Description of Neorhizobium tunisiense sp. nov., reclassification of Neorhizobium xiangyangii as Pseudorhizobium xiangyangii comb. nov. and proposal of Terrirhizobium terrae gen. nov., comb. nov. to accommodate the divergent species Aliirhizobium terrae.

Abstract

The taxonomic affiliations, genomic divergence and ecological potential of strains IRAMC 0178ᵀ and IRAMC 0179, isolated from nodules of Retama raetam growing in coastal northern Tunisia, were investigated using genome-scale phylogenomics, average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and protein metrics (average amino acid identity, percentage of conserved proteins and core-proteome average amino acid identity). Taxogenomic, ecogenomic and phenotypic analyses were used to classify strains IRAMC 0178ᵀ and IRAMC 0179 - each isolated from nodules of distinct R. raetam trees in northern Tunisia - and to revise the taxonomic status of Neorhizobium xiangyangii and Aliirhizobium terrae. Strain IRAMC 0178ᵀ (=HAMBI 3839=CGMCC 1.65424=DSM 119302^T) was placed in Neorhizobium, showing low genomic similarity to known species (dDDH <45% and ANI <93%) supporting its recognition as a novel genomic species. Its distinct phenotypic characteristics further justify the proposal of the new species Neorhizobium tunisiense sp. nov. Further genomic analyses revealed discrepancies in the current taxonomy, supporting the reclassification of N. xiangyangii as Pseudorhizobium xiangyangii comb. nov. and the transfer of A. terrae to the newly proposed genus Terrirhizobium terrae gen. nov., comb. nov. Several non-nodulating Neorhizobium strains, including IRAMC 0178ᵀ, either lacked or carried incomplete nod and nif gene sets, suggesting a loss of symbiotic capacity across these lineages. However, strains retained diverse plant growth-promoting traits and stress-adaptive functions. Notably, N. tunisiense sp. nov. exhibited genomic features indicative of a rhizosphere-associated lifestyle, such as osmoprotective systems, moderate growth rates and metabolic versatility. These results highlight the diverse evolutionary pathways within Rhizobiaceae, including both symbiotic and non-symbiotic lineages, and emphasize the overlooked genomic diversity with potential implications for sustainable agriculture.