A ground-based and rocket investigation of the response of the neutral atmosphere to E region auroral heating has been carried out at Poker Flat, Alaska. The temporal evolution of the atomic oxygen to molecular nitrogen ratio (O/N2) in the lower thermosphere has been monitored using the optical emissions from the aurora as a diagnostic. Comparisons between the changes in the O/N2 ratio and the auroral Joule and particle heating have shown several examples of close similarity between the durations of the heating events and the depletions. Using the thermospheric winds measured during the rocket flights and the temporal structure of the depletions, the upper limit on the horizontal scale size of the depletions has been estimated at 200--400 km. Moreover, in situ rocket measurements of atomic oxygen showed significant differences at points separated horizontally by approximately 220 km. It is also concluded from the near coincidence between the depletion events and the Joule heating events that the dynamical mechanism(s) that drive the depletions were not far distant from the observing site, that is, local processes are sometimes dominant during periods of moderate auroral activity. We suggest that the observation of a strong wind shear in the 100-to 120-km altitude region [Larsen et al., 1997> could be responsible for turbulence that contributes to the changes in minor constituent composition. ¿ 1997 American Geophysical Union