Genome mining revealed polyhydroxybutyrate biosynthesis by Ramlibacter agri sp. nov., isolated from agriculture soil in Korea

A white-colony-forming, facultative anaerobic, motile and Gram-stain-negative bacterium, designated G-1-2-2 T was isolated from soil of agriculture field near Kyonggi University, Republic of Korea. Strain G-1-2-2 T synthesized the polyhydroxybutyrate and could grow at 10–35 °C. The phylogenetic analysis based on 16S rRNA gene sequence showed that, strain G-1-2-2 T formed a lineage within the family Comamonadaceae and clustered as a member of the genus Ramlibacter. The 16S rRNA gene sequence of strain G-1-2-2 T showed high sequence similarities with Ramlibacter ginsenosidimutans BXN5-27 T (97.9%), Ramlibacter monticola G-3-2 T (97.9%) and Ramlibacter alkalitolerans CJ661T (97.5%). The sole respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, and an unidentified phospholipid. The principal cellular fatty acids were C16:0, cyclo-C17:0, summed feature 3 (C16:1ω7c and/or C16:1ω6c) and summed feature 8 (C18:1ω7c and/or C18:1ω6c). The genome of strain G-1-2-2 T was 7,200,642 bp long with 13 contigs, 6,647 protein-coding genes, and DNA G + C content of 68.9%. The average nucleotide identity and in silico DNA–DNA hybridization values between strain G-1-2-2 T and close members were ≤ 81.2 and 24.1%, respectively. The genome of strain G-1-2-2 T showed eight putative biosynthetic gene clusters responsible for various secondary metabolites. Genome mining revealed the presence of atoB, atoB2, phaS, phbB, phbC, and bhbD genes in the genome which are responsible for polyhydroxybutyrate biosynthesis. Based on these data, strain G-1-2-2 T represents a novel species in the genus Ramlibacter, for which the name Ramlibacter agri sp. nov. is proposed. The type strain is G-1-2-2 T (= KACC 21616 T = NBRC 114389 T).