Bradyrhizobium cedriense sp. nov., a novel rhizobial species isolated from Acacia saligna nodules grown in polluted soils in Tunisia

Abstract

Acacia saligna, a leguminous plant known for its ability to thrive under challenging environmental conditions, plays an important role in bioremediation by enhancing soil fertility and facilitating pollutant degradation. In this study, three slow-growing rhizobial strains, designated 1.29L, 1.27L and 5.13L, were isolated from root nodules of A. saligna growing naturally in two contaminated sites in Tunisia. A polyphasic taxonomic approach was applied. Phylogenetic analysis based on the 16S rRNA gene placed the isolates within the genus Bradyrhizobium, clustering within the Bradyrhizobium japonicum superclade. Multilocus sequence analysis using concatenated housekeeping genes (recA, atpD, glnII and gyrB: 1,734 bp) positioned the strains as a distinct lineage, with Bradyrhizobium arachidis, Bradyrhizobium stylosanthis and Bradyrhizobium shewense as the closest relatives, sharing 94.5–94.8% sequence identity. Comparative genomic analyses further supported their taxonomic distinctiveness. The proposed type strain, 1.29Lᵀ, exhibited average nucleotide identity (ANI) values of 90.6%, 90.1% and 89.1% with Bradyrhizobium liaoningense, Bradyrhizobium diversitatis and Bradyrhizobium forestalis, respectively, and digital DNA–DNA hybridization (dDDH) values ranging from 34.4 to 42.5%. In contrast, strains 1.29LT, 1.27L and 5.13L shared >99.9% ANI and 100% dDDH, confirming their conspecificity. Phylogenomic analyses conducted using the Type Strain Genome Server and GTDB-Tk pipelines further confirmed their placement within the B. japonicum supergroup while clearly separating them from all described species. Phenotypically, the isolates tolerated high concentrations of heavy metals and were capable of producing indole-3-acetic acid, solubilizing phosphate and producing siderophores. Based on the combined genomic, phylogenetic and phenotypic evidence, these strains represent a novel species, for which the name Bradyrhizobium cedriense sp. nov. is proposed, with strain 1.29LT (=LMG 33169T=DSM 116455T) designated as the type strain.