Genome-based analyses of the genus Frateuria: proposal of the two novel genera Parafrateuria gen. nov., Pseudofrateuria gen. nov., and the identification of Pseudofrateuria alba sp. nov., Pseudofrateuria humi sp. nov., and Pseudofrateuria lycopersici sp. nov. from tomato rhizosphere soil.

Abstract

Four aerobic, Gram-stain-negative, straight rod-shaped bacterial strains designated GZRe12ᵀ, GZRe14, GZRR33ᵀ and GZRR35ᵀ were isolated from tomato rhizosphere soil and characterised by polyphasic taxonomy. 16S rRNA gene analysis affiliated these isolates with the family Rhodanobacteraceae and the polyphyletic genus Frateuria. Phylogenomic reconstruction and genome-wide relatedness indices including ANI, dDDH and AAI supported the establishment of two novel genera Parafrateuria gen. nov. and Pseudofrateuria gen. nov., with Frateuria defendens transferred to Parafrateuria defendens comb. nov. Chemotaxonomic traits, including ubiquinone Q-8, polar lipid compositions and fatty acid profiles, together with genomic features (3.52-3.78 Mbp genome size, 67.7-68.5% G+C content) distinguished these strains as three novel species within Pseudofrateuria. The names Pseudofrateuria alba sp. nov. (GZRe12ᵀ = GDMCC 1.4121ᵀ = JCM 36337ᵀ), Pseudofrateuria humi sp. nov. (GZRR33ᵀ = GDMCC 1.4118ᵀ = JCM 36339ᵀ) and Pseudofrateuria lycopersici sp. nov. (GZRR35ᵀ = GDMCC 1.4119ᵀ = JCM 36340ᵀ) are proposed. Functional assays confirmed their capacities for indole-3-acetic acid and siderophore production, and strains GZRe12ᵀ and GZRe14 exhibited significant phosphate-solubilizing potential. Six previously published species originally classified within Frateuria and Fulvimonas were formally transferred to the genus Pseudofrateuria. This study resolves the polyphyletic taxonomic confusion of the traditional genus Frateuria and provides novel insights into the diversified ecological functions and plant-growth-promoting potential of rhizosphere colonising bacteria in the family Rhodanobacteraceae.