GeoChip 4.2 hybridization
Fungal functional genes were accessed by GeoChip 4.2 (Roche NimbleGen Inc., Madison, WI, USA), which is a functional microarray containing more than 107,950 oligonucleotide probes of 792 bacterial, archaeal and fungal genes associated with C, nitrogen (N), phosphorus (P) and sulfur (S) cycling, stress, virulence, energy process, to name a few. These oligonucleotide probes are designed from functional gene sequences of microbial organisms with known taxonomy in the NCBI database (He et al., 2007). Before hybridization, 1 μg of purified DNA was labeled with the fluorescent dye Cy3. After overnight hybridization, unbound DNA was removed. Then GeoChip was scanned by a NimbleGen MS 200 Microarray Scanner (Roche, Basel, Switzerland) at 532 nm and 635 nm. Probes with signal-to-noise ratio lower than 2 were considered to be unreliable and hence removed. The normalized signal intensity of each detected probe was calculated by dividing total signal intensity by each detected probe and log-transformed.