Central infected zone tissue of soybean (Glycine max L. Merr.) nodules was fractionated into separate subcellular compartments using density gradient centrifugation in nonaqueous solvents to better understand how exposure to Ar:O(2) (80:20%, v/v) atmosphere affects C and N metabolism, and to explore a potential role for adenylates in regulating O(2) diffusion. When nodules were switched from air to Ar:O(2), adenylate energy charge (AEC) in the plant cytosol rose from 0.63 +/- 0.02 to 0.73 +/- 0.02 within 7 min and to 0.80 +/- 0.01 by 60 min. In contrast, AEC of the mitochondrial compartment of this central zone tissue remained high (0.80 +/- 0.02 to 0.81 +/- 0.02) following Ar treatment while that of the bacteroid compartment was unchanged, at 0.73 +/- 0.02, after 7 min, but declined to 0.57 +/- 0.03 after 60 min. These results were consistent with a simulation model that predicted Ar:O(2) exposure would first reduce ATP demand for ammonia assimilation and rapidly increase cytosolic AEC, before the Ar:O(2)-induced decline mediated by a decrease in nodule O(2) permeability reduces bacteroid AEC. The possibility that adenylates play a key, integrating role in regulating nodule permeability to oxygen diffusion is discussed.