The first FGA developed used PCR-amplicon probes and targeted four N-cycling genes (nirS, nirK, amoA, and pmoA; Wu et al., 2001) . However, since PCR-amplicons were used, only a limited number of genes could be included because conserved primers can only be designed for a few functional genes. In addition, it would be cost-and time-prohibitive to amplify genes from hundreds of microorganisms or clones in order to achieve a truly diverse probe set. Most microarrays now use oligonucleotide probes, which are more specific (Zhou, 2003) , can be easily customized (Denef et al., 2003; Zhou, 2003; Gentry et al., 2006) , and are relatively inexpensive.