In April and September 2009, sediments were collected from 10 stations located across the continental shelf: inshore (IS9, IS10); mid-shelf (MS7, MS8, BR1, GR1); outer GBR lagoon (PRC4, PRC5); and the shelf break off the Pompey Complex (SB13, SB14). Sediments were collected to a maximum depth 25 cm using a modified 0.027 m² Bouma boxcorer (IS9, IS10, MS7, MS8, BR1, GR1, SB13, SB14) or a 0.25 m² Smith-McIntyre grab (PRC4, PRC5). Sub-samples were taken with methanol washed polycarbonate tubes. The core tubes were opened for deeper layers to be sampled. Surface sediments (0-1 cm) were taken with a clean stainless spoon. Sediments were stored frozen in glass jars and later freeze-dried in the laboratory to remove water.
A moored sediment trap (made of stainless steel, 1 m tall and 10 cm diameter with 5 traps in an aluminium frame) was deployed for 10 days at 30 m in a 65 m deep water column, in September 2009 near reef station PRC4. The traps were filled with 2 x salinity brine containing 4 mg of HgCl2 to retard bacterial activity. However, the windy turbulent conditions caused the trap to drift approximately 8 nautical miles south toward station PRC5 during deployment. In February 2010 sediment traps (made of polycarbonate 0.8 m tall and 8 cm in diameter with 12 traps in a frame) were tethered to the anchored research vessel by a 100 m line at stations PRC4, PCR5, GR1. The tethered traps floated in mid water with a slight tilt in the direction of the currents. Offshore from station IS9, the trap array was free floating. The traps were only deployed during daylight hours (~10 h) and no bacterial retardant was added. Sediment trap samples were filtered though pre-weighed and pre-combusted glass fibre filters. After rinsing with SuperQ water to remove salt, the filters were folded in half and wrapped in pre-combusted aluminium foil and frozen. Prior to analysis, the trap filters were examined and visible crustacean zooplankton removed with tweezers.
The following analyses were carries out on sediment and sediment trap samples: Trace elements; CHN; Organic carbon; Total extractable organic matter (EOM); Extraction of neutral lipids and separation by column chromatography into classes (F1-2 hydrocarbons, F3 esters and ketone, F4 sterols and n-alcohols); Extraction of F5 fatty acids from the polar fraction of the extracts; Full scan gas chromatography-mass spectroscopy (GC-MS) quantification of alkanes, Archaea biomarkers and unresolved complex mixtures (UCM); Selected ion monitoring (SIM) GC-MS quantification of a series of 298 PAHs and standards, plus the hopane and sterane series of petroleum biomarkers and the microbial biomarker, diploptene; and Crenarchaeol analysis using normal phase high performance chromatography (API-MS).
