The Value of Adding Optics to Ecosystem Models: A Case Study

Many ecosystem models have been developed to study the ocean's biogeochemical properties, but most of these models use simple formulations to describe light penetration and spectral quality. Here, an optical model is coupled with a previously published ecosystem model that explicitly represents two phytoplankton (picoplankton and diatoms) and two zooplankton functional groups, as well as multiple nutrients and detritus. Surface ocean color fields and subsurface light fields are calculated by coupling the ecosystem model with an optical model that relates biogeochemical standing stocks with inherent optical properties (absorption, scattering); this provides input to a commercially available radiative transfer model (Ecolight). We apply this bio-optical model to the equatorial Pacific upwelling region, and find the model to be capable of reproducing many measured optical properties and key biogeochemical processes in this region. Our model results suggest that non-algal particles largely contribute to the total scattering or attenuation (> 50% at 660 nm) but have a much smaller contribution to particulate absorption (< 20% at 440 nm), while picoplankton dominate the total phytoplankton absorption (> 95% at 440 nm). These results are consistent with the field observations. In order to achieve such good agreement between data and model results, however, key model parameters, for which no field data are available, have to be constrained. Sensitivity analysis of the model results to optical parameters reveals a significant role played by colored dissolved organic matter through its influence on the quantity and quality of the ambient light. Coupling explicit optics to an ecosystem model provides advantages in generating: (1) a more accurate subsurface light-field, which is important for light sensitive biogeochemical processes such as photosynthesis and photo-oxidation, (2) additional constraints on model parameters that help to reduce uncertainties in ecosystem model simulations, and (3) model output which is comparable to basic remotely-sensed properties. In addition, the coupling of biogeochemical models and optics paves the road for future assimilation of ocean color and in-situ measured optical properties into the models.

A Comparison of Hydrographically and Optically Derived Mixed Layer Depths

Efforts to understand and model the dynamics of the upper ocean would be significantly advanced given the ability to rapidly determine mixed layer depths (MLDs) over large regions. Remote sensing technologies are an ideal choice for achieving this goal. This study addresses the feasibility of estimating MLDs from optical properties. These properties are strongly influenced by suspended particle concentrations, which generally reach a maximum at pycnoclines. The premise therefore is to use a gradient in beam attenuation at 660 nm (c660) as a proxy for the depth of a particle-scattering layer. Using a global data set collected during World Ocean Circulation Experiment cruises from 1988-1997, six algorithms were employed to compute MLDs from either density or temperature profiles. Given the absence of published optically based MLD algorithms, two new methods were developed that use c660 profiles to estimate the MLD. Intercomparison of the six hydrographically based algorithms revealed some significant disparities among the resulting MLD values. Comparisons between the hydrographical and optical approaches indicated a first-order agreement between the MLDs based on the depths of gradient maxima for density and c660. When comparing various hydrographically based algorithms, other investigators reported that inherent fluctuations of the mixed layer depth limit the accuracy of its determination to 20 m. Using this benchmark, we found a similar to 70% agreement between the best hydrographical-optical algorithm pairings.

Study of Basic Wood Decay Mechanisms and Their Biotechnological Applications

The overall objective of this thesis was to gain further understanding of the non-enzymatic mechanisms involved in brown-rot wood decay, especially the role of pH, oxalic acid, and low molecular catecholate compounds on the dissolution and reduction of iron, and the formation of reactive oxygen species. Another focus of this study will be the potential application of a biomimetic free radical generating system inspired from fungi wood decay process, especially the non-enzymatic mechanism. The possible pathways of iron uptake and iron redox cycling in non-enzymatic brown-rot decay were investigated in this study. UV-Vis spectroscopy and HPLC were employed to study the kinetics and pathways of the interaction between iron and model catecholate compounds under different pH and chelator/iron molar ratio conditions. Iron chelation and reduction during early non-enzymatic wood decay processes have been studied in this thesis. The results indicate that the effects of the chelator/iron ratio, the pH, and other reaction parameters on the hydroxyl radical generation in a Fenton type system can be determined using ESR spin-trapping techniques. Data also support the hypothesis that superoxide radicals are involved in chelator-mediated Fenton processes. The mechanisms involved in free radical activation of Thermal Mechanical Pulp fibers were investigated. The activation of TMP fibers was evaluated by ESR measurement of free phenoxy radical generation on solid fibers. The results indicate that low molecular weight chelators can improve Fenton reactions, thus in turn stimulating the free radical activation of TMP fibers. A mediated Fenton system was evaluated for decolorization of several types of dyes. The result shows that the Fenton system mediated by a catecholate-type chelator effectively reduced the color of a diluted solution of synthetic dyes after 90 minutes of treatment at room temperature. The results show that compared to a neat Fenton process, the mediated Fenton decolorization process increased the production, and therefore the effective longevity, of hydroxyl radical species to increase the decolorization efficiency.