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Metabolomics Approach to Explore Bioactive Natural Products Derived From Plant-Root-Associated Streptomyces

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Abstract

Streptomyces, a prominent genus within the Actinomycetota phylum, is responsible for over 60% of clinically relevant antibiotics. Streptomyces strains inhabiting plant roots possess the potential to synthesize bioactive natural products, conferring defense and resilience to plants against pathogenic microorganisms. However, this potential remains largely unexplored. This study aims to screen for bioactive metabolites produced by Streptomyces strains in the plant rhizosphere.

Six Streptomyces isolates were cultivated using three modified media to induce the production of diverse metabolites, employing the One Strain Many Compounds (OSMAC) approach. The metabolites present in extracts from fermentation broths were examined through a non-targeted Liquid Chromatography-Tandem Mass Spectrometry (LC–MS/MS) approach coupled with Global Natural Products Social Molecular Networking (GNPS MN). The antimicrobial activity of the extracts was assessed using the disc diffusion method.

The strains demonstrated a wide-ranging antimicrobial efficacy against all examined organisms. The GNPS molecular network analyses reveal that metabolite profiles in extracts can exhibit variations based on the medium and solvent system employed. Notably, the ethyl acetate and dichloromethane extracts from Streptomyces sp. CAH29, cultivated in Glucose-Yeast Extract Medium (GYM), exhibited inhibition diameters of up to 30 mm against both Staphylococcus aureus and Candida albicans. Within the metabolomes of these strains, the antibiotics spiramycin and actinomycin were detected. Additionally, lyngbatoxin, a tumor promoter, and potential new analogs were identified. Significantly, a considerable portion of the produced metabolites did not align with any known compounds, indicating the existence of unidentified metabolites generated by these strains. This suggests the possibility of introducing novel chemical entities.

Our study illustrated that Streptomyces strains associated with plant roots could be considered a valuable source of bioactive secondary metabolites. Furthermore, the metabolomics approach utilized in this study serves as a rapid and valuable tool for the screening of microorganisms capable of producing bioactive metabolites.

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Data Availability

The data that support the findings of this study are openly available in the GNPS database at https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=b4d62c82bdc446ddb073b0aab6194587.

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Funding

This study was supported by the Dicle University Scientific Research Projects Committee [Grant number: FEN.17.016].

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Authors and Affiliations

  1. The Institute of Natural and Applied Science, Dicle University, Diyarbakır, Turkey

    Ekrem Kum

  2. Department of Biology, Faculty of Science, Dicle University, Diyarbakır, Turkey

    Ebru İnce

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  1. Ekrem Kum
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Correspondence to Ebru İnce.

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Kum, E., İnce, E. Metabolomics Approach to Explore Bioactive Natural Products Derived From Plant-Root-Associated Streptomyces. Appl Biochem Biotechnol (2024). https://doi.org/10.1007/s12010-024-04905-7

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