Peteryoungia gen. nov. with four new species combinations and description of Peteryoungia desertarenae sp. nov., and taxonomic revision of the genus Ciceribacter based on phylogenomics of Rhizobiaceae

Abstract

A novel bacterial strain designated as ADMK78^T was isolated from the saline desert soil. The cells were rod-shaped, Gram-stain-negative, and non-motile. The strain ADMK78^T grows best at 28 °C. Phylogeny of 16S rRNA gene placed the strain ADMK78^T with the members of genera Ciceribacter and Rhizobium, while the highest sequence similarity was with Rhizobium wuzhouense W44^T (98.7%) and Rhizobium ipomoeae shin9-1 ^T (97.9%). Phylogenetic analysis based on 92 core-genes extracted from the genome sequences and average amino acid identity (AAI) revealed that the strain ADMK78^T forms a distinct cluster including five species of Rhizobium, which is separate from the cluster of the genera Rhizobium and Ciceribacter. We propose re-classification of Rhizobium ipomoeae, R. wuzhouense, R. rosettiformans and R. rhizophilum into the novel genus Peteryoungia. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of ADMK78^T were less than 82 and 81%, respectively, among all type strains included in the genus Peteryoungia. The strain ADMK78^T showed differences in physiological, phenotypic, and protein profiles estimated by MALDI-TOF MS to its closest relatives. Based on the phenotypic, chemotaxonomic properties, and phylogenetic analyses, the strain ADMK78^T represents a novel species, Peteryoungia desertarenae sp. nov. The type strain is ADMK78^T (= MCC 3400^T; KACC 21383^T; JCM 33657^T). We also proposed the reclassification of Rhizobium daejeonense, R. naphthalenivorans and R. selenitireducens, into the genus Ciceribacter, based on core gene phylogeny and AAI values.

Keywords: MALDI-TOF MS biotyping; Phylogenomics; Polyphasic taxonomy; Saline Desert.