The increasing atmospheric concentration of greenhouse gases is known to affect the whole atmosphere-ionosphere system at least to F2-region heights. Also other drivers of long-term changes and trends like long-term change of geomagnetic activity or changes of stratospheric ozone concentration affect significant parts of the atmosphere-ionosphere system. Therefore the vertical coupling in the atmosphere-ionosphere system can also be affected by long-term changes and trends. Here I will present some examples of such effects, as impact of the stratospheric ozone changes on the neutral density in the lower thermosphere and on the E-region ionosphere, or possible long-term changes in the mesopause region winds and atmospheric wave activity. All that clearly indicates that there are three channels of vertical coupling: (1) atmospheric waves, (2) electromagnetic through phenomena like sprites, field-aligned currents etc., and (3) on long-term scale antropogenic changes of concentration of minor chemical constituents (greenhouse gases, ozone etc.).