Variovorax palleresanus sp. nov., a novel plant growth-promoting rhizobacterium isolated from sulphur-rich soil in Spain

During a screening of sulphur-oxidizing bacteria from different Spanish soils, a strain designated AFSI2.2^T was isolated from the rhizosphere soil of a mulberry plant thriving in a sulphur-rich environment. Cells of this strain were Gram-stain-negative motile rods with flagella. Its taxonomic classification was determined through a polyphasic approach. Phylogenetic analysis of the 16S rRNA gene revealed that strain AFSI2.2^T shares high similarity (99.64%) with certain <i>Variovorax</i> species, suggesting that the isolate belongs to this genus. Whole-genome phylogeny showed that the novel strain forms a distinct lineage within the genus <i>Variovorax</i>. Whole-genome analysis of AFSI2.2^T exhibited average nucleotide identity values of 78.37-89.63% and digital DNA-DNA hybridization values of 21.90-38.90% with closely related <i>Variovorax</i> species, both below the established thresholds for species delineation. The predominant cellular fatty acids of strain AFSI2.2^T were C_{16 : 0}, Summed Feature 3 (C_{16 : 1} <i> ω</i>6<i>c</i> and/or C_{16 : 1} <i> ω</i>7<i>c</i>) and Summed Feature 8 (C_{18 : 1} <i> ω</i>7<i>c</i> and/or C_{18 : 1} <i> ω</i>6<i>c</i>). Apart from the ability of oxidizing inorganic sulphur compounds, AFSI2.2^T presented further <i>in vitro</i> plant growth-promoting (PGP) activities such as production of indole-3-acetic acid and siderophores and 1-aminocyclopropane-1-carboxylate deaminase activity. Genes associated with these PGP traits, as well as with cytokinin and gamma-aminobutyric acid biosynthesis, were identified in the AFSI2.2^T genome, supporting its potential as a PGP bacterium. In conclusion, phylogenetic, genomic, phenotypic and chemotaxonomic analyses support the classification of the isolate as a novel species within the genus <i>Variovorax</i>, for which the name <i>Variovorax palleresanus</i> sp. nov. is proposed. The type strain is AFSI2.2^T (=CECT 31217^T=CIP 112526^T).