Sediment samples were collected from 2 sites in Bowling Green Bay, a shallow coastal embayment located between Townsville and the Burdekin River delta in the central Great Barrier Reef province. A sediment core was collected at Station U for use in a depth profile study. The core was collected using a plastic, 51 mm diameter, core tube. The core was returned to the laboratory within 3 hours of collection, subsectioned and transferred to centrifuge tubes for pore water isolation. A surface sediment sample, collected at nearby Station 11 was used for an intact lipid study. The surface sediment (0-1 cm depth) was collected using a frame supported grab sampler and immediately frozen.All sediment samples were freeze dried and ground to < 100 µm in a stainless steel ring mill. Total carbon was measured using a LECO CHN Analyser. Total phosphorus was determined by ICPES after nitric acid/perchloric acid digestion. Pore waters were analysed for ammonium, phosphate, nitrite and nitrate using an Autoanalyser system.The results of pore water analyses indicated that bacterial activity responsible for the mineralization of the nutrients was confined to the upper 15-20 cm of the core. On this basis, samples from five depths were selected for lipid analysis (0-1 cm, 3-4 cm, 7-9 cm, 11-13 cm and for comparison 30-35 cm). Sediment samples (1-5 g dry wt) were extracted (x2) with hexane:isopropanol:water (HIP) 30:20:1.25. An aliquot of the extract was saponified and the resultant fatty acids were isolated and esterified to methyl esters. Lipid phosphate was determined by P analysis of an aliquot of the TSE after combustion and acid hydrolysis.An aliquot of the lipid extract from the surface sediment sample was separated into fractions by silica column chromatography. Four fractions were obtained. Each fraction was evaporated just to dryness under nitrogen and then transesterified. Non-ionic compounds were extracted from the resultant mixture with toluene. The toluene extract was evaporated to a small volume, treated and analysed by capillary GC and GC-MS.
