Abstract
The direct retrieval and sequencing of environmental RNA is emerging as a powerful technique to elucidate the in situ activities of microbial communities. Here we provide a metatranscriptomic protocol describing environmental sample collection, rRNA depletion, mRNA amplification, cDNA synthesis, and bioinformatic analysis. In addition, the preparation of internal RNA standards and their addition to the sample are discussed, providing a method by which transcript numbers can be expressed as absolute abundances in the environment and more readily compared to other biogeochemical and ecological measurements.
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Acknowledgements
We wish to thank Christa Smith for help in protocol development and Camille English for creating the figure artwork.
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Gifford, S., Satinsky, B., Moran, M.A. (2014). Quantitative Microbial Metatranscriptomics. In: Paulsen, I., Holmes, A. (eds) Environmental Microbiology. Methods in Molecular Biology, vol 1096. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-712-9_17
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DOI: https://doi.org/10.1007/978-1-62703-712-9_17
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Publisher Name: Humana Press, Totowa, NJ
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Online ISBN: 978-1-62703-712-9
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