Actinorhizal plants form nitrogen-fixing root nodules in symbiosis with soil-dwelling actinobacteria within the genus ， and specific taxonomic clusters nodulate plants in corresponding host infection groups. In same-soil microcosms， we observed that some host species were nodulated (， ， ， ) while others were not (， ). Nodule populations were represented by eight different sequences of gene fragments. Two of these sequences characterized frankiae in nodules， and three others characterized frankiae in nodules. Frankiae in nodules were represented by five sequences， one of which was also found in nodules from and ， while another was detected in nodules from Quantitative PCR assays showed that vegetation generally increased the abundance of frankiae in soil， independently of the target gene (i.e.， or the 23S rRNA gene). Targeted Illumina sequencing of -specific gene fragments detected 24 unique sequences from rhizosphere soils， 4 of which were also found in nodules， while the remaining 4 sequences in nodules were not found in soils. Seven of the 24 sequences from soils represented >90% of the reads obtained in most samples; the 2 most abundant sequences from soils were not found in root nodules， and only 2 of the sequences from soils were detected in nodules. These results demonstrate large differences between detectable populations in soil and those in root nodules， suggesting that root nodule formation is not a function of the abundance or relative diversity of specific populations in soils. The nitrogen-fixing actinobacterium forms root nodules on actinorhizal plants， with members of specific taxonomic clusters nodulating plants in corresponding host infection groups. We assessed diversity in root nodules of different host plant species， and we related specific populations to the abundance and relative distribution of indigenous frankiae in rhizosphere soils. Large differences were observed between detectable populations in soil and those in root nodules， suggesting that root nodule formation is not a function of the abundance or relative diversity of specific populations in soils but rather results from plants potentially selecting frankiae from the soil for root nodule formation. These data also highlight the necessity of using a combination of different assessment tools so as to adequately address methodological constraints that could produce contradictory data sets.