Genotypic diversity of an indigenous Rhizobium meliloti field population assessed by plasmid profiles, DNA fingerprinting, and insertion sequence typing

Abstract

One hundred and twenty-five Rhizobium meliloti isolates nodulating field-grown Medicago sativa cv. Europe were evaluated for plasmid content and for symbiotic effectiveness with this host. Relative to the strain used commercially in France (RCR2011), isolates showed a comparable level of symbiotic effectiveness, although two isolates were poorly effective. Twenty-four distinct plasmid profiles were observed among these isolates, with a plasmid number varying between one and five per isolate. All isolates but one harboured a plasmid equivalent in size to that of the R. meliloti 41 megaplasmid. Sizes of the other plasmids varied from 45 to >600 kb. The major plasmid group (representing 30% of the whole population) consisted of isolates carrying a megaplasmid plus a large plasmid with an average size of 230 kb. To assess the validity of plasmid grouping, 32 isolates representative of 12 plasmid groups were further characterized on the basis of their genomic DNA restriction patterns and their insertion sequence (IS) fingerprints, using the indigenous insertion sequence ISRm1 as a probe. The DNA restriction patterns and IS fingerprints were highly distinctive among the 32 isolates examined since 20 and 16 types, respectively, were observed. These two characteristics are strongly correlated with the plasmid profiles of the strains, confirming the validity of plasmid grouping in assessing diversity of natural populations of R. meliloti. Plasmid profile analysis, although less discriminating than DNA restriction patterns or IS fingerprinting, is the method of choice when many isolates need to be typed. Key words: Rhizobium meliloti, ecology, diversity, field population, symbiotic effectiveness.