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

Abstract

18The diversity of indigenous bradyrhizobia from soils collected at 11 locations in the 19 Philippines was investigated using PSB-SY2 local soybean cultivar as the host plant. 20 Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) 21 treatment for 16S rRNA, 16S-23S rRNA internal transcribed spacer (ITS) region and rpoB 22 housekeeping gene was performed primarily to detect the genetic variation among the 424 23 isolates collected. Then, sequence analysis of 16S rRNA, ITS region and rpoB gene was 24 performed for the representative isolates. Majority of the isolates were classified under 25 Bradyrhizobium elkanii, B. diazoefficiens, B. japonicum, Bradyrhizobium sp., and few 26 isolates were related to B. yuanmingense. Genetic variations observed through PCR-RFLP 27 and sequence analyses of the ITS region and rpoB gene generally occurred in B. elkanii, 28 suggesting an occurrence of gene transfer. Shannon's diversity index showed varied results 29 with a lowest score of 0.00 and highest at 0.98 indicating a very diverse population of 30 bradyrhizobia across the country. Among all the factors considered in this work, soil 31 management such as period of flooding and some soil properties provided major influence 32 on the distribution and diversity of soybean bradyrhizobia in the country. Thus, it is 33 proposed that the major micro-symbiont of soybean in the Philippines are B. elkanii for 34 3 non-flooded soils, then B. diazoefficiens and B. japonicum for flooded soils. 35 Importance 36Agriculture production in the Philippines has been and is currently heavily dependent on 37 chemical inputs with mainly rice or corn mono-cropping that it rendered the soil acidic and 38 unproductive. Legume research in the country are mainly focused on plant varietal 39 improvements and very few are aimed at understanding the ecological niche of rhizobia 40 present in the soil. Since soybean has mutual relationship with rhizobia, this legume is a 41 good fallow crop or a rotation crop after rice and corn to help build up the nitrogen stock in 42 the soil. The significance of this research is the better understanding of the ecological niche 43 of indigenous soybean bradyrhizobia, particularly in a tropical archipelago like the 44 Philippines. This work was conceptualized with the utmost goal to increase soybean yield 45 by harnessing and evaluating the indigenous rhizobia in the soil to make production more 46 sustainable and human-friendly. 47 48 KEYWORDS 49 B. elkanii, B. diazoefficiens, B. japonicum, flooded soil, non-flooded, soil management 50 51 52 The genus Bradyrhizobium is a major micro-symbiont of soybean (Glycine max [L.] 53 Merrill) that could form nodule with legumes through symbiosis. The symbiotic 54 relationship between rhizobia and legume is a highly specific, complicated and 55 energy-exhaustive process (50) which may lead to improved crop yield if efficient and 56 sustained. It is considered that Bradyrhizobium is the predominant genus of rhizobia in the 57 tropics (9). Tropical regions ...