1887

Abstract

Summary: A 16S rRNA-based molecular ecological study was performed to search for dominant bacterial sequences in Drentse A grassland soils (The Netherlands). In the first step, a library of 165 clones was generated from PCR-amplified 16S rDNA. By sequence comparison, clone DA079 and two other identical clones could be affiliated to a group of recently described uncultured Actinobacteria. This group contained 16S rDNA clone sequences obtained from different environments across the world. To determine whether such uncultured organisms were part of the physiologically active population in the soil, ribosomes were isolated from the environment and 16S rRNA was partially amplified via RT-PCR using conserved primers for members of the domain Bacteria. Subsequent sequence-specific separation by temperature-gradient gel electrophoresis (TGGE) generated fingerprints of the amplicons. Such community fingerprints were compared with the TGGE pattern of PCR-amplified rDNA of clone DA079 which was generated with the same set of primers. One of the dominant fingerprint bands matched with the band obtained from the actinobacterial clone. Southern blot hybridization with a probe made from clone DA079 confirmed sequence identity of clone and fingerprint band. This is the first report that a member of the novel actinobacterial group may play a physiologically active role in a native microbial community.

Loading

Article metrics loading...

/content/journal/micro/10.1099/00221287-143-9-2983
1997-09-01
2021-10-27
Loading full text...

Full text loading...

/deliver/fulltext/micro/143/9/mic-143-9-2983.html?itemId=/content/journal/micro/10.1099/00221287-143-9-2983&mimeType=html&fmt=ahah

References

  1. Bakken L. R., Olsen R. A. 1987; The relationship between cell size and viability of soil bacteria. Microb Ecol 13:103–114
    [Google Scholar]
  2. Borneman J., Skroch P. W., O'Sullivan K. M., Palus J. A., Rumjanek N. G., Jansen J. L., Nienhuis J., Triplett E. W. 1996; Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol 62:1935–1943
    [Google Scholar]
  3. Brosius J., Palmer M. L., Kennedy P. J., Noller H. F. 1978; Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli . Proc Natl Acad Sci USA 75:4801–4805
    [Google Scholar]
  4. Clark D. A., Norris P. R. 1996; Acidimicrobium ferrooxidans gen. nov., sp. nov.: mixed-culture ferrous iron oxidation with Sulfobacillus species. Microbiology 142:785–790
    [Google Scholar]
  5. Engelen B., Heuer H., Felske A., Nübel U., Smalla K., Backhaus H. 1995; Protocols for the TGGE. In Abstracts for the Workshop on Application of DGGE and TGGE in Microbial Ecology 1995. BBA for Agriculture And Forestry, Braunschweig;
    [Google Scholar]
  6. Felsenstein J. 1993; phylip (Phylogeny Inference Package) version 3.5.1.. Seattle: Department of Genetics, University of Washington;
    [Google Scholar]
  7. Felske A., Engelen B., Nübel U., Backhaus H. 1996; Direct ribosome isolation from soil to extract bacterial rRNA for community analysis. Appl Environ Microbiol 62:4162–4167
    [Google Scholar]
  8. Fuhrman J. A., McCallum K., Davis A. A. 1993; Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific oceans. Appl Environ Microbiol 59:1294–1302
    [Google Scholar]
  9. Hartung K. 1996 Entwicklung von Sonden zur Interpretation von TGGE-Gelen für die Analyse mikrobieller Gemeinschaften. Diploma thesis Fachhochschule Lippe;
    [Google Scholar]
  10. Heuer H., Smalla K. 1997; Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) for studying soil microbial communities. In Modern Soil Microbiology pp. 353–373 Edited by van Elsas J. D., Wellington E. M. H., Trevors J. T. New York: Marcel Dekker;
    [Google Scholar]
  11. Josephson K. L., Gerba C. P., Pepper T. L. 1993; Polymerase chain reaction of nonviable bacterial pathogens. Appl Environ Microbiol 59:3513–3515
    [Google Scholar]
  12. Jukes T. H., Cantor C. R. 1969; Evolution of protein molecules. In Mammalian Protein Metabolism pp. 21–132 Edited by Munro H. N. New York: Academic Press;
    [Google Scholar]
  13. Liesack W., Stackebrandt E. 1992a; Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J Bacteriol 174:5072–5078
    [Google Scholar]
  14. Liesack W., Stackebrandt E. 1992b; Unculturable microbes detected by molecular sequences and probes. Biodivers Conserv 1:250–262
    [Google Scholar]
  15. Lorenz M. G., Wackernagel W. 1987; Adsorption of DNA to sand and variable degradation rates of adsorbed DNA. Appl Environ Microbiol 53:2948–2952
    [Google Scholar]
  16. Maidak B. L., Larsen N., McCaughey M. J., Overbeck R., Olsen G. J., Fogel K., Blandy J., Woese C. R. 1994; The ribosomal database project. Nucleic Acids Res 22:3483–3487
    [Google Scholar]
  17. Muyzer G., De Waal E. C., Uitterlinden A. G. 1993; Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700
    [Google Scholar]
  18. Nübel U., Engelen B., Felske A., Snaidr J., Wieshuber A., Amann R. I., Ludwig W., Backhaus H. 1996; Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J Bacteriol 178:5636–5643
    [Google Scholar]
  19. Rainey F. A., Ward N. L., Stackebrandt E. 1993; Molecular ecology study of a New Zealand acidothermal soil. In Thermophiles ’93, Hamilton, New Zealand abstract A7. Hamilton: University of Waikato;
    [Google Scholar]
  20. Rheims H., Rainey F. A., Stackebrandt E. 1996a; A molecular approach to search for diversity among bacteria in the environment. J Ind Microbiol 17:159–169
    [Google Scholar]
  21. Rheims H., Spröer C., Rainey F. A., Stackebrandt E. 1996b; Molecular biological evidence for the occurrence of uncultured members of the actinomycete line of descent in different environments and geographical locations. Microbiology 142:2863–2870
    [Google Scholar]
  22. Rosenbaum V., Riesner D. 1987; Temperature-gradient gel electrophoresis – thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts. Biophys Chem 26:235–246
    [Google Scholar]
  23. Roszak D. B., Grimes D. J., Colwell R. R. 1984; Viable but nonrecoverable stage of Salmonella enteritidis in aquatic systems. Can J Microbiol 30:334–338
    [Google Scholar]
  24. Saano A., Lindström K., Van Elsas J. D. 1995; Eubacterial diversity in Finnish forest soil. In 7th International Symposium on Microbial Ecology, Santos, Brazil abstract P1-3.9. Santos: Brazilian Society for Microbiology;
    [Google Scholar]
  25. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  26. Stackebrandt E., Liesack W., Goebel B. M. 1993; Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis. FASEB J 7:232–236
    [Google Scholar]
  27. Stackebrandt E., Rainey F. A., Ward-Rainey N. L. 1997; Proposal for a hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47:479–491
    [Google Scholar]
  28. Stienstra A. W., Klein Gunnewiek P., Laanbroek H. J. 1994; Repression of nitrification in soils under climax grassland vegetation. FEMS Microbiol Ecol 14:45–52
    [Google Scholar]
  29. Torsvik V., Goksøyr J., Daae F. L. 1990; High diversity in DNA of soil bacteria. Appl Environ Microbiol 56:782–787
    [Google Scholar]
  30. Ueda T., Suga Y., Matsuguchi T. 1995; Molecular phylogenetic analysis of a soil microbial community in a soybean field. Eur J Soil Sci 46:415–421
    [Google Scholar]
  31. Wagner R. 1994; The regulation of ribosomal RNA synthesis and bacterial cell growth. Arch Microbiol 161:100–106
    [Google Scholar]
  32. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. 1991; 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703
    [Google Scholar]
  33. Weller R., Weller J. W., Ward D. M. 1991; 16S rRNA sequences of uncultivated hot spring cyanobacterial mat inhabitants retrieved as randomly primed complementary DNA. Appl Environ Microbiol 57:1146–1151
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/00221287-143-9-2983
Loading
/content/journal/micro/10.1099/00221287-143-9-2983
Loading

Data & Media loading...

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error