Microevolution of symbiotic Bradyrhizobium populations associated with soybeans in east North America

Abstract

Microevolution and origins of Bradyrhizobium populations associated with soybeans at two field sites (A and B, 280 km apart in Canada) with contrasting histories of inoculation was investigated using probabilistic analyses of six core (housekeeping) gene sequences. These analyses supported division of 220 isolates in five lineages corresponding either to B. japonicum groups 1 and 1a or to one of three novel lineages within the genus Bradyrhizobium. None of the isolates from site A and about 20% from site B (the only site with a recent inoculation history) were attributed to inoculation sources. The data suggest that most isolates were of indigenous origin based on sequence analysis of 148 isolates of soybean-nodulating bacteria from native legumes (Amphicarpaea bracteata and Desmodium canadense). Isolates from D. canadense clustered with B. japonicum group 1, whereas those from A. bracteata were placed in two novel lineages encountered at soybean field sites. One of these novel lineages predominated at soybean sites and exhibited a significant clonal expansion likely reflecting selection by the plant host. Homologous recombination events detected in the 35 sequence types from soybean sites had an effect on genetic diversification that was approximately equal to mutation. Interlineage transfer of core genes was infrequent and mostly attributable to gyrB that had a history of frequent recombination. Symbiotic gene sequences (nodC and nifH) of isolates from soybean sites and native legumes clustered in two lineages corresponding to B. japonicum and B. elkani with the inheritance of these genes appearing predominantly by vertical transmission. The data suggest that soybean-nodulating bacteria associated with native legumes represent a novel source of ecologically adapted bacteria for soybean inoculation.

Genetic Divergence of Bradyrhizobium Strains Nodulating Soybeans as Revealed by Multilocus Sequence Analysis of Genes Inside and Outside the Symbiosis Island

“…All the gene trees of island genes (nifA, nifH, nodC, nodV, fixA, rhcC2, and trpD) were significantly different (P Ͻ 0.001) from the species tree based on the SMc00019-truA-thrA concatenate, whereas no significantly incongruent signals could be detected for the gene tree of each offisland gene compared to the species tree (P Ͼ 0.05). This result is similar to earlier findings on nifH, nodA, nodC, nodY, nodK, nodZ, nolL, and noeI (14,(18)(19)(20), where Bradyrhizobium formed a monophyletic clade in the phylogeny of these symbiosis genes but showed a topology that was incongruent with the reference species tree. In the well-resolved ML tree of the concatenated off-island genes (Fig.…”

“…Recent evolutionary genetics studies have shown that recombination could make a contribution compara- ble to or greater than that of mutation in creating diversity of rhizobia (7,18,49 (5). The discrepancy could be due to either the higher diversity of test strains in this study or different sets of off-island genes used in the two studies.…”

“…In contrast to some strains such as BTAi1 and ORS278, which use a Nod- independent pathway to form a symbiosis with Aeschynomene species (53), most Bradyrhizobium strains use the Nod-dependent strategy and are characterized by the genomic feature that key symbiotic functions are encoded by genes localized in a symbiosis island region (26,27). However, our understanding of the diversity of genes in this island is limited to nifH, nifD, and several nod/nol/noe genes, such as nodA, nodC, nodY, nodK, nodZ, nolL, and noeI (14,(18)(19)(20)54). In this study, island genes nifA, nifH, nodC, nodV, fixA, rhcC2, and trpD were sequenced (25,(28)(29)(30)(31)55).…”

“…Moreover, these core genes provide a gap of 2% for intraspecies/ interspecies average nucleotide identity (ANI) for rhizobia, including Bradyrhizobium (17), implying their potential role as useful markers in taxonomy, phylogeny, and population genetics. In most studies on the phylogenetics and evolutionary genetics of housekeeping genes in Bradyrhizobium, no symbiosis genes were analyzed, or only nifH and/or nodC on the symbiosis island (5,(14)(15)(16)18). On the other hand, studies on the evolution of nodu-…”

Genetic Diversity and Geographical Distribution of Indigenous Soybean-Nodulating Bradyrhizobia in the United States

“…Total DNA was extracted from the isolates using BL extraction buffer, as described previously (22), based on the method reported by Hiraishi et al (29). As reference strains, we used B. japonicum USDA strains 4,6 T , 38, 110, 115, 123, 124, and 135 and B. elkanii USDA strains 46,76 T , and 94 (30). Total DNAs of the reference strains were extracted by means of the same procedure as that used for the isolates.…”