The complex atmospheric swirls and bands of Jupiter are as distinctive as Saturn’s ring or Mars' color, but they are still very mysterious. To understand how the gas giant's atmosphere works, an international team of astronomers decided to peer through the thick clouds.

The feat was possible by using the recently upgraded Jansky Very Large Array. The data from the radio telescope looked 100-kilometers (62-miles) deep into the planet and studied how ammonia, which is the main component of the clouds, moves in the deeper layers.

The team discovered that ammonia has a complex and turbulent life on Jupiter. Ammonia-rich gasses moves upwards and form the upper cloud layer, either by reacting with sulfide ions or by freezing and forming ammonia-ice clouds.

The radio maps also show where ammonia is missing. Ammonia-poor air moves down, sinking deeper into the planet like cool dry air on Earth, and the data shows that there are ammonia-poor regions that encircle the planet in bands north of the equator. Between the bands, the maps reveal billowing plumes of ammonia from deeper within the planet.

The findings also explain the mystery of the Jovian atmosphere that was reported by the Galileo probe in the 1990s. Speaking to IFLScience, lead author Professor Imke de Pater said: "In the past, when we made observations it looked like Jupiter’s atmosphere had roughly the same abundance of ammonia observed in the Sun. When the Galileo probe went down found that the abundance was actually 4 to 5 times higher than what was observed.

"It was a big discrepancy. But using these new observations and understanding the dynamics we can explain it now."

^{Radio image (top), made with the VLA, and visible-light image (bottom) made with the Hubble Space Telescope, of Jupiter's famous Great Red Spot, a giant storm in the planet's atmosphere. The radio image shows the complex upwellings and downwellings of ammonia gas 30-90 kilometers below the visible clouds.de Pater, et al., NRAO/AUI/NSF; NASA.}

The NASA spacecraft released a probe in one of the cloud-free regions, which are ammonia-poor, and discovered the overabundance of ammonia in the deeper layer. The recent observation indicates this should exactly be the case.

The maps and discovery are reported in the latest issue of Science and they shed interesting new insights into the evolution of atmospheres in gas giants.

"What you observe for gas giants might not be the exact composition of the atmosphere as a whole or in the deeper layers. We really have to be cautious about what we measure and then interpret," added de Pater.

The team is planning more analysis of current data and they will also provide important complementary information for the Juno probe, which will begin analyzing the Jovian atmosphere next month. 

"We are planning to get more data when Juno is there, as the atmosphere is changing all the time. We will provide context images to match their particular observation to the global changes on Jupiter. And they will provide us with ammonia observations to a deeper level," she concluded.

The secrets hiding underneath Jupiter's cover of clouds are finally being exposed.