Applied Microbiology and Biotechnology

, Volume 101, Issue 2, pp 843–857 | Cite as

Biotechnological potential of Actinobacteria from Canadian and Azorean volcanic caves

  • Cristina Riquelme
  • Maria de Lurdes Enes Dapkevicius
  • Ana Z. Miller
  • Zachary Charlop-Powers
  • Sean Brady
  • Cohord Mason
  • Naowarat Cheeptham
Environmental biotechnology


Caves are regarded as extreme habitats with appropriate conditions for the development of Actinobacteria. In comparison with other habitats, caves have not yet been the target of intensive screening for bioactive secondary metabolites produced by actinomycetes. As a primary screening strategy, we conducted a metagenomic analysis of the diversity and richness of a key gene required for non-ribosomal peptide (NRP) biosynthesis, focusing on cave-derived sediments from two Canadian caves (a lava tube and a limestone cave) to help us predict whether different types of caves may harbor drug-producing actinobacteria. Using degenerate PCR primers targeting adenylation domains (AD), a conserved domain in the core gene in NRP biosynthesis, a number of amplicons were obtained that mapped back to biomedically relevant NRP gene cluster families. This result guided our culture-dependent sampling strategy of actinomycete isolation from the volcanic caves of Canada (British Columbia) and Portugal (Azores) and subsequent characterization of their antibacterial and enzymatic activities. Multiple enzymatic and antimicrobial activities were identified from bacterial of the Arthrobacter and Streptomyces genera demonstrating that actinomycetes from volcanic caves are promising sources of antibacterial, antibiofilm compounds and industrially relevant enzymes.


Caves Actinobacteria Metagenomics Antimicrobial activity Enzymatic activity 



C. Riquelme was funded by the Regional Fund for Science and Technology and Pro-Emprego program of the Regional Government of the Azores, Portugal [M3.1.7/F/013/2011, M3.1.7/F/030/2011]. Her work was partly supported by National funds from the Foundation for Science and Technology of the Portuguese Government [Understanding Underground Biodiversity: Studies in Azorean Lava Tubes (reference PTDC/AMB/70801/2006)]. A.Z. Miller acknowledges the support from the Marie Curie Intra-European Fellowship of the European Commission’s 7th Framework Programme (PIEF-GA-2012-328689). The authors would like to thank the TRU Innovation in Research Grant, TRU Undergraduate Research Enhancement (UREAP) Fund, Western Economic Diversification Canada Fund, Kent Watson (assisted with the Helmcken Falls Cave sample collection), Dr. Mario Jacques (U of Montreal for his assistance in biofilm culture), Nicholaus Vieira, Christian Stenner, and the Raspberry Rising Expedition team. We acknowledged the Canadian Ministry of Forests, Lands, and Natural Resource Operations for Park Use Permit#102172. The work done in the Brady lab was funded by NIH grant GM077516. Z. Charlop-Powers was also supported by NIH grant AI110029. The authors also wish to thank Fernando Pereira, Ana Rita Varela, Pedro Correia, Berta Borges, and Guida Pires for help during field and lab work in the Azores. The authors would like to thank Dr. Steven Van Wagoner (TRU) and Drs. Julian Davies and Vivian Miao (UBC) for their invaluable comments in manuscript preparation.

Compliance with ethical standards

This article does not contain any studies with human participants or animals performed by any of the authors.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

253_2016_7932_MOESM1_ESM.pdf (45 kb)
ESM 1 (PDF 45 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Food Science and Health Group (CITA-A), Departamento de Ciências AgráriasUniversidade dos AçoresAngra do HeroísmoPortugal
  2. 2.Instituto de Recursos Naturales y Agrobiología de SevillaConsejo Superior de Investigaciones Científicas (IRNAS-CSIC)SevillaSpain
  3. 3.Laboratory of Genetically Encoded Small MoleculesThe Rockefeller UniversityNew YorkUSA
  4. 4.Department of Biological Sciences, Faculty of ScienceThompson Rivers UniversityKamloopsCanada

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