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Ecological Strategies Behind the Selection of Cultivable Actinomycete Strains from the Yucatan Peninsula for the Discovery of Secondary Metabolites with Antibiotic Activity

  • Microbiology of Aquatic Systems
  • Published:
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Abstract

The quest for novel natural products has recently focused on the marine environment as a source for novel microorganisms. Although isolation of marine-derived actinomycete strains is now common, understanding their distribution in the oceans and their adaptation to this environment can be helpful in the selection of isolates for further novel secondary metabolite discovery. This study explores the taxonomic diversity of marine-derived actinomycetes from distinct environments in the coastal areas of the Yucatan Peninsula and their adaptation to the marine environment as a first step towards novel natural product discovery. The use of simple ecological principles, for example, phylogenetic relatedness to previously characterized actinomycetes or seawater requirements for growth, to recognize isolates with adaptations to the ocean in an effort to select for marine-derived actinomycete to be used for further chemical studies. Marine microbial environments are an important source of novel bioactive natural products and, together with methods such as genome mining for detection of strains with biotechnological potential, ecological strategies can bring useful insights in the selection and identification of marine-derived actinomycetes for novel natural product discovery.

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Acknowledgements

Authors would like to acknowledge Dr. Emanuel Hernández-Núñez at the Department for Marine Resourcesin CINVESTAV, Mérida for his help with the GC-MS analysis of the crude extracts.

Funding

We would like to recognize the Mexican Council of Science and Technology (CONACyT) for their support through fellowships for Parera-Valadez (Masters in Science fellowship: 560614) and Yam-Puc (Postdoctoral fellowship). We would like to recognize the National Autonomous University of Mexico (UNAM) for their funding through PAPIIT TA200212 and TA200415 and UNAM School of Chemistry for their funding through PAIP.

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Authors and Affiliations

  1. Laboratorio de Ecología Microbiana y Productos Naturales Marinos, Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Sisal, Yucatán, Mexico

    Yessica Parera-Valadez, Alejandro Yam-Puc, Lluvia Korynthia López-Aguiar, Norma Angélica Márquez-Velázquez & Alejandra Prieto-Davó

  2. CICY - Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida, Yucatán, Mexico

    Rocío Borges-Argáez & Mirbella Cáceres-Farfán

  3. Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Av. Universidad 3000, Conjunto E., 04510, Mexico City, Mexico

    Mario Alberto Figueroa-Saldivar

Authors
  1. Yessica Parera-Valadez
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  2. Alejandro Yam-Puc
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  8. Alejandra Prieto-Davó
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Contributions

Parera-Valadez contributed by heading the research and writing the paper. Yam-Puc and Figueroa-Saldivar contributed with chemical analyses, bioautography assays, and manuscript writing. López-Aguiar and Márquez-Velázquez contributed with field collections, laboratory procedures, and manuscript revisions. Borges-Argáez and Cáceres-Farfán contributed with bioautography assays.

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Correspondence to Alejandra Prieto-Davó.

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The authors declare that they have no conflict of interest.

Electronic Supplementary Material

Figure S1

Phylogenetic tree with all actinomycete isolates from the coast of the Yucatan peninsula. Alignment and phylogeny were performed following same methods as those reported in Fig. 1 (PDF 37 kb)

Figure S2

Rarefaction curves for the 12 locations sampled. No location was thoroughly sampled and more processing or sampling are needed to reach saturation. (PDF 299 kb)

Figure S3

Detection of the antimicrobial activity of the ethyl acetate extract (5%) from actinomycete NCA004 against Staphylococcus aureus by the bioautography assay. The highly active yellow compound corresponds to resistomycin. 1) Ethyl acetate extract of strain NCA002. 2) Ethyl acetate extract of strain NCA004. 3) Dichloromethane extract of strain NCA004. 4) Acetone extract of strain NCA004. Positive control: amikacin (0.1 mg/mL), negative control: 5 μl of dichloromethane/methanol 1:1. (PDF 728 kb)

Figure S4

Chromatogram displaying resistomycin peak at 12.057 min. Figure S4: UPLC-MS analysis of Ethyl Acetate extract for strain NCA004 showing UV peaks and mass consistent with resistomycin. (PDF 5364 kb)

Figure S5 UV profile and MS data that confirm presence of resitomycin in extract Figure S5 was mentioned in the text but the corresponding data is missing. Please provide.Figure S5 has been uploaded

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Parera-Valadez, Y., Yam-Puc, A., López-Aguiar, L.K. et al. Ecological Strategies Behind the Selection of Cultivable Actinomycete Strains from the Yucatan Peninsula for the Discovery of Secondary Metabolites with Antibiotic Activity. Microb Ecol 77, 839–851 (2019). https://doi.org/10.1007/s00248-019-01329-3

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