Most GeoChip analysis has involved the use of DNA, so that only gene abundance can be determined. These changes can be used to infer microbial activity, but cannot provide direct proof of activity. mRNA can be used for FGA analysis to monitor activity (Dennis et al., 2003; Bodrossy et al., 2006; Gao et al., 2007; Wawrik et al., 2012a) , although as mentioned above, working with environmental RNA can be challenging. Stable isotope probing (SIP) has also been used with GeoChip to monitor microbial activity (Leigh et al., 2007) . Gao et al. (2007) used amplified community mRNA from a denitrifying fluidized bed reactor to examine microbial activity. Genes for nitrate and nitrite reduction, organic contaminant degradation, sulfite reduction, and polyphosphate kinase were detected, consistent with reactor operation (Gao et al., 2007) . Another study used amplified community mRNA to examine nitrate utilization in marine bacterial communities (Wawrik et al., 2012a) . Hybridization results indicated activity by ureC, nirS, nirK, narG, nosZ, napA, nrfA, amoA, and nifH genes, indicating that urea cycling, denitrification, dissimilatory nitrate, nitrite reduction, and N fixation were occurring (Wawrik et al., 2012a) .