Abstract: Provided herein are methods for detecting and discriminating bacteria and fungal species by nucleic acid amplification, then hybridization analysis on a microarray. Primer pairs are used to simultaneously amplify multiple ribosomal Hypervariable regions from the rDNA or rRNA in bacteria and/or fungi as a multiplex amplification reaction, wherein the resulting hypervariable region amplicon mix is analyzed by hybridization to nucleic acid probes that are complementary to unique sequence determinants within those amplified hypervariable regions. The combination of multiplex amplification and microarray hybridization is used for detection and differentiation of specific species within a microbial set relevant to human or animal health or environmental or agricultural analysis, based on simultaneous analysis of the sequence in two or more hypervariable regions, concurrently.

Abstract: Provided herein is a method of quantitating a fungus in a plant, plant product or agricultural product. Total nucleic acids are isolated from a sample of the plant or plant product, and an asymmetric PCR amplification reaction is performed using fluorescent labeled primer pairs to obtain fluorescent labeled fungal amplicons. These amplicons are hybridized to fungus specific nucleic acid probes that are attached on a microarray support. The microarray is imaged to detect fluorescent signals from the fluorescent labeled fungal amplicons. The fluorescent signal intensity is correlated to the quantity of fungus.