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The ecosystem of Lake Macquarie, N.S.W., has been subject to heavy metal and metalloid inputs since 1897 from a lead-zinc smelter, and subsequently coal-fired power stations, coal mines and washeries and sewage treatment plants. Reports in 1994 of contamination of commercial fish species from the Lake with selenium levels up to twelve times those recommended for human consumption has lead to calls for bans on commercial and recreational fishing in the Lake, which could potentially devastate local fishing and tourism industries. Selenium biogeochemical cycling in estuarine environments such as Lake Macquarie is subject to factors including sediment redox potential, sediment characteristics, solubility of Se-containing mineral phases, ligand complexing ability, and microbially-mediated oxidation-reduction, mineralisation and methylation reactions. Understanding this biogeochemistry is important so as to evaluate the potential risk to ecosystems and human health posed by selenium, and to determine the likely impact of potential management strategies. The research described in this paper examines the importance and role of two of these specific factors which impact selenium biogeochemical cycling in Lake Macquarie: sediment redox potential and microbial methylation reactions. The role of sediment redox potential was examined utilising sediment from the Lake, dosed with known quantities of selenium and then studied under different conditions, comprising: addition of various macrofauna to the sediments to examine the impact of bioturbation on sediment redox status and therefore selenium availability; and exposure of sediment plugs to oxygenated and deoxygenated seawater to quantify selenium release. Bioturbation caused deepening of the oxidised conditions in the sediment, impacting upon speciation and mobility of selenium, whilst exposure of contaminated reduced sediment to oxidising porewater arising from bioturbation resulted in selenium mobilisation from the strongly binding “organic fraction” of the sediment. Separately, bacterial cultures were isolated from the Lake with the ability to tolerate high selenium levels. Organisms were cultured in flasks with nutrient broth containing selenate (Se(VI)) at 100mg/l and incubated at 28oC for several weeks. Analysis by hydride generation atomic absorption spectroscopy revealed that the mass balance on the flasks would not close, indicating loss of selenium to the culture headspace. Samples of culture headspace gases were then collected using a cryogenic trapping system and injected into a GC/MS where methylated selenium species including dimethylselenyl sulfide and dimethylselenyl disulfide were identified. These experiments indicated that both sediment redox potential and microbial methylation are important in the biogeochemical cycling of selenium in Lake Macquarie. The impact of bioturbation upon sediment redox potential is important for any consideration of capping sediments, as the depth of the cap must be sufficient to prohibit bioturbative organisms from accessing the sediment below the cap, whilst the demonstrated ability of indigenous microorganisms from the Lake to methylate selenium may represent a potential remediation options for contaminated sediments or selenium-containing waste streams.