Metatranscriptomics of soil eukaryotic communities

Abstract

Functions expressed by eukaryotic organisms in soil can be specifi cally studied by analyzing the pool of eukaryotic-specifi c polyadenylated mRNA directly extracted from environmental samples. In this chapter, we describe two alternative protocols for the extraction of high-quality RNA from soil samples. Total soil RNA or mRNA can be converted to cDNA for direct high-throughput sequencing. Polyadenylated mRNA-derived full-length cDNAs can also be cloned in expression plasmid vectors to constitute soil cDNA libraries, which can be subsequently screened for functional gene categories. Alternatively, the diversity of specifi c gene families can also be explored following cDNA sequence capture using exploratory oligonucleotide probes.