Mathematical Ecology Analysis of Geographical Distribution of Soybean-Nodulating Bradyrhizobia in Japan

Soybeans (Glycine max. L. Merr.) establish a symbiotic relationship with soybean-nodulating bacteria during the development of their nitrogen-fixing organs, the root nodules. The major soybean-nodulating rhizobia that have been identified are Bradyrhizobium japonicum, Bradyrhizobium elkanii, and Ensifer/Sinorhizobium fredii (4, 13, 14, 18, 37, 47). Additional species of soybean-nodulating rhizobia have also been discussed extensively in the literature because of the complexity of their taxonomic classification (10, 23, 41, 43, 45). Major symbionts of soybeans for nodulation in acidic-neutral soil in Japan are B. japonicum and B. elkanii (21, 28, 36, 40). Soybean-nodulating bacteria are found throughout wide regions of the world, and their genetic diversity may reflect geographical and climatic differences as well as the diversity of local hosts. Therefore, analysis of the genetic diversity and field distributions of indigenous soybean-nodulating rhizobia is important for improving our understanding of rhizobial ecology under various conditions. Our previous research (28, 31) demonstrated the genetic diversity and field distributions of indigenous soybean-nodulating bradyrhizobia isolated from weakly acidic soils from five fields in Japan and suggested that indigenous bradyrhizobia cluster in association with strains listed in north-to-south order as follows: B. japonicum USDA 123, 110, 6T, and B. elkanii USDA 76T. Suzuki et al. (40) reported the dominance of B. elkanii strains in weakly acidic-neutral soils of the islands of Okinawa, Miyakojima and Ishigaki and the dominance of S. fredii strains in alkaline soils of the Okinawa island. Risal et al. (25) reported the genetic diversity of native soybean bradyrhizobia isolated from different topographical regions along the southern slopes of the Himalayan Mountains in Nepal. Furthermore, Adhikari et al. (1) demonstrated the genetic diversity and distribution of soybean-nodulating bradyrhizobia in relation to climate and soil properties in Nepal. Li et al. (19) reported that the genetic diversity and biogeography of soybean rhizobia were related to soil determinant factors such as pH, electrical conductivity (EC), and phosphorus content in Hebei Province, China. These results suggest that a relationship exists between the genetic diversity and field distribution of indigenous soybean-nodulating rhizobia and soil properties such as temperature (as influenced by latitude and altitude), phosphorus content, EC, and soil pH. In the host soybean, the genes related to nodulation, the Rj genes, are known as nodulation regulatory genes, and Rj genotypes of rj1, Rj2, Rj3, Rj4 and non-Rj, which lack these genetical phenotypes, have been confirmed to exist naturally (6). Soybean cultivars harboring Rj genes are involved in the inhibition of effective nodulation by certain serogroups of rhizobia as well as in the preferential selection of appropriate rhizobia for nodulation (11, 20, 26). Thus, in an analysis of indigenous soybean-nodulating bacteria, it is necessary to use several types of Rj genotypes of soybean cultivars for the isolation of rhizobia. To examine the relationship between bradyrhizobial genetic diversity and their geographical distribution in an ecological study of indigenous soybean rhizobia, we used three types of Rj-genotype soybeans to isolate indigenous soybean-nodulating bradyrhizobia from weakly acidic soils in Japan. We investigated their genetic diversity, community structure, and allocation among fields by PCR-RFLP analysis of internal transcribed spacer (ITS) regions of the 16S–23S rRNA gene. Furthermore, we used data from the present and previous studies to conduct mathematical ecological analyses to clarify the relationship between the community structures of soybean-nodulating bradyrhizobial and their geographical distributions.