The phenotype of an individual organism can have important consequences for processes operating at the scale of populations and ecosystems. However, explicit linkages between a gene and its phenotype, and their impact on population structure and ecosystem function are not understood. The multidisciplinary HERMES (Hierarchical Experimental Responses at Macromolecular to Ecosystem Scales) project was initiated to investigate linkages in a model ecosystem where wild type and mutant Arabidopsis plants, with a reduced capacity to assimilate nitrate, were grown in mesocosms at current and elevated levels of carbon dioxide concentration. A fundamental step in understanding the gene-ecosystem continuum is to characterize relationships between a gene transcript and the functional activity of the enzymes it encodes. This is difficult to predict because post-transcriptional and post-translational regulation can significantly alter the response predicted from transcript alone. Traditional enzyme activity analysis is labor intensive, making it unsuitable for the kind of data intensive studies that are necessary to advance understanding. We have adopted a microplate-based enzyme analysis platform that has higher throughput than traditional approaches. We present enzyme activity data for 20+ key enzymes in central carbon and nitrogen metabolism from several generations of arabidopsis grown in model ecosystems. Preliminary results from the first generation show significantly lower activity in over half of the measured enzyme activities in plants with a reduced capacity for nitrate assimilation and some changes in plants grown at elevated CO₂. Results are displayed on a metabolic map that allows visualization of the impacts of a single gene mutation in nitrate metabolism and growth at elevated carbon dioxide concentrations on the metabolic pathways associated with carbon and nitrogen metabolism. We discuss how this data, alone and when combined with observations taken across a range of biological levels of organization can provide insights into the structure and function of terrestrial ecosystems.