Sites used for this study of the coral disease atramentous necrosis (AN) were located in two adjacent bays, Nelly Bay and Geoffrey Bay, on the south-eastern side of Magnetic Island, which is situated within the inner shelf region of the Great Barrier Reef. Both bays have fringing coral reefs and are similar in shape, physical structure, and hydrodynamic setting. The study was conducted between December 2007 and December 2009. Sampling was conducted every 2 weeks in the austral summer (Nov-Apr) and once a month in the winter (May-Oct). Increased sampling frequency in summer was based on the hypothesis that AN increases with warm water temperatures. Disease dynamics were assessed in three permanent 5x5 m quadrats at 3-5 m depth at each site. Coral colonies demonstrating signs of AN were tagged with numbered plastic tags attached to cable ties. Visual surveys were able to clearly distinguish the four stages in the development of AN lesions: Stage 1 lesions are small (1-2 cm diameter) areas of bleached but intact tissue; Stage 2 lesions are white skeleton devoid of tissue; Stage 3 lesions are covered with a white bacterial film; and in Stage 4, a black, sulphurous deposit accumulates under the white film likely the result of opportunistic secondary microbial community. The last two stages were combined in this study because they generally occur simultaneously and an additional stage (S) was used when disease progression stopped.The diseased corals were all colonies of Montipora aequituberculata, which was the most prevalent species of Montipora in the quadrats. New disease cases (disease incidence) were counted and tagged in each plot during each survey. New AN infections, in addition to both lesion progression and cessation, were monitored on individual colonies to elucidate spatio-temporal patterns in disease dynamics. Due to logistical constraints, Geoffrey Bay was not sampled in February 2008.On each sampling occasion, two replicate water samples were collected in 1-L plastic bottles 1 m above the coral and on opposite sides of the quadrats for the analysis of concentrations of: dissolved organic carbon (DOC), chlorophyll a (chl-a), particulate organic carbon (POC), particulate nitrogen (PN), particulate phosphorus (PP) and suspended solids (SS). Due to logistical reasons, only two replicate water samples were used. Salinity was measured at each sampling occasion with a handheld refractometer (r2 Mini, Reichert GmbH, Germany). Temperature was measured using a temperature logger (ODYSSEY data recording systems, Christchurch, New Zealand) attached underneath a sediment trap in both Nelly Bay and Geoffrey Bay. It was retrieved and downloaded approximately every 2 months. Temperature data from sensors were combined with data collected by the Australian Institute of Marine Science (AIMS) sea surface temperature monitoring program in the same two bays (data available at http://www.aims.gov.au). Maximum temperatures were calculated for the periods of 7 and 14 days up to and including the sampling date.Two sediment traps (40 cm high with a diameter of 10 cm) were deployed 10 m apart close to the permanent 5x5 m quadrats at each site. Traps were collected at every second sampling occasion in the winter and on each occasion in the summer. The ash-free dry weight (AFDW) of the sediment was used as a coarse measure of the organic content of the sediment.Rainfall data for Townsville were obtained from the Australian Bureau of Meteorology web site (http://www.bom.gov.au).
