Phylogenetic Analysis of Soybean-Nodulating Rhizobia Isolated from Alkaline Soils in Vietnam

Abstract

In order to analyze the phylogeny of soybean-nodulating bacteria in alkaline soils in Vietnam, indigenous soybean-nodulating bacteria were isolated from root nodules by cultivating three kinds of &j-soybean cultivam on two alkaline soils in Vietnam. The 120 isolates were classified into two major genera of soybean-nodulating rhizobia, namely Brudyrhizobium and Sinorhizobium genera, based on a growth analysis on medium and PCR-RFLP analyses of 16s rDNA and of the 165-23s rDNA internal transcribed spacer (ITS) region. Most of the isolates of B. juponicum were extra-slow-growing and their ITS types were similar to that of B. juponicum USDA 136. They were not isolated €kom the soybean cultivar CNS used as &jm, genotype. Isolates of Sinorhizobium were divided into two groups, S. fredii and S. sp., based on a PCR-RFLP analysis of 16s rDNA. Furthermore, PCR-RFLP analysis of the 165-23s rDNA ITS region enabled to separate them into Ave types, three ITS types associated with S. fkedii and two with S. sp. Sinorhizobium was frequently isolated from the three soybean cultivars on two soils. From the isolate ratio, it was suggested that B. juponicum strains similar to B. juponicum USDA 136 and S.Pedii predominated in the alkaline soils of Vietnam. Additionally, our findings indicated that the &j-genotypes affected not only the compatibility, but also the preference for nodulation between the host soybean and rhizobia.

Incompatible Nodulation of <i>Bradyrhizobium elkanii</i> Strains BLY3-8 and BLY6-1 with <i>Rj</i>3 Gene-Harboring Soybean Cultivars

“…Saeki et al [5] reported that Rj gene soybean cultivars affect compatibility and preference for nodule formation between the host cultivar and rhizobial bacteria.…”

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members

“…Direct sequencing was carried out by using the PCR products as templates and the PCR primers with an ABI PRISM 310 DNA sequencer and Big Dye Terminator v.3.1 Cycle Sequencing Kit (Applied Biosystems, Foster City, CA, USA). PCR amplification and sequence analysis of 16S-23S rDNA ITS sequences were performed as described by Saeki et al (2005Saeki et al ( , 2006. Table 1 lists the DDBJ/GenBank/EMBL accession numbers for the 16S rRNA genes and ITS sequences between 16S-and 23S-rRNA that are used in this study.…”

Characterization of Soybean-Nodulating Rhizobial Communities and Diversity

“…As soybean-nodulating sinorhizobia will inhabit alkaline soils exclusively (Saeki et al, 2005;Suzuki et al, 2008), and because the soils sampled in this study were all acidic, it is reasonable to assume that all isolates in the present study belonged to genus Bradyrhizobium, and that most were B. japonicum, as suggested by the soybean root nodulation, alkaline production on YMA medium, and the PCR-RFLP analysis results. Bradyrhizobial community diversities, determined by pair-wise comparison, among soybean cultivars of each Rj genotype are shown in Table 4 and Fig.…”

“…Specific rhizobial strains can be incompatible with soybean cultivars harboring a particular Rj gene. In addition, indigenous soybean-nodulating rhizobia may show a preference for particular genotypes among the compatible genotypes, even among soybean plants cultivated in soil samples from the same field (Ishizuka et al, 1991;Saeki et al, 2000Saeki et al, , 2005. It is therefore important to use soybean cultivars with different Rj genotypes for both isolating and analyzing indigenous soybean-nodulating rhizobia.…”

“…For amplifications of 23S-5S rDNA, the following primer set was used (van Berkum et al, 2003;Saeki et al, 2007): 23S-F1 (5'-GRYGGATGCCTTGGC-3') and 5S-R (5'-GGCAGCGACCTACTCTC-3'). Furthermore, for amplifications of the 16S-23S rDNA ITS region from Sinorhizobium/ Ensifer, the primer set ITS1512F (5'-GTCGTAACAAGGTAGCCGT-3') and ITSLS23R (5'-TGCCAAGGCATCCACC-3'), based on Hiraishi et al (1997) with slight modification for Sinorhizobium/ Ensifer (Saeki et al, 2005), was used. …”