Microarray technology provides the opportunity to identify thousands of microbial genes or populations simultaneously, but adapting such technologies for characterizing microbial communities in natural settings is of great changes. To address the needs for environmental applications, a very comprehensive functional gene array (FGA) containing ~23,000 probes from the genes important for biogeochemical cycling of C, N, S, P, metal resistance and contaminant degradation were designed and constructed. To address the great challenge related to detection sensitivity, a novel microarray-based method in combination with whole community genome amplification (WCGA) was developed to achieve representative, sensitive, and quantitative detection of microbial populations/communities that could not be studied using conventional microarray approaches. This new technology was used to analyze the spatial variation of microbial communities in a temperate, mixed-hardwood forest. Composite surface (15 cm deep) soil samples were collected at a central point and at sampling points placed 1, 5, 10, 50, 250, and 500 m distances from the center point along transects in a north, south, east, and west direction. Altogether 25 samples were collected. Various soil properties (e.g., soil texture, C and N concentrations, C-to-N ratios) and processes (i.e., asymbiotic N2-fixation, urease activity, potential soil C mineralization) were measured for each sample, and the microbial community structure was determined using FGA. Further data analysis is on-going.