Surveys of phytoplankton and zooplankton were conducted by a licensed fishing vessel (Permit number: R1710033; issued by AFCD) at two stations in each of Sections A, B, C and D. Sampling of plankton communities were conducted twice in the wet and the dry season respectively.
Physical parameters of water samples, including water temperature, salinity, dissolved oxygen and pH, were measured in situ using a YSI multiprobe system and the sampling interval was 1 s. Water samples (150 mL) were collected from the surface (1 m) and bottom (1 m above the seafloor) layers by a water sampler. The samples were stored in a cold box and brought to the laboratory for further analyses. Inorganic nutrients (NO3, NO2, NH4, PO4 and SiO4) were be analysed using a Skalar nutrient autoanalyser with standard seawater methods and colorimetric detection. To measure chlorophyll-a (Chl-a) concentration, water samples were filtered through 20 and 5 μm polycarbonate filters and then a GF/F glass fibre filter using a cascade filtration system. Filters were extracted in 90% acetone for 24 h at - 20 oC in the dark and the extracts were measured with a Turner Designs fluorometer. Surface and bottom waters were analysed separately. The water depth of each sampling station was measured by using a weighted measuring tape.
Two 500 mL bottles of seawater (surface and bottom layers, same as the nutrient and Chl-a samples) were fixed with formalin (4% final concentration) for further identification and counting. An aliquot of subsamples was placed in an Utermöhl sedimentation chamber and left to settle for at least 24 h before being counted by using an inverted microscope (Nikon-TMD 300) at 200× or 400× magnification. A species accumulation curve was constructed according to the cumulative number of species recorded for a set of samples taken at one station with a gradient of sampling volume (equivalent to sampling effort). The result of the species cumulative curve indicated that a sample volume of 500 mL was sufficient to recover the majority of phytoplankton species in the study area.
A 250 μm mesh Bongo net with 0.5 m diameter mouth was employed to collect mesozooplankton samples, which can increase filtration efficiency for zooplankton, reduce net avoidance, and sampling replication. The Bongo net is an appropriate instrument because 1) it provides duplicate samples with a single tow given its paired-net design and 2) less disturbance to the water is created on account of the net bridle being located in-between the two nets, and hence, this helps reduce escape responses of the zooplankton. Ten-minute long oblique tows were conducted at each station after determining this to be an appropriate sampling time from the results of a preliminary trial. During the preliminary trial, we compared the bio-volume and dry mass collected from tows of different duration (as the volume of water sampled is proportional to towing time). It is extremely important to note that plankton distributions are highly dynamic spatially and temporally, i.e., samples collected minutes apart can have very different species compositions. On account of this high variability in species composition, we opted to compare bio-volume and dry mass to estimate if we have sampled a representative portion of the community. Contents were preserved with 4% paraformaldehyde and split into quarters with a Folsom plankton splitter for the following purposes: 1) dry mass; and 2) settling volume measurements; 3) identification and enumeration of species using light microscopy; and finally 4) a back-up sample. We computed the species composition based on the identification and counts of the subsample (1/16 of the original volume) and we followed up with sorting through the remaining samples for rare species for building a species inventory.