Frankia bacteria in Alnus rubra forests: genetic diversity and determinants of assemblage structure

To quantify the genetic diversity of Frankia bacteria associated with Alnus rubra in natural settings and to examine the relative importance of site age, management, and geographic location in structuring Frankia assemblages in A. rubra forests, root nodules from four A. rubra sites in the Pacific Northwest, USA were sampled. Frankia genetic diversity at each site was compared using sequence-based analyses of a 606 bp fragment of the nifH gene. At a 3% sequence similarity cutoff, a total of 5 Frankia genotypes were identified from 317 successfully sequenced nodules. Sites varied in the total number of genotypes present, but were typically dominated by only one or two genotypes. Phylogenetic analyses showed that all of the A. rubra-Frankia genotypes grouped with other Alnus-infective Frankia. Analysis of similarity (ANOSIM) and chi-square analyses indicated that Frankia assemblages were more strongly influenced by site age/management than geographic location. This study demonstrates that the Frankia assemblages in A. rubra forests have low genotype diversity, but that genotype abundance can differ significantly in forests of different age/management history.