Screening and identification of a new antimicrobial, Streptomyces rehmanniae, from the rhizosphere of Rehmannia glutinosa

Abstract

Objectives: we aimed to isolate and characterize antimicrobial-producing strains from the rhizosphere soil of Rehmannia glutinosa, with the goal of identifying novel antimicrobial agents to address the escalating crisis of antimicrobial resistance. Methods: strain Rer75 was isolated from rhizosphere soil and characterized based on morphology, phylogenetic analyses, average nucleotide identity (ANI), and digital DNA–DNA hybridization (dDDH). Bioactive compounds were extracted and purified from the strain. The antimicrobial activity of isolated compounds was evaluated against E. coli CGMCC 1.1521, S. aureus ATCC 25923, and the pathogenic fungus B. berengeriana CFCC 85789. Genome mining was performed using antiSMASH to identify biosynthetic gene clusters (BGCs). Inhibition of key genes in the nigericin-like gene cluster was performed to elucidate the relationship between the antibacterial activity of the strain and the gene cluster. Results: strain Rer75, identified as a novel species named “Streptomyces rehmanniae”, exhibited strong antagonistic activity against six types of plant pathogenic fungi. Seven compounds were isolated from its crude extract, including a new unsaturated hydroxy ester (compound 1) and six known compounds (compounds 2–7). Compound 1 showed moderate antibacterial activity against E. coli and S. aureus, but no activity against B. berengeriana. Genomic analyses revealed 40 BGCs encoding polyketides, nonribosomal peptides, and terpenes, many of which displayed low similarity to known clusters. Notably, the nigericin-like BGC No. 37 was essential for the antibacterial activity of the strain. Conclusions: Streptomyces rehmanniae Rer75 is a promising source of novel antimicrobial compounds. The genomic insights into its diverse and unique biosynthetic potential highlight its ecological and biotechnological importance for developing new antimicrobial agents.