GeoChip: Recent Development, and Its Applications to Bioenergy and Sustainability

Microarray technology provides the opportunity to identify thousands of microbial genes or populations simultaneously. A comprehensive functional gene array (GeoChip) was developed to detect and monitor microbial communities important to various biogeochemical, ecological and environmental processes. Based on the second generation of GeoChip, a new generation, GeoChip 3.0, has been developed, which has several new features. First, GeoChip 3.0 contains ~25,000 probes and covers ~47,000 sequences for 292 gene families. Second, the homology of automatically retrieved sequences by key words is verified by HUMMER using seed sequences so that the sequence retrieving process is automated. Third, a universal standard has been implemented so that data normalization and comparison of different microbial communities can be conducted. Fourth, a genomic standard is used to quantitatively determine absolute gene abundance. In addition, GeoChip 3.0 includes phylogenic markers, such as gyrB. Finally, a software package has been developed to facilitate the management of such a complicated array, especially for data analysis and future update. Here, we have used GeoChips to successfully analyze microbial functional structure from a variety of environments, including several samples related to bionergy production such as Microbial Fuel Cells (MFC) for hydrogen production from plant biomass. Seven microbial communities from MFCs set up in both the US and China with inocula of different geographic origins were analyzed by GeoChip. Our results indicate that the microbial communities for electricity production are well separated from those for hydrogen production despite the differences of original inocula. Also, GeoChip analysis suggested that Shewanella, Geobacter, Pseudomonas, Desulfovibrio and Rhodopseudomonas are key organisms for hydrogen production, which was also validated by 454 sequencing.