Description of Streptomyces naphthomycinicus sp. nov., an endophytic actinobacterium producing naphthomycin A and its genome insight for discovering bioactive compounds

Abstract

Endophytic actinobacteria are a group of bacteria living inside plant tissue without harmful effects, and benefit the host plant. Many can inhibit plant pathogens and promote plant growth. This study aimed to identify a strain of Streptomyces as a novel species and study its antibiotics production. An endophytic actinobacterium, strain TML10^T was isolated from a surface-sterilized leaf of a Thai medicinal plant (Terminalia mucronata Craib and Hutch). As a result of a polyphasic taxonomy study, strain TML10^T was identified as a member of the genus Streptomyces. Strain TML10^T was an aerobic actinobacterium with well-developed substrate mycelia with loop spore chains and spiny surface. Chemotaxonomic data, including cell wall components, major menaquinones, and major fatty acids, confirmed the affiliation of strain TML10^T to the genus Streptomyces. The results of the phylogenetic analysis, including physiological and biochemical studies in combination with a genome comparison study, allowed the genotypic and phenotypic differentiation of strain TML10^T and the closest related type strains. The digital DNA-DNA hybridization (dDDH), Average nucleotide identity Blast (ANIb), and ANIMummer (ANIm) values between strain TML10^T and the closest type strain, Streptomyces musisoli CH5-8^T were 38.8%, 88.5%, and 90.8%, respectively. The name proposed for the new species is Streptomyces naphthomycinicus sp. nov. (TML10^T = TBRC 15050^T = NRRL B-65638^T). Strain TML10^T was further studied for liquid and solid-state fermentation of antibiotic production. Solid-state fermentation with cooked rice provided the best conditions for antibiotic production against methicillin-resistant Staphylococcus aureus. The elucidation of the chemical structures from this strain revealed a known antimicrobial agent, naphthomycin A. Mining the genome data of strain TML10^T suggested its potential as a producer of antbiotics and other valuable compounds such as ε-Poly-L-lysine (ε-PL) and arginine deiminase. Strain TML10^T contains the arcA gene encoding arginine deiminase and could degrade arginine in vitro.

Keywords: Streptomyces naphthomycinicus; endophyte; genome insight; naphthomycin A; solid-state fermentation.

Figure 1

Phylogenomic tree based on TYGS result showing relationship between Streptomyces naphthomycinicus TML10^T with related type strains. The numbers above branches are GBDP pseudo-bootstrap support values >60% from 100 replications, with an average branch support of 97.5%. The tree was rooted at the midpoint (Farris, 1972). Leaf labels are annotated by affiliation to species (1) and subspecies clusters (2) and genomic G+C content (3) (Meier-Kolthoff and Göker, 2019).

Figure 2

Antibiotic production of strain TML10^T in F26 liquid medium and solid state with rice grain inhibit Staphylococcus aureus ATCC 29213 for 6 days.

Figure 3

Maximum-likelihood phylogenetic tree based on protein of arginine deiminase sequences of strains TML10^T and its nearest phylogenetic neighbors in genus Streptomyces and Bacillus licheniformis as the out-group (414 bp). Bootstrap values based on 1,000 replicates are shown at the branch nodes. The scale bar represents 0.010 changes per nucleotide.