Curtobacterium allii sp. nov., the actinobacterial pathogen causing onion bulb rot

Abstract

A Gram-stain-positive, aerobic, and non-spore-forming bacterial strain, 20TX0166^T, was isolated from a diseased onion bulb in Texas, USA. Upon testing its pathogenicity on onion bulb, it produced pathogenic response which makes it first species of pathogen belonging to the phylum actinobacteria detected in onion. Phylogenetic analysis of the 16S rRNA gene sequence revealed that the strain belonged to the genus Curtobacterium and was most similar to Curtobacterium flaccumfaciens LMG 3645^T (100%), C. pusillum DSM 20527^T (99.5%), and C. oceanosedimentum ATCC 31317^T (99.5%). The estimated genome size of the novel species was 4.0 Mbp with a G + C content of 70.8%. The orthologous ANI (orthoANIu), ANI based on blast (ANIb), and dDDH values between the novel strain and the closest relative, C. flaccumfaciens LMG 3645^T, were 95.7%, 95.4%, and 63.3%, respectively. These values were below the recommended species cut-off threshold of 96% (ANI) and 70% (dDDH), suggesting the strain may be a novel species. Physiologic and phenotypic characters of this novel strain were also unique when compared with the closely related species. The major cellular fatty acids of this strain were anteiso-C_15:0 and anteiso-C_17:0. Using a polyphasic approach based on phenotypic and genotypic analyses, strain 20TX0166^T represents a novel species of the genus Curtobacterium, and the name Curtobacterium allii sp. nov. is proposed. The type strain is 20TX0166^T (= LMG 32517^T = CIP112023^T = NCIMB 15427^T).