This research evaluates the decomposition of leaf litter while in litter traps. More specifically this study asks, ‘Does sugar maple (Acer saccharum Marsh.), American basswood (Tilia Americana L.) and American beech (Fagus grandifolia Ehrh.) leaf litter collected bi-weekly from litter traps undergo a loss of dry mass and nutrient content (C, N, P, K, Ca and Mg) in comparison to freshly abscised leaf litter?’The objective of the initial experiment was to determine if sugar maple, basswood and beech leaf litter collecting in litter traps, while exposed to in-situ conditions, experienced decomposition. Results indicated that sugar maple, basswood and beech leaf litter experienced early stages of decomposition and identified precipitation, freezing temperatures and microbial activity as possible mechanisms for the observed decomposition. It was found that the dry weight of sugar maple and basswood differed significantly (p < 0.05 and p < 0.10, respectively) post- 14-day experiment period as compared to the initial dry weight. Consequently, three experiments were completed to examine the aforementioned variables. Conclusions were based on measured changes in the mass and nutrient (C, N, P, K, Ca and Mg) content of freshly abscised sugar maple, basswood and beech leaf litter under ex-situ conditions. It was found that the dry weight sugar maple and basswood leaf litter exposed to 30 mm, 60 mm and 100 mm of precipitation differed significantly (p < 0.05) as compared to freshly abscised leaf litter. In general, this research affirmed that precipitation and freezing temperature contribute to a change in mass and nutrient content of leaf litter collecting in litter traps. Furthermore, through measurable production of CO2 and Community Level Physiological Profiling it was determined that microbes are present and active on the leaf surface and contribute to the decomposition of leaf litter in litter traps.

Before January 2003, the Dapeng Bay lagoon was occupied by oyster culture racks and fish farming cages. Along with the development of the Dapeng Bay National Scenic Area Administration, the government has started taking actions on removing oyster culture racks, and has kept improving the quality of lagoon water. Nowadays, the government is implementing sediment dredging plan. As to discuss the change of biogeochemical processes, this study is divided by three parts, including the first stage, before the removal of oyster culture rafts; second stage, after the removal of oyster culture rafts, and the third stage, after implementation of sediment dredging. At the first stage, the annual mean of water exchange time at the Dapeng Bay was approximately 10 days. At the second and third stage, the annual mean of water exchange time were 6.2 days and 8.3 days, respectively. The difference is not significant between the second stage and third stage. The trend of water exchange time is similar to the seawater exchange rate. Distributions of chlorophyll a were controlled by temperature and solar radiation, rather than by nutrient concentration throughout three-stage periods. Although the change tendency between chlorophyll a, DIN, and DIP at the third stage is similar, chlorophyll a correlated positively with DIN and DIP only in fall. The net ecosystem production (NEP) was positive (p¡Ðr > 0) at all three stages, so the Dapeng Bay was always an autotrophic system throughout the study period. Before the removal of the oyster culture racks, the NEP was 5.64 mole C m-2 yr-1, after that, it increase to 11.64 mole C m-2 yr-1. During the sediment dredging period, the NEP was 14.31 mole C m-2 yr-1. The NEP increases 106 % from the first stage to the second stage, and increases 23% from the second stage to the third stage. The environmental remediation appears to produce significant influence on NEP. The concentration of DIN¡BDSi¡BDIP decreases by removing the oyster culture of racks. But the concentrations of particulate and dissolved organic carbon and nitrogen increase sharply after removing the oyster culture racks. Nevertheless, the concentration of dissolved organic carbon, nitrogen and the phosphorus decreases during the third stage, resulted mainly from the improvement of water quality. The system changed from the condition of phosphorus surplus (Si/N=1.8¡Ó1.2 and N/P=7.4¡Ó5.2) during the first and second stage to the condition of phosphorus limitation (Si/N=1.0¡Ó1.2 and N/P=22.2¡Ó18.7) during the third stage. The ratios of particulate organic carbon and nitrogen (POC/PN) are 7.7¡Ó1.1, 8.0¡Ó1.0, 6.5¡Ó1.3, respectively. The ratio at the third stage is very close to the Redfield ratio (C/N=6.6), which may result from the improvement of water quality. In terms of temporal and spatial variation of various parameters, DO variability was strong in the time scale than in the spatial scale, but nutrients and POC show a decrease of spatial variability from the first stage to the third stage. The removal of oyster culture racks, and the implementation of sediment dredging plan at the Dapeng Bay have significant influence on the improvement of lagoon environment for the past ten years.

This study aims to understand the role of the Tapong Bay on carbon biogeochemical cycle in the coastal zone and the influence of terrigenous inputs on ecosystem functioning in the Tapong Bay. The Tapong Bay is a semi-enclosed lagoon, occupied largely by fish farming cages and oyster culture racks. There is only one tidal inlet for exchanging water between the Tapong Bay and Taiwan Strait, which results in a low water exchange rate and oxygen deficient condition in the bottom water of the inner bay. The annual mean of water exchange time is about 10.6 days that is much longer than that in the Chiku Lagoon (5.8 days). Experimental results show that biological activity and variations of hydrochemistry primarily control the distributions of carbon and nutrients. Excess of DIP likely occurred in the Tapong Bay. Seasonal variations of primary productivity are apparently controlled by temperature, solar radiation and turbidity. The regression slope between particulate organic carbon and nitrogen approaches the Redfield ratio, indicating that organic carbon is derived primarily from biological production. The stratification of water column in the Tapong Bay was observed throughout the year. Diffusion from sediment may thus contribute significantly to nutrient distributions in bottom water. Diffusion flux estimated from porewater to bottom water is about 7.6% of annual mean input for DIN and is about 1.0% for DIP. Calcification process was observed in the Tapong Bay indicating that the oyster culture would affect the carbon budget in the bay. The annual mean production rate of organic carbon estimated from the biogeochemical model is about 5.80 mole C m-2 yr-1, implying that the Tapong Bay is an autotrophic system. The net ecosystem production (NEP) derived from diel observation is about 6.29 mmole C m-2 d-1 that is closed to 6.65 mmole C m-2 d-1 estimated from the biogeochemical modeling. The annual nitrogen fixation exceeds the annual denitrification [(nfix-denit)¡×1.30 mole m-2 yr-1] in the Tapong Bay. Carbon biogeochemical fluxes and budgets differ significantly between the Tapong Bay and the Chiku Lagoon, which may be arisen from pronounced difference in terrigenous inputs and seawater exchange rates.

A 3D numerical model ¡V COHERENS has been applied to construct a coupled hydrodynamic and ecological model for studying Tapeng Bay, which is a coastal lagoon situated in southwest of Taiwan. The simulations have been carried out to study the influences and their interacting mechanisms among the tidal currents, nutrients and micro planktons in the Lagoon. Model results have been compiled for calculating the nutrient fluxes and the primary productions in the Tapeng Bay. Tapeng Bay is a semi-enclosed coastal lagoon, which has only one tidal inlet for exchanging lagoon water with the coastal currents along the Kaoping coast on the narrow shelf in southwest of Taiwan. The study area is situated in the tropical climate zone where has sunshine through out the year except the rainy days concentrated in the summer season, which is influenced by the southwest monsoon. There are several drainage channels that collect the untreated domestic sewerage and wastewater discharged from the fish farms surround the lagoon. The discharges in these channels are usually low during the dry season. The solid contained in the water are mostly settled on the channel beds. During the raining season, high discharges due to the storm rainfalls re-suspend the sediments and carry into the lagoon. These sediments, which contain high concentrations of suspended solids and nutrients, cause the Bay water highly eutrophied. Therefore, the Bay is fully influenced by the seasonal variations. There are a lot of aquaculture, i.e. oyster farming and fish cage, in the Bay area since the water is calm and rich. But the balance between the nature and the anthropogenic disturbance is breaking. Besides the water level variation generated from the tidal inlet, the fresh water inflow from 3 major channels are included in the model to simulate their influences to the hydrodynamics and the density driven circulation due to changing salinities and temperatures from these inlets. Plankton, detritus, dissolved nutrients and dissolved oxygen is taking into account as the model variables for this marine eco-system. The plankton growth is mainly generated due to temperature, light intensity and nutrient level. Only the nitrogen cycle has been considered in the model by assuming there are enough supply of phosphate and silicate. Model runs have been carried out according to different seasonal situations of the boundary conditions. Furthermore, climates (heats, lights, winds, etc) are also included in the model to distinct seasonal characteristics. It is shown, from the model results, that the currents mainly dominate the distribution of nutrients in the Tapeng Bay. The nutrient level controls plankton growth. The nutrient sources are mainly coming from the coastal currents (through tidal inlet) in the wintertime, whereas the summer source was from the drainage channels due to the wash out by the high discharge rates. Beside these, dissolved oxygen concentrations in the Bay water are strongly influenced by the plankton growth rate, faster the photosynthesis higher the DO concentrations. The eutrophication levels of the Tapeng Bay water have been compiled using the plankton carbon level modeled at various situations. According to the Nixon standard (1995), Tapeng Bay has eutrophication through out the year. Mesotrophic condition can be observed during the wintertime, whereas the hypereutrophic level can be concluded during the raining season.

Contaminated sediments are periodically subjected to resuspension processes during either storm events or due to dredging. In sediments, metals are often contained in insoluble low bioavailability forms. Upon resuspension, however, biogeochemical processes associated with the exposure to more oxic conditions may lead to transformation and release of the metals, giving rise to exposure and risk in the water column. Batch experiments suggested that oxidation of reduced species and corresponding pH decrease were the most importance processes controlling metals release upon sediment resuspension. A mathematical model was implemented to better understand the complex underlying biogeochemical reactions that affect metals release. The model described the metals dynamics and other inter-related important biogeochemical factors well and was successful at predicting the metals release from different sediment reported in the literature. Tidal and other cyclic variations in oxygen, pH and other relevant parameters in the overlying water may also lead to cyclic transformations and release of metals from surficial sediments. In simulated estuarine microcosm experiments, cyclic variations in pH and salinity due to freshwater/saltwater exchange were shown to lead to cyclic variations in metal release. Both pH and salinity were important factors controlling interstitial dissolved metals concentrations, however, in terms of freely dissolved metals concentrations, which have been considered to be more related with toxicity and bioavailability, pH was the single most important parameter. The mathematical model was extended to the conditions of the cyclic behavior in an estuary and successfully described metals release under such conditions. It is believed that the model can be used to predict the metals behavior in other sediments and conditions by model calibration with a similar experimental approach to that used in this study. / text

Thalassiosira oceanica, a marine centric diatom, possesses an extracellular reductase that reduces iron (Fe(III)) bound to organic complexes as part of a high-affinity Fe transport mechanism. A number of Fe(III) organic complexes are reduced, including siderophores---effective Fe chelates produced by microorganims in response to Fe stress. Reduction rates are inversely related to the relative stability constants of the oxidized and reduced Fe chelates (log Kox/Kred), and vary by a factor of 2.4 in accordance with theoretical predictions. Under Fe-limiting conditions, reduction rates increase and the ability of T. oceanica to transport Fe from siderophores is enhanced. Iron bound to the siderophore desferrioxamine B (DFB) is reduced 2 times faster than it is taken up, suggesting that the reductase is well coupled to the Fe transporter, and can provide all the inorganic Fe to account for the measured Fe uptake rates in the presence of excess DFB. The efficacy of the reductase in providing inorganic Fe for uptake and growth is ultimately dependent on the relative concentrations of excess ligands in solution and cell surface Fe transporters competing for inorganic Fe. The rates of Fe reduction and uptake are twice as fast in cells grown in NO3- compared to those grown in NH 4+, suggesting a link with cellular N metabolism and with NO3- utilization in particular. Enhanced Fe reductase activity in NO3--grown cells enables them to maintain a 1.6-fold higher cellular Fe concentration under low Fe conditions. / Experiments conducted in the subarctic Pacific, an Fe-limited oceanic region, demonstrated that even indigenous plankton (both prokaryotic and eukaryotic plankton) have the ability to acquire Fe bound to strong organic chelates. Large phytoplankton species (>3 mum) reduce Fe bound to siderophores extracellularly. Because the predominant form of dissolved Fe in the sea is bound to strong organic complexes, a reductive mechanism as described here may be a critical step in Fe acquisition by phytoplankton.

No description available.

I examined the distribution of stable isotope ratios of nitrogen $( delta sp{15}$N) and carbon $( delta sp{13}$C) in fish and aquatic invertebrates. Animals are enriched in $ delta sp{15}$N compared to their diet and I hypothesized that among-lake variation in the $ delta sp{15}$N of a top predator should reflect variation in the length of the food chain leading to it. A comparative study of a biomagnifying contaminant, mercury, confirmed that the presence or absence of certain key organisms such as pelagic forage fish and the crustacean Mysis relicta determined among-lake variation in mercury in lake trout, a top predator in the lakes. Mercury levels from the longest food chains where pelagic forage fish and Mysis were present were higher than those from the shortest food chains where these last two components were missing. This biogeographic variation in food chain length was correlated with variation in the $ delta sp{15}$N of trout. The use of $ delta sp{15}$N as a continuous, integrative measure of trophic position was further supported by its correlation to mercury in lake trout. However, such cross-system comparisons in $ delta sp{15}$N can be complicated by differences in $ delta sp{15}$N at the base of the food chain. Using large primary consumers (unionid mussels) as bio-indicators, I showed that $ delta sp{15}$N increases markedly with the human population in the lake watershed, an effect of the high $ delta sp{15}$N of human sewage. Correcting for this baseline variation in $ delta sp{15}$N, I reported that food chains leading up to nearshore fish species varied by about only one trophic level among the 35 lakes studied. A study of the $ delta sp{15}$N of coral reef and intertidal organisms collected along the coast of the the Carribean island of Barbados extended these patterns observed in lakes to coastal systems: baseline variation in $ delta sp{15}$N was related to human density on the adjacent watershed and within-site variation $ delta sp{15}$N

This dissertation focuses on understanding the complex interactions between hydrological and geochemical processes, and specifically how these interactions are affected by subsurface heterogeneity across scales. Heterogeneity in the form of macropores and fractures provide preferential flowpaths and affect contaminant transport. Biogeochemical processes are also strongly affected by such heterogeneities. Any lithological layering or interface (e.g. plume fringe, wetland-aquifer boundary, etc.) increases biogeochemical activity around that interface. Hydrologic conditions, rainfall events, drainage patterns, and pH variations are also dominant controls on redox processes and thereby affect contaminant distribution and migration. An inherent limitation of modeling fate and transport of contaminants in the subsurface is that the interactions among biogeochemical processes are complex and non-linear. Therefore, this research investigates the effect of hydrological variations and physical heterogeneity on coupled biogeochemical processes across column and landfill scales. Structural heterogeneity in the form of macropore distributions (no macropore, single macropore, and multiple macropores) in experimental soil columns is investigated to accurately model preferential flow and tracer transport. This research is crucial to agricultural systems where soil and crop management practices modify soil structure and alter macropore densities. The comparison between deterministic and stochastic approaches for simulating preferential flow improved the characterization of interface parameters of the dual permeability model, and outlined the need for efficient sampling algorithms or additional datasets to yield unique (equifinal) soil hydraulic parameters. To evaluate the effect of heterogeneity on redox processes, repacked soil columns with homogeneous and heterogeneous (layered) profiles from soil cores collected at the Norman Landfill site, Oklahoma, USA were employed. Results indicate that heterogeneity in the form of textural layering is paramount in controlling redox processes in the layered column. To evaluate the effect of hydrologic conditions on redox processes, temporal data at the Norman landfill site was used. Results indicate that seasonal hydrologic variations exert dominant control over redox-sensitive concentrations. An integrated MCMC algorithm was devised to upscale linked biogeochemical processes from the column to the field scale. Results indicate that heterogeneity and hydrologic processes are paramount in controlling effective redox concentrations at the Norman landfill site.

[Truncated abstract] Estimating internal biogeochemical fluxes is essential to the understanding of the dynamic of aquatic ecosystems. Different ecological approaches have been used to gain insight into the internal cycling, but success has been limited. A critical point is the identification of the characteristic scales of patterns and the underlying processes affecting the behaviour of biological and chemical species. Failing to capture these scales leads to misinterpretation of field and numerical data. In this study, key aspects in the design of ecological surveys are identified to ensure that the internal biogeochemical processes are well represented. In the first part of this thesis, a 1D reaction-diffusion-advection equation is used to investigate the formation of patterns and relevant time and spatial scales. This is used to define an approach for the determination of a critical domain size that allows differentiation of the role of local and internal cycling from advective fluxes across the open boundaries in a shallow coastal ecosystem. By using a 3D numerical model, in conjunction with an extensive field data set, it is shown that domain sizes must be larger than this critical value in order to capture the patterns generated within the system. For smaller domains, transport processes control the evolution of the system across the boundaries misleading the interpretation of the internal ecological dynamics. The study of the influence of boundary fluxes on ecological patchiness was motivated by the need to define the size of the domain necessary for the assessment of the impact of a sewage outflow on a coastal regime. The quantification of biogeochemical processes has proven to be difficult to achieve especially under conditions of high spatial and temporal hydrodynamic and biogeochemical variability. In the second part of this thesis, a Lagrangian experimental design is employed to estimate biogeochemical rate coefficients in situ. A set of four drogues and a cross-transect sampling design is used to capture the patchy distribution of phytoplankton and nutrient species, and high transport and mixing rates. ... Total chlorophyll from both models shows similar behavior when the variability in the 3D model, expressed as Chlamax/Chlamin, is low. When Chlamax/Chlamin is high, the difference between the biomass predicted by the two models reaches 30% due to the generation of localised patches. Comparison of the 1D and 3D results highlights the need of using models that are able to resolve the spatial complexity to some extent, as the use of averaged properties may produce misleading results. This is especially important in the presence of patches with differential physiological and biogeochemical characteristics, and nonlinear processes, in which case biomass average is not necessarily linearly related to the averaged environment.