Taxonomic and genomic characterization of a siderophore-producing bacterium, Rhodoligotrophos ferricapiens sp. nov isolated from lettuce cultivation soil

Abstract

A Gram-stain-negative, aerobic, non-spore-forming, non-motile, coccus-shaped, and red-pigmented bacterial strain designated as CJ14^T was isolated from lettuce cultivation soil in Yong-In, South Korea. Strain CJ14^T grew optimally on Luria–Bertani agar at 37 ℃ and pH 7.0 in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CJ14^T belonged to the genus Rhodoligotrophos in the family Rhodoligotrophaceae and was closely related to Rhodoligotrophos defluvii lm1^T (98.4% similarity). The genome size of strain CJ14^T was 4.8 Mbp consisting of a single contig, and the DNA G + C content of strain CJ14^T was 61.8%. The genomic comparison of strain CJ14^T to R. defluvii lm1^T showed an average nucleotide identity value of 77.9%, and the digital DNA–DNA hybridization value was 22.4%. Genomic analyses revealed that strain CJ14^T possessed a gene cluster for ochrobactin biosynthesis, highly homologous to the siderophore gene cluster from Nitratireductor thuwali Nit1536^T. Strain CJ14^T contained ubiquinone (Q-10) as the predominant respiratory quinone. The major cellular fatty acids of strain CJ14^T were C_16:0, C_19:0 cyclo ω8c and summed feature 8. The polar lipid profile was composed of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, one unidentified aminolipid, one unidentified glycolipid and five unidentified lipids. Based on polyphasic taxonomy study, strain CJ14^T could be classified as a novel species of the genus Rhodoligotrophos, for which the name Rhodoligotrophos ferricapiens sp. nov. is proposed. The type strain is CJ14^T (= KACC 23063^T = JCM 36057^T).