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Extraction Protocol for Nontargeted NMR and LC-MS Metabolomics-Based Analysis of Hard Coral and Their Algal Symbionts

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Metabolomics Tools for Natural Product Discovery

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1055))

Abstract

Metabolomics and in particular, nontargeted metabolomics, has become a popular technique for the study of biological samples as it provides considerable amounts of information on extractable metabolites and is ideal for studying the metabolic response of an organism to stressors in its environment. One such organism, the symbiotic hard coral, presents its own complexity when considering a metabolomics approach in that it forms intricate associations with an array of symbiotic macro- and microbiota. While not discounting the importance of these many associations to the function of the coral holobiont, the coral-Symbiodinium relationship has been the most studied to date and as such, is the primary focus of this extraction protocol. This protocol provides details for the sample collection, extraction, and measurement of hard coral holobiont metabolites using both 1H nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography coupled with mass spectrometry (LC-MS). Using this nontargeted metabolomics approach, the holobiont metabolism can be investigated for perturbations resulting from either (1) natural or anthropogenic environmental challenges, (2) the controlled application of stressors, and (3) differences between phenotypes or species. Consequently, this protocol will benefit both environmental and natural products based research of hard coral and their algal symbionts. Every effort has been made to provide the reader with all the details required to perform this protocol, including many of the costly and time consuming “pitfalls” or “traps” that were discovered during its development. As a result, this protocol can be confidently accomplished by those with less experience in the extraction and analysis of symbiotic hard coral, requiring minimal user input whilst ensuring reproducible and reliable results using readily available lab ware and reagents.

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Acknowledgments

This work was supported by the Australian Research Council, Centre of Excellence for Coral Reef Studies, and a Science for Management grant from the Great Barrier Reef Marine Park Authority (GBRMPA), Australia. We would also like to thank João Paulo Krajewski for kindly allowing us to use his photograph and Mark Viant and Christian Ludwig for their kind assistance with the DSE-JRES pulse program.

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Authors and Affiliations

  1. Australian Research Council Centre of Excellence for Coral Reef Studies, AIMS@JCU, The Comparative Genomics Centre and School of Pharmacy and Molecular Sciences, James Cook University, Townsville, QLD, Australia

    Benjamin R. Gordon

  2. Australian Research Council Centre of Excellence for Coral Reef Studies, The Comparative Genomics Centre and School of Pharmacy and Molecular Sciences, James Cook University, Townsville, QLD, Australia

    William Leggat

  3. Australian Institute of Marine Science, Cape Cleveland, Australia

    Cherie A. Motti

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  1. Benjamin R. Gordon
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  2. William Leggat
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  3. Cherie A. Motti
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Editors and Affiliations

  1. Parkville, Australia

    Ute Roessner

  2. School of Botany, The University of Melbourne, Parkville, Victoria, Australia

    Daniel Anthony Dias

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Gordon, B.R., Leggat, W., Motti, C.A. (2013). Extraction Protocol for Nontargeted NMR and LC-MS Metabolomics-Based Analysis of Hard Coral and Their Algal Symbionts. In: Roessner, U., Dias, D. (eds) Metabolomics Tools for Natural Product Discovery. Methods in Molecular Biology, vol 1055. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-577-4_10

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  • DOI: https://doi.org/10.1007/978-1-62703-577-4_10

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-576-7

  • Online ISBN: 978-1-62703-577-4

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