Raina MacIntyre receives funding from influenza vaccine manufacturers GSK and CSL Biotherapies for investigator-driven research. These payments were not associated with this study. The remaining authors have no competing interests. Use of functional gene arrays for elucidating in situ biodegradation Microarrays have revolutionized the study of microbiology by providing a high-throughput method for examining thousands of genes with a single test and overcome the limitations of many culture-independent approaches. Functional gene arrays (FGA) probe a wide range of genes involved in a variety of functions of interest to microbial ecology (e.g., carbon degradation, N fixation, metal resistance) from many different microorganisms, cultured and uncultured. The most comprehensive FGA to date is the GeoChip array, which targets tens of thousands of genes involved in the geochemical cycling of carbon, nitrogen, phosphorus, and sulfur, metal resistance and reduction, energy processing, antibiotic resistance and contaminant degradation as well as phylogenetic information (gyrB). Since the development of GeoChips, many studies have been performed using this FGA and have shown it to be a powerful tool for rapid, sensitive, and specific examination of microbial communities in a high-throughput manner. As such, the GeoChip is well-suited for linking geochemical processes with microbial community function and structure. This technology has been used successfully to examine microbial communities before, during, and after in situ bioremediation at a variety of contaminated sites. These studies have expanded our understanding of biodegradation and bioremediation processes and the associated microorganisms and environmental conditions responsible. This review provides an overview of FGA development with a focus on the GeoChip and highlights specific GeoChip studies involving in situ bioremediation. As the most phylogenetically and functionally diverse group of organisms on the planet (estimated 2000-50,000 microbial species per gram of soil; Torsvik et al., 1990; Hong et al., 2006; Schloss and Handelsman, 2006; Roesch et al., 2007) , microorganisms are critical to ecosystem functioning and are involved in the biogeochemical cycling of carbon, nitrogen, sulfur, phosphorus, and metals, as well as degradation or stabilization of contaminants in the environment. However, because a vast majority (>99%) of microorganisms remain uncultured (Amann et al., 1995; Fuhrman and Campbell, 1998; Whitman et al., 1998) , culture-independent approaches must be used to gain a comprehensive picture of microbial communities. However, many of the culture-independent methods, such as 16S rRNA genebased cloning or quantitative PCR, require a PCR amplification step, which introduces well-known biases (Suzuki and Giovannoni, 1996; Warnecke et al., 1997; Lueders and Friedrich, 2003) . In addition, since many functional genes have too much variance or too few sequences available, conserved PCR primers cannot be designed for many functional genes. Even if primers could be designed for many functional genes, performing PCR with many different primer sets would be cost-and time-prohibitive.