Abstract:
Contemporary microbial analysis of groundwater quantifies biomarker genes (i.e., DNA) that are indicative of a process of interest, and the results influence site management decisions. For example, the presence of Dehalococcoides biomarker genes suggests that reductive dechlorination is a feasible bioremediation strategy; however, DNA-based analysis provides no direct evidence that the key organism(s) (e.g., Dehalococcoides) are alive and active. The analysis of biomarker transcripts (i.e., RNA) promises to provide information about the activity of the organism(s) of interest, and recent procedural advances expand RNA analysis to environmental samples. This chapter presents two procedures for isolating RNA from biomass collected from groundwater, a method to quantify target transcripts as cDNA, and the process of data analysis. The protocols provide general guidance and information for refining and adjusting methods to an environmental sample (e.g., volume of groundwater), the method of biomass collection, and user preference.
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Ritalahti, K.M., Cruz-García, C., Padilla-Crespo, E., Hatt, J.K., Löffler, F.E. (2010). RNA Extraction and cDNA Analysis for Quantitative Assessment of Biomarker Transcripts in Groundwater. In: Timmis, K.N. (eds) Handbook of Hydrocarbon and Lipid Microbiology. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-77587-4_289
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DOI: https://doi.org/10.1007/978-3-540-77587-4_289
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-77584-3
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