Evaluation of BOX-PCR and REP-PCR as Molecular Typing Tools for Antarctic Streptomyces
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Evaluation of BOX‑PCR and REP‑PCR as Molecular Typing Tools for Antarctic Streptomyces Marcela Proença Borba1 · Ana Elisa Ballarini1 · Joao Paulo Duarte Witusk1 · Paris Lavin2,3 · Sueli Van Der Sand1 Received: 5 May 2020 / Accepted: 3 September 2020 © Springer Science+Business Media, LLC, part of Springer Nature 2020
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.
Introduction Microorganisms play an important role in the production of interesting compounds to the pharmaceutical industry. Among the most varied products, we can highlight antibiotics, antitumor, antivirals, vaccines, enzyme inhibitors, polymers and bioherbicides [1]. It is estimated that only a small fraction of compounds has been discovered in past years Marcela Proença Borba and Ana Elisa Ballarini contributed equally to this work. * Marcela Proença Borba [email protected] 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
2
Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
3
Facultad de Ciencias del Mar y Recursos Biológicos, Departamento de Biotecnología, Universidad de Antofagasta, Antofagasta, Chile
and post-sequencing DNA studies have been pointing to the great potential of natural products production by bacteria from the phylum Actinobacteria [2]. The genus Streptomyces are distinct in this phylum because they have genomes that contain a l
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