Strain-specific early, host-shaped late: the rhizobial transcriptome across symbiosis

The two ends of the rhizobial symbiotic trajectory have only been described separately. Here we report strand-specific RNA-seq of bacteroids of two strains, each against free-living cells of the same strain and alongside its flavonoid response: Sinorhizobium fredii HH103 from soybean (Glycine max), Glycyrrhiza uralensis and Lotus burttii, and Rhizobium tropici CIAT 899 from common bean (Phaseolus vulgaris) and L. burttii, the one legume both strains nodulate. Between 1877 and 2284 genes respond per strain-host combination, and most of that response is host-common: 1171 of 2855 genes respond in all three hosts of HH103 and 1664 of 2703 in both hosts of CIAT 899. What distinguishes the remainder is host identity rather than nodule type, since HH103 bacteroids from the indeterminate-nodule G. uralensis resemble those from L. burttii more than either resembles those from soybean, its natural host. Nitrogen fixation and the stress response are over-represented in every bacteroid and motility is almost entirely repressed, yet the shared core of CIAT 899 is the only repression-dominated gene set here and its translational machinery is induced where that of HH103 is repressed. Dismantling of the early programme is selective: in HH103 the type III apparatus is switched off, the Nod factor operons are attenuated but retained, and the fixABCX operon under a nod box is amplified, so a nod box does not by itself mark a gene as early. CIAT 899, lacking a type III system and placing no nif/fix gene under flavonoid control, keeps that block flat until the nodule, then engages 26 of its 30 genes. Across genera, 26% of responding orthologue pairs are shared in the bacteroid against 5% in the flavonoid response: each bacterium negotiates entry in a dialect of its own and converges on a shared end state whose amplitude, rather than content, the host modulates.