Human activities such as urban settlement, farming, forestry and recreation, have caused deterioration of water quality in many freshwater lakes worldwide. Apart from anthropogenic impacts, it is also recognized that climate has a direct influence on lake water temperature, nutrient loads, phytoplankton abundance and chemistry. However, little is known about the potential effects of future climate change on lake water quality. Understanding the dynamics, abundance and availability of nutrient pools in lake bottom sediments is fundamentally important for predicting how, and over what time-scales, lake ecosystems will respond to future scenarios such as climate change, in-lake restoration or altered external nutrient loading. Through a sediment field study on 14 different lakes, and applications of complex lake ecosystem models to three New Zealand lakes, this study examined the spatial and temporal dynamics of sediment nutrient concentrations, and made considerations of the effects of restoration measures and future climate change on lake water quality. To gain insight into processes influencing the dynamics of horizontal and vertical gradients of sediment nutrient concentrations, intact sediment cores were collected from twelve lakes within the Bay of Plenty province, North Island of New Zealand. In addition, intact sediment cores were collected from shallow Lake Te Waihora (Ellesmere) in the Canterbury province, South Island of New Zealand and shallow Lake Taihu in the Jaingsu province, China. The observed vertical concentration profiles of total phosphorus (TP) in the sediments revealed that the shape of these profiles can be similar across gradients of widely differing trophic status. Empirical and mechanistic steady state profile models were derived to describe the vertical distribution of total carbon (TC), total nitrogen (TN) and TP concentrations in the sediments. These models revealed that density-driven burial and biodiffusive mixing, which in the models also includes effects of redox-driven gradients, are strongly correlated with vertical gradients of sediment TC, TN and TP content, whereas lake trophic status was not. Despite enhancing knowledge of the processes influencing vertical gradients of sediment nutrient concentrations, little is known about the rates at which sediment nutrient concentrations may change as a response to changes in external loading or climate. Studies into the composition of bottom sediments have been undertaken intermittently over the past three decades for the 12 lakes in the Bay of Plenty. These studies, together with the data collected in this study, were used to quantify temporal changes in sediment chemistry across the lakes. Comparison of the data collected in this study with results from a survey in 1995 showed that surficial sediment (0-2 cm) TP concentrations have increased in three of the 12 lakes, at rates ranging from 27.5 to 114.4 mg P kg-1 dry wt yr-1. TN concentrations in surficial sediments have increased in nine of the 12 lakes at rates ranging from 51.8 to 869.2 mg N kg-1 dry wt yr-1. A correlation analysis revealed that temporal changes in sediment TP and TN concentrations were not significantly linearly related (pgt0.05) to catchment area or temporal changes of different water column indices considered to reflect lake trophic state, including annual mean water column concentrations of TP, TN or chlorophyll a (Chl a). While vertical profiles of sediment nutrient concentrations can be used to provide information about historical changes of trophic status in lakes, little is known about horizontal variability of sediment nutrient concentrations, including possibly relationships with horizontal variations in water column variables. In the large, shallow and eutrophic Lake Taihu, China, there are distinct horizontal water column concentration gradients of nutrients and Chl a. Concentrations are generally high in the north, where some of the major polluted tributaries enter the lake, and relatively low in the south, where macrophytes generally are abundant. To test whether these water column concentration gradients are similarly reflected in spatial heterogeneity of nutrient concentrations within the bottom sediments of Lake Taihu, I examined correlations between concentrations of TP and TN in surficial sediments (0-2 cm) and TP, TN and Chl a concentrations in water column samples determined for 32 sites in 2005. Linear correlation analysis revealed that surficial sediment TP concentrations across the 32 stations were related significantly, though weakly, to annual mean water column concentrations of TP and TN as well as Chl a. Correlations of surficial sediment TN with water column variables were, however, not significant (p gt 0.05). To better understand the effects of future climate change on lakes of different trophic status, I applied the one-dimensional lake ecosystem model, DYRESM-CAEDYM, to oligo-mesotrophic Lake Okareka, eutrophic Lake Rotoehu and highly eutrophic Lake Te Waihora. All three models were calibrated based on a three-year period (July 2002 - June 2005) and validated on a separate two-year period (July 2005 - June 2007). The model simulations generally showed good agreement with observed data for temperature, dissolved oxygen (DO), and total nutrient and Chl a concentrations. To represent a possible future climate of 2100, temperature predictions were derived from the regional climate model, DARLAM, based on the Intergovernmental Panel on Climate Change (IPCC) A2 scenario, which suggests that air temperatures by the year 2100 will increase by an average of 2.5 'C and 2.7 'C for the Bay of Plenty and the Canterbury province, respectively, relative to the base scenario (years 2002-2007). Model simulations of the future climate scenarios indicate that climatic changes generally will lead to a degradation of lake water quality in all three lakes, especially during summer months, and further suggest that the effects on annual mean surface concentrations of TP, TN and Chl a will be equivalent to an increase in external TN and TP loading by 25-50%. Simulations for Lake Rotoehu, where diatoms and cyanophytes were represented in the conceptual model, further suggest that cyanophytes will be more abundant in the future, increasing by gt15% in annual mean biomass. Although the effects of climate change may be delayed or slightly mediated by the chemical resilience of the sediment nutrient pools, the effects of climate change on lake water quality in the New Zealand lakes will be of a magnitude that should be considered as management strategies are planned and implemented, thus increasing the probability of successful preservation or improvement in water quality in future decades.

In this research, a recent version of the Boreal Ecosystem Productivity Simulator (BEPS), called BEPS-TerrainLab, was adapted to northern peatlands and evaluated using observations made at the Mer Bleue bog located near Ottawa, Ontario, and the Sandhill fen located near Prince Albert, Saskatchewan. The code was extended and modified with a major focus on the adequate representation of northern peatlands' multi-layer canopy and the associated processes related to energy, water vapour and carbon dioxide fluxes through remotely-sensed leaf area index (LAI) maps. An important prerequisite for the successful mapping of LAI based on remote sensing imagery is the accurate measurement of LAI in the field with a standard technique such as the LAI-2000 plant canopy analyzer. As part of this research, a quick and reliable method to determine shrub LAI with the LAI-2000 instrument was developed. This method was used to collect a large number of LAI data at the Mer Bleue bog for the development of a new remote sensing-based methodology using multiple endmember spectral unmixing that allows for separate tree and shrub LAI mapping in ombrotrophic peatlands. A slight modification of this methodology allows for its application to minerotrophic peatlands and their surrounding landscapes. These LAI maps were used to explicitly represent the tree and shrub layers of the Mer Bleue bog and the tree and shrub/sedge layers of the Sandill fen within BEPS-TerrainLab. The adapted version of BEPS-TerrainLab was used to investigate the in fluence of mescoscale topography (Mer Bleue bog) and macro- and mesoscale topography (Sandhill fen) on wetness, evapotranspiration, and gross primary productivity during the snow-free period of 2004. This research suggests that future peatland ecosystem modelling efforts at regional and continental scales should include a peatland type-specific differentiation of macro- and mesoscale topographic effects on hydrology, to allow for a more realistic simulation of peatlands' soil water balance. This is an important prerequisite for the reduction of currently existing uncertainties in wetlands' contribution to North America's carbon dioxide and methane annual fluxes from an ecosystem modelling perspective.

The potential for life to control its environment was first suggested by Lovelock (1972). Charlson et al (1987) proposed a role for marine planktonic ecosystems in global climate regulation via the production and ventilation to the atmosphere of dimethylsulphide (DMS), a by-product of phytoplankton metabolism. Once in the atmosphere DMS contributes to the formation of cloud condensation nuclei, and increases the amount and brightness of cloud. This affects the albedo of the planet, reflecting more incident sunlight back into space, and cooling the earth. In common with many other 'hypotheses' regarding complex adaptive systems, the hypothesis proposed by Charlson et al (1987) is not experimentally testable. The production and ventilation to the atmosphere of DMS is the result of complex interactions between biological, chemical and physical processes. Consequently, increasing use is being made of mathematical models that simulate these processes to advance understanding of it (Archer et al. 2002). This study examines one of the fundamental mechanisms proposed by the Charlson et al (1987) hypothesis, that increasing global temperatures will lead to increased ventilation of DMS from the ocean to the atmosphere. The study develops one-dimensional biogeochemical models of DMS production by upper ocean ecosystems, based on the model proposed by Gabric et al. (1993b). The models are examined to elucidate their fundamental mathematical properties, and are subjected to sensitivity analysis to identify important processes and parameters. These investigations identify a simpler model that can reproduce the predictions of the Gabric et al. (1993b) model. Predictions derived from model simulations forced by climatologies of measured physical data are compared to a global database of measurements of sea surface DMS concentrations, and to observed depth profiles of DMS in the upper ocean. These comparisons confirm that all models are in good qualitative agreement with measured data. The fifteen global climate prediction models currently in use around the globe all predict substantial warming effects from the ventilation of anthropogenic carbon dioxide to the atmosphere. A simplified DMS model is calibrated to climatologies of Antarctic chlorophyll and DMS data and reproduces the data with great precision. The calibrated model is applied in global warming scenarios to 'test' the efficacy of the mechanism proposed by the Charlson et al (1987) hypothesis. This simulation provides evidence that the response predicted by the hypothesis is indeed feasible, and that substantial increases (up to 45%) in the ventilation of DMS to the atmosphere could be possible in some circumstances. The results of the modelling study provide impetus for further examination of field data. If couplings between marine biota and atmosphere are feasible, then they may be operating contemporarily, and may be detectable. Atmospheric DMS is oxidised to form aerosols (Miller et al. 2002) that influence the aerosol optical depth of the atmosphere. Archives of remote sensed ocean chlorophyll a concentration and aerosol optical depth are examined for evidence of the biologically mediated couplings. A clear coupling between aeolian dust and marine phytoplankton is evident from this analysis, suggesting that the deposition of dust from the atmosphere is a major factor controlling phytoplankton growth in many parts of the ocean. A second coupling between marine phytoplankton and atmospheric aerosols is also detected. This coupling is apparently not related to dust and is symmetrical about the equator, despite the substantial differences in the atmospheres and oceans of each hemisphere. It is speculated that this coupling may reflect the influence of the ventilation of DMS produced by marine phytoplankton on the atmosphere. This thesis provides new evidence supporting the important role of marine ecosystems in global climate regulation by the production of DMS. This evidence is principally obtained from a biogeochemical modelling approach, but is supported by analyses of empirical data. The concordance of results obtained from different approaches suggests that the contribution of marine ecosystems to global climate regulation is real, important and currently active.

In this research, a recent version of the Boreal Ecosystem Productivity Simulator (BEPS), called BEPS-TerrainLab, was adapted to northern peatlands and evaluated using observations made at the Mer Bleue bog located near Ottawa, Ontario, and the Sandhill fen located near Prince Albert, Saskatchewan. The code was extended and modified with a major focus on the adequate representation of northern peatlands' multi-layer canopy and the associated processes related to energy, water vapour and carbon dioxide fluxes through remotely-sensed leaf area index (LAI) maps. An important prerequisite for the successful mapping of LAI based on remote sensing imagery is the accurate measurement of LAI in the field with a standard technique such as the LAI-2000 plant canopy analyzer. As part of this research, a quick and reliable method to determine shrub LAI with the LAI-2000 instrument was developed. This method was used to collect a large number of LAI data at the Mer Bleue bog for the development of a new remote sensing-based methodology using multiple endmember spectral unmixing that allows for separate tree and shrub LAI mapping in ombrotrophic peatlands. A slight modification of this methodology allows for its application to minerotrophic peatlands and their surrounding landscapes. These LAI maps were used to explicitly represent the tree and shrub layers of the Mer Bleue bog and the tree and shrub/sedge layers of the Sandill fen within BEPS-TerrainLab. The adapted version of BEPS-TerrainLab was used to investigate the in fluence of mescoscale topography (Mer Bleue bog) and macro- and mesoscale topography (Sandhill fen) on wetness, evapotranspiration, and gross primary productivity during the snow-free period of 2004. This research suggests that future peatland ecosystem modelling efforts at regional and continental scales should include a peatland type-specific differentiation of macro- and mesoscale topographic effects on hydrology, to allow for a more realistic simulation of peatlands' soil water balance. This is an important prerequisite for the reduction of currently existing uncertainties in wetlands' contribution to North America's carbon dioxide and methane annual fluxes from an ecosystem modelling perspective.

No description available.

Object - oriented ecosystem modelling was introduced in the early of 1990s ( Silvert, 1992 ). From that time on, ecosystem models using object - oriented programming ( OOP ) has earned significant achievements with increasing upgraded information technology. The common purposes of ecosystem modellers are to build a model with flexible structure, which allow continuous modifications on the model content. In last decade, ecosystem modellers have put a large number of efforts to practice the OOP approaches in order to implement a true object - oriented ecosystem model. However, these previous work have not fully take advantage of object - orientation because of misusing more or less this technique. This paper explains the shortcoming of these previous endeavours therewith points out a practical solution that using the methodology of object - oriented software engineering and some relative novel information techniques. A case study SALMO - OO will be presented in this paper to prove Silvert ' s assumption that OOP play an important role on ecosystem modelling approaches. Moreover, the results of SALMO - OO convince that object - oriented ecosystem modelling can be achieved by using object - oriented software engineering associating with a true object - oriented programming language ( Java in this case ). / Thesis (M.Sc.)--School of Earth and Environmental Sciences, 2006.

A three dimensional time-dependent coupled ecosystem model is applied to Izmir Bay for the first time. Delft3D modelling suite&rsquo / s FLOW and ECO modules are adapted and tuned for the region. A reference model with a time frame of three years is produced that represents the current physical and biogeochemical status of the bay. Model skill assessment methods are used as a measure of model performance and to address the shortcomings of it. The hydrodynamics model is able to produce physical features in terms of seasonality and spatial distribution within reasonable ranges, whereas the ecosystem model has certain discrepancies which can be reduced with improved quality of model inputs, such as open boundary conditions, and fresh water and nutrient fluxes. The reference model is used as a tool with predictive capacity to assess the ecosystem response of the bay to possible changes it may undergo in the future. Five nutrient enrichment/reduction scenarios are constructed to predict the reactions of the bay to changing external inputs of DIN and PO4. Results suggest that both physical and biogeochemical properties of the bay show strong horizontal gradients between outer and inner regions in which both natural and anthropogenic influences are effective. It is revealed that Outer bays are mostly occupied by waters originating from the oligotrophic Aegean Sea, while eutrophicated inner regions are mainly controlled by local influences such as increased fresh water inputs and excessive wastewater discharges. Results of the nutrient enrichment/reduction scenarios suggest that the N-limited Inner and Middle bays and the P-limited Outer bays, give contrasting reactions to changes in inputs of DIN and PO4 such that the former is more sensitive to DIN input whereas the latter is more sensitive to PO4 input. Due to the existence of these two contrasting environments in the bay, availability of one nutrient is dependent on the availability of the other, therefore treatment of both should be considered in parallel. Among the scenarios tested in this study, the best possible option to reduce eutrophication in Izmir Bay is to prevent the increase of PO4 input and to reduce the DIN input simultaneously. These outcomes are aimed to provide a scientific insight for coastal policy makers and environmental managers on how changes in anthropogenic influences can impact the marine ecosystem of the bay.

Recent shifts towards ecosystem based fisheries management (EBFM) around the world have necessitated consideration of effects of fishing on a larger range of species than previously. Non-selective multispecies fisheries are particularly problematic for EBFM, as they can contribute to erosion of ecosystem structure. The trade-off between catch of productive commercial species and abundance of low-productivity species is unavoidable in most multispecies fisheries. A first step in evaluation of this trade-off is estimation of productivity of different species but this is often hampered by poor data. This thesis develops techniques for estimating productivity for data-limited species and aims to help clarify EBFM policy objectives for the fisheries of New South Wales (NSW), Australia. It begins with development of an age-structured model parameterised in terms of optimal harvest rate, UMSY. UMSY is a measure of productivity, comparable among species and easily communicated to managers. It also represents a valid threshold for prevention of overfishing. The model is used to derive UMSY for 54 Atlantic fish stocks for which recruitment parameters had previously been estimated. In most cases, UMSY was strongly limited by the age at which fish were first caught. However, for some species, UMSY was more strongly constrained by life history attributes. The model was then applied to twelve species of Australian deepwater dogshark (Order Squaliformes), known to have been severely depleted by fishing. Results showed that the range of possible values of UMSY for these species is very low indeed. These findings enabled a preliminary stock assessment for three dogsharks (Centrophorus spp.) currently being considered for threatened species listing. Preliminary results suggest they have been overfished and that overfishing continues. Finally, an Ecopath with Ecosim ecosystem model, representing the 1976 NSW continental slope, is used to illustrate trade-offs in implementation of fishing policies under alternative policy objectives. Results are compared with those of a biogeochemical ecosystem model (Atlantis) of the same system, built by scientists from CSIRO. While there were large differences in model predictions for individual species, they gave similar results when ranking alternative fishing policies, suggesting that ecosystem models may be useful for exploring broad-scale strategic management options.

Recent shifts towards ecosystem based fisheries management (EBFM) around the world have necessitated consideration of effects of fishing on a larger range of species than previously. Non-selective multispecies fisheries are particularly problematic for EBFM, as they can contribute to erosion of ecosystem structure. The trade-off between catch of productive commercial species and abundance of low-productivity species is unavoidable in most multispecies fisheries. A first step in evaluation of this trade-off is estimation of productivity of different species but this is often hampered by poor data. This thesis develops techniques for estimating productivity for data-limited species and aims to help clarify EBFM policy objectives for the fisheries of New South Wales (NSW), Australia. It begins with development of an age-structured model parameterised in terms of optimal harvest rate, UMSY. UMSY is a measure of productivity, comparable among species and easily communicated to managers. It also represents a valid threshold for prevention of overfishing. The model is used to derive UMSY for 54 Atlantic fish stocks for which recruitment parameters had previously been estimated. In most cases, UMSY was strongly limited by the age at which fish were first caught. However, for some species, UMSY was more strongly constrained by life history attributes. The model was then applied to twelve species of Australian deepwater dogshark (Order Squaliformes), known to have been severely depleted by fishing. Results showed that the range of possible values of UMSY for these species is very low indeed. These findings enabled a preliminary stock assessment for three dogsharks (Centrophorus spp.) currently being considered for threatened species listing. Preliminary results suggest they have been overfished and that overfishing continues. Finally, an Ecopath with Ecosim ecosystem model, representing the 1976 NSW continental slope, is used to illustrate trade-offs in implementation of fishing policies under alternative policy objectives. Results are compared with those of a biogeochemical ecosystem model (Atlantis) of the same system, built by scientists from CSIRO. While there were large differences in model predictions for individual species, they gave similar results when ranking alternative fishing policies, suggesting that ecosystem models may be useful for exploring broad-scale strategic management options.

Recent shifts towards ecosystem based fisheries management (EBFM) around the world have necessitated consideration of effects of fishing on a larger range of species than previously. Non-selective multispecies fisheries are particularly problematic for EBFM, as they can contribute to erosion of ecosystem structure. The trade-off between catch of productive commercial species and abundance of low-productivity species is unavoidable in most multispecies fisheries. A first step in evaluation of this trade-off is estimation of productivity of different species but this is often hampered by poor data. This thesis develops techniques for estimating productivity for data-limited species and aims to help clarify EBFM policy objectives for the fisheries of New South Wales (NSW), Australia. It begins with development of an age-structured model parameterised in terms of optimal harvest rate, UMSY. UMSY is a measure of productivity, comparable among species and easily communicated to managers. It also represents a valid threshold for prevention of overfishing. The model is used to derive UMSY for 54 Atlantic fish stocks for which recruitment parameters had previously been estimated. In most cases, UMSY was strongly limited by the age at which fish were first caught. However, for some species, UMSY was more strongly constrained by life history attributes. The model was then applied to twelve species of Australian deepwater dogshark (Order Squaliformes), known to have been severely depleted by fishing. Results showed that the range of possible values of UMSY for these species is very low indeed. These findings enabled a preliminary stock assessment for three dogsharks (Centrophorus spp.) currently being considered for threatened species listing. Preliminary results suggest they have been overfished and that overfishing continues. Finally, an Ecopath with Ecosim ecosystem model, representing the 1976 NSW continental slope, is used to illustrate trade-offs in implementation of fishing policies under alternative policy objectives. Results are compared with those of a biogeochemical ecosystem model (Atlantis) of the same system, built by scientists from CSIRO. While there were large differences in model predictions for individual species, they gave similar results when ranking alternative fishing policies, suggesting that ecosystem models may be useful for exploring broad-scale strategic management options. / Science, Faculty of / Resources, Environment and Sustainability (IRES), Institute for / Graduate