Genomic and phenotypic characterization of phosphate-solubilizing strain YNK-FB0058, which potentially represents a novel species within the genus Phyllobacterium

Abstract

Phosphate-solubilizing bacteria are soil-dwelling probiotics that promote plant growth and convert unavailable phosphorus into absorbable forms for plants. A phosphate-solubilizing strain, YNK-FB0058, which potentially represents a novel species within the genus Phyllobacterium , was isolated from the rhizosphere of safflower in a tobacco–safflower rotation field. Whole-genome sequencing and in vitro verification tests were conducted to explore its genetic basis and functional traits. Phylogenetic analysis based on the 16 S rRNA gene, together with comprehensive ANIm and dDDH comparisons against the available Phyllobacterium type-strain genomes and genome-scale taxonomic analysis using TYGS, suggested that strain YNK-FB0058 may represent a novel species within the genus Phyllobacterium . Its draft genome assembly size is 4,694,147 bp with a GC content of 61.14%, and a total of 4,459 CDSs were annotated. The genome harbors gene clusters involved in inorganic phosphorus solubilization, organic phosphorus mineralization, phosphorus transport and regulation. It also carries growth-promoting genes related to indole-3-acetic acid (IAA) synthesis, nitrogen-related functions, a putative nonribosomal peptide metallophore/nonribosomal peptide synthetase biosynthetic gene cluster, iron acquisition and homeostasis, and zinc solubilization. The strain exhibited high efficiency in solubilizing organic and inorganic phosphorus, with solubilization capacities of 566.3 mg/L − 1 and 474.46 mg/L − 1 , respectively, and showed a maximum IAA-equivalent concentration of 19.319 µg/mL. It also grew under the tested nitrogen-free-medium conditions, exhibited zinc-solubilizing activity, and showed CAS-detectable siderophore production. Inoculation with this strain significantly increased plant height, stem diameter, leaf area and biomass of flue-cured tobacco, elevated nitrogen and phosphorus contents and enzyme activities in rhizosphere soil, and promoted phosphorus accumulation in tobacco plants. Strain YNK-FB0058 may represent a novel species within the genus Phyllobacterium and exhibits efficient phosphate-solubilizing activity and multiple plant growth-promoting traits. This strain provides a high-quality microbial resource and theoretical basis for reducing chemical phosphorus fertilizer application and developing high-efficiency microbial inoculants in green agriculture.