Description of a Novel Species Quadrisphaera endophytica sp. nov., a Potential Strain as a Plant Growth Promotor and Comparative Genome Analysis of the Genus Quadrisphaera.

Quadrisphaera is a rare genus of the phylum Actinomycetota which is rarely studied for functional characteristics of its phenotype and genome. The endophytic actinobacterium, strain KR29T, was isolated from the surface-sterilized Jasmine rice leaf (Oryza sativa KDML 105). This strain was an aerobic actinobacterium that formed cocci cells with tetrad arrangements. The type strains that shared the highest 16S rRNA gene sequence similarity with strain KR29T were Quadrisphaera oryzae TBRC 8486T (99.6%), Quadrisphaera setariae NBRC 113770T (99.4%), and Quadrisphaera granulorum JCM 16010T (99.0%). Chemotaxonomic data confirmed the affiliation of strain KR29T to the genus Quadrisphaera. Strain KR29T contained MK-8(H2) as a major menaquinone; the whole-cell sugar of strain KR29T was galactose, glucose, and mannose. Strain KR29T exhibited the highest similarity values with Q. oryzae TBRC 8486T and Q. setariae NBRC 113770T, showing average nucleotide identity (ANI)-MUMmer (ANIm), average amino acid identity (AAI), and digital DNA-DNA hybidization (dDDH) values of 87.5%, 84.8%, and 28.5%, respectively. In comparison, its values with Q. granulorum JCM 16010T were 86.8% (ANIm), 81.5% (AAI), and 26.1% (dDDH). The polyphasic taxonomy confirmed that strain KR29T represents a novel species, and the name Quadrisphaera endophytica sp. nov. is proposed. The type strain is KR29T (= TBRC 17753T = NRRL B-65687T). Strain KR29T could produce a high amount of indole acetic acid and hydrolyze L-asparagine. Genome data mining of strain KR29T revealed that its genome contained genes encoding proteins relating to plant growth promotion, bioactive compounds, and beneficial enzymes, including L-asparaginase. The genomic insight into strain KR29T and the three type strains of genus Quadrisphaera was studied. The findings suggest that Quadrisphaera strains possess metabolic pathways relating to useful plant bioactive compound production, such as brassinosteroid, diterpenoid, and isoquinoline alkaloid biosynthesis and xenobiotic biodegradation, and 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation.