The Impact of Domesication on Nitrogen Fixation in Chickpea: Parrallel Shifts in Bacterial Genome Structure and Host Selectivity

Legume crops are significant for their ability to host a diverse group of nitrogen-fixing bacterial symbionts, collectively called rhizobia. However, there is evidence to suggest that crop legumes form less-efficient symbioses than their wild relatives. This study attempts to examine differences in nitrogen fixation between wild and domesticated chickpea (Cicer spp.), by using whole-genome sequencing to characterize the population of chickpea’s rhizobial symbionts (Mesorhizobium spp.). 1,800 root nodules were collected from three species of chickpea (cultivated: C. arietinum, and two wild relatives: C. reticulatum and C. echinospermum) grown in a field in India. Metagenomic DNA sequences from 95 root nodules revealed two Mesorhizobium species to be present: M. mediterraneum (previously isolated from chickpea) and M. plurifarium (previously only isolated from native tropical legumes). The two species diverge based on core, housekeeping-gene phylogenies, but have phylogenetically identical symbiosis loci. This suggests that the observed M. plurifarium strains are adapted to tropical Indian soil, but obtained symbiosis genes from chickpea’s co-evolved symbiont (M. mediterraneum). M. plurifarium was observed to be more prevelant than M. mediterraneum in nodules from all three species. However, based on a PCR assay developed from metagenomic data, C. reticulatum nodules are more commonly occupied by M. mediterraneum than nodules of C. arietinum. This suggests that in exotic soils, chickpea’s wild progenitor preferentially selects its co-evolved symbiont over novel symbionts, relative to C. arietinum.