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Evaluation of BOX-PCR and REP-PCR as Molecular Typing Tools for Antarctic Streptomyces

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Abstract

Molecular studies led to the resurgence of natural products research from genus Streptomyces, already known for their long history and importance for the pharmaceutical industry. However, species belonging to this genus are difficult to identify and the most commonly used techniques, which are based on 16S rRNA sequencing, do not discriminate between related species. In this work, amplification profiles generated from BOX-PCR and REP-PCR of 49 Antarctic soil streptomycetes were compared to evaluate the diversity present in the group and to characterize the bacterial isolates, along with some 16S rRNA amplifications. The BOX-A1R primer exhibit clearer amplification fragments, different from the amplification patterns obtained using the REP 1R and 2R primers. A higher diversity was observed with REP-PCR amplifications, even though a larger number of fragments was obtained with BOX-A1R primer amplifications. There are at least four isolates that showed great similarity (about 90%) in both techniques. In other hand, there are two others that are 90% similar in BOX-PCR, but distant in REP-PCR, showing only 40% of similarity. Results of the combination of BOX-PCR and REP-PCR represent a simple and low-cost method to discriminate between Streptomyces strains. There is no species identification with only the 16S rRNA, most isolates seem to be related to S. globisporus. Further studies added to the obtained results may provide better data to help the characterization of these microorganisms.

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Acknowledgements

This work was supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (FAPERGS) by the grants receveid. The author also thanks to Voltaire Neto for the figures artwork.

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Author notes

  1. Marcela Proença Borba and Ana Elisa Ballarini contributed equally to this work.

Authors and Affiliations

  1. Laboratório de Microbiologia Aplicada, Instituto de Ciências Básicas da Saúde, Departamento de Microbiologia, Imunologia e Parasitologia, Rua Sarmento Leite, 500, Bairro Farroupilha, Porto Alegre, 90050-170, Brazil

    Marcela Proença Borba, Ana Elisa Ballarini, Joao Paulo Duarte Witusk & Sueli Van Der Sand

  2. Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile

    Paris Lavin

  3. Facultad de Ciencias del Mar y Recursos Biológicos, Departamento de Biotecnología, Universidad de Antofagasta, Antofagasta, Chile

    Paris Lavin

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  1. Marcela Proença Borba
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Contributions

MPB isolated the Streptomyces, extracted DNA, supervised the PCR fingerprinting reactions, performed the 16S rRNA PCR reactions, analyzed the data and wrote the manuscript. AEB extracted DNA, performed the PCR fingerprinting reactions, analyzed the data and wrote the manuscript. JPDW contributed to the isolation and DNA extraction. PL collected the soil samples and supervised the manuscript writing. SVDS supervised the experiments, data analysis and manuscript writing. All the authors have approved the final manuscript.

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Correspondence to Marcela Proença Borba.

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Borba, M.P., Ballarini, A.E., Witusk, J.P.D. et al. Evaluation of BOX-PCR and REP-PCR as Molecular Typing Tools for Antarctic Streptomyces. Curr Microbiol 77, 3573–3581 (2020). https://doi.org/10.1007/s00284-020-02199-6

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  • DOI: https://doi.org/10.1007/s00284-020-02199-6

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