Frankia populations were analyzed in three soils devoid of actinorhizal plants but containing monocultures of birch (Betula pendula Roth), pine (Pinus sylvestris L.) or spruce (Picea abies (L.) Karsten). Bioassays using seedlings of Alnus incana as capture plants resulted in nodulation capacities of 3160±7, 2267±13, and 2747±6 nodulation units g−1 of these soils, respectively. Comparative sequence analysis of an actinomycetes-specific insertion in domain III of the 23S rRNA allowed a grouping of isolates obtained from nodules of the capture plants into three distinct groups of the Alnus host infection group. This separation was confirmed by the analysis of genomic fingerprints of the isolates generated by rep-PCR fingerprinting with the BOX primer. Genomic fingerprints also demonstrated that all isolates differed from each other. The isolates accounted for a significant proportion of the Frankia population in root nodules of the capture plants as shown by in situ hybridization with specific probes. However, only those Frankia strains isolated from soil of the birch stand via Alnus seemed to represent the total Frankia population in root nodules. Nodules induced after inoculation with soil from the pine or spruce stand also contained Frankia populations which were not isolated during this study and which could not be identified by in situ hybridization. Depending upon whether the soil originated from a birch, pine or spruce stand, different Frankia populations were found in the nodules of the capture plants. Because a nested PCR on nucleic acids extracted from these different soils did not indicate differences in the diversity of the total Frankia populations, it was concluded that Frankia populations in nodules of the capture plants represent the fraction of physiologically active, infecting frankiae in the soils rather than the total Frankia populatio
