We report on subauroral plasma density troughs observed by Defense Meteorological Satellite Program (DMSP) satellites during the major magnetic storm of 6 April 2000. The troughs were embedded within strongly irregular, ≥500-km wide subauroral convection streams, composed of two distinctive parts. The poleward part coincided with strong wave structures, energetic (ring current) ion precipitations, and enhanced vertical ion flows. One or several narrow density decreases were present here. The equatorward part was marked by a density trough coincident with a local maximum of the electron temperature ~7000--9000 K. Here the ion temperatures and downward vertical ion velocities were ~2000 K and <20 m/s, respectively. The mean convection velocity was typically ≤500 m/s. We develop analytical approximations for the rate coefficients of the charge exchange reactions based on recent laboratory experiments. These have been used in local modeling of the equatorward F peak density depletions. Topside steady-state density profiles were evaluated assuming diffusive equilibrium in a given Te profile. A scenario for the transition of an initial density-height profile to a flat profile is described. Substantial agreement between the modeling results and DMSP observations indicates that the vibrational mechanism contributes significantly to the formation of high-Te-related density troughs.