Ecological assessment of the Scott Reef system using environmental DNA metabarcoding (WEL)

In October 2021, a total of 94 seawater samples were collected approximately 1m below the surface from the Scott reef system (Figure 1). Samples were collected at 10 sites spread across the three atolls (South Scott, North Scott, and Seringapatam). At each site, a minimum of five replicate 1L samples were collected in sterile Nalgene bottles sites by snorkellers. We also included for comparison seawater samples collected from the Rowley Shoals (n=13), a neighbouring oceanic atoll system with pristine coral reef communities, and from inside the Darwin Harbour (n=6), a tidally-dominated turbid inshore environment. Samples inside Darwin Harbour were collected using the RV Solander’s Niskin array. Water samples were stored on ice until filtration within 6 hours of sample collection.

A series of control samples that consisted of the 10-20% bleach solution used to rinse collection bottles were also collected. All samples were filtered using a 250 mL funnel EZ-Fit filtration unit with 0.48 μm mixed cellulose ester membranes and an EZ-Fit Manifold base (3-place) from Merck Millipore (Merck Group, Burlington, USA). Gloves were changed and the manifold base and cup were sterilized with a 10% bleach solution between the filtering of samples from different sites. Following filtration, the filter papers were rolled and kept in cryogenic tubes at -20°C until transport and storage at -80°C.