Large amounts of DNA (e.g., 1 μg) or RNA (e.g., 5 μg) are needed for GeoChip hybridization. However, it can be difficult to get sufficient quantities of nucleic acid from some types of samples (e.g., water) or the sample is too difficult or impossible to replace to use such large quantities of nucleic acid. In this case, amplification of DNA or RNA can be done using either whole community genome amplification (WCGA; Wu et al., 2006a) or whole community RNA amplification (WCRA; Gao et al., 2007) . WCGA uses the Templiphi 500 amplification kit (phi 29 DNA polymerase, GE Healthcare, Piscataway, NJ, USA) with a modified amplification buffer and using 1-100 ng DNA provides a sensitive (10 fg detection limit) and representative amplification (<0.5% of amplified genes showed >2-fold difference from unamplified; Wu et al., 2006a) . WCRA provides a representative amplification with 50-100 ng of starting material.