Pseudomonas retamae sp. nov., a novel endophytic bacterium with plant growth-promoting potential, isolated from root nodules of Retama monosperma in Northwestern Algeria.

Abstract

A thorough polyphasic taxonomic study, integrating genome-based taxonomic approaches, was carried out to characterize the RB5^T strain isolated from root nodules of Retama monosperma growing on the coastal dunes of Bousfer Beach (Oran, Algeria). The 16S rRNA gene sequence analysis revealed that strain RB5^T had the highest similarity to Pseudomonas granadensis LMG27940^T (98.94%) and Pseudomonas gozinkensis IzPS32d^T (98.73%). Phylogenetic studies, including both 16S rRNA gene sequence and multilocus sequence analysis using 16S rRNA, gyrB and rpoD housekeeping genes, positioned RB5^T in a distinct branch alongside its closest relative, P. granadensis LMG27940^T. Phylogenomic analysis using the Bac120 marker set and Type (Strain) Genome Server confirmed the unique position of RB5^T and its close relationship with P. granadensis LMG27940^T. Similarly, genomic comparisons using average nucleotide identity based on blast (ANIb) and digital DNA-DNA hybridization (dDDH) revealed values of 92.85 and 59.3%, respectively, when compared with its closest relative, P. granadensis LMG27940^T. Both values fall below the established species delimitation thresholds of 95-96% for ANIb and 70% for dDDH, providing strong genomic evidence that strain RB5^T represents a novel species. Further average nucleotide identity comparisons with unclassified Pseudomonas spp. (384 genomes) and metagenomic-derived genomes from the Genome Taxonomy Database (GTDB) showed values between 84.27 and 89.2%, indicating that strain RB5^T belongs to a unique evolutionary line. The genome of RB5^T, with a size of 6 311 310 bp and a G+C content of 60%, harbours several key genes associated with plant growth-promoting traits, making it a promising candidate for sustainable agriculture. Phenotypically, RB5^T strain is an aerobic, rod-shaped, Gram-negative, non-spore-forming bacterium that is motile with a single polar flagellum. It grows under a wide range of temperature (4-42 °C) and pH (5-10) conditions and tolerates up to 6% (w/v) NaCl. The main cellular fatty acid composition of RB5^T includes C_16:0, C_17:0 cyclo and the summed features 3 consisting of C_16:1 ω7c/_C16:1 ω6c. Based on the phylogenetic, phenotypic, chemotaxonomic and genome comparison analyses, strain RB5^T was identified as a novel species of the genus Pseudomonas, for which the name Pseudomonas retamae sp. nov. is proposed. The type strain is RB5^T (=DSM 117471^T=LMG 33633^T=CIP 112482^T).