The present invention relates to methods for isolating a gene encoding an enzyme, comprising: (a) adding a mixture of labeled first nucleic acid probes from a microbial strain cultured on medium without the substrate, and labeled second nucleic acid probes from a microbial strain cultured on medium with the substrate, to an array of random nucleic acid fragments of the microbial strain where the labeled nucleic acids hybridize to complementary sequences of the genomic fragments in the array, wherein the first nucleic acid probes are labeled with a first reporter and the second nucleic acid probes are labeled with a second reporter; (b) examining the array under conditions wherein the relative expression of the genes of the microbial strain is determined by the observed hybridization reporter signal of each spot in the array; and (c) isolating a gene from the microbial strain that encodes an enzyme that degrades the substrate. The present invention also relates to isolated genes obtained by such methods.