Genome insight and description of antibiotic producing Massilia antibiotica sp. nov., isolated from oil-contaminated soil

Abstract

Abstract An ivory-coloured, motile, Gram-stain-negative bacterium, designated TW-1 T was isolated from oil-contaminated experimental soil in Kyonggi University. The phylogenetic analysis based on 16S rRNA gene sequence revealed, strain TW-1 T formed a lineage within the family Oxalobacteraceae and clustered as members of the genus Massilia . The closest members were M. pinisoli T33 T (98.8% sequence similarity), M. putida 6NM-7 T (98.6%), M. arvi THG-RS2O T (98.5%), M. phosphatilytica 12-OD1 T (98.3%) and M. niastensis 5516S-1 T (98.2%). The sole respiratory quinone is ubiquinone-8. The major cellular fatty acids are hexadeconic acid, cis -9, methylenehexadeconic acid, summed feature 3 and summed feature 8. The major polar lipids are phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The DNA G + C content of the type strain is 66.3%. The average nucleotide identity (ANI) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain TW-1 T and closest members were below the threshold value for species demarcation. The genome size is 7,051,197 bp along with 46 contigs and 5,977 protein-coding genes. The genome showed 5 putative biosynthetic gene clusters (BGCs) that are responsible for different secondary metabolites. Cluster 2 showed thiopeptide BGC with no known cluster blast, indicating TW-1 T might produce novel antimicrobial agent. The antimicrobial assessment also showed that strain TW-1 T possessed inhibitory activity against Gram-negative pathogens ( Escherichia coli and Pseudomonas aeruginosa ). This is the first report of the species in the genus Massilia which produces antimicrobial compounds. Based on the polyphasic study, strain TW-1 T represents novel species in the genus Massilia , for which the name Massilia antibiotica sp. nov. is proposed. The type strain is TW-1 T (= KACC 21627 T = NBRC 114363 T ).

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