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Extraction of Microbial and Host DNA, RNA, and Proteins from Oak Bark Tissue

1
School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
2
Department of Biosciences, Faculty of Natural and Environmental Sciences, University of Helsinki, Biocenter 2, Viikinkaari 5, 00790 Helsinki, Finland
*
Author to whom correspondence should be addressed.
Methods Protoc. 2019, 2(1), 15; https://doi.org/10.3390/mps2010015
Received: 30 November 2018 / Revised: 30 January 2019 / Accepted: 1 February 2019 / Published: 5 February 2019
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Abstract

The application of high-throughput nucleic acid and protein sequencing technologies is transforming our understanding of plant microbiomes and their interactions with their hosts in health and disease. However, progress in studying host-microbiome interactions in above-ground compartments of the tree (the phyllosphere) has been hampered due to high concentrations of phenolic compounds, lignin, and other compounds in tree bark that severely limit the success of DNA, RNA, and protein extraction. Here we present modified sample-preparation and kit-based protocols for the extraction of host and microbiome DNA and RNA from oak (Quercus robus and Quercus petraea) bark tissue for subsequent high-throughput sequencing. In addition, reducing the quantity of bark tissue used for an established protein extraction protocol yielded high quality protein for parallel analysis of the oak-microbiota metaproteome. These procedures demonstrate the successful extraction of nucleic acids and proteins from oak tissue using as little as 50 mg of sample input, producing sufficient quantities for nucleic acid sequencing and protein mass spectrometry of tree stem tissues and their associated microbiota. View Full-Text
Keywords: oak tissue; oak bark; DNA extraction; RNA extraction; protein extraction; DNA/RNA sequencing; shotgun proteomics oak tissue; oak bark; DNA extraction; RNA extraction; protein extraction; DNA/RNA sequencing; shotgun proteomics
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Broberg, M.; McDonald, J.E. Extraction of Microbial and Host DNA, RNA, and Proteins from Oak Bark Tissue. Methods Protoc. 2019, 2, 15.

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