Very low frequency (VLF) radio waves propagate over long distances within the Earth-ionosphere waveguide, reflected off the Earth's surface and the ionospheric D-region. The characteristics of these signals depend on several parameters along the path, which apart from the D-region's properties, are fairly constant over short periods of time. This allows probing of perturbations in the lower ionosphere to be made using VLF measurements. In this paper, we present an analysis of VLF narrowband signals, transmitted from Sicily, Italy, and detected in Tel-Aviv, Israel. We show observations of the interaction between both pressure waves and electromagnetic perturbations from thunderstorms with the VLF waves aloft. We clearly observe long period acoustic wave signatures (up to 4 minutes) and short period gravity wave signatures (5-10 minutes), while also many transient events related to heating and ionization of the D-region. Comparisons with the World Wide Lightning Location Network (WWLLN) data show the possible link between tropospheric thunderstorms and D-region short-Term variability. Finally, we conclude that gravity wave signatures are a common and significant feature in VLF measurements.