May I add this link as well form Physorg:

First Global Connection Between Earth And Space Weather Found

"Weather on Earth has a surprising connection to space weather occurring high in the electrically-charged upper atmosphere, known as the ionosphere, according to new results from NASA satellites. "This discovery will help improve forecasts of turbulence in the ionosphere, which can disrupt radio transmissions and the reception of signals from the Global Positioning System," said Thomas Immel of the University of California, Berkeley, lead author of a paper on the research published August 11 in Geophysical Research Letters."

Although it is postulated that thunderheads affect the plasma above, the opposite might also be true, creating a reinforcing effect - plasma causes thunder, thunder focuses plasma and back we go.