ALBERT

Description: Insight in the biogeochemistry and ecology of sandy sediments crucially depends on a quantitative description of pore water flow and the associated transport of various solutes and particles. We show that widely different problems can be modelled by the same flow and tracer equations. The principal difference between model applications concerns the geometry of the sediment-water interface and the pressure conditions that are specified along this boundary. We illustrate this commonality with four different case studies. These include biologically and physically induced pore water flows, as well as simplified laboratory set-ups versus more complex field-like conditions: [1] lugworm bio-irrigation in laboratory set-up, [2] interaction of bio-irrigation and groundwater seepage on a tidal flat, [3] pore water flow induced by rotational stirring in benthic chambers, and [4] pore water flow induced by unidirectional flow over a ripple sequence. The same two example simulations are performed in all four cases: (a) the time-dependent spreading of an inert tracer in the pore water, and (b) the computation of the steady-state distribution of oxygen in the sediment. Overall, our model comparison indicates that model development for sandy sediments is promising, but within an early stage. Clear challenges remain in terms of model development, model validation, and model implementation.

Description: Oxygen depletion in coastal and estuarine waters has been increasing rapidly around the globe over the past several decades, leading to decline in water quality and ecological health. In this study we apply a numerical model to understand how salt wedge dynamics, changes in river flow and temperature together control oxygen depletion in a micro-tidal riverine estuary, the Yarra River estuary, Australia. Coupled physical–biogeochemical models have been previously applied to study how hydrodynamics impact upon seasonal hypoxia; however, their application to relatively shallow, narrow riverine estuaries with highly transient patterns of river inputs and sporadic periods of oxygen depletion has remained challenging, largely due to difficulty in accurately simulating salt wedge dynamics in morphologically complex areas. In this study we overcome this issue through application of a flexible mesh 3-D hydrodynamic–biogeochemical model in order to predict the extent of salt wedge intrusion and consequent patterns of oxygen depletion. The extent of the salt wedge responded quickly to the sporadic riverine flows, with the strength of stratification and vertical density gradients heavily influenced by morphological features corresponding to shallow points in regions of tight curvature ("horseshoe" bends). The spatiotemporal patterns of stratification led to the emergence of two "hot spots" of anoxia, the first downstream of a shallow region of tight curvature and the second downstream of a sill. Whilst these areas corresponded to regions of intense stratification, it was found that antecedent conditions related to the placement of the salt wedge played a major role in the recovery of anoxic regions following episodic high flow events. Furthermore, whilst a threshold salt wedge intrusion was a requirement for oxygen depletion, analysis of the results allowed us to quantify the effect of temperature in determining the overall severity and extent of hypoxia and anoxia. Climate warming scenarios highlighted that oxygen depletion is likely to be exacerbated through changes in flow regimes and warming temperatures; however, the increasing risk of hypoxia and anoxia can be mitigated through management of minimum flow allocations and targeted reductions in organic matter loading. A simple statistical model (R2 〉 0.65) is suggested to relate riverine flow and temperature to the extent of estuary-wide anoxia.

Description: Oxygen depletion in estuarine waters is an important factor governing water quality and ecological health. A complex and dynamic balance of physical and biogeochemical factors drive the extent and persistence of hypoxia and anoxia making it difficult to predict. An increased understanding of the effect of changing flow regimes and temperature on patterns of estuarine oxygen depletion is required to support ongoing management. Coupled physical and biogeochemical models have been applied to study the interaction of physical processes and seasonal hypoxia, however, application to riverine estuaries with tight curvature and more sporadic periods of oxygen depletion is rare. In this study we apply a finite volume 3-D hydrodynamic-biogeochemical model (TUFLOW-FV–FABM) to the Yarra River estuary, Australia, in order to predict the extent of salt-wedge intrusion and consequent patterns of oxygen depletion. The predictive capacity of the model was evaluated using a series of model verification metrics and the results evaluated to determine the dominant mechanisms affecting salt-wedge position and the extent and persistence of anoxia and hypoxia. Measures of model fit indicated that the model reasonably captured the strength of stratification and the position and extent of the salt wedge (r2 ~ 0.74). The extent of the salt wedge intrusion was controlled by riverine flow and the strength of stratification or mixing dominated by topographical features corresponding to areas of tight curvature ("horseshoe" bends). The model predicted that the extent of anoxic waters generally mimicked the extent of the salt wedge (r2 ~ 0.65) increasing during periods of low flow and reduced following episodic high flow events. The results showed two sporadically isolated "hot spots" of anoxia, the first downstream of the horseshoe bend and the second downstream of a sill. Simulated oxygen concentrations indicated that whilst a threshold salt wedge intrusion was a requirement of oxygen depletion, temperature was critical in determining the extent of hypoxia and anoxia in the estuary. These findings highlight the importance of how seasonal changes in flow events and environmental flow management can impact on estuarine oxygen depletion in a warming climate. This study provides an improved understanding of the controls on hypoxia and anoxia in riverine estuaries, which is essential to support improved prediction of nutrient dynamics and ecological heath.

Description: Dissolved inorganic carbon, CO2 and alkalinity fluxes from intertidal sediments were investigated during periods of exposure and inundation, using laboratory core incubations, field data and reactive transport model simulations. In the incubations and field data, it was found that during periods of alkalinity production, the flux of dissolved inorganic carbon (DIC) out of the sediment was significantly greater during inundation periods. This alkalinity production was attributed to the accumulation of reduced sulfur species within the sediment. This finding was supported by computational simulations which indicated that large amounts of sulfate reduction and reduced solute burial (FeS) induce an alkalinity flux from the sediment during high tide conditions. As the fate of sulfide is controlled by Fe, the sensitivity of alkalinity flux to Fe concentrations was investigated, and it was found that amount of reactive Fe in the sediment was a major driver of net alkalinity production. The finding the CO2 fluxes can be significantly lower than total metabolism during exposure has implications for how total metabolism is quantified on tidal flats.

Description: Blooms of noxious N2 fixing cyanobacteria such as Nodularia spumigena are a recurring problem in some estuaries. Here we report the results of a palaeoecological study on a temperate Australian lagoon system (The Gippsland Lakes) where we used stable isotopes and pigment biomarkers in dated cores as proxies for eutrophication and blooms of cyanobacteria. Pigment proxies show a clear signal, with an increase in cyanobacterial pigments (echinenone, canthaxanthin and zeaxanthin) in the period coinciding with recent blooms. Another excursion in these proxies was observed prior to the opening of an artificial entrance to the lakes in 1889, which markedly increased the salinity of the Gippsland Lakes. A coincident increase in the sediment organic carbon content in the period prior to the opening of the artificial entrance suggests the bottom waters of the lakes were increasingly stratified and hypoxic, which would have led to an increase in the recycling of phosphorus. After the opening of the artificial entrance there was a ~ 60 year period with low values for the cyanobacterial proxies as well as a low sediment organic carbon content suggesting a period of low bloom activity associated with the increased salinity of the lakes. During the 1940s, the current period of re-eutrophication commenced as indicated by a steadily increasing sediment organic carbon content and cyanobacterial pigments. We suggest increasing nitrogen inputs from the catchment led to the return of hypoxia and increased phosphorus release from the sediment, which drove the re-emergence of cyanobacterial blooms.

Description: Dissolved inorganic carbon (DIC), gaseous CO2 and alkalinity fluxes from intertidal sediments were investigated during periods of exposure and inundation, using laboratory core incubations, previously published field data and reactive transport model simulations. In the incubations and previous field data, it was found that during periods of alkalinity production (attributed to the accumulation of reduced sulfur species within the sediment), the flux of DIC out of the sediment was greater during inundation than the gaseous CO2 flux during exposure by a factor of up to 1.8. This finding was supported by computational simulations which indicated that large amounts of sulfate reduction and reduced sulfur burial (FeS) induce an alkalinity flux from the sediment during high tide conditions. Model simulations also found that the amount of reactive Fe in the sediment was a major driver of net alkalinity production. Our finding that CO2 fluxes can be significantly lower than total metabolism during exposure has implications for how total metabolism is quantified on tidal flats.

Description: Insight in the biogeochemistry and ecology of sandy sediments crucially depends on a quantitative description of pore water flow and the associated transport of various solutes and particles. Here, we compare and analyse existing models of tracer dynamics in permeable sediments. We show that all models can be derived from a generic backbone, consisting of the same flow and tracer equations. The principal difference between model applications concerns the geometry of the sediment-water interface and the pressure conditions that are specified along this boundary. We illustrate this commonality with four different case studies. These include biologically and physically induced pore water flows, as well as simplified laboratory set-ups versus more complex field-like conditions: [1] lugworm bio-irrigation in laboratory set-up, [2] interaction of bio-irrigation and groundwater seepage on a tidal flat, [3] pore water flow induced by rotational stirring in benthic chambers, and [4] pore water flow induced by unidirectional flow over a ripple sequence. To illustrate the potential of the generic model approach, the same two example simulations are performed in all four cases: (a) the time-dependent spreading of an inert tracer in the pore water, and (b) the computation of the steady-state distribution of oxygen in the sediment. Overall, our model comparison indicates that model development is promising, but within an early stage. Clear challenges remain in terms of model development, model validation, and model implementation.