Background: Rahnella perminowiae S11P1 and Variovorax sp. S12S4 are two plant growth-promoting rhizobacteria that were previously isolated from the rhizosphere of Crocus sativus L. (saffron), and have demonstrated interesting PGP activities and promising results when used as inoculants in field trials. To further elucidate the molecular mechanisms underlying their beneficial effects on plant growth, comprehensive genome mining of S11P1 and S12S4 and comparative genomic analysis with closely related strains were conducted. Results: Functional annotation of the two strains predicted a large number of genes involved in auxin and siderophore production, nitrogen fixation, sulfur metabolism, organic acid biosynthesis, pyrroloquinoline quinone production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, volatile organic compounds production, and polyamine biosynthesis. In addition, numerous genes implicated in plant-bacteria interactions, such as those involved in chemotaxis and quorum sensing, were predicted. Moreover, the two strains carried genes involved in bacterial fitness under abiotic stress conditions. Comparative genomic analysis revealed an open pan-genomic structure for the two strains. COG annotation showed that higher fractions of core and accessory genes were involved in the metabolism and transport of carbohydrates and amino acids, suggesting the metabolic versatility of the two strains as effective rhizosphere colonizers. Furthermore, this study reports the first comparison of Multilocus sequence analysis (MLSA) and core-based phylogenies of the Rahnella and Variovorax genera. Conclusions: The present study unveils the molecular mechanisms underlying plant growth promotion and biocontrol activity of S11P1 and S12S4, and provides a basis for their further biotechnological application in agriculture.

Three slow-growing rhizobial strains, designated as 1AS2L^T, 1AS20L and 1AS5L, were isolated from nodules of Acacia saligna in Borj Cedria, northern Tunisia. These strains, which belong to the symbiovar cyanophyllae, were characterized using a polyphasic approach. Phylogenetic analysis of the 16S rRNA (rrs) gene placed these strains within the genus Bradyrhizobium, specifically in the superclade associated with Bradyrhizobium japonicum. Further phylogenetic analysis using concatenated sequences of the recA, atpD, glnII and gyrB genes (totalling 1,734 bp) positioned the strains in a distinct lineage, with Bradyrhizobium shewense identified as their closest related species, sharing a sequence identity of 95.2%. The type strain, 1AS2L^T, exhibited average nucleotide identity values of 89.10%, 89.08% and 89.00% with the type strains of the closest valid species: Bradyrhizobium frederickii, B. shewense and Bradyrhizobium ottawaense, respectively. Additionally, digital DNA–DNA hybridization values confirmed the novelty of strain 1AS2L^T, showing low similarity (38.0%–38.3%) with the type strains of the closest known species. Phylogenomic analyses based on up-to-date bacterial core genes, Type (Strain) Genome Server and the Genome Taxonomy Database (GTDB) pipelines further supported the uniqueness of the 1AS2L^T, 1AS20L and 1AS5L strains. The GTDB analysis also robustly clustered two strains (SZCCT0449 and NSD-1) with our strains, suggesting putative members of the proposed novel species. The differentiation of these novel strains from their closest phylogenetic neighbours was also corroborated by phenotypic, physiological and fatty acid content analyses. Based on genomic, phenotypic and biochemical data, we propose the establishment of a novel species, Bradyrhizobium tunisiense sp. nov., with strain 1AS2L^T (=LMG 33170^T=DSM 114401^T) as the type strain.

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 ( rec A, atp D, gln II and gyr B: 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.

Deserts are among the most hostile terrestrial ecosystems, where all life forms face harsh environmental constraints. Indigenous desert bacteria have developed special survival mechanisms, making them valuable resources for uncovering interesting biotechnological traits. This study investigates the genetic basis of environmental adaptation and biotechnological potential in Enterobacter xiangfangensis MDMC82 isolated from the Merzouga desert in Morocco. Genomic analysis predicted a robust apparatus involved in heat/cold shock response, drought and salinity tolerance, carbon storage/starvation response, polyamine metabolism, DNA repair, biofilm formation, motility, heavy metal resistance, aromatic compound degradation, and a variety of industrial enzymes, reflecting remarkable genome plasticity. Pan-genome analysis and COG classification highlighted pronounced metabolic and transcriptional versatility among environmental E. xiangfangensis isolates. Their core-based phylogenetic patterns in relation to their ecological niches were also discussed. Homologous gene analysis revealed a conserved repertoire of environmental adaptation genes across different taxonomic levels of the Enterobacteriaceae family, suggesting shared ecological strategies. To our knowledge, this is the first genomic analysis of an E. xiangfangensis isolate from desert environment. The study provides favorable support for its further exploration for environmental and industrial purposes, and sheds light on the genomic basis of putative core functions across higher taxonomic levels within the Enterobacteriaceae family.

We report the draft genome sequences of plant growth-promoting Rahnella perminowiae strain S11P1, Variovorax sp. strain S12S4, and Pseudomonas sp. strains S11A4 and S11P7, which were isolated from saffron ( Crocus sativus L.) rhizosphere. Several genes were predicted to be involved in auxin production, phosphate solubilization, and other specialized functions in plant growth and defense.

This study investigates nitrogen-fixing rhizobia associated with Pisum sativum, a member of the tribe Vicieae (Fabaceae), whose species establish symbioses with bacteria belonging predominantly to the symbiovar viciae within the Rhizobium leguminosarum complex (Rlc). Based on a comprehensive taxonomic revision of the F-clade within this complex, we report the identification and characterization of a novel rhizobial subspecies, Rhizobium laguerreae subsp. mediterraneum subsp. nov., isolated from pea nodules in Tunisia. Phylogenetic analyses based on 16S rRNA and multilocus sequence analysis (recA, atpD, dnaK, and glnII) placed strains 25PS6 and 10PS4 within the Rlc, while whole-genome phylogenomics using 2960 single-copy orthologues supported their assignment to a distinct monophyletic clade (Q-II). Subspecies-level clustering consistency was maximized using an optimized ANIm criterion of 97.40%, corresponding to 76.65% dDDH. Both strains belong to symbiovar viciae and exhibited improved symbiotic performance on pea plants compared to the reference strain, indicating strong symbiotic performance and potential relevance for biological nitrogen fixation. Cluster-specific SNP analysis identified 63 exclusive non-synonymous mutations with putative functional effects predicted in silico. These results suggest that cluster-specific nsSNPs may contribute to genomic differentiation within the Q-II lineage. Phenotypic and chemotaxonomic analyses further distinguished the novel subspecies based on carbon utilization, enzymatic activity, antibiotic resistance, and fatty acid profiles. Together, these findings highlight the genomic diversity within nitrogen-fixing rhizobia associated with legumes and identify a novel subspecies with potential agronomic relevance for improving symbiotic nitrogen fixation in pea cultivation. The proposed subspecies, Rhizobium laguerreae subsp. mediterraneum, is represented by strains 10PS4 and 25PS6, with strain 25PS6^T (=DSM 116212^T = LMG 33205^T) designated as the type strain.