252-263.
4. DeLong E.F., Pace N.R. Environmental diversity of bacteria and archaea. Syst. Biol. 50:2001;470-478.
5. Don R.H., Cox P.T., Wainwright B.J., Baker K., Mattick J.S. 'Touchdown' PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res. 19:1991;4008.
6. Finch-Savage W.E. Influence of seed quality on crop establishment, growth and yield. Basra A.S. Seed Quality. Basic Mechanisms and Agricultural Implications. 1995;361-384 Haworth Press, USA.
7. Hampton J.G. What is seed quality? Seed Sci. Technol. 30:2002;1-10.
8. ISTA, 1999. International rules for seed testing, 1999. Seed Sci. Technol. 27 (supplement). pp. 27-32 and 155-159.
9. Kowalchuk G.A. New perspectives towards analysing fungal communities in terrestrial environments. Curr. Opin. Biotechnol. 10:1999;247-251.
10. Kowalchuk G.A., Gerards S., Woldendorp J.W. Detection and characterization of fungal infections of Ammophila arenaria (marram grass) roots by denaturing gradient gel electrophoresis of specifically amplified 18s rDNA. Appl. Environ. Microbiol. 63:1997;3858-3865.
11. Kurtzman C.P., Droby S. Metschnikowia fructicola, a new ascosporic yeast with potential for biocontrol of postharvest fruit rots. Syst. Appl. Microbiol. 24:2001;395-399.
12. Morris C.E., Bardin M., Berge O., Frey-Klett P., Fromin N., Girardin H., Guinebretière M.-H., Lebaron P., Thiéry J.M., Troussellier M. Microbial biodiversity, approaches to experimental design and hypothesis testing in primary scientific literature from 1975 to 1999. Microbiol. Mol. Biol. Rev. 66:2002;592-616.
13. Muyzer G. DGGE/TGGE, a method for identifying genes from natural ecosystems. Curr. Opin. Microbiol. 2:1999;317-322.
14. Muyzer G., Smalla K. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek Int. J. G. 73:1998;127-141.
15. 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. 59:1993;695-700.
16. Noots I., Delcour J.A., Michiels C.W. From field barley to malt: detection and specification of microbial activity for quality aspects. Crit. Rev. Microbiol. 25:1999;121-153.
17. Perry D.A. Report of the vigour test committee 1974-1977. Seed Sci. Technol. 6:1978;159-181.
18. 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. 86:1989;232-236.
19. Skinner F.A., Jones P.C.T., Mollison J.E. A comparison of a direct and a plate counting technique for the quantitative estimation of soil microorganisms. J. Gen. Microbiol. 6:1952;261-271.
20. Stephen J.R., Kowalchuk G.A. Ribotyping methods for assessment of in situ microbial community structure. Bitton G. Encyclopedia of Environmental Microbiology. vol. 5:2002;2728-2741 Wiley, New York, USA.
21. Stephen J.R., Chang Y.-J., Macnaughton S.J., Whitaker S.L., Hicks C.L., Leung K.T., Flemming C.A., White D.C. Fate of a mixture of five metal resistant bacteria introduced into pristine and heavy-metal-contaminated soil microcosms assessed by DGGE. Environ. Toxicol. Chem. 18:1999;1118-1123.
22. Vainio E.J., Hantula J. Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNA. Mycol. Res. 104:2000;927-936.
23. van Hannen E.J., van Agterveld M.P., Gons H.J., Laanbroek H.J. Revealing genetic diversity of eukaryotic microorganisms in aquatic environments by denaturing gradient gel electrophoresis. J. Phycol. 34:1998;206-213.
24. White T.J., Bruns T., Lee S., Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Innins M.A., Gelfand D.H., Sninsky J.J., White T.J. PCR Protocols. 1990;315-322 Academic Press, San Diego, CA.