Phylogenetic clustering of Bradyrhizobium symbionts on legumes indigenous to North America

Abstract

To analyse determinants of biogeographic structure in members of the genus Bradyrhizobium, isolates were obtained from 41 legume genera, originating from North American sites spanning 48.5 6 of latitude (Alaska to Panama). Sequencing of portions of six gene loci (3674 bp) in 203 isolates showed that there was only a weak trend towards higher nucleotide diversity in tropical regions. Phylogenetic relationships for nifD, in the symbiosis island region of the Bradyrhizobium chromosome, conflicted substantially with a tree inferred for five housekeeping gene loci. For both nifD and housekeeping gene trees, bacteria from each region were significantly more similar, on average, than would be expected if the source location was permuted at random on the tree. Within-region permutation tests also showed that bacteria clustered significantly on particular host plant clades at all levels in the phylogeny of legumes (from genus up to subfamily). Nevertheless, some bacterial groups were dispersed across multiple regions and were associated with diverse legume host lineages. These results indicate that migration, horizontal gene transfer and host interactions have all influenced the geographical divergence of Bradyrhizobium populations on a continental scale.

Genetic Diversity and Evolution of Bradyrhizobium Populations Nodulating Erythrophleum fordii, an Evergreen Tree Indigenous to the Southern Subtropical Region of China

“…Although both the symbiotic genes and the housekeeping genes are located on the same chromosome in bradyrhizobia, their evolution has been affected by different factors. The evolution of symbiotic genes in rhizobia was strongly forced by the selection of host plants (44)(45)(46), while the divergence of housekeeping genes was usually a time-dependent event. Therefore, it was not surprising that the rhizobia, especially in the same species, harbored different symbiotic genes and that the phylogenetic relationships of the symbiotic genes were different from those of the two housekeeping genes in the same rhizobia ( Fig.…”

Metapopulation dominance and genomic-island acquisition ofBradyrhizobiumwith superior catabolic capabilities

“…Parallel processes are also possible in bacterial symbionts, with the host possibly promoting rather than countering bacterial spread. In rhizobial populations, host plants can favour beneficial over ineffective rhizobial genotypes [20,22,23] and thus select certain symbiosis alleles over others [18,19,32]. However, only under very specific conditions has there been evidence of plant selection promoting selective sweeps of symbiosis genotypes.…”

“…Host control models of symbiosis posit that hosts must exhibit mechanisms to constrain exploitation in their associated symbionts, for instance via discrimination among symbionts during initial host colonization or via within host control over symbiont proliferation [14][15][16][17]. Consistent with these models, legume hosts have been shown to select certain rhizobial genotypes over others for nodulation [18,19] and favour beneficial rhizobia over less-effective strains in planta [20][21][22][23]. However, ex planta selection on rhizobia has remained poorly understood [4,24].…”

Disparate origins ofBradyrhizobiumsymbionts for invasive populations ofCytisus scoparius(Leguminosae) in North America

“…For a marker in the SI region, we analyzed an 822 bp portion of nifD gene (which codes for dinitrogenase α subunit) as described (Parker et al ., ). Four markers outside of the SI region (in addition to 23S rRNA) were also sequenced as described (Koppell & Parker, ; Parker, ): dnaK (603 bp), gyrB (781 bp), rplC (432 bp) and rpoB (537 bp).…”

“…strain ORS278). Parker () and Koppell & Parker () analyzed strains from diverse indigenous legumes in nine regions of the United States and Mexico (number of strains per region in parenthesis): Oaxaca (34), Chihuahua (21), south Texas (21), California (2), Washington State (25), Alaska (3), Illinois (1), North Carolina (27) and northeastern U.S. (28). Finally, we obtained sequence data for 37 additional isolates (Supporting Information, Table S1), from indigenous legumes in Ireland (2), Scotland (2), Belgium (5), Poland (2), Portugal (2), Spain (11), Hawaii (2) and Australia (11).…”