Comparative genomic analysis of diverse rhizobia and effective nitrogen-fixing clover-nodulating Rhizobium strains adapted to Egyptian dry ecosystems

Abstract

Rhizobium strains that nodulate Egyptian winter clover belong to two symbiotic species, Rhizobium aegyptiacum sv. trifolii and Rhizobium bangladeshense sv. trifolii. Rhizobia from Egyptian clover are often tolerant of extreme environmental conditions and are generally poorly characterized, despite the importance of this crop species. Here, we report on the comparative genomic analysis of four stress-tolerant, highly effective nitrogen-fixing, Egyptian-clover-nodulating rhizobia, R. aegyptiacum sv. trifolii strain Rhiz950 and Rhizobium bangladeshense sv. trifolii strains Rhiz1002, Rhiz1017 and Rhiz1024, as well as other diverse Rhizobium strains. While Rhizobium bangladeshense sv. trifolii strains Rhiz1002, Rhiz1017, and Rhiz1024 had similar genome sizes of around 6.6 Mb, the salt tolerant strain Rhiz950 had a slightly larger genome size of 7.4 Mb. All four strains lacked genes responsible for methylation and sulfation of nod factors (nodS and nodHPQ). They also lacked nodZ, and instead had the functionally-equivalent nod factor fucosylation gene nolK. No strains contained homocitrate synthase (encoded by nifV) that is essential for free-living nitrogen fixing by diazotrophs. A number of genes unique to the Egyptian clover strains and to other rhizobia are potential candidates for variation in stress tolerance and host-range.