Owing to their vast diversity and recalcitrance to laboratory cultivation, the detection, characterization and quantification of microorganisms in natural settings can be very challenging, and linking microbial diversity to ecosystem processes and functions is often even more difficult. Several molecular methods have begun to bridge this divide.  Microarray-based methods and complementary technologies for analyzing functional genes and processes have a great promise of overcoming such obstacles.
Results/Conclusions

We have developed and applied one such array comprehensive microarray (coined the “GeoChip”) to studies that attempt to link microbial community characteristics to functional processes in environments such as soils and contaminated sediments.  This array contains >24,000 oligonucleotide (50 mer) probes and covering >10 000 genes in >150 functional groups involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance, and organic contaminant degradation. Examples of the application of this technology to studies of soil biogeochemistry under afforestation regimes, organic and conventional agriculture, the spatial variability of microbial communities, and the remediation of contaminated environments from past and ongoing efforts will be discussed along with methods for integration environmental data and appropriate complimentary methods.   These studies show that when applied correctly such technologies are beginning to provide direct linkages between microbial genes/populations and environmental processes and functions.