The most comprehensive FGAs reported to date are the GeoChip arrays. The GeoChip 1.0 had 2006 oligonucleotide probes (50-mers) for genes involved in nitrification, denitrification, nitrogen fixation, methane oxidation, sulfate reduction (Tiquia et al., 2004) , organic contaminant degradation, and metal resistance (Rhee et al., 2004) . This array was used in several studies examining microbial communities at uranium (U)-contaminated sites (Wu et al., 2006a; Waldron et al., 2009) , in the Gulf of Mexico (Wu et al., 2008) , and under different land use strategies (Zhang et al., 2007b) and showed FGAs to be useful for microbial community studies. GeoChip 2.0 was developed to provide a truly comprehensive probe set for multiple functional gene categories and to provide increased specificity for highly homologous gene variants . GeoChip 2.0 contains 24,243 (50-mer) oligonucleotide probes targeting ∼10,000 functional genes from 150 gene families involved in the geochemical cycling of C, N, and P cycling, sulfate reduction, metal reduction and resistance, and organic contaminant degradation. This array has been used in numerous studies to examine microbial communities at metals contaminated sites (Gao et al., 2007; Van Nostrand et al., 2009 , oil or diesel-contaminated sites (Rodríguez-Martínez et al., 2006; Liang et al., 2009a,b) , coral mucus (Kimes et al., 2009) , lake or river samples (Taş et al., 2009; Parnell et al., 2010) , deep sea samples (Mason et al., 2009; Wang et al., 2009) , Antarctic soils (Yergeau et al., 2007) and to examine the taxa-area relationship .