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Marine Actinobacteria from the Gulf of California: diversity, abundance and secondary metabolite biosynthetic potential

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Abstract

The Gulf of California is a coastal marine ecosystem characterized as having abundant biological resources and a high level of endemism. In this work we report the isolation and characterization of Actinobacteria from different sites in the western Gulf of California. We collected 126 sediment samples and isolated on average 3.1–38.3 Actinobacterial strains from each sample. Phylogenetic analysis of 136 strains identified them as members of the genera Actinomadura, Micromonospora, Nocardiopsis, Nonomuraea, Saccharomonospora, Salinispora, Streptomyces and Verrucosispora. These strains were grouped into 26–56 operational taxonomic units (OTUs) based on 16S rRNA gene sequence identities of 98–100 %. At 98 % sequence identity, three OTUs appear to represent new taxa while nine (35 %) have only been reported from marine environments. Sixty-three strains required seawater for growth. These fell into two OTUs at the 98 % identity level and include one that failed to produce aerial hyphae and was only distantly related (≤95.5 % 16S identity) to any previously cultured Streptomyces sp. Phylogenetic analyses of ketosynthase domains associated with polyketide synthase genes revealed sequences that ranged from 55 to 99 % nucleotide identity to experimentally characterized biosynthetic pathways suggesting that some may be associated with the production of new secondary metabolites. These results indicate that marine sediments from the Gulf of California harbor diverse Actinobacterial taxa with the potential to produce new secondary metabolites.

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Acknowledgments

We acknowledge financial support from the Universidad Autónoma de Baja California Internal Assembly (grants No. 357 and 369), the Consejo Nacional de Ciencia y Tecnología (México) for the pre-doctorate fellowship given to A.B.E (number 5892). P.J. acknowledges financial support from the National Institutes of Health (grant GM0886261) and the NOAA California Sea Grant College Program Project R/NMP-100 (Grant NA100AR4170060) through NOAA’S National Sea Grant College Program, U.S. Dept. of Commerce. We thank W. Fenical for facilitating the field collections, M. Woolery for LC/MS assistance and D. Guillen, H. Ocampo-Alvarez, C. Barrila, S. Gomez, N. Millán and M. Torres for help with strain preservation.

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Authors and Affiliations

  1. Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, km 103 Carretera Tijuana- Ensenada, 22830, Ensenada, Baja California, Mexico

    Amayaly Becerril-Espinosa & Irma E. Soria-Mercado

  2. Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92093-0204, USA

    Kelle C. Freel & Paul R. Jensen

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  1. Amayaly Becerril-Espinosa
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  2. Kelle C. Freel
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  3. Paul R. Jensen
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  4. Irma E. Soria-Mercado
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Correspondence to Irma E. Soria-Mercado.

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Becerril-Espinosa, A., Freel, K.C., Jensen, P.R. et al. Marine Actinobacteria from the Gulf of California: diversity, abundance and secondary metabolite biosynthetic potential. Antonie van Leeuwenhoek 103, 809–819 (2013). https://doi.org/10.1007/s10482-012-9863-3

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  • DOI: https://doi.org/10.1007/s10482-012-9863-3

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