Abstract
Polimerase Chain Reaction (PCR)-based genomic fingerprints of 16 Frankia isolates were obtained using two different primers. rep-PCR DNA fingerprints were obtained by using DR1R primer, and Randomly Amplified Polymorphic DNA (RAPD) fingerprints by using a large primer derived from the 16S rDNA sequence of Escherichia coli (879F primer). According to the results obtained, primer DR1R generates strain-specific patterns. However, primer 879F yielded an identical band patterns in two Frankia strains, Cc13 and UGL 020603, isolated from different Casuarina species and geographical origins, indicating that it could identify genomic fingerprints at a higher taxonomic level (subspecies or species) than DR I R primer. To verify this hypothesis, we tested the primer 879F with eight strains of Clavibacter michiganensis, another actinobacterium with high G+C content, which includes several well-defined subspecies. Primer 879F identified a unique hand pattern in all strains within the same subspecies but different patterns for other subspecies, indicating that it generates subspecies-specific genomic fingerprints. Consequently, Frankia Ccl3 and Frankia UGL 020603 should be included in the same subspecies and the remaining Frankia strains used in this study in different subspecies. An UPGMA dendrogram of the 879F-PCR fingerprint patterns shows that the Frankia strains used in this study could be clustered into groups that broadly reflects the host plants from which they were derived. These results are consistent with those obtained by other authors using different techniques. Because primer 879F yields genomic fingerprints at taxonomic level upper than strain level, it may be a valuable tool in the polyphasic approach to Frankia taxonomy, where other classical taxonomic methods are barely applicable. Taking into account that several primers can be designed from ribosomal sequences in order to obtain RAPD patterns, we propose to name these methods according to the position of such primers in the 16S rRNA sequences of Escherichia coli. In this way, we name 879F-RAPD fingerprinting the procedure used in this study.
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References
Baker D D 1987 Relationships among pure cultured strain of Frankia based on host-specifity. Physiol. Plant. 70, 245–248.
Benson D R and Silvester W B 1993 Biology of Frankia Strains, Actinomycete Symbionts of Actinorhizal Plants. Microbiol. Rev. 57, 293–319.
Benson D R, Stephens D W, Clawson M L and Silvester W B 1996 Amplification of 16S rRNA genes from Frankia strains in root nodules of Ceanothus griseus, Coriaria arborea, Cori-aria plumosa, Discaria toumatou and Purshia tridentata. Appl. Environ. Microbiol. 62, 2904–2909.
Beyazova M and Lechevalier M P 1992 Low-Frequency Restriction Fragment Analysis of Frankia Strains (Actinorn’cetales). Int. J. Syst. Bacteriol. 42, 422–433.
Callahan 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.
Clawson M L, Caru M and Benson D R 1998 Diversity of Frankia strains in root nodules of plants from the families Elaeagnaceae and Rhamnaceae. Appl. Environ. Microbial. 64, 3539–3543.
Dong X, Cheng G and Jian W 2000 Simultaneous identification of five Bifidobacterium species isolated from human beings using multiple PCR primers. System. Appl. Microbiol. 23, 386–390.
Fernandez M P, Meugnier H, Grimant P A D and Bardin R 1989 Deoxyribonucleic acid relatedness among members of the genus Frankia. Int. J. Syst Bacterial. 39, 424–429.
Fox G E, Wisotzkcy J D and Jurtshuk P Jr 1992 How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int. J. Syst. Bacterial. 42, 166–170.
Hahn S, Lechevalier M P, Fisher A and Stackebrandt E 1989 Evidence far a close phylogenetic relationship between members of the genera Frankia, Geodermatophilus, and Blastococcus’ and emendation of the family Frankiaceae. Syst. Appl. Microbial. 11, 236–242.
Hahn D, Nickel A and Dawson J 1999 Assessing Frankia populations in plants and soil using molecular methods. FEMS Microbial. Ecol. 29, 215–227.
Honerlage W, Hahn D, Zepp K, Zeyer J and Normand P 1994 A hypervariable 23S rRNA region provides a discriminating target for specific characterization of uncultured and cultured Frankia. Syst. Appl. Microbial. 17, 433–443.
Jeong S C and Myrold D 1999 Genomic fingerprinting of Frankia microsymbionts from Ceanothus copopulations using repetitive sequences and polymerase chain reactions. Can. J. Bat. 77, 1220–1230.
Lechevalier M P 1986 Catalog of Frankia strains. Actinomycetes 19, 131–162.
Maggia L, Nazaret S and Simonet P 1992 Molecular characterization of Frankia isolates from Casuarina equisetifolia root nodules harvested in West Africa ( Senegal and Gambia ). Acta Oecol. 13, 453–461.
Maunuksela L, Zepp K, Koivula T, Zeyer J, Haahtela K and Hahn D 1999 Analysis of Frankia populations in three soils devoid of actinorhizal plants. FEMS Microbial. Ecol 28, 11–21.
Mirza M S, Hahn D, Dobritsa S V and Akkermans A D L 1994 Phylogenetic studies on uncultured Frankia populations in nodules of Dati.sca cannahina. Can. J. Microbial. 40, 313–318.
Murry M A, Fontaine M S and Torrey J G 1984 Growth kinetics and nitrogenase induction in Frankia sp HFPAr13 grown in batch culture. Plant Soil 78, 61–78.
Murry M A, Zhang D, Schneider M and De Bruijn F 1995 Use of Repetitive Sequences and the Polymerase Chain Reaction (repPCR) to fingerprint the genomes of Frankia isolates. Symbiosis 19, 223–240.
Nazaret S, Simonet P, Normand P and Bardin 1989 Genetic diversity among Frankia strains isolated from Casuarina nodules. Plant Soil 118, 241–247.
Nazaret S, Cournoyer B, Normand P and Simonet P 1991 Phylogenetic relationships among Frankia genomic species determined by use of amplified 16S rllNA sequences. J. Bacteriol. 173, 4072–4078.
Normand P and Lalonde M 1982 Evaluation of Frankia strains isolated from provenances of two Alnus species. Can. J. Microbial. 28, 1133–1142.
Normand P, Orso S, Cournoyer B, Jeannin P, Chapelon C. Dawson J, Evtushenko L and Misra A K 1996 Molecular Phylogeny of the Genus Frankia and Related Genera and Emendation of the Family Frankiaceae. Int. J. Syst. Bacterial. 46, I -9.
Pastrik K H and Rainey F A 1999 Identification and differentiation of Clavibacter michiganensis subspecies by Polymerase Chain Reaction-based techniques. J. Phytopathol. 147, 687–693.
Pérez O, Olivera H, Vasquez L and Valdés M 1999 Genetic characterization of Mexican Frankia strains nodulating Casuarina equisetifolia. Can. J. Bot 77. 1214–1219
Ramirez-Saad H, Janse J D and Akkermans A D L 1998 Root nodules of Ceanothus caerulcus contain both the Nn-fixing Frankia endophyte and a phylogenetically related Nod/Fix actinomycete. Can. J. Microbial. 44, 140–148.
Ritchie N J and Myrold D D 1999 Phylogenetic placement of uncultured Ceanothus microsymbionts using I 6S rRNA gene sequences. Can. J. Bot. 77, 1208–1213.
Rivas R, Velazquez E, Valverde A, Mateos P F and Mart nez-Molina E 2001 A two primers random amplified polimorphic DNA procedure to obtain polymerase chain reaction fingerprints of bacterial species. Electrophoresis 22, 1086–1089.
Rouvier C, Nazaret S, Fernandez M P, Picard B, Simonet P and Normand P 1992 rrn and //if intergenic spacers and isoenzyme patterns as tools to characterize Casuarina infective Frankia strains. Acta Oecol. 13, 487–495.
Rouvier C, Prim Y, Reddel P, Normand P and Simonet P 1996 Genetic diversity among Frankia strains nodulating members of the family Casuarinaceae in Australia revealed by PCR and restriction fragment length polymorphism analysis with crushed root nodules. Appl. Environ. Microbial. 62, 979–985.
Sayed W F, Wheeler C T, Zahran H H and Shoreit A A M 1997. The effect of temperature and soil moisture on the survival and symbiotic effectivity of Frankia. J. Soil. Biol. Fert. 25, 349–353
Simonet F, Navarro E, Rouvier C, Reddell P, Zimpfer J, Dawson J. Dommergues Y, Bardin R, Combarro P. Domenach A, Hamelin J, Gourbière F, Aim Y and Normand P 1998. Evidence for co-evolution between Frankia and host plants in the family Casuarinaceae. 11th International Conference on Frankia and Actinorhizal Plants, Urbana. Illinois (USA) 7–11 June.
Stackebrandt E and Goebel B M 1994 Taxonomic note: a place for DNA DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44, 846–849.
Vandamme P, Pot B, Gillis M, de Vos F, Kersters K and Swings J 1996 Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbial. Rev. 60, 407–438.
Velazquez E, Cervantes E, Igual J M. Peix A, Mateos P F, Benamar S, Moiroud A, Wheeler C T, Dawson J, Labeda D, Rodriguez-B arrueco C and Martinez-Molina E 1998a Analysis of LMW RNA profiles of Frankia strains by Staircase Electrophoresis. System. Appl. Microbial. 21, 539–545.
Versalovic J, Schneider M, de Bruijn F J and Lupski J R 1994 Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol. Cell. Biol. 5, 25–40.
Williams J G, Kubelikt A R, Livak K J, Rafalski J A and Tingey S V 1990 DNA polymorphism amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18, 6531–6535.
Woese C R 1987 Bacterial evolution. Microbial. Rev. 51, 221–271.
Zhang Z, Lopez M F and Torrey J G 1984 A comparison of cultural characteristic and infectivity of Frankia isolates from root nodules of Casuarina species. Plant Soil 78, 79–90.
Zimpfer J F, Kennedy G J, Smyth C A, Hamelin J, Navarro E and Dawson J 0 1999 Localization of Casuarina-infective Frankia near Casuarina cunninghamiana trees in Jamaica. Can J. Bot. 77, 1248–1256.
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Igual, J.M. et al. (2003). Genomic fingerprinting of Frankia strains by PCR-based techniques. Assessment of a primer based on the sequence of 16S rRNA gene of Escherichia coli . In: Normand, P., Dawson, J.O., Pawlowski, K. (eds) Frankia Symbiosis. Developments in Plant and Soil Sciences, vol 100. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-1601-7_14
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DOI: https://doi.org/10.1007/978-94-017-1601-7_14
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