title: Typing method for N2-fixing bacteria based on PCR-RFLP--application to the characterization of Frankia strains.
abstract: DNA sequences of an intergenic spacer (IGS) and parts of genes in the nif cluster were amplified by the polymerase chain reaction (PCR) using two primers derived from nifD- and nifK-conserved sequences. The PCR products were cleaved by ten 4-base cutting restriction enzymes and the restriction patterns were used as fingerprints to type Frankia strains. The feasability of this PCR-RFLP method for typing Frankia strains was investigated on Frankia reference strains belonging mainly to the Elaeagnaceae infectivity group but also on new Frankia isolates and on other N2-fixing microorganisms. By modulating the stringency of the amplifications, we showed the method allowed to target either Frankia strains or the whole N2-fixing microbial community. DNA digestion patterns were used to estimate the sequence divergence between the Frankia nifD-K fragment. The estimated relationships deduced from these genotypic data correlated well with established Frankia taxonomic schemes.
authors.affiliation: Laboratoire d'Ecologie microbienne du Sol, URA CNRS 1450, Université Claude Bernard, Villeurbanne, France.
authors.forename: S
authors.initials: S
authors.lastname: Jamann
authors.forename: M P
authors.initials: MP
authors.lastname: Fernandez
authors.forename: P
authors.initials: P
authors.lastname: Normand
mesh_terms: D000192:Actinomycetales / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D015373:Bacterial Typing Techniques; D001483:Base Sequence; D016172:DNA Fingerprinting; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D017753:Ecosystem; D005798:Genes, Bacterial; D005838:Genotype; D007709:Klebsiella / Q000235:genetics; D008969:Molecular Sequence Data; D009586:Nitrogen Fixation / Q000235:genetics*; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial; D004275:DNA, Ribosomal