Rhizobium zaerense sp. nov., a novel member of the Rhizobium leguminosarum species complex with a broad geographic distribution and multiple legume hosts.

Abstract

A novel nitrogen-fixing rhizobial strain, designated Z1P35ᵀ, was isolated from root nodules of Pisum sativum grown in the Zaër region of Morocco. Phylogenetic analysis of the 16S rRNA gene placed strain Z1P35ᵀ within the genus Rhizobium, showing 100% sequence identity with several undescribed genospecies of the Rhizobium leguminosarum species complex (Rlc). Strain Z1P35ᵀ exhibited low average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values with all described Rhizobium species, but high ANI and dDDH values (97.62 and 78.8%, respectively) with Rhizobium sp. SRDI565, representing genospecies M (GsM) of the Rlc, suggesting that Z1P35ᵀ represents a novel species corresponding to GsM within this complex. FastANI screening against all Rhizobium genomes available in GenBank revealed that Z1P35ᵀ shares ANI values above the bacterial species delimitation threshold with 17 unclassified strains, which, together with Z1P35ᵀ and Rhizobium sp. SRDI565 (GsM), form a distinct lineage within the Rlc. These 17 strains originate from root nodules of diverse legume hosts and are distributed across the Mediterranean region and Australia, including representatives of the symbiovars viciae and trifolii. Phylogenomic analysis further confirms the clustering of Z1P35ᵀ with Rhizobium sp. SRDI565 (GsM) and several undescribed Rhizobium strains, forming a unique taxonomic unit clearly distinct from other members of the Rlc. Strain Z1P35ᵀ has a genome of 7.6 Mb with a G+C content of 61 mol% and carries numerous genes associated with chemotaxis, nodulation, nitrogen fixation, phosphate solubilization, iron acquisition and abiotic stress tolerance. Differentiation of Z1P35ᵀ from described Rhizobium species was further supported by phenotypic and chemotaxonomic analyses. Based on these results, we conclude that Z1P35T belongs to a novel species, corresponding to genospecies M within the Rlc, for which we propose the name Rhizobium zaerense sp. nov. The type strain is Z1P35ᵀ (DSM 120601ᵀ=CCMM B1365ᵀ).