Abstract
Ecological studies on the actinomyceteFrankia are often influenced by the difficulty to isolate and identify this microorganism. The application of molecular biological techniques offers possibilities to detect microbes without isolation and cultivation.Nif genes or whole plasmids can serve as targets for the design of specific probes. Alternatively, ribosomal RNA (rRNA), commonly used in modern phylogenetic studies, can be used as a target molecule in ecological studies. This paper gives an overview of new developments on the use of 16S rRNA as a target molecule for oligonucleotide probes. Group-specific sequences in the 16S rRNA ofFrankia can be used as targets for oligonucleotide probes that a) recognize ineffectiveFrankia strains onAlnus, b) recognize effective strains onAlnus, c) recognize allFrankia strains tested so far. The present paper summarizes the essential steps needed for the use of these probes for the detection ofFrankia strains in soil without isolation and cultivation.
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References
Amann R I, Krumholz I, and Stahl D A 1990 Fluorescent oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in mierobiology. J. Bacteriol. 172, 762–770.
An C S, Riggsby W S, and Mullin B C 1985 Relationship ofFrankia isolates based on deoxyribonucleic acid homology studies. Int. J. System. Bacteriol. 35, 140–146.
An C S, Riggsby W S and Mullin B C 1987 DNA relatedness ofFrankia isolates ArI4 and EuI1 to other actinomycetes of cell wall type III. The Actinomycetes 20, 50–54.
Baker D, Kidd G H and Torrey J G 1979a Separation of actinomycete nodule endophytes from crushed nodule suspensions by Sephadex fractionation. Bot. Gaz. 140 (Suppl.), S49-S51.
Baker D, Torrey J G and Kidd G H 1979b Isolation by sucrose-density fractionation and cultivation in vitro of actinomycetes from nitrogen-fixing root nodules. Nature 281, 76–78.
Baker D 1987 Relationship among pure cultured strains ofFrankia based on host specificity. Physiol. Plant. 70, 245–248.
Baker D and O'Keefe D 1984 A modified sucrose fractionation procedure for the isolation of frankiae from actinorhizal root nodules and soil samples. Plant and Soil 78, 23–28.
Becking J H 1970 Frankiaceae Fan. nov. (Actinomycetales) with one new combination and six new species of the genusFrankia Brunchorst 1886 174. Int. J. Syst. Bacteriol. 20, 201–220.
Becking J H 1974 The Family Frankiaceae.In Bergey's Mannual of Determinative Bacteriology. Eds. R EBuchanan and N EGibbons. pp. 701–706. Williams and Wilkins Co., Baltimore, MD.
Berry A and Torrey J G 1979 Isolation and characterization in vivo and in vitro of an actinomycetous endophyte fromAlnus rubra Bong.In Symbiotic Nitrogen Fixation in the Management of Temperate Forests. Eds. J C Gordon, C T Wheeler and D A Perry. pp 69–83. Oregon University Press.
Callaham D, Del Tredici P and Torrey J G 1978 Isolation and cultivation in vitro of the actinomycete causing root nodulation in Comptonia. Science 199, 899–902.
De Long E F, Wickham G S and Pace N R 1989 Phylogenetic strains: ribosomal RNA-based probes for the identification of single cells. Science 243, 1360–1363.
Dorbitsa S V 1985 Restriction analysis of theFrankia spp. genome. FEMS Microbiol. Lett. 29, 123–128.
Embley T M, Smida J and Stackerbrandt E 1988 Reverse transcriptase sequencing of 16S ribosomal RNA fromFaenia rectivirgula, Pseudonocardia thermophila andSaccharopolyspora hirsuia, three Wall type IV actinomycetes which lack mycolic acids. J. Gen. Microbiol. 134, 961–966.
Fernandez M P, Meugnier H, Grimont P A D and Bardin R 1989 Deoxyribonucleic acid relatedness in the genusFrankia. Int. J. System. Bacteriol. 39, 424–429.
Fuhrman J A, Comeau D E, Hagstrom A and Chan A M 1988 Extraction from natural planctonic microorganisms of DNA suitable for molecular biological studies. Appl. Environ. Microbiol. 54, 1426–1429.
Giovannoni S J, De Long E F, Olsen G J and Pace N R 1988 Phylogenetic Group-specific oligonucleotide probes for identification of single microbial cells. J. Bacteriol. 170, 720–726.
Goebel U B, Geiser A and Stanbridge E J 1987 Oligonucleotide probes complementary to variable regions of ribosomal RNA discriminate betweenMycoplasma species. J. Gen. Microbiol. 133, 1969–1974.
Hahn D 1990 16S rRNA as molecular marker in ecology ofFrankia. Ph.D. Thesis, Agricultural University, Wageningen, The Netherlands.
Hahn D, Starrenburg M J C and Akkermans A D L 1988 Variable compatibility of clonedAlnus glutinosa ecotypes against ineffectiveFrankia strains. Plant and Soil 107, 233–243.
Hahn D, Dorsch M, Starrenburg M J C and Akkermans A D L 1989a Synthetic oligonucleotide probes for identification ofFrankia strains. Plant and Soil 118, 210–219.
Hahn D, Kester R, Starrenburg M J C and Akkermans A D L 1990a Extraction of ribosomal RNA from soil for detection ofFrankia with oligonucleotide probes. Arch. Microbiol. 154, 329–335.
Hahn D, Lechevalier M P, Fischer A and Stackebrandt E 1989b Evidence for a close phylogenetic relationship between members of the generaFrankia, Geodermatophilus, andBlastococcus and emendation of the family Frankiaceae. Syst. Appl. Microbiol. 11, 236–242.
Hahn D, Starrenburg M J C and Akkermans A D L 1990b Oligonucleotide probes that hybridize with rRNA as a tool to studyFrankia strains in root nodules. Appl. Environ. Microbiol. 56, 1342–1346.
Henneke H, Kaluza K, Thony B, Fuhrmann M, Ludwig W and Stackebrandt E 1985 Concurrent evolution of nitrogenase genes and 16S rRNA inRhizobium species and other nitrogen fixing bacteria. Arch. Microbiol. 142, 342–348.
Holben W E, Jansson J K, Chelm B K and Tiedje J M 1988 DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl. Environ. Microbiol. 54, 703–711.
Kohne D, Hogan J, Jonas V, Dean E and Adams T H 1986 Novel approach for rapid and sensitive detection of microorganisms: DNA probes to rRNA.In Microbiology-1986. Ed. LLeive. pp. 110–12, American Society for Microbiology, Washington DC.
Lane D J, Pace B, Olsen G J, Stahl D A, Sogin M L and Pace N R 1985 Rapid determination of 16S rRNA sequences for phylogenetic analyses. Proc. Natl. Acad. Sci. USA 82, 6955–6959.
Lechevalier M P 1984 The taxonomy of the genusFrankia.In Frankia Symbiosis and Actinorhizal Plants. Eds. A D LAkkermans, DBaker, KHuss-Danell and J DTjepkema. pp. 1–6. Nijhoff/Junk Publishers, The Hague.
Lechevalier M P and Lechevalier H A 1984 Taxonomy ofFrankia In Biological, Biochemical and Biomedical Aspects of Actinomycetes. Eds LOrttiz-Ortiz, L FBojalil and VYakoleff. Academic Press, New York. pp 575–582.
Meesters T M 1988 The function of vesicles in the actinomyceteFrankia. Ph.D. Thesis, Agricultural University, Wageningen, The Netherlands.
Normand P and Lalongde M 1986 The genetics of actinorhizalFrankia: A review. Plant and Soil 90, 429–453.
Normand P, Simonet P and Bardin R 1988 Conservation of Nif sequences inFrankia. Mol. Gen. Genet. 213, 238–246.
Ogram A, Sayler G S and Barkay T 1988 DNA extraction and purification from sediments. J. Microbiol. Methods 7, 57–66.
Ruvkun G B and Ausubel F M 1980 Interspecies homology of nitrogenase genes. Proc. Natl. Acad. Sci. USA 77, 191–195.
Saiki R K, Gelfand D H, Stoffel S, Scharf S J, Higuchi R, Horn G T, Mullis K B and Erlich H A 1988 Primerdirected enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239, 487–491.
Simonet P, Le N T, Teissierdu Cros E and Bardin R 1988 Identification ofFrankia strains by direct DNA hybridization of crushed nodules. Appl. Environ. Microbiol. 54, 2500–2503.
Sommerville C C, Knight I T, Straube W L and Colwell R R 1989 Simple, rapid method for direct isolation of nucleic acids from aquatic environments. Appl. Environ. Microbiol. 55, 548–554.
Smolander A 1990Frankia populations in soils under different tree species-with special emphasis on soils underBetula pendula. Plant and Soil 121, 1–10.
Stahl D, Flesher B, Mansfield R H and Montgomery L 1988 Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl. Environ. Microbiol. 54, 1079–1084.
Steffan R J and Atlas R M 1988 DNA amplification to enhance detection of genetically engineered bacteria in environmental samples. Appl. Environ. Microbiol. 54, 2185–2191.
Steffan R J, Goksoyr J, Bej A K and Atlas R M 1988 Recovery of DNA from soils and sediments. Appl. Environ. Microbiol. 54, 2908–2915.
Tenover F C 1988 Diagnostic deoxyribonucleic acid probes for infectious diseases. Clin. Microbiol. Rev. 1, 82–101.
Van Dijk C 1984 Ecological aspects of spore formation in theFrankia-Alnus symbiosis. Ph.D. Thesis, Univ. Leiden, The Netherlands
Van Dijk C and Sluimer-Stolk A 1990 An ineffective strain type ofFrankia in the soil of natural stands of Alnus glutinosa (L.) Gaertn. Plant and Soil 127, 107–121.
Viscidi R P and Yolken R G 1987 Molecular diagnosis of infectious diseases by nucleic acid hybridization. Molecular Cellular Probes 1, 3–14.
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Akkermans, A.D.L., Hahn, D. & Mirza, M.S. Molecular ecology ofFrankia: Advantages and disadvantages of the use of DNA probes. Plant Soil 137, 49–54 (1991). https://doi.org/10.1007/BF02187431
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DOI: https://doi.org/10.1007/BF02187431