Skip to main content
SpringerLink
Log in
Book cover

Nucleic Acids in the Environment pp 111–139Cite as

Specific DNA Sequences for Detection of Soil Bacteria

  • Chapter

Part of the book series: Springer Lab Manuals ((SLM))

Abstract

Soils are colonized by numerous microorganisms reaching up to 1011 bacterial cells per g soil (Torsvik et al. 1990). They also can be considered as a reservoir for biodiversity which remains largely unknown, since only 10%–20% of the species living in soil have been isolated and characterized (Ward et al. 1990). This includes nitrogen-fixing bacteria such as Rhizobium, Frankia or Azospirillum, plant pathogens such as Agrobacterium and various fungi, and free-living bacteria involved in various biological processes. Concern has also been voiced about the fate of genetically engineered microorganisms (GMO) released in soils. Consequently, soil microbial populations as well as their in situ activities have remained largely unknown, indicating the need for new techniques which can provide detection tests with high levels of specificity and sensitivity regardless of physical and chemical characteristics of the environment.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Araujo RS, Maya-Flores J, Barnes-McConnell D, Yokoyama C, Dazzo FB, Bliss FA (1986). Semienclosed tube cultures of bean plants (Phaseolus vulgaris L.) for enumeration of Rhizobium phaseoli by the Most-Probable-Number technique. Appl Environ Microbiol 52: 954–956

    Google Scholar 

  • Bej AK, Steffan RJ, diCesare J, Haff L, Atlas RM (1990) Detection of coliform bacteria in water by polymerase chain reaction and genes probes. Appl Environ Microbiol 56: 307–314

    Google Scholar 

  • Bej AK, Steffan RJ, diCesare J, Haff L, Atlas RM (1991) Detection of coliform bacteria and Escherichia coli and Shigella spp. in water by using the polymerase chain reaction and gene probes for ucd. Appl Environ Microbiol 57: 1013–1017

    Google Scholar 

  • Bollet C, Gevaudan MC, de Lamballerie X, Zandotti C, de Mieco P (1991) A simple method for the isolation of chromosomal DNA from gram-positive or acid-fast bacteria. Nucleic Acids Res 19: 1955

    Google Scholar 

  • 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 

  • Bouzard H, Ouadah D, Krimi Z, Jones JB, Travato M, Petit A, Dessaux Y (1993) Correlative association between resident plasmids and the host chromosome in a diverse Agrobacterium soil population. Appl Environ Microbiol 49: 1310–1317

    Google Scholar 

  • Bruce KD, Hiorns WD, Hobman JL, Osbom AM, Strike P, Ritchie DA (1992) Amplification of DNA from native populations of soil bacteria by using the polymerase chain reaction. Appl Environ Microbiol 58: 3413–3416

    Google Scholar 

  • Chen Y, Senesi N, Schnitzer M (1977) Information provided on humic substances by E4/E6 ratios. Soil Sci Soc Am J 41: 352

    Article  Google Scholar 

  • Cochran WG (1950) Estimation of bacterial densities by means of the most probable number. Biometrics 1950: 105–116

    Article  Google Scholar 

  • Crozat Y, Cleyet-Marel JC, Corman A (1987) Use of fluorescent antibody technique to characterize equilibrium survival concentrations of Bradyrhizobium japonicum strains in soil. Biol Fertil Soils 4: 85–90

    Google Scholar 

  • Deragon JM, Sinnett D, Mitchell G, Potier M, Labuda D (1990) Use of Gamma irradiation to eliminate DNA contamination for PCR. Nucleic Acids Res 18: 6149

    Article  Google Scholar 

  • Gilliand G, Perrin ST, Bunn HF (1990) Competitive PCR for quantitation of mRNA. In: Innis MA, Gelfand DH, Sninsky JJ, White IJ (eds). PCR protocols. A guide to methods and amplifications. Academic, San Diego, pp 21–27

    Google Scholar 

  • Golsteyn Thomas EJ, King RK, Burchak J, GannonVPJ (1991) Sensitive and specific detection of Listeria monocytogenes in milk and ground beef with the polymerase chain reaction. Appl Environ Microbiol 57: 2576–2580

    Google Scholar 

  • Grosjean MC, Picard C, Nesme X, Nazaret S, Cournoyer B, Paget E, Simonet P, Normand P, Bardin R (1991) L’amplification enzymatique de l’ADN: un outil d’étude en écologie microbienne. Phytoma 430: 34

    Google Scholar 

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

    Article  Google Scholar 

  • Hobbie JE, Daley RJ, Jasper S (1977) Use of Nucleopore filters for counting bacteria by fluorescence microscopy. Appl Environ Microbiol 54: 2859–2861

    Google Scholar 

  • Holben WE, Jansson 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 

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

    Article  Google Scholar 

  • Jacobsen CJ, Rasmussen OF (1992) Development and application of a new method to extract bacterial DNA from soil based on separation of bacteria from soil with cation-exchange resin. Appl Environ Microbiol 58: 2458–2462

    Google Scholar 

  • Jinno Y, Yoshiura K, Niikawa N (1990) Use of psoralen as extinguisher of contaminated DNA in PCR. Nucleic Acids Res 18: 6739

    Article  Google Scholar 

  • Kitchin PA, Szotyori Z, Fromholc C, Almond N (1990) Avoidance of false positives. Nature 344: 201

    Article  Google Scholar 

  • Liesack W, Ward N, Stackebrandt E (1991) Strategies for molecular microbial ecological studies. Actinomycete 2: 63–76

    Google Scholar 

  • Lorenz MG, Wackernagel W (1987) Adsorption of DNA to sand and variable degradation rate of adsorbed DNA. Appl Environ Microbiol 53: 2948–2952

    Google Scholar 

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

    Article  Google Scholar 

  • Major JG (1992) A rapid PCR method of screening for small mutations. BioTechniques 12: 40–43

    Google Scholar 

  • Mullis KB, Faloona FA (1989) Specific synthesis of DNA in vitro via a polymerase catalysed chain reaction. Methods Enzymol 155: 335–350

    Article  Google Scholar 

  • Nannipieri P, Ciardi C, Badalucco L (1986) A method to determine soil DNA and RNA. Soil Biol Biochem 18: 275–281

    Article  Google Scholar 

  • Navarro E, Simonet P, Normand P, Bardin R (1992) Characterization of natural populations of Nitrobacter spp. using PCR/RFLP analysis of the ribosomal intergenie spacer. Arch Microbiol 157: 107–115

    Google Scholar 

  • Nazaret, S.,B. Cournoyer, P. Normand, and P. Simonet. 1991. Phylogenetic relationships among Frankia genomic species determined by use of amplified 16S rDNA sequences. J Bacteriol 173: 4072–4078

    Google Scholar 

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

    Google Scholar 

  • Nick G, Paget E, Simonet P, Moiroud A, Normand P (1992) The nodular endophytes of Coriaria spp. from a distinct lineage within the genus Frankia. Mol Ecol 1: 175–181

    Article  Google Scholar 

  • Normand P, Cournoyer B, Nazaret S, Simonet P (1992) Analysis of a ribosomal RNA operon in the actinomycete Frankia. Gene 111: 119–124

    Article  Google Scholar 

  • Ogram A, Sayler GS, Barkay T (1987) The extraction and purification of microbial DNA from sediments. J Microb Methods 7: 57–66

    Article  Google Scholar 

  • 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 

  • 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 

  • Picard C, Ponsonnet C, Recorbet G, Antonelli F, Simonet P, Nesme X (1994) Detection of pathogenic Agrobacterium in soils by PCR. Plant pathogenic bacteria. 8th International conference. Les Collogues, INRA-Editions, Paris, 66: 729–734

    Google Scholar 

  • Pillai SD, Josephson KL, Bailey RL, Gerba CP, Pepper IL (1991) Rapid method for processing soil samples for polymerase chain reaction amplification of specific gene sequences. Appl Environ Microbiol 57: 2283–2286

    Google Scholar 

  • 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 

  • Postma J, Van Elsas JD, Govaert JM, Van Veen JA (1988) The dynamics of Rhizobium leguminosarum bv. trifolii introduced in soil as determinated by immunofluorescence and selective plating techniques. FEMS Microbiol Ecol 53: 251–260

    Google Scholar 

  • Richard GM (1974) Modifications of the diphenylamine reaction giving increased sensitivity and simplicity in the estimation of DNA. Anal Biochem 57: 369–376

    Article  Google Scholar 

  • Rochelle PA, Olson BH (1991) A simple technique for electroelution of DNA from environmental samples. Biotechniques 11: 724–728

    Google Scholar 

  • Ruano G, Fenton W, Kidd KK (1989) Biphasic amplification of very dilute DNA samples via “booster” PCR. Nucleic Acids Res 17: 5407

    Article  Google Scholar 

  • Sarkar G, Kapelner S, Sommer SS (1990) Formamide can dramatically improve the specificity of PCR. Nucleic Acids Res 18: 7465

    Article  Google Scholar 

  • Sarkar G, Sommer SS (1991) Parameters affecting susceptibility of PCR contamination to UV inactivation. BioTechniques 10: 591–593

    Google Scholar 

  • Selenska S, Klingmüller W (1991) DNA recovery and direct detection of Tn5 sequences from soil. Lett Appl Microbiol 13: 21–24

    Article  Google Scholar 

  • Sheng Zhu Y, Isaacs ST, Cimino GD, Hearst JE (1991) The use of exonuclease III for polymerase chain reaction sterilization. Nucleic Acids Res 19: 2511

    Article  Google Scholar 

  • Simonet P, Capellano A, Navarro E, Bardin R, Moiroud A (1984) An improved method for lysis of Frankia with achromopeptidase allows detection of new plasmids. Can J Microbiol 30: 1292–1295

    Article  Google Scholar 

  • 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 

  • 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 

  • 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 674: 78–85

    Google Scholar 

  • Soltanpour PN, Jones JB, Workman SM (1982) Optical emission spectrometry. In Page AL, Miller RH, Keeney DR (eds) Methods of soil analysis. 2 Chemical and microbiological properties. Agronomy 9: 29–65

    Google Scholar 

  • Steffan RJ, Atlas RM (1988) DNA amplification to enhance detection of genetically engineered bacteria in environmental samples. Appl Environ Microbiol 54: 2185–2191

    Google Scholar 

  • Steffan RJ, Goksoyr J, Bej AK, Atlas RM (1988) Recovery of DNA from soils and sediments. Appl Environ Microbiol 54: 2908–2915

    Google Scholar 

  • Suggs SV, Hirose T, Miake T, Kawashima EH, Johnson MJ, Itakura K, Wallace RB (1981) ICN-UCLA Symp Mol Cell Biol 231: 683

    Google Scholar 

  • Tebbe CC, Vahjen W (1993) Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast. Appl Environ Microbiol 59: 2657–2665

    Google Scholar 

  • Torsvik VL (1980) Isolation of bacterial DNA from soil. Soil Biol Biochem 12: 15–21

    Article  Google Scholar 

  • Torsvik V, Goksoyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56: 782–787

    Google Scholar 

  • Trevors JT (1992) DNA extraction from soil. Microb Releases 1: 3–9

    Google Scholar 

  • Tsai YL, Olson BJ (1991) Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol 57: 1070–1074

    Google Scholar 

  • 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 

  • Ward DM. Weller R, Bateson MM (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 344: 63–65

    Google Scholar 

  • Weyant RS, Edmonds P, Swaminathan B (1990) Effect of ionic and nonionic detergents on the Taq polymerase. Biofeedback 9: 308–309

    Google Scholar 

  • Wu D.Y, Ugozzoli L, Pal BK, Qian J, Wallace RB (1991) DNA Cell Biol 10: 233–238

    Article  Google Scholar 

  • Yap EPH, McGee JOD (1991) Short PCR product yields improved by lower denaturation temperatures. Nucleic Acids Res 19: 1713

    Article  Google Scholar 

Download references

Authors
  1. X. Nesme
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. C. Picard
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. P. Simonet
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Environmental Biology, University of Guelph Lab. Microbial Techniques, N1G 2W1, Guelph, Ontario, Canada

    Jack T. Trevors

  2. DLO-Institute for Soil Fertility Research c/o IPO-DLO, Binnenhaven 12, P.O. Box 9060, 6700 GW, Wageningen, The Netherlands

    J. Dick van Elsas

Rights and permissions

Reprints and permissions

Copyright information

© 1995 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Nesme, X., Picard, C., Simonet, P. (1995). Specific DNA Sequences for Detection of Soil Bacteria. In: Trevors, J.T., van Elsas, J.D. (eds) Nucleic Acids in the Environment. Springer Lab Manuals. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-79050-8_7

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-79050-8_7

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-58069-0

  • Online ISBN: 978-3-642-79050-8

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation