Sediment diagenesis in aquatic systems is usually understood to be controlled by the concentrations of both organic carbon and the oxidant. However, the concept that sediment respiration may be limited by the supply of organic carbon, even in systems with moderate concentrations of organic carbon in the water column, has yet to be fully explored. Typically we assume that a direct coupling between water column and sediment diagenesis processes occurs and the chemical evolution of porewater and surface water are linked through fluxes of chemical species across the sediment-water interface. While the dynamics of supply of particulate organic carbon (POC) to the sediments via plankton deposition and resuspension, has previously been examined, the fate of dissolved organic carbon (DOC) once in the sediments, has rarely been investigated. A series of experiments comprising batch tests, microcosms and sediment cores were conducted on sediment and water from four diverse field sites in which sediment respiration was considered to be carbon limited. Three sites were oligotrophic, acidic lakes and the fourth an oligotrophic coastal embayment. During each experiment dissolved organic carbon was added and measurements were undertaken of solutes that were considered participants in diagenetic processes. While each system differed in its chemical, biological and geological makeup, a key commonality was the rapid onset of anoxic conditions in the sediments irrespective of the overlying water oxygen concentrations, indicating lack of direct coupling between biogeochemical processes in the water column and sediments. Also, similar apparent DOC remineralisation rates were observed, measured solute fluxes after the addition of DOC indicated adherence to the ecological redox sequence, and increased ammonium concentrations were measured in the overlying waters of the acidic microcosms. In marine system experiments it was noted that diagenetic respiration, as indicated by decreasing concentrations of oxygen in the overlying water, increased rapidly after labile DOC was added. To explore the influence of geochemical processes on sediment respiration, a diagenetic model was tested against the laboratory data. The model was able to capture the rapid changes observed in the microcosms after addition of DOC in both the marine and acidic systems experiments. The model has the potential to serve as an essential tool for quantifying sediment organic matter decomposition and dissolved chemical fluxes. This work has focussed our attention on the control of DOC availability on sediment respiration and thus its ultimate control on solute fluxes across the sediment water interface. The results highlight the need to understand and quantify the supply of DOC to the sediment (as POC or already as the dissolved form), its transport through the sediment and its eventual remineralisation. This understanding is critical for improved management of aquatic systems, possibly even in systems where water column organic carbon is plentiful but sediment respiration is constrained by high organic carbon turnover rates in the water column and a resulting low flux of organic carbon to the sediment.

[Truncated abstract] Acidic mine lakes are formed as a result of the oxidation and dissolution of metal sulfide minerals and are primarily characterized by low pH values of 2 – 4. Many strategies for the bioremediation of acidic mine lakes depend on the alkalinity generation capabilities of microbial ferric and/or sulfate reducing bacteria. However nearly all mine lakes are oligotrophic, with very low concentrations of available organic carbon and nutrients; all required for healthy microbial growth. There is also an unusual class of mine lakes characterized by low concentrations of organic carbon and also very low concentrations of dissolved iron and sulfate. Our ability to promote microbial activity in these systems is especially challenging. This study focuses on one of these systems, Lake Kepwari, a coal mine lake in Western Australia. Numerical modeling of remediation strategies is an efficient way of testing scenarios prior to expensive in-field trials. However such modeling relies on good descriptions of microbial processes, including kinetic parameterizations of ferric and sulfate reduction. There has been little research to date on the study of kinetic parameterizations of the chemical and biological alkalinity generation in acidic mine lakes. The objectives of this thesis were to investigate the viability of microbial ferric and sulfate reduction in an ultraoligotrophic, acidic mine lake, to assess the impact of these microbial processes on water quality and to parameterize the Dual Monod kinetics of neutralization under dual limitation conditions. Molecular analyses including most probable number, DNA extraction, polymerase chain reaction, polymerase chain reaction – denaturing gradient gel electrophoresis were used to examine the microbial communities in the lake sediments. ... The Monod maximum specific microbial growth rates with respect to dissolved organic carbon and ferric, and as determined in batch experiments, were 0.07 ± 0.01 and 0.048 ± 0.02 day-1, respectively, and their corresponding Monod half saturation constants and were 14.37 and 5.6 mmol L-1. The Monod maximum consumption rates under ferric and OC limitation were also estimated. The Monod maximum specific microbial growth rates with respect to dissolved organic carbon and sulfate, , and were 0.05 ± 0.01, 0.08 ± 0.01 and 0.07 ± 0.02 day-1, respectively, and their corresponding Monod half saturation constants, and were 75.5, 131.8 and 10.2 mmol L-1. The Monod maximum consumption rates under sulfate and OC limitation were also estimated. The results of this study suggest that strategies for the remediation of ultraoligotrophic, acidic mine lakes may rely on microbial ferric and sulfate reduction, however additions of both organic carbon and sulfate/ferric are essential. These results can be immediately applied to mesocosm studies in outdoor enclosures and to the management of acidic mine lakes. Furthermore, this thesis has provided a new, valuable understanding on the Dual Monod kinetic parameterizations of neutralization for an ultraoligotrophic, acidic mine lake environment. These parameterizations are essential for the lake ecological models that will be used to investigate remediation scenarios for acidic mine lakes.