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The rise in global energy demand has motivated the exploration and production of oil and gas in increasingly challenging marine environments and there is a continuous risk of accidental oil spills. One of the many fates of spilled oil is deposition on the seabed, which has been extensively studied following the Deepwater Horizon oil spill. However, post-depositional fates of oil in sediments are not well understood. Similarly, the effects of chemical dispersant on oil fate are currently under investigation as their overall contribution to mitigating oil spills environmental impacts remains debated. This project aimed to evaluate the potential for spilled oil to entrain marine sediments and the effects dispersant application had on the process under three transport regimes; (1) post-depositional transport via oil-sediment aggregate deposition in deep-sea sediments, (2) percolative transport in intertidal sands and (3) advective pore-water transport in intertidal and subtidal sands. Investigations into the sorption dynamics of two polyaromatic hydrocarbons in sediment-dispersantseawater systems were also undertaken to evaluate the influence of dispersant application on sorption of hydrocarbons to sediments. Finally, the effects of oil exposure at in situ conditions of pressure and temperature on sediment bacterial community composition were investigated. Oil transport experiments revealed that the tested regimes resulted in significant entrainment of hydrocarbons in marine sediments. Dispersant application resulted in enhanced oil entrainment into sands but not in silts and this effect depended on the water-solubility of hydrocarbons. Watersoluble components were less affected by dispersant than less water-soluble ones. Investigations into sediment bacterial responses to oil exposure at in situ conditions of pressure and temperature revealed a significant effect of both variables on diversity and community composition, highlighting the importance of conducting deep-sea microbial studies at conditions as close to in situ as possible.

The objective of this thesis is the development of a unifying framework for the integration and upscaling of the fluid mechanical, ecological and biomechanical processes occurring in aquatic flows. Particular focus is on the interactions of the fluid motion with aquatic plants and sediments in aquatic systems. Appropriately formulated coupled conservation equations are developed for fluid, sediment, and plant motions. The starting points for their derivation are the continuity and momentum equations written for instantaneous local field variables, for fluid, sediment and aquatic plants. The equations of motion for fluid, sediment and plants (at the stem scale) are averaged over time and space to cope with the temporal and spatial heterogeneity of the flow field near the interfacial boundary and couple the fluid and non-fluid equations of motion. To deal with the possible discontinuity of the time-averaged fields within the averaging time, appropriate definitions and theorems for time-averaging are proposed. Time-averaging is then applied on the equations of motion for each phase to obtain the respective time-averaged equations. Time-averaged equations for the second-order velocity moments are also proposed for mobile-boundary flows. The application of consecutive time-space averaging on the continuum equations led to the development of the double-averaged equations of motion for each phase. Double-averaged continuity and momentum equations have been recently proposed for mobile-boundary flows. In this thesis, the coupled double-averaged continuity and momentum equations are proposed for the sediment material and aquatic plants at the reach scale. Double-averaged equations for the second-order velocity moments have been derived for the case of fluid and sediments. By applying the double-averaging methodology (i) the governing equations are upscaled to the scales relevant to applications, (ii) the fluid motion is rigorously coupled with the non-fluid (plants or sediments) motions, and (iii) the effect of the moving interfacial boundary is introduced explicitly in the governing averaged equations. The derived second-order hydrodynamic double-averaged equations are applied to the analysis of extensive data from Direct Numerical Simulations of turbulent open-channel flows over mobile granular beds (the simulations were performed in the Dresden Technical University by Professor J. Fröhlich's Group). The use of the double-averaged equations provides significant data reduction and assists in the data interpretation. The key physical mechanisms involved in the energy transfers between the fluid mean, form-induced and turbulent fields as well as sediment motions are identified based on the assessment of the terms in the double-averaged balances of kinetic energy.

Sediments in the South Slough Estuarine Sanctuary, Coos Bay, Oregon, were sampled and studied in order to determine the sources, dispersal systems and depositional facies of sedimentation. The purpose of the study was to establish baseline measurements and observations on the existing sediment conditions within the relatively undisturbed South Slough Estuarine Sanctuary

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To gain an understanding of the transfer of nutrients and trace elements from sediment pore waters to surface waters of eutrophic Lake Rotorua and the early diagenetic processes controlling the transfer, pore water chemistry in the sediments of Lake Rotorua was investigated over a one year period in 2006 by collection of sediment cores on three occasions and deployment of pore water equilibrators on two occasions. Pore water concentrations of Fe2+, Mn2+, S, PO4, NH4, As, Cd, and Pb were analysed. Phosphate and ammonium fluxes to the water column from the sediments were calculated from measured concentration gradients by Fick's law of diffusion. Gas present in the sediments was analysed for composition, and source, and its ebullition rate measured. Anaerobic oxidation of organic matter is indicated by negative Eh values. Sulfate reduction was indicated near the sediment-water interface and releases of Fe2+, Mn2+, PO4 and NH4 into the pore water from particulate material were associated with the reducing conditions. Peaks in concentration of nutrients and elements occurred at the sediment surface over summer and deeper in the pore water profile over the cooler months of May and September. Sampling with peepers at fine scales immediately above the sediment-water interface indicated the presence of a nepheloid layer where elements are actively being recycled. Sulfate reduction appears to occur in the layer above the sediment-water interface, indicating that dissolved oxygen has already been reduced. Phosphorus is possibly being removed by iron and manganese oxide/hydroxide precipitation 5 to 15 cm above the sediment-water interface. Pore water saturation calculations indicate that sulfides may be controlling concentrations of iron and possibly other metals in the pore water by formation of pyrite in the zone of sulfate reduction. Below the zone of sulfate reduction, siderite and vivianite may be precipitating and acting as an additional sink for iron and phosphorus. ii Nutrient release rates based on Fick's law of diffusion indicated 430 tonnes of dissolved phosphorus and 1150 tonnes of ammonium were released to Lake Rotorua's water column in 2006, suggesting nutrient release from the sediments is the dominant flux of nutrients to the water column of Lake Rotorua. Methanogenesis, from acetate fermentation, occurs below the zone of sulfate reduction, where it becomes the dominant process in organic matter degradation. Ebullition of gas was measured at 126 ml m-2 d-1 and this gas was comprised dominantly of methane. Possible remediation techniques that could reduce the internal load of nutrients released from the lake sediments include sediment removal by dredging or capping the sediments with an adsorbent or sealing layer. Capping the sediments could be compromised by ebullition of gas that would disrupt the capped layer, opening up pathways that allow more readily for exchange between pore water nutrients and the water column. Dredging is likely to stimulate the ebullition of most of the trapped gas and result in a rapid efflux of much of the nutrient rich pore water into the lake, however dredging the top 10 to 20 cm of the sediments may partially reduce phosphorus in the pore waters but would not substantially reduce ammonium and fluxes would remain similar to current levels. Improving redox conditions in the sediments could reduce pyrite formation improving phosphorus binding with iron.

Concentrations of heavy metals (Cu, Cd, Cr, Zn, Mn, Fe and Pb) in the water columns, aquatic plants and sediments of fourteen lakes of varied levels of pollution were measured. Correlation analysis was carried out between heavy metal concentrations in aquatic plants and heavy metal concentrations in water and sediment. The aquatic plants which accumulated heavy metals in their tissues in proportion to that in water and sediments were identified. The aquatic plants studied were: 8/yxa auberti Rich, Cabomba caroliniana Gray, Ceratophyllum demersum L, Ceratopteris thalictroides (L.) Bron, Chara globularis, Eichhornia crassipes Solmn, Hydrilla verticillata Royle, Ipomoea aquatica Forsk, Limnophila aromatica (Lam.) Merr., Ludwigia adscendens (L) Hara, Nelumbo nucifera Gaertn, Nymphaea stallata Linn, Nymphoides indica (L.) Kuntze, Typha angustata Bony & Chaub and Utricularia aurea Lour. Metal uptake by aquatic plants varied between different species and within the same species depending on lake water contamination levels. The level of metal uptake to a great extent was a function of the environment water metal concentration. Results showed that Utricularia accumulated Mn, Zn, Cr, Cd and Pb in direct proportion to the overlying waters (r2 = 0.69, 0.63, 0.69, 0.65 and 0.39 respectively). Hydrilla accumulated Cu, Mn, Zn, Fe, Cr, Cd and Pb in direct proportion to the overlying waters (r2 = 0.65, 0.66, 0.44, 0.72, 0.38, 0.63, and 0.73 respectively). Blyxa leaves accumulated Zn, Fe, Cr, Cd and Pb in direct proportion to the overlying waters (r2 = 0.74, 0.74, 0.72, 0.60 and 0.82 respectively). Echhornia leaf accumulated only Cr in direct proportion to the overlying waters r2 = 0.81. Nymphaea leaf and Chara did not accumulate any metal in direct proportion to the overlying waters. Roots of Blyxa auberti, Ceratopteris thalictroides, and Eichhornia crassipes contained higher concentrations of heavy metals than their leaves. Roots of Blyxa accumulated Cr, Cd and Pb in direct proportion to the overlying waters (r2 = 0.91, 0.65 and 0.69 respectively). Echhornia root accumulated Cd in direct proportion to the overlying waters with r2 = 0.90. Nymphaea stem showed no significant correlations between the metal concentrations in the waters and in the plant. Utricularia accumulated Zn, Fe, Cr, Cd and Pb in direct proportion to the metals in the underlying sediment extracted by cold hydrochloric acid (r2 = 0.84, 0.51, 0.47, 0.68 and 0.80 respectively). Hydrilla accumulated Cu, Zn, Cr, Cd and Pb in direct proportion to the underlying sediment (r2 = 0.34, 0.37, 0.91, 0.49 and 0.96 respectively). Blyxa accumulated Zn, Fe, Cr, Cd and Pb in direct proportion to the underlying sediments (r2 = 0.99, 0.61, 0.82, 0.75 and 0.64 respectively) . Echhornia leaf showed significant correlation between the Cu (r2 = 0.83) and Cr (i2 = 0.88) concentration in underlying sediment and the plant. Nymphaea leaf showed a significant correlation between the Zn (r2 = 0.83) concentration in the plant and the underlying sediments. Roots of Blyxa showed significant correlation between concentrations of Cu, Cr and Pb in sediment extracted by hydrochloric acid and plant (r2 = 0.9, 0.7 and 0.9 respectively). Roots of Echhornia had no significant correlation with the sediment metal concentrations (hydrochloric acid extractable). Two techniques (cold hydrochloric acid extractable and nitric acid extractable) to extract metals from sediment were compared. Based on correlations of metal concentrations in plant tissue and metal extracted from the sediment, it was concluded that the cold hydrochloric acid extractable metal technique is more suitable for determining bioavailable sediment metal concentration in environmental studies. Laboratory studies investigations on the bioaccumulation of Zn and Cu in Hydrilla confirmed that Hydrilla is a good bioindicator of Cu as it accumulated 20360 ug/g dry weight of Cu in 72 hours. Hydrilla showed higher bioaccumulation factor with low concentration of Cu in the solution, in the laboratory studies. Hydrilla was determined to be the best indicator species as it reflected the heavy metal concentration in the environment which was supported by the laboratory studies.

Macroalgae are abundant on shallow temperate reef environments, often forming complex communities that comprise several strata. In southern Australia, these assemblages are dominated by large canopy forming taxa from the Orders Laminariales and Fucales. The presence of subtidal fucoid macroalgae differentiates these communities from that elsewhere, and emphasises the need for local studies rather than relying on generalisations made elsewhere. Like most natural systems, temperate reefs are often threatened by human activity with degradation reported from many locations in close proximity to urban settlements. The work presented in this thesis involves an examination of the temporal and spatial variability in the structure of macroalgal communities from reefs along the Adelaide (South Australia) metropolitan coast. The work looked specifically at the effects of a dispersed sediment plume, resulting from the 1997 beach sand-replenishment dredging program, on shallow sub-tidal reef systems. An examination of the structure of canopy forming phaeophycean macroalgae in Gulf St Vincent (South Australia), noted large amounts of both spatial and temporal heterogeneity. Notwithstanding, this variation was not random, but demonstrated considerable structure that could be linked to a number of important underlying processes. In particular, macroalgal assemblages appeared as a mosaic of patches, each of which comprised a high-density state clearly dominated by a single genus (Cystophora, Sargassum, or Ecklonia), or alternatively a lower density mixed assemblage (Variable Low Abundance, VLA). Macroalgal community structure appeared to be driven by biotic interactions at small scales (metres), such that patches comprised of different species of algae in high density states rarely abutted one another. Instead, VLA assemblages frequently formed a buffer being situated between these mono generic patches. In terms of successional processes, the high-density states appeared to be relatively stable whereas the VLA state, at least in some systems, was transitory. This finding was supported by the absence of intermediary high- density states (e.g. a mix of Cystophora and Ecklonia) implying that state changes must occur via the VLA state following some form of disturbance. Larger scale patterns appeared to be driven by environmental variation, with factors such as wave exposure influencing habitat suitability for individual species and thereby affecting community composition. These phenomena were examined in terms of life history strategies that tend to promote stability, and which are common in late successional taxa. The importance of properties enhancing stability and the role of disturbance was investigated experimentally using a dispersed sediment plume, which entirely engulfed two reefs, as a pulse impact. This disturbance was of particular relevance given that degradation of macroalgal communities in close proximity to the City of Adelaide has been, at least in part, attributed to the effects of elevated levels of sediment. Follow up surveys revealed that the sedimentation from the plume had primarily affected newly recruiting individuals, with few juveniles surviving to one year of age. Over the following few years, the effect of this recruitment failure cascaded into the adult stand. In broader terms, unfavourable climatic conditions prior to the start of the study, including a particularly severe El Nino event, had a widespread effect on local assemblages, causing high levels of both adult and juvenile mortality. As such, at the commencement of the study, macroalgal communities across the study area were in the process of recovery. This was observed at control sites over the duration of the study. In contrast, recruitment failure at the sediment-affected sites retarded the recovery process, exacerbating the problems associated with prior unfavourable climatic events and leaving them in a degraded state. This study demonstrated that macroalgal assemblages are equipped (under natural conditions) to handle 'normal' environmental fluctuations (such as inter-annual variability). However, the additional stress associated with certain anthropogenic impacts has the potential to push them over the limit, causing degradation. The loss of canopy macroalgae reduces the structural complexity of the system, leading to a concomitant reduction in their ability to recover. As such, these findings are of particular relevance to those charged with the responsibility for managing near-shore marine environments. The plume was created accidentally during a dredging operation for beach sand replenishment of Adelaide's eroding shoreline. / Thesis (Ph.D.)--School of Earth and Environmental Sciences, 2004.

Thesis (M.A.)--State University of New York at Binghamton, Geological Sciences and Environmental Studies Department, 2006. / Includes bibliographical references.