2.1 | Zooplankton community sample collection and preservation
Zooplankton community samples were collected from plankton trawls in coral reef areas around Green Island, Taiwan. The samplings were carried out along two transects, one on the island’s southern side and the other on its western side (Figure 1). Sample collection was performed twice a day: once during the day (approx. 10:00-12:00) and once at night (18:00-20:00). The specific GPS locations and sampling times are available in Table S1. A plankton net with a mouth opening of 45 cm in diameter and mesh size of 63 µm (NORPAC net, Rigosha & Co., Ltd, Saitama, Japan) was used for the sampling. For each sampling event, the net was towed at the sea surface for 10 minutes with the slowest operational speed of the boat. The plankton net was washed with fresh water after use to ensure that no sample carry-over occurred between collections. The collected zooplankton were kept alive in aerated tanks (5 litres of filtered surface water) during transportation back to the Marine Science Centre, Green Island Research Station, Academia Sinica, Taiwan. All samples were brought to the laboratory within 2 hours of the collection.
In the laboratory, the samples were size-fractionated into three size ranges: F1: 63 – 100 µm, F2: 100 – 200 µm, and F3: 200 – 300 µm using plankton meshes. After the size fractionation, the samples were weighed and then homogenized with 10 times the volume of the TriPure Isolation reagent (Roche, Base, Switzerland) and kept at - 20 °C until total RNA extraction.