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Detection and enumeration of soil bacteria using the MPN-PCR technique

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Molecular Microbial Ecology Manual

Abstract

The complexity and heterogeneity of soils lead to an important variability among the microbial community which colonize this environment. Depending upon the physical and chemical properties of the soil, including texture, minerals, pH and presence of plants, the diversity and density of microorganisms will be distinct [14, 40].

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References

  1. Aardema BW, Lorenz MG, Krumbein WE (1983) Protection of sediment-adsorbed transforming DNA against enzymatic inactivation. Appl Environ Microbiol 46: 417–420.

    Google Scholar 

  2. Bosco M, Fernandez MP, Simonet P, Materassi, R, Normand P (1992) Evidence that some Frankia sp. strains are able to cross boundaries between Alnus and Elaeagnus host specificity groups. Appl Environ Microbiol 58: 1569–1576.

    Google Scholar 

  3. Bouzar H, Moore LW (1987) Isolation of different Agrobacterium biovars from a natural oak savanna and tallgrass prairie. Appl Environ Microbiol 53: 717–727.

    Google Scholar 

  4. Bouzar H., Ouadah D, Krimi Z, Jones JB, Trovato M, Petit A, Dessaux Y (1993) Correlative association between resident plasmids and the host chromosome in a diverse Agrobacterium soil population. Appl Environ Microbiol 59: 1310–1317.

    Google Scholar 

  5. Brauns LA, Hudson MC, Oliver JC (1991) Use of the polymerase chain reaction in detection of culturable and nonculturable Vibrio vulnificus cells. Appl Environ Microbiol 57: 2651–2655.

    Google Scholar 

  6. Chelly J, Kaplan JC, Maire, Gautron PS, Kahn A (1988) Transcription of the dystrophin gene in human muscle and non-muscle tissues. Nature 333: 858–860.

    Article  Google Scholar 

  7. Cochran W.G. (1950) Estimation of bacterial densities by means of the most probable number. Biometrics. March 1950: 105–116.

    Google Scholar 

  8. Dallman M, Porter AC (1991) Semi-quantitative PCR for the analysis of gene expression. In: PCR, A Practical Approach. MJ Mc Pherson, P. Quirke & GR Taylor (eds) IRL Press, Oxford University Press. pp 215–224.

    Google Scholar 

  9. Hazen TC, Jimenez L (1988) Enumeration and identification of bacteria from environmental samples using nucleic acid probes. Microbiol Sci 5: 340–343.

    Google Scholar 

  10. Dallman M, Porter AC (1991) Semi-quantitative PCR for the analysis of gene expression. In: PCR, A Practical Approach. MJ Mc Pherson, P. Quirke & GR Taylor (eds) IRL Press, Oxford University Press. pp 215–224.

    Google Scholar 

  11. Hazen TC, Jimenez L (1988) Enumeration and identification of bacteria from environmental samples using nucleic acid probes. Microbiol Sci 5: 340–343.

    Google Scholar 

  12. Higuchi R, Dolliger G, Walsh PS, Griffith R (1992) Simultaneous amplification and detection of specific DNA sequences. Biotechnology 10: 413–417.

    Article  Google Scholar 

  13. Holben WE, Janson JK, Chelm BK, Tiedje JM (1988) DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl Environ Microbiol 54: 703–711.

    Google Scholar 

  14. Horn GT, Richards B, Klinger KW (1989) Amplification of a highly polymorphic VNTR segment by the polymerase chain reaction. Nucl Acids Res 16: 2140.

    Article  Google Scholar 

  15. Loyer MW, Hamilton MA (1984) Interval estimation of the density of organisms using a serial dilution experiment. Biometrics 40: 907–916.

    Article  Google Scholar 

  16. Lynch JM (1987) In M Fletcher, TRG Gray & JG Jones (eds). Ecology of Microbial Communities. Cambridge Univ. Press, Cambridge, p 55.

    Google Scholar 

  17. McCrady MH (1915) The numerical interpretation of fermentation-tube results. J Infec Dis 17: 183–212.

    Article  Google Scholar 

  18. Myrold DD, Huss-Danell K (1994) Population dynamics of Alnus-infective Frankia in a forest soil with and without host trees. Soil Biol Biochem 26: 533–540.

    Article  Google Scholar 

  19. Nesme X, Simonet P, Jocteur-Montrozier L, Normand P (1993) La PCR appliquée à l’étude des bactéries du sol. In D Larzul (ed) La PCR un procédé de réplication in vitro. Lavoisier, Paris, France. pp. 262–272.

    Google Scholar 

  20. Nesme X, Michel MF, Digat B (1987) Population heterogeneity of Agrobacterium tumefaciens in galls of Populus L. from a single nursery. Appl Environ Microbiol 53: 655–659.

    Google Scholar 

  21. Nesme X, Ponsonnet C, Picard C, Normand P (1992) Chromosomal and pTi genotypes of agrobacterium strains isolated from Populus tumors in two nurseries. FEMS Microbiol Ecol 101: 189–196.

    Google Scholar 

  22. Nesme X, Leclerc MC, Bardin R (1990) PCR detection of an original endosymbiont: the Ti plasmid of Agrobacterium tumefaciens. In P Nardon, V Gianinazzi, AM Grenier, L Margulis & DC Smith (eds) Endocytobiology IV, INRA edition, Paris, France. pp 47–50.

    Google Scholar 

  23. Paget E, Jocteur Monrozier L, Simonet P (1992) Adsorption of DNA on clay minerals: protection against DNase I and influence on gene transfer. FEMS Microbiol Lett 97: 31–40.

    Article  Google Scholar 

  24. Picard C, Ponsonnet C, Paget E, Nesme X, Simonet P (1992) Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Appl Environ Microbiol 58: 2717–2722.

    Google Scholar 

  25. Picard C, Ponsonnet C, Recorbet G, Antonelli F, Simonet P, Nesme X (1994) Detection of pathogenic Agrobacterium in soils by PCR. In Plant Pathogenic Bacteria. M Lemattre, S Freigoun, K Rudolph & JG Swings (eds). Les colloques No66, INRA edition-ORSTOM edition, Paris, France. pp 729–734.

    Google Scholar 

  26. Ponsonnet C, Nesme X (1994) Identification of Agrobacterium strains by PCR-RFLP analysis of pTi and chromosomal regions. Arch Microbiol 161: 300–309.

    Google Scholar 

  27. Recorbet G, Picard C, Normand P, Simonet P (1993) Kinetics of the persistence of chromosomal DNA from genetically engineered Escherichia coli introduced into soil. Appl Environ Microbiol 59: 4289–4294.

    Google Scholar 

  28. Rochelle P, Day M, Fry J (1988) Occurrence, transfer and mobilization in epilithic strains of Acinetobacter of mercury-resistance plasmids capable of transformation. J Gen Microbiol 134: 2933–2941.

    Google Scholar 

  29. Romanowski G, Lorenz M, Wackernagel W (1993) Use of polymerase chain reaction and electroporation of Escherichia coli to monitor the persistance of extracellular plasmid DNA introduced into natural soil. Appl Environ Microbiol 59: 3438–3446.

    Google Scholar 

  30. Rowe R, Todd R, Waide J (1977) Microtechnique for most probable number analysis. Appl Environ Microbiol 33: 675–680.

    Google Scholar 

  31. Seal S, Jackson L, Daniels M (1992) Isolation of a Pseudomonas solanacearum specific DNA probes by subtraction hybridization and construction of species-specific oligonucleotide primers for sensitive detection by the Polymerase Chain Reaction. Appl Environ Microbiol 58: 3751–3758.

    Google Scholar 

  32. Selenska S, Klingmüller W (1992) DNA recovery and direct detection of Tn5 sequences from soil. Lett Appl Microbiol 13: 21–24.

    Article  Google Scholar 

  33. Simonet P, Normand P, Moiroud A, Bardin R (1990) Identification of Frankia strains in nodules by hybridization of polymerase chain reaction products with strain-specific oligonucleotide probes. Arch Microbiol 153: 235–240.

    Article  Google Scholar 

  34. Simonet P, Grosjean, MC, Misra AK, Nazaret S, Cournoyer B, Normand P (1991) Frankia genus-specific characterization by polymerase chain reaction. Appl Environ Microbiol 57: 3278–3286.

    Google Scholar 

  35. Simonet P, Bosco M, Chapelon C, Moiroud A, Normand P (1994) Molecular characterization of Frankia microsymbionts from spore-positive and spore-negative nodules in a natural alder stand. Appl Environ Microbiol 60: 1335–1341.

    Google Scholar 

  36. Smalla K, Cresswell N, Mendonca-Hagler LC, Wolters A, Van Elsas JD (1993) Rapid DNA extraction protocol from soil for polymerase chain reaction-mediated amplification. J Appl Bacteriol 74: 78–85.

    Article  Google Scholar 

  37. Smolander A (1990) Frankia populations in soils under tree species with special emphasis on soils under Betula pendula. Plant Soil 121: 1–10.

    Article  Google Scholar 

  38. Torsvik V, Goksoyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56: 782–878.

    Google Scholar 

  39. Tsai YL, Olson BH (1992) Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Appl Environ Microbiol 58: 2292–2295.

    Google Scholar 

  40. Van Dijk C (1979) Endophyte distribution in the soil. In Symbiotic nitrogen fixation in the management of temperate forests. J. C Gordon, CT Wheeler & D A. Perry (eds). Oregon State University Press, Corvallis, pp. 84–94.

    Google Scholar 

  41. Walia S, Khan A, Rosenthal N (1990) Construction and applications of DNA probes for detection of polychlorinated biphenyl-degrading genotypes in toxic organic-contaminated soil environments. Appl Environ Microbiol 5656: 254 259.

    Google Scholar 

  42. Wang AM, Doyle MV, Mark DF (1989) Quantitation of mRNA by the polymerase chain reaction. Proc Natl Acad Sci USA. 86: 9717–9721.

    Article  Google Scholar 

  43. Yanagita T (1990) Natural microbial communities: Ecological and physiological features. Japan Scientific Societies Press, Tokyo.

    Google Scholar 

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Author information

Authors and Affiliations

  1. Laboratoire d’Ecologie Microbienne du Sol, UMR. Centre National de la Recherche, Scientifique 5557, Bâtiment 741, Université Lyon I, 43 bd du 11 Novembre 1918, 69622, Villeurbanne Cedex, France

    Christine Picard, Xavier Nesme & Pascal Simonet

Authors
  1. Christine Picard
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  2. Xavier Nesme
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  3. Pascal Simonet
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Editor information

Editors and Affiliations

  1. Department of Microbiology, Wageningen Agricultural University, The Netherlands

    Antoon D. L. Akkermans

  2. IPO-DLO, Wageningen, The Netherlands

    Jan Dirk Van Elsas

  3. MSU-DOE Plant Research Lab, Michigan State University, USA

    Frans J. De Bruijn

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© 1996 Springer Science+Business Media Dordrecht

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Picard, C., Nesme, X., Simonet, P. (1996). Detection and enumeration of soil bacteria using the MPN-PCR technique. In: Akkermans, A.D.L., Van Elsas, J.D., De Bruijn, F.J. (eds) Molecular Microbial Ecology Manual. Springer, Dordrecht. https://doi.org/10.1007/978-94-009-0215-2_4

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  • DOI: https://doi.org/10.1007/978-94-009-0215-2_4

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-94-011-7660-6

  • Online ISBN: 978-94-009-0215-2

  • eBook Packages: Springer Book Archive

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