GeoChip 3.0 covers 56,990 sequences from 292 gene families, greatly increasing the number of genes and categories covered compared to GeoChip 2.0 and added new control features (He et al., 2010a) . New gene categories include antibiotic resistance, energy processing, and phylogenetic markers (i.e., gyrB). A set of 16S rRNA gene probes were added as positive controls, human, plant, or hyperthermophile gene probes were added as negative controls, and a common oligo reference standard (CORS) was added for data normalization and comparison. The CORS is composed of an artificial sequence probe that is co-spotted with each gene probe and the complementary CORS target, labeled with a contrasting fluorescent dye to the sample, which is then spiked into each sample prior to hybridization (Liang et al., 2010) . The signal intensity of the CORS probe can then used to normalize the signal intensity of the sample and allows comparison of samples hybridized at different times. In addition, a computational pipeline has been developed for GeoChip probe design and data analysis. The GeoChip 3.0 has been used to examine microbial communities associated with elevated CO 2 (He et al., 2010b) , to examine communities within coal formation production waters (Wawrik et al., 2012b) or rhizosphere communities in As-contaminated sites (Xiong et al., 2010) . GeoChip 4.0, the newest version, is synthesized by Nimblegen (Madison, WI, USA) in their 12-plex format and contains 83,992 probes targeting 152,414 genes in 410 gene categories (Lu et al., 2012a) . In addition to added genes in most categories, new categories added include stress response, antibiotic resistance, and bacteriophage genes. It has been used to examine microbial communities during the 2010 Gulf oil spill (Lu et al., 2012a) ,