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

Abstract

We investigated the relationship between the genetic diversity of indigenous soybean-nodulating bradyrhizobia and their geographical distribution in the United States using nine soil isolates from eight states. The bradyrhizobia were inoculated on three soybean Rj genotypes (non-Rj, Rj 2 Rj 3 , and Rj 4 ). We analyzed their genetic diversity and community structure by means of restriction fragment length polymorphisms of PCR amplicons to target the 16S-23S rRNA gene internal transcribed spacer region, using 11 USDA Bradyrhizobium strains as reference strains. We also performed diversity analysis, multidimensional scaling analysis based on the Bray-Curtis index, and polar ordination analysis to describe the structure and geographical distribution of the soybean-nodulating bradyrhizobial community. The major clusters were Bradyrhizobium japonicum Bj123, in the northern United States, and Bradyrhizobium elkanii, in the middle to southern regions. Dominance of bradyrhizobia in a community was generally larger for the cluster belonging to B. elkanii than for the cluster belonging to B. japonicum. The indigenous American soybean-nodulating bradyrhizobial community structure was strongly correlated with latitude. Our results suggest that this community varies geographically.

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

“…Recent studies not only suggested differences in the biogeographic distribution of rhizobial species nodulating soybeans but also demonstrated a biased selection of rhizobial species by different genotypes of soybeans (2,4,10,11). Consistent with these findings, comparative genomics of rhizobia revealed that the phyletic distribution of rhizobial functional genes involved in environmental adaptations and symbiotic interactions generally agrees with the phylogeny of rhizobial species (7).…”

“…One of the key features of soybean is its ability to form symbiotic nitrogen-fixing nodules with diverse rhizobial species (2,3), implying its important role in sustainable agriculture. It has been recurrently reported that Bradyrhizobium japonicum, Bradyrhizobium elkanii, Bradyrhizobium liaoningense, Bradyrhizobium yuanmingense, and Sinorhizobium fredii could nodulate soybeans (2)(3)(4)(5). Recently, Bradyrhizobium huanghuaihaiense, Bradyrhizobium daqingense, Sinorhizobium sojae, and several unnamed species were also found to be effective microsymbionts of soybeans (2,3,(6)(7)(8).…”

“…Recently, Bradyrhizobium huanghuaihaiense, Bradyrhizobium daqingense, Sinorhizobium sojae, and several unnamed species were also found to be effective microsymbionts of soybeans (2, 3, 6-8). Strain USDA110 represents a widely distributed type formerly known as B. japonicum Ia, but it has recently been proposed as a member of the new species Bradyrhizobium diazoefficiens (9).Recent studies not only suggested differences in the biogeographic distribution of rhizobial species nodulating soybeans but also demonstrated a biased selection of rhizobial species by different genotypes of soybeans (2,4,10,11). Consistent with these findings, comparative genomics of rhizobia revealed that the phyletic distribution of rhizobial functional genes involved in environmental adaptations and symbiotic interactions generally agrees with the phylogeny of rhizobial species (7).…”

Morphological and Biochemical Characterization of Soybean Nodulating Rhizobia Indigenous to Zambia

“…Following successful infection with soybean-nodulating rhizobia, soybean forms root nodules where rhizobia symbiotically fix atmospheric nitrogen. The main soybean-nodulating rhizobia are Bradyrhizobium japonicum, Bradyrhizobium elkanii, Sinorhizobium xinjiangense, Mesorhizobium tianshanense, Ensifer fredii, and Rhizobium tropici (Shiro et al, 2013). Of these, Bradyrhizobium japonicum and Bradyrhizobium elkanii are both slow growing while Ensifer fredii, and Rhizobium tropici are fast growing (Li et al, 2011).…”

“…While inoculation with Bradyrhizobia has been shown to improve nitrogen fixation and subsequent soybean yield (Shiro et al, 2013), the efficiency of the inoculants maybe poor if the inoculated strains cannot out-compete the indigenous ones or cannot establish an efficient symbiosis with the host plant (Mweetwa et al, 2014). Therefore, a complete understanding of the ecology of indigenous soybean-nodulating rhizobia with respect to their genetic diversity and the environmental factors associated with their localization and dominance in the soil is important.…”