Advertisement

Archives of Microbiology

, Volume 157, Issue 2, pp 107–115 | Cite as

Characterization of natural populations of Nitrobacter spp. using PCR/RFLP analysis of the ribosomal intergenic spacer

  • Elisabeth Navarro
  • Pascal Simonet
  • Philippe Normand
  • René Bardin
Original Papers
  • 314 Downloads

Abstract

DNA sequences from the intergenic spacer (IGS) region of the ribosomal operon were amplified by the polymerase chain reaction (PCR) technique using two primers derived from 16S and 23S rRNA conserved sequences. The PCR products, cleaved by 4 base cutting restriction enzymes, were used to differentiate Nitrobacter strains. This method offered a convenient alternative to serological testing for characterization of Nitrobacter isolates and enabled a large number of strains to be genotypically characterized easily and rapidly. This method was successfully used to characterize natural populations of Nitrobacter from various soils and a lake. A diversity was demonstrated in various soils, and in a lake both in freshwater and in sediments. Strains closely related to both WL and LL were found in these eco-systems. It seems that the diversity of Nitrobacter populations was not associated with global environments but may be related to the presence of locally coexisting niches.

Key words

Nitrobacter Nitrification Natural population soil freshwater sediments Restriction fragment length polymorphism Polymerase chain reaction Intergenic spacer ribosomal RNA 

Non-commun abbreviations

PCR

polymerase chain reaction

RFLP

restriction fragment length polymorphism

IGS

intergenic spacer

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Belser LW (1979) Population ecology of nitrifying bacteria. Ann Rev Microbiol 33: 309–333CrossRefGoogle Scholar
  2. Belser LW, Mays EL (1982) Use of activity measurements to estimate the efficiency of viable nitrifier counts in soil and sediments. Appl Environ Microbiol 43: 945–948PubMedPubMedCentralGoogle Scholar
  3. Beynon JL, Josey DE (1980) Demonstration of heterogeneity in a natural population of Rhizobium phaseoli using variation in intrinsic antibiotic resistance. J Gen Microbiol 118: 437–442Google Scholar
  4. Bock E, Koops H-P, Möller UC, Rudert M (1990) A new facultatively nitrite oxidizing bacterium, Nitrobacter vulgaris sp. nov. Arch Microbiol 153: 105–110CrossRefGoogle Scholar
  5. Bock E, Sundermeyer-Klinger H, Stackebrandt E (1983) New facultative lithotrophic nitrite-oxydizing bacteria. Arch Microbiol 136: 281–284CrossRefGoogle Scholar
  6. Bradbury WC, Pearson AD, Marko MA, Congi RV, Penner JL (1984) Investigation of a Campylobacter jejuni outbreak by serotyping and chromosomal restriction endonuclease analysis. J Clin Microbiol 19: 342–346PubMedPubMedCentralGoogle Scholar
  7. Brenner DJ, McWorter AC, Leete Knutson JK, Steigerwalt AG (1982) Escherichia vulneris: a new species of Enterobacteriaceae associed with human wounds. J Clin Microbiol 15: 1133–1140PubMedPubMedCentralGoogle Scholar
  8. Brosius J, Dull TJ, Sleeter DD, Noller HF (1981) Gene organisation and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol 148: 107–127CrossRefGoogle Scholar
  9. Fitch WM, Margoliash E (1967) Construction of phylogenetic trees. Science 155: 279–284CrossRefGoogle Scholar
  10. Fliermans CB, Bohlool BB, Schmidt EL (1974) Autecological study of chemoautotroph Nitrobacter by immunofluorescence. Appl Microbiol 27: 124–129PubMedPubMedCentralGoogle Scholar
  11. Gay G, Corman A (1984) Comparative study of the growth of two strains of Nitrobacter in batch and continuous culture. Microb Ecol 10: 99–105CrossRefGoogle Scholar
  12. Hall GH (1986) Nitrification in lakes. In: Prosser JI (ed) Nitrification. SGM IRL Press, Oxford Washington, pp. 127–156Google Scholar
  13. Hartskeerl RA, DeWit MYL, Klatser PR (1989) Polymerase chain reaction for detection of Mycobacterium lepra. J Gen Microbiol 135: 2357–2364PubMedGoogle Scholar
  14. Josserand A, Cleyet-Marel JC (1979) Isolation from soils of Nitrobacter and evidence for novel serotypes using immunofluorescence. Microb Ecol 5: 207–213CrossRefGoogle Scholar
  15. Li W-H (1981) Simple method for constructing phylogenetic trees from distance matrices. Proc Natl Acad Sci USA 78: 1085–1089CrossRefGoogle Scholar
  16. MacDonald RM (1986) Nitrification in soil: introductory history. In: Prosser JI (ed). Nitrification. SGM IRL Press, Oxford Washington, pp 17–38Google Scholar
  17. Mullis KB, Faloona FA (1987) Specific synthesis of DNA in vitro via a polymerase-catalized chain reaction. Methods Enzymol 155: 335–350CrossRefGoogle Scholar
  18. Navarro E, Josserand A, Bernillon B, Bardin R (1987) Aspects microbiens de la nitrification: effets des variations quantitatives et diversité des souches de Nitrobacter. Rev Ecol Biol Sol 24: 591–602Google Scholar
  19. Nazaret S, Cournoyer B. Normand P, Simonet P (1991) Phylogenetic relationships between Frankia genomic species determined using amplified 16S rDNA sequences. J Bacteriol 173: 4072–4078CrossRefGoogle Scholar
  20. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkCrossRefGoogle Scholar
  21. Nei M, Li W-H (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76: 5269–5273CrossRefGoogle Scholar
  22. Normand P, Cournoyer B, Nazareth S, Simonet P (1992) Study of Frankia ribosomal rRNA genes. Gene (in press)Google Scholar
  23. Pernodet JL, Boccard F, Allegre MT, Cagnat J, Guérineau M (1989) Organisation and nucleotide sequence analysis of a ribosomal RNA gene cluster from Streptomyces ambofaciens. Gene 79: 33–46CrossRefGoogle Scholar
  24. Pérolat P, Grimont F, Regnault B, Grimont PAD, Fournié E, Thevenet H, Baranton G (1990) rRNA gene restriction of Leptospira: a molecular typing system. Res Microbiol 141: 159–171CrossRefGoogle Scholar
  25. Prosser JI, Cox DJ (1982) Nitrification. In: Burns RG, Slater JH (eds) Experimental microbial ecology. Blackwell Scientific Publications, Oxford, pp. 178–193Google Scholar
  26. Regnery RL, Spruill CL, Plikaytis BD (1991) Genotypic identification of Rickettsiae and estimation of intraspecies sequence divergence for portions of two rickettsial genes. J Bacteriol 173: 1576–1589CrossRefGoogle Scholar
  27. Saitou M, Nei M (1987) A Neighbor-Joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 44: 406–425Google Scholar
  28. Schmidt EL, Belser LW (1982) Nitrifying Bacteria. In: Miller RH, Keeney DR (eds) Methods of soil analysis, 2nd edn. Am Soc Agron Madisson, pp. 1027–1042Google Scholar
  29. Schmidt EL, Molina JAE, Chiang C (1973) Isolation of chemoautotrophic nitrifiers from Moroccan soils. Bull Ecol Res Commun 17: 166–167Google Scholar
  30. Seewaldt E, Schleifer KH, Bock E, Stackebrant E (1982) The close phylogenetic relationship of Nitrobacter and Rhodopseudomonas palustris. Arch Microbiol 131: 287–290CrossRefGoogle Scholar
  31. Simonet P, Capellano A, Navrro E, Bardin R, Moiroud A (1984) An improved method for lysis of Frankia with achromopeptidase allows detection of new plasmid. Can J Microbiol 30: 1292–1295CrossRefGoogle Scholar
  32. 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: 235–240CrossRefGoogle Scholar
  33. Sokal RR, Sneath PHA (1963) Principles of numerical taxonomy. WH Freeman, San FranciscoGoogle Scholar
  34. Soriano S, Walker N (1968) Isolation of ammonia oxidizing autotrophic bacteria. J Appl Bacteriol 31: 493–498CrossRefGoogle Scholar
  35. Stanley PM, Gage MA, Schmidt EL (1979) Enumeration of specific populations by immunofluorescence. In: Costerton JW, Colwell RR (eds). Native aquatic bacteria enumeration, activity and ecology. ASTM STP 695, pp. 46–55Google Scholar
  36. Stanley PM, Schmidt EL (1981) Serological diversity of Nitrobacter spp. from soil and aquatic habitats. Appl Environ Microbiol 41: 1069–1071PubMedPubMedCentralGoogle Scholar
  37. Takahashi M, Yoshioka T, Saijo Y (1982) Nitrogen metabolism in lake Kizaki, Japan. III. Active nitrification in early summer. Arch Hydrobiol 92: 272–286Google Scholar
  38. Tezuka Y (1985) The number of nitrifying bacteria in the north basin of lake Biwa. Jap J Limnol 46: 145–148CrossRefGoogle Scholar
  39. Watson SW, Bock E, Harms H, Koops H-P, Hooper AB (1989) Nitrifying bacteria. In: Holt JC, Staley JT, Bryant MP, Pfenning N (eds) Bergey's manual of systematic bacteriology, vol 3. Williams and Wilkins, Baltimore, pp 1808–1834Google Scholar
  40. Watson SW, Valois FW, Waterbury JB, (1981) The family Nitrobacteraceae. In: Starr MP, Stolp P, Truper HG, Balows A, Schlegel HG (eds) The procaryotes, vol I. Springer, Berlin, Heidelberg, New York, pp 1005–1022Google Scholar
  41. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S Ribosomal amplification for phylogenetic study. J Bacteriol 173: 697–703CrossRefGoogle Scholar
  42. White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, White TJ (eds) PCR protocols: a guide to methods and applications. Academic Press, INC San Diego, pp 315–322Google Scholar
  43. Winogradsky S (1892) Contributions à la morphoplogie des organismes de la nitrification. Arch Sci Biol St Petersb 1: 88–137Google Scholar
  44. Woese CR (1987) Bacterial evolution. Microbiol Rev 51: 221–271PubMedPubMedCentralGoogle Scholar
  45. Woldendorp JW, Laanbroek HJ (1989) Activity of nitrifiers in relation to nitrogen nutrition of plants in natural ecosystems. Plant Soil 115: 217–228CrossRefGoogle Scholar
  46. Wood PM (1986) Nitrification as a bacterial energy source. In: Prosser JI (ed) Nitrification. SGM IRL Press, Oxford Washington, pp 39–62Google Scholar
  47. Yoshioka T, Saijo Y (1984) Photoinhibition and recovery of NH4+ oxidizing bacteria and NO2 oxidizing bacteria. J Gen Microbiol 30: 151–166CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 1992

Authors and Affiliations

  • Elisabeth Navarro
    • 1
  • Pascal Simonet
    • 1
  • Philippe Normand
    • 1
  • René Bardin
    • 1
  1. 1.Laboratoire d'Ecologie Microbienne du Sol, U.R.A. CNRS 1450Université Lyon IVilleurbanneFrance

Personalised recommendations