The photosynthetic algae and bacteria are there in abundance whether they're macroscopic or not. Anything that affects oxygen consumption, off-gassing, production, or solubility will affect the amount of pearling- lighting intensity, photoperiod, nutrients, stocking levels, water motion, surface area of the tank, surface area of the rock, temperature, salinity, etc.
In most cases where there isn't an obvious algae problem, cyanobacteria are the culprit. Most people only recognize cyano as the scummy mats that form in stagnant areas, but in fact they're ubiquitous and usually aren't visible.