Genomic and physiological characterization of Kitasatospora sp. nov., an actinobacterium with potential for biotechnological application isolated from Cerrado soil

Abstract

An Actinobacteria - Kitasatospora sp. K002 - was isolated from the soil of Cerrado, a savanna-like Brazilian biome. Herein, we conducted a phylogenetic, phenotypic and physiological characterization, revealing its potential for biotechnological applications. Kitasatospora sp. K002 is an aerobic, non-motile, Gram-positive bacteria that forms grayish-white mycelium on solid cultures and submerged spores with vegetative mycelia on liquid cultures. The strain showed antibacterial activity against Bacillus subtilis, Pseudomonas aeruginosa and Escherichia coli. Genomic analysis indicated that Kitasatospora xanthocidica JCM 4862 is the closest strain to K002, with a dDDH of 32.8-37.8% and an ANI of 86.86% and the pangenome investigations identified a high number of rare genes. A total of 60 gene clusters of 22 different types were detected by AntiSMASH, and 22 gene clusters showed low similarity (< 10%) with known compounds, which suggests the potential production of novel bioactive compounds. In addition, phylogenetic analysis and morphophysiological characterization clearly distinguished Kitasatospora sp. K002 from other related species. Therefore, we propose that Kitasatospora sp. K002 should be recognized as a new species of the genus Kitasatospora - Kitasatospora brasiliensis sp. nov. (type strains = K002).

Keywords: Bacterial phylogenomic; Cerrado; Natural products; Soil.

Fig. 1

Phylogenetic tree based on the partial sequence of the 16 S rRNA of Kitasatospora K002. The evolutionary position of the strain was estimated after constructing a phylogenetic tree using the Maximum-likelihood (ML) method with 1000 repetitions of sampling (Bootstrap), using representative 16 S rRNA sequences from valid strains of the genus listed in the List of Prokaryotic names with Standing in Nomenclature - LPSN

Fig. 2

Circular map of the hybrid genome assembly of the Kitasatospora K002 showing the coding regions and the GG content. Outside to center: forward CDS (dark blue), reverse CDS (red), GC content and GC slope (dark gray andlight gray)

Fig. 3

Circular visualization of the genome alignment between Kitasatospora K002 (in gray) and its closest strain according to TYGS-DSMZ, K. xanthocidica JCM 4862 (in blue). Genome alignment blocks with at least 1000 nucleotides and 90% identity are shown. The outer band is the size scale of the contigs

Fig. 4

Maximum likelihood phylogenetic tree based on concatenated 520 major orthologous genes from genomic sequences of 12 Kitasatospora strains, including Kitasatospora K002, the closely related strains according to the TYGS-DSMZ, and Streptomyces violaceorubidus as the outgroup

Fig. 5

Comparative pangenome analysis performed at Roary. The genome of Kitasatospora K002 and the 10 genomes closest to it, according to TYGS-DSMZ, were used. A minimum percentage identity for BLASTp of 80% was defined to group genes encoding complete protein sequences into core genomes. Distribution of genes in genomes: Core genes (genes present in 99–100% of genomes), Shell genes (genes present in 15–95% of genomes) and Cloud genes (genes present in 0–15% of genomes) (A). Venn diagram demonstrating the number of genes in common between Kitasatospora sp. K002 and its closest strain K. xanthocidica JCM 4862 (B). Maximum likelihood phylogenetic tree based on the presence and absence of genes from the pangenome. The blue bar indicates the pangenome, each line corresponds to a strain and each column corresponds to the variation in the genes. The presence of genes is shown in decreasing frequency. Empty space indicates the absence of genes (C). The tree was generated from Roary’s output files and the Phandango interactive viewer

Fig. 6

Predicted proteins of Kitasatospora K002 genome as classified according to COG categories. Classification was performed using the eggNOG mapper against the Kyoto Encyclopedia of Genes and Genomes (KEGG) database

Fig. 7

Comparison between phenotypic predictions of the hybrid genome assembly of Kitasatospora K002 and its closest strains according to the TYGS-DSMZ obtained from the NCBI database. Zero value stands for a negative phenotype, whereas values 1 and 2 correspond to the positive in the phypat and phypat + PGL predictors, respectively. Value 3 indicated that the phenotype was positive in both predictions

Fig. 8

Scanning (A and B) and transmission (C and D) electron micrographs of the Kitasatospora sp. K002 showing its vegetative mycelia (elongated shape) and submerged spores (rounded shape)