Streptomyces amazonensis sp. nov. isolated from Madeira river sediments with genomic potential for secondary metabolite production

The genus Streptomyces is recognized as a source of secondary metabolites (SMs) with applications in medicine, industry, and agriculture. This study presents the description and characterization of a new Streptomyces species, isolated from sediments of the Madeira River in the Brazilian Amazon. Four strains (CPAA MAD 27, CPAA MAD 39, CPAA MAD 42, and CPAA MAD 51) were obtained from sampling sites distributed along the river. The strains were analyzed for morphological, phenotypic, and biochemical characteristics, as well as their potential for SM production using genome mining. Phylogenetic and phylogenomic analyses indicated that Streptomyces murinus is the most closely related species; however, the dDDH value of 55% and ANI of 94%, combined with biochemical analysis, support the proposal of the isolates as a new species, herein named Streptomyces amazonensis. This species exhibits adaptability to diverse environmental conditions, growing across a wide range of pH values (4–11) and temperatures (15–40 °C), with optimal growth at 35 °C and pH 8, and utilizing various carbon sources, including L-arabinose, unlike S. murinus. Genomic analysis revealed 39 to 46 biosynthetic gene clusters (BGCs) per strain, related to polyketides, nonribosomal peptides, and ribosomally synthesized and post-translationally modified peptides (RiPPs). Notably, BGCs showed high similarity to thioligamide (antitumor) and tetracenomycin (antibiotic) metabolites. Additionally, numerous BGCs with matches in the MIBiG database were identified, suggesting genomic potential related to the biosynthesis of molecules of scientific interest. This discovery expands our understanding of Amazonian microbial diversity and offers new prospects for the bioprospecting of natural products, highlighted by the unexplored biosynthetic potential of S. amazonensis for the development of new natural compounds.