Sphingobium salicis sp. nov., is a plant endophyte isolated from pioneer species of willow, poplar, and salvia growing on primary rock substrate

Three Gram-negative Sphingobium endophyte strains, designated WW5^T, 11R-BB, and HT1-2, were isolated from stems of Salix sitchensis, roots of Populus trichocarpa, and shoots of Pluchea carolinensis, respectively, growing on nutrient limited rock substrate undergoing primary succession. Phylogenetic analysis based on 16S rRNA gene sequences placed all three strains within the genus Sphingobium, with highest sequence identity to S. yanoikuyae JCM 7371^T. Digital DNA-DNA hybridization analysis revealed values of 66.2-68.2% to S. yanoikuyae JCM 7371^T, falling below the 70% species delineation threshold, while 99.9% identity between WW5^T and 11R-BB and 70.1% between WW5^T and HT1-2 confirmed their assignment to a single species. Average WGS nucleotide identity values to S. yanoikuyae JCM 7371^T were 95.68% (WW5^T), 95.56% (11R-BB), and 96.65% (HT1-2), while phylogenomic WGS analysis using GTDB-Tk classified the strains as distinct from the S. yanoikuyae lineage, placing them under the placeholder Sphingobium yanoikuyae_A. Hybrid Illumina-Nanopore genome sequencing generated high-quality assemblies of 5.39-5.72 Mb with approximately 64% GC content. Comparative genomic analysis revealed 96 gene families conserved across all three strains but absent from other Sphingobium genomes, with 80 classified as highly conserved hypothetical proteins and 16 functionally annotated genes including arylsulfatases, heavy metal efflux systems, and ion transporters that may support their plant-associated niche. Chemotaxonomic analysis demonstrated predominant fatty acids distinguishing them from S. yanoikuyae JCM 7371^T, while physiological tests showed the strains metabolized plant-derived carbon compounds not utilized by S. yanoikuyae JCM 7371^T. Based on phylogenomic, genomic, and phenotypic analyses, these strains represent a novel species, for which the name Sphingobium salicis sp. nov. was proposed, with WW5^T (DSM 120182, NCCB 101075) designated as the type strain.