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All organisms are constantly metabolising, which is the process of converting sugars and oxygen into carbon dioxide and energy. This means that at any time an organism is generating carbon dioxide, which can lower the pH if it can accumulate (poor gas exchange) or the alkalinity is insufficient.
Photosynthetic organisms metabolise as well, generating carbon dioxide. However, during daylight hours there is a net uptake of carbon dioxide and conversion to sugars and oxygen by photosynthetic organisms.
When the lights are on a reef aquarium, due to significant amount of algae present within a reef aquarium, photosynthesis uses up more carbon dioxide than metabolism generates for all organisms within the system. Therefore, carbon dioxide levels fall, increasing the pH. In the case of lights out, everything is metabolising (including the photosynthetic organisms). Therefore, carbon dioxide levels rise and the pH falls.
This daily pH swing is an entirely natural phenomena. However, it should not be too large of a swing, if that is the case then the alkalinity and gas exchange issues should be explored.
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