Phylogenetic analysis of actinobacterial populations associated with Antarctic Dry Valley mineral soils

Authors

  • Olubukola O. Babalola,

    1. Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, Cape Town, South Africa.
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  • Bronwyn M. Kirby,

    1. Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, Cape Town, South Africa.
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  • Marilize Le Roes-Hill,

    1. Biotransformations & Technical Biology Group, Department of Chemical Engineering, University of Cape Town, Private Bag 1, Rondebosch 7701, South Africa.
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  • Andrew E. Cook,

    1. Advanced Water Management Centre, the University of Queensland, Brisbane, Qld, Australia.
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  • S. Craig Cary,

    1. Department of Biological Science, University of Waikato, Hamilton, New Zealand.
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  • Stephanie G. Burton,

    1. Biotransformations & Technical Biology Group, Department of Chemical Engineering, University of Cape Town, Private Bag 1, Rondebosch 7701, South Africa.
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  • Don A. Cowan

    Corresponding author
    1. Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, Cape Town, South Africa.
      *E-mail: dcowan@uwc.ac.za; Tel. (+27) 219592093; Fax (+27) 219593505.
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*E-mail: dcowan@uwc.ac.za; Tel. (+27) 219592093; Fax (+27) 219593505.

Summary

Despite the apparent severity of the environmental conditions in the McMurdo Dry Valleys, Eastern Antarctica, recent phylogenetic studies conducted on mineral soil samples have revealed the presence of a wide diversity of microorganisms, with actinobacteria representing one of the largest phylotypic groups. Previous metagenomic studies have shown that the majority of Antarctic actinobacterial populations are classified as ‘uncultured’. In this study, we assessed the diversity of actinobacteria in Antarctic cold desert soils by complementing traditional culture-based techniques with a metagenomic study. Phylogenetic analysis of clones generated with actinobacterium- and streptomycete-specific PCR primers revealed that the majority of the phylotypes were most closely related to uncultured Pseudonocardia and Nocardioides species. Phylotypes most closely related to a number of rarer actinobacteria genera, including Geodermatophilus, Modestobacter and Sporichthya, were also identified. While complementary culture-dependent studies isolated a number of Nocardia and Pseudonocardia species, the majority of the cultured isolates (> 80%) were Streptomyces species – although phylotypes affiliated to the genus Streptomyces were detected at a low frequency in the metagenomic study. This study confirms that Antarctic Dry Valley desert soil harbours highly diverse actinobacterial communities and suggests that many of the phylotypes identified may represent novel, uncultured species.

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