To compare measurements within the ECM in different regions of the microcolony, pH and CO32− were also measured under the coral polyps. For this, glass slides with microcolonies were placed in a temperature-controlled seawater bath (100 ml) under a Leica Z16 APO macroscope (Leica Microsystems) connected to a camera system and computer screen, allowing macroscopic online observations. To minimize the effects of a photosynthesis- or respiration-driven diffusive boundary layer over the colony, a gentle surface current (~2 cm/s) was applied by blowing air with an air pump through a bent Pasteur pipette along the water surface. After calibration, the microsensor was moved to the seawater bath containing the sample, and the tip was positioned above the polyp mouth. This depth was set as zero. Generally starting from 1000 μm above the mouth (negative depths), the sensor was moved toward the polyp and inserted through the mouth (depth zero) until it could not be advanced any further (presumably reaching the skeleton and referred to as measurements “at the skeleton” in the text; maximum positive depths in the profiles). Contact with the skeleton could not be verified directly but was defined as when either the microsensor tip started to bend or the glass slide with the colony was moved in the water bath. Profiles were recorded in the light (200 μmol photons m−2 s−1) with a dark period of 10 min at maximum depth. After the dark period, the light was switched back on for 10 min before an upward profile was recorded until the sensor had reached its original position in the seawater again. Data from experiments during which the sensor tip broke were excluded from the data presented within this study (this also applies to measurements in the growing edge).

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