Development of an environmental microarray to study bacterial and archaeal functional genes in Australian soil agroecosystems

Soil biota is responsible for the majority of ecosystem functions in soil, in particular carbon transformations, nutrient cycling, soil structure maintenance, and biological population regulation. An environmental microarray was designed to study key functional genes that facilitate soil processes required for sustainable and productive management of agricultural systems, providing a useful tool for assessing the biological condition of soil. Processes represented included nitrogen and phosphorus cycling, one-carbon degradation, biodegradation of complex organic toxins, and the production of antibiotics. A set of 2934 unique probes was designed from 6420 gene sequences for the target functions across the Bacterial and Archaeal domains. Soil DNA extracted from paired land-use sites (agricultural management and remnant vegetation) and associated with two agriculturally significant Soil Orders, the Dermosols and Calcarosols, was hybridised to the array. A multivariate analysis indicated that the major differences in microbial function could be associated with modification of the soil N cycle following agricultural management. Soils under cropping were associated with higher levels of ammonium (NH4+), and increased frequency of abundance of ammonia monooxygenase genes (amoA). In contrast, soils under grazing management were associated with higher levels of nitrate (NO3−) and increased abundance of nitrogenase genes (nifH). The microarray prototype described here may be a valuable tool in the assessment and description of microbial processes in agriculturally significant Australian soils.