Genome mining and description of Streptomyces albidus sp. nov., an endophytic actinobacterium with antibacterial potential

An endophytic actinobacterium, strain CAP215ᵀ was isolated from the root sample of a native pine tree (Callitris preissii), Adelaide, South Australia. This strain was a Gram stain-positive, aerobic actinobacterium with well-developed substrate mycelia. It produced spiral chains of spores. The closest phylogenetic members which shared the highest 16S rRNA gene sequence similarity were Streptomyces marinus DSM 41968ᵀ, Streptomyces haliclonae DSM 41970ᵀ and Streptomyces karpasiensis K413ᵀ at 98.2%, 98.0% and 97.9%, respectively. The major cellular fatty acid of this strain was anteiso-C₁₅:₀ and major menaquinone was MK-9(H₄). Polar lipids of strain CAP215ᵀ contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol dimannoside and two unknown glycolipids. Chemotaxonomic data confirmed strain CAP215ᵀ belonged to the genus Streptomyces. Genome of strain CAP215ᵀ was 6.65 Mb with 69.8% DNA G + C content and contains 5992 coding sequences (CDS). Biosynthesis Genes Clusters (BGCs) comprised post-translationally modified peptides (RiPPs) cluster, genes encoding enzyme relating to antibiotic production; actinorhodin, surfactin and tetracenomycin. Genome mining of this strain identified genes encoding proteins relating to plant growth promotion such as pyrophosphatase, ectoine synthase, superoxide dismutase and siderophore production; penibactin and desferrioxamine E. Genes encoding beneficial enzymes; amylase, β-xylosidase, chitinase, lipase and protease were detected. The genome of this strain contained genes encoding enzymes degrading xenobiotic compounds such as 2,4-dichlorophenol 6-monooxygenase, nitroreductase and epoxide hydrolase. Also, genes encoding squalene, hopene and betacarotenoid production were observed. Digital DNA–DNA (dDDH) hybridization, Average Nucleotide Identity BLAST (ANIb), ANI-MUMmer (ANIm) between strain CAP215ᵀ and S. marinus DSM 41968ᵀ were 25.4 %, 82% and 86.4%, respectively. The data on the genotypic and phenotypic characteristics and genome analysis recognized the differentiation of strain CAP215ᵀ with the closest species with valid names. The name Streptomyces albidus sp. nov. was proposed for which the type strain is CAP215ᵀ (= DSM 42025ᵀ = NRRL B-24815ᵀ).