The flashing fountains on the world map are Soul Spots. These are areas that are bursting with soul energy, and you can collect it here once the allotted time passes. You can spend Zell to increase the amount of souls it generates and the maximum capacity.

Leveling up Soul Spots is really important because soul energy does double duty in this game. Soul energy doubles as currency and this game's "stamina" system. To bring Arks with you into battle, you need a certain amount of soul energy. Most Arks costs blue souls, but some take red.

Arks also require a LOT of souls to upgrade them, so you are going to need a lot of blue souls. Upgrade as many Soul Spots as you come across!