Genetic diversity and distribution of indigenous soybean-nodulating bradyrhizobia in the Philippines

Abstract

ABSTRACTThe diversity of indigenous bradyrhizobia from soils collected at 11 locations in the Philippines was investigated using PSB-SY2 local soybean cultivar as the host plant. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) treatment for 16S rRNA, 16S-23S rRNA internal transcribed spacer (ITS) region and rpoB housekeeping gene was performed primarily to detect the genetic variation among the 424 isolates collected. Then, sequence analysis of 16S rRNA, ITS region and rpoB gene was performed for the representative isolates. Majority of the isolates were classified under Bradyrhizobium elkanii, B. diazoefficiens, B. japonicum, Bradyrhizobium sp., and few isolates were related to B. yuanmingense. Genetic variations observed through PCR-RFLP and sequence analyses of the ITS region and rpoB gene generally occurred in B. elkanii, suggesting an occurrence of gene transfer. Shannon’s diversity index showed varied results with a lowest score of 0.00 and highest at 0.98 indicating a very diverse population of bradyrhizobia across the country. Among all the factors considered in this work, soil management such as period of flooding and some soil properties provided major influence on the distribution and diversity of soybean bradyrhizobia in the country. Thus, it is proposed that the major micro-symbiont of soybean in the Philippines are B. elkanii for non-flooded soils, then B. diazoefficiens and B. japonicum for flooded soils.ImportanceAgriculture production in the Philippines has been and is currently heavily dependent on chemical inputs with mainly rice or corn mono-cropping that it rendered the soil acidic and unproductive. Legume research in the country are mainly focused on plant varietal improvements and very few are aimed at understanding the ecological niche of rhizobia present in the soil. Since soybean has mutual relationship with rhizobia, this legume is a good fallow crop or a rotation crop after rice and corn to help build up the nitrogen stock in the soil. The significance of this research is the better understanding of the ecological niche of indigenous soybean bradyrhizobia, particularly in a tropical archipelago like the Philippines. This work was conceptualized with the utmost goal to increase soybean yield by harnessing and evaluating the indigenous rhizobia in the soil to make production more sustainable and human-friendly.