Original Article

Microbial Ecology and Functional Diversity of Natural Habitats

Deep sequencing of non-ribosomal peptide synthetases and polyketide synthases from the microbiomes of Australian marine sponges

  • The ISME Journal (2013) 7, 18421851 (2013)
  • doi:10.1038/ismej.2013.65
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Abstract

The biosynthesis of non-ribosomal peptide and polyketide natural products is facilitated by multimodular enzymes that contain domains responsible for the sequential condensation of amino and carboxylic subunits. These conserved domains provide molecular targets for the discovery of natural products from microbial metagenomes. This study demonstrates the application of tag-encoded FLX amplicon pyrosequencing (TEFAP) targeting non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) genes as a method for determining the identity and diversity of natural product biosynthesis genes. To validate this approach, we assessed the diversity of NRPS and PKS genes within the microbiomes of six Australian marine sponge species using both TEFAP and metagenomic whole-genome shotgun sequencing approaches. The TEFAP approach identified 100 novel ketosynthase (KS) domain sequences and 400 novel condensation domain sequences within the microbiomes of the six sponges. The diversity of KS domains within the microbiome of a single sponge species Scopalina sp. exceeded that of any previously surveyed marine sponge. Furthermore, this study represented the first to target the condensation domain from NRPS biosynthesis and resulted in the identification of a novel condensation domain lineage. This study highlights the untapped potential of Australian marine sponges for the isolation of novel bioactive natural products. Furthermore, this study demonstrates that TEFAP approaches can be applied to functional genes, involved in natural product biosynthesis, as a tool to aid natural product discovery. It is envisaged that this approach will be used across multiple environments, offering an insight into the biological processes that influence the production of secondary metabolites.

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Acknowledgements

We would like to acknowledge the financial support from the Australian Research Council and the Gordon and Betty Moore Foundation.

Author Contributions

JNW, MVB and BAN designed research; JNWand LF performed research; JNW, MVB, LF, TT and BAN analysed data; and JNW, MVB, TT and BAN wrote the manuscript.

Author information

Affiliations

  1. School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia

    • Jason N Woodhouse
    • , Lu Fan
    • , Mark V Brown
    • , Torsten Thomas
    •  & Brett A Neilan
  2. Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, New South Wales, Australia

    • Lu Fan
    •  & Torsten Thomas

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Competing interests

The authors declare no conflict of interest.

Corresponding author

Correspondence to Brett A Neilan.

Supplementary information

Supplementary Information accompanies this paper on The ISME Journal website (http://www.nature.com/ismej)