Characterization and genome sequence of chitinase-producing Chitiniphilus shinanonensis

Abstract

Chitinolytic bacteria play a crucial role in the degradation of chitin and have been widely applied for green crop production. In this work, 4 chitinase-producing strains were isolated from chitin flakes placed in the water of Suoi Hong Lake, Yok Don National Park, Vietnam, and identified as Chitiniphilus shinanonensis by 16S rDNA phylogeny. Experimental characterization demonstrated that all strains produced cellulases, amylases, biofilms, siderophores, IAA, GA3, and zeatin, and solubilized inorganic phosphate and potassium sources. The genome sequence of the most potent bacterium, C. shinanonensis YWS-5.2, contained 4302709 bp with 66.3 % GC content, 3874 coding sequences, 60 tRNAs, and 3 rRNAs. It displayed 98.45 % ANI and 86.5 % dDDH to those of the C. shinanonensis NBRC 104970 genome. Of the coding sequences, KEGG assigned 2058, and COG clarified 3249. The genome possessed 29 sequences concerning plant growth promotion and 122 carbohydrate-active enzymes. The chitinolytic system of the strain contained 28 enzymes, among them, 9 was not present in the reported C. shinanonensis. Furthermore, it harbored 9 BGCs responsible for antibiotic metabolites, with 2 being novel clusters. These results implied that 4 chitinolytic bacteria have great potential as plant growth promoters, and strain YWS-5.2 is a promising candidate as a novel chitinase and antibiotic producer. This is the first report demonstrating plant growth-promoting traits and BGCs of C. shinanonensis.