Molecular Analysis of Effectiveness in Soybean-Rhizobia Symbioses

Abstract

Soybean-rhizobia symbioses can be highly variable in nitrogen fixing effectiveness. Identification of the genetic regulation for symbiotic effectiveness could enable improvement of the understanding and manipulation of biological nitrogen fixation (BNF). The aim of this study is to evaluate effectiveness of symbioses between a range of soybean cultivars and rhizobial strains, and identify genomic traits that account for differences between highly and poorly effective N2 fixing strains. In this study, thirteen strains from genera Bradyrhizobium and Sinorhizobium were differentiated using their ribosomal fingerprints and phylogenies based on symbiotic and housekeeping genes. The selected strains were evaluated for their symbiotic efficiency with six soybean cultivars in three glasshouse experiments. Greatly varied symbiotic outcomes were observed due to highly variable compatibility between symbiotic partners. A poorly effective N2 fixing B. elkanii strain CC717 caused sub-optimal BNF on five out of the six tested cultivars. A time-course experiment showed CC717 induced nitrogen fixation activity to decrease five weeks after sowing, and early nodule senescence coupled with leaf senescence and minor foliar chlorosis in soybean cv. Soya 791. Whole genome sequencing yielded a large number of contigs for the poorly effective strain CC717, indicating a high volume of repeated sequences in this genome. The genome of a highly effective N2 fixing B. diazoefficiens strain CB1809 showed highly conserved similarity to its type strain USDA110. However, no direct relatedness was found between the level of conservation of the symbiotic region and the symbiotic efficiency. The BNF efficiency is likely to be controlled by specific genes of both host and rhizobia e.g., the rhizobial T3SS and soybean Rj genes. The results obtained in this study provide important information for better understanding and future manipulation of rhizobia-associated biological nitrogen fixation.