Streptomyces sediminimaris sp. nov., a novel actinobacterium with anticancer potential isolated from mangrove sediments

Abstract

Two marine actinomycete-like strains, MCC20^T and MCC57, were isolated from Chanthaburi (Thailand) mangrove sediment. Their taxonomic classifications were established through a polyphasic approach. Despite differences in colony morphotypes, genetic and chemotaxonomic analyses confirmed them as the same species within the genus Streptomyces. Both strains contained ll-diaminopimelic acid in their cell wall, with glucose, mannose, ribose and rhamnose identified as whole-cell sugars. Their phospholipid profile comprises phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. The predominant fatty acids were iso-C_15:0, anteiso-C_15:0, iso-C_16:0 and anteiso-C_17:0 with MK-9(H₈) as the primary menaquinone, while MK-9(H₆) and MK-9(H₄) were unique to strain MCC57. Both strains exhibited anticancer activity against colorectal (HCT116) and lung (A549) cancer cells, with strain MCC20^T being more potent. Their 16S rRNA gene sequences showed 100% similarity, with 99.2% similarity to Streptomyces fumigatiscleroticus NBRC 12999^T. Nevertheless, a phylogenomic tree placed them closer to Streptomyces spinosirectus CRSS-Y-16^T, Streptomyces plumbidurans KC 17012^T and Streptomyces spinosisporus 7R016^T. Nearly 100% average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values highlighted the identity of strains MCC20^T and MCC57, while ANI (89.4%) and dDDH (35.5%) values were well below the respective 95 and 70% thresholds for related species. This supported their novelty. Based on their genotypes and phenotypes, strains MCC20^T (=NBRC 117131^T=TBRC 19240^T) and MCC57 (=NBRC 117132=TBRC 19241) are identified as phenotypic variants of a new species, Streptomyces sediminimaris sp. nov., with strain MCC20^T designated as the type strain (~9.2 Mb genome, 72.0 mol% G+C content).

Keywords: anticancer activity; mangrove sediment; novel Streptomyces; phenotypic variants.

Fig. 1.. 16S rRNA gene-based phylogeny built by the NJ algorithm. Genetic relationships among strains MCC20^T, MCC57 and their closely related type strains are shown, with Kitasatospora setae KM-6054^T (AB022868) serving as the outgroup. Bootstrap values >50% from 1,000 replications are displayed above the branches. The branch lengths are scaled to represent 0.005 substitutions per nucleotide position. Dots indicate branches that are also supported by the ME and ML trees (see Figs S1and S2).

Fig. 2.. Genome-based phylogeny of strains MCC20^T and MCC57 inferred with the FastME 2.1.6.1 algorithm [65] based on genome blast distance phylogeny (GBDP) distances automatically calculated by TYGS. Kitasatospora setae NRRL B-16185^T (GCA 000716965.1) is applied as the outgroup. GBDP pseudo-bootstrap values >60% from 100 replications are shown above the branches, with the branch lengths scaled according to the GBDP distance formula d₅.

Fig. 3.. Scanning electron micrographs visualizing the polysporous chains of strains (a) MCC20^T and (b) MCC57 grown on ISP 3 agar at 30 °C for 14 days of incubation. Scale bar, 2 µm.