GeoChip can be hybridized with either DNA or RNA. Most DNA samples used for GeoChip analysis are extracted using a 1 http://hmmer.wustl.edu/ well-established freeze-grind method with detergent lysis (Zhou et al., 1996; Hurt et al., 2001) since it provides high molecular weight DNA, important for later amplification steps. The use of RNA presents some challenges as mRNA is unstable and has a low abundance in environmental samples. Several papers have described methods for extracting environmental RNA, including a protocol for the dual extraction of both DNA and RNA Burgmann et al., 2003) or RNA alone (McGrath et al., 2008; Poretsky et al., 2009a) . Methods for mRNA enrichment include size separation by gel electrophoresis (McGrath et al., 2008) or use of commercial kits [MICROBExpress (Ambion) and/or mRNA-ONLY (Epicentre Biotechnologies); Poretsky et al., 2009b; Mettel et al., 2010] . Size separation obtained 115-155 ng mRNA from 4.6-5.3 μg total RNA (McGrath et al., 2008) . Using commercial kits, Mettel et al. (2010) were able to obtain 140-530 ng of mRNA from 0.4-2.0 μg total RNA per 0.5 g soil.