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Moss dominated ecosystems are an important part of the global terrestrial carbon cycle. Over large areas, remote sensing can be useful to provide an improved understanding of these ecosystems. Two boreal mossess (Pleurozium and Sphagnum) were assessed using remote sensing based spectral vegetation indices for estimating biochemical capacity and photosynthetic efficiency by varying net photosynthesis rate via changes in water content. In the laboratory, changes in the normalized difference vegetation index (NDVI) and chlorophyll index coincided with declining photosynthetic capacity due to desiccation. This effect was more dramatic in Sphagnum. The photochemical reflectance index (PRI) did not vary with changes in CO2 supply as anticipated, possibly due to overriding effects of changing water content. The water band index (WBI) was strongly related to water content but this relationship showed an uncoupling in the field. Bi-directional reflectance measurements indicated what WBI was sensitive to sensor, sun, and moss surface slope angles. / xi, 110 leaves : ill. (some col.) ; 29 cm.

Complex biogenic habitats created by large canopy-forming macroalgae on intertidal and shallow subtidal rocky reefs worldwide are increasingly affected by degraded environmental conditions at local scales and global climate-driven changes. A better understanding of the mechanisms underlying the impacts of complex suites of anthropogenic stressors on algal forests is essential for the conservation and restoration of these habitats and of their ecological, economic and social values. This thesis tests physical and biological mechanisms underlying the impacts of different forms of natural and human-related disturbance on macroalgal assemblages dominated by fucoid canopies along the east coast of the South Island of New Zealand. A field removal experiment was initially set up to test assemblage responses to mechanical perturbations of increasing severity, simulating the impacts of disturbance agents affecting intertidal habitats such as storms and human trampling. Different combinations of assemblage components (i.e., canopy, mid-canopy and basal layer) were selectively removed, from the thinning of the canopy to the destruction of the entire assemblage. The recovery of the canopy-forming fucoids Hormosira banksii and Cystophora torulosa was affected by the intensity of the disturbance. For both species, even a 50% thinning had impacts lasting at least eighteen months, and recovery trajectories were longer following more intense perturbations. Independently of assemblage diversity and composition at different sites and shore heights, the recovery of the canopy relied entirely on the increase in abundance of these dominant fucoids in response to disturbance, indicating that functional redundancy is limited in this system. Minor understory fucoids, which could have provided functional replacement for the dominant habitat formers, had reduced rates of growth or recruitment when the overlying canopy was disturbed. I then used a combination of field and laboratory experiments to test the impacts of physical and biotic stress sources on the dominant fucoids H. banksii and C. torulosa. The large fucoid Durvillaea antarctica was also included in one of the laboratory investigations. I assessed how altered physical and biotic conditions affect these important habitat formers, both separately and in combination. Physical stressors included increased sedimentation, nutrient enrichment and warmer water temperatures. Biotic stress originated from interspecific competition with turfs of articulated coralline algae and ephemeral, fast-growing green and brown algae. Sediment deposition severely reduced the survival and growth of recently settled H. banksii, C. torulosa and D. antarctica germlings in laboratory experiments. In the field, the recruitment of H. banksii on unoccupied substrates was significantly higher than in treatments in which sediments or mats of turf-forming coralline algae covered the substrate. This shows that sediment deposition and space pre-emption by algal turfs can synergistically affect the development of fucoid beds. Further impacts of sediment accumulation in the benthic environment were investigated using in situ and laboratory photorespirometry techniques to assess the contribution of coralline algae to assemblage net primary productivity (NPP), both in the presence and absence of sediment. The NPP of articulated corallines was reduced by sediment. Sediment accumulation among the thalli limited the access of the corallines to the light and induced photoinhibitive mechanisms. In the absence of sediment, however, coralline algae enhanced the NPP of assemblages with a fucoid canopy, showing the importance of synergistic interactions among the components of multi-layered assemblages in optimizing light use. Nutrient enrichment had a less pervasive influence on the dominant fucoids H. banksii and C. torulosa than sedimentation. In laboratory experiments, nutrients stimulated the growth of H. banksii and C. torulosa germlings. However, negative impacts of high nutrient levels were observed for the early life stages of D. antarctica. The abundance of opportunistic, fast-growing algae rapidly increased in response to nutrient enrichment both in the laboratory and in the field. Impacts of ephemeral species on fucoid early life stages were only evident in laboratory contexts, where green algae of the genus Ulva impaired both the settlement of H. banksii zygotes and the growth of its germlings. Fucoid recruitment in the field was not affected by increased covers of ephemeral algae caused by enhanced nutrient regimes, indicating that H. banksii and C. torulosa may be resistant to short-term (one year) nutrient pollution. In the laboratory, increased temperatures within the range predicted for the end of the 21st century caused increased mortality in the H. banksii, C. torulosa and D. antarctica germlings. In a separate experiment, a combination of warmer water temperatures and nutrient enrichment enhanced the growth of ephemeral green algae. These results suggest that opposite responses to altered climate conditions may contribute to shifts from complex biogenic habitats dominated by macroalgal canopies to simplified systems monopolized by a limited number of stress-tolerant species. This research contributes to a clearer mechanistic understanding of biotic and physical mechanisms shaping the structure of coastal marine hard bottom communities under increasingly stressful conditions worldwide. These findings may provide insights for other studies investigating the complex mosaic of challenges facing marine coastal ecosystems.

Strong light can cause damage and be lethal for photosynthetic organisms. An increase of thermal dissipation of excess absorbed energy at the level of photosynthetic antenna is one of the processes protecting against deleterious effects of light. In cyanobacteria, a soluble photoactive carotenoid binding protein, Orange Carotenoid Protein (OCP) mediates this process. The photoactivated OCP by interacting with the core of phycobilisome (PB; the major photosynthetic antenna of cyanobacteria) triggers the photoprotective mechanism, which decreases the energy arriving at the reaction centres and PSII fluorescence. The excess energy is dissipated as harmless heat. To regain full PB capacity in low light intensities, theFluorescence Recovery Protein (FRP) is required. FRP accelerates the deactivation of OCP.In this work, I present my input in the understanding of the mechanism underlying the OCPrelated photoprotection. I further characterized the FRP of Synechocystis PCC6803, the model organism in our studies. I established that the Synechocystis FRP is shorter than what it was proposed in Cyanobase and it begins at Met26. Our results also revealed the great importance of a high OCP to FRP ratio for existence of photoprotection. The most remarkable achievement of this thesis is the in vitro reconstitution of the OCPrelated mechanism using isolated OCP, PB and FRP. I demonstrated that light is only needed for OCP photoactivation but OCP binding to PB is light independent. Only the photoactivated OCP is able to bind the PB and quench all its fluorescence. Based on our in vitro experiments we proposed a molecular model of OCP-related photoprotection. The in vitro reconstituted system was applied to examine the importance of a conserved salt bridge (Arg155-Glu244) between the two domains of OCP and showed that this salt bridge stabilises the inactive form of OCP. During photoactivation this salt bridge is broken and Arg155 is involved in the interaction between the OCP and the PB. The site of OCP binding in the core of a PB wasalso investigated with the in vitro reconstituted system. Our results demonstrated that the terminal energy emitters of the PB are not needed and that the first site of fluorescence quenching is an APC trimer emitting at 660 nm. Finally, we characterised the properties of excited states of the carotenoid in the photoactivated OCP showing that one of these states presents a very pronounced charge transfer character that likely has a principal role in energy dissipation. Our results strongly suggested that the OCP not only induces thermal energy dissipation but also acts as the energy dissipator.

Fourier transform infrared difference spectroscopy (FTIR DS) is widely used to study the structural details of electron transfer cofactors in photosynthetic protein complexes. In photosynthetic proteins quinones play an important role, functioning as a cofactor in light-driven electron transfer. In photosystem I (PS I) phylloquinone (PhQ) functions as an intermediary in electron transfer. To investigate the properties of PhQ that occupies the, so called, A1 binding site in PS I, time-resolved step-scan FTIR DS, with 5µs time resolution at 77K has been used. By replacing PhQ in the A1 binding site with specifically isotope labeled version, information on the vibrational frequencies associated specifically with the quinone in the binding site were obtained, which could be compared to the vibrational properties of quinone in solution or quinones in other protein binding sites. To further aid in assessing the origin of bands in the spectra, quantum mechanics /molecular mechanics (QM/MM) ONIOM type calculations were undertaken. ONIOM is an acronym for Our own N-layered Integrated molecular Orbital and molecular Mechanics. We find that the phytyl tail of PhQ does not play an important role in the orientation of PhQ in the A1 binding site. We also find that PhQ, in both neutral and reduced states, is strongly hydrogen bonded. To test and verify the applicability of our QM/MM approach, ONIOM calculations were also undertaken for ubiquinone and a variety of other quinones incorporated into the, so called, QA binding site in purple bacteria photosynthetic reaction centers. The calculated and experimental spectra agree well, demonstrating the utility and applicability of our ONIOM approach. Hydrogen bonding to the carbonyl groups of quinones in the QA binding site was shown to be relatively weak, and it was found that hydrogen bonding to neutral ubiquinone in purple bacterial reaction centers can be considered in purely electrostatic terms, contrary to the widely held belief that the hydrogen bonding amino acids should be treated quantum mechanically.

The main aim of this study was to investigate the effects of water availability and SO2 pollution, imposed separately or simultaneously, on the photosynthetic metabolism of Augea capensis Thunb., a succulent of the Namib Desert in the region of Skorpion Zinc mine, Namibia. The main driver for this investigation was the need to distinguish between the effects of water availability on plants native to a desert environment, where water availability dominates plant response, but where the possibility of anthropogenic SO2 pollution poses a new threat to the unique succulent vegetation. Fifteen measuring sites were selected in the vicinity of the mine to determine how rainfall influenced the physiological status of the vegetation. Chlorophyll a fluorescence measurements, and analysis of recorded OJlP fluorescence transients with the JIP-test, were used for this purpose. A series of laboratory experiments were also conducted on A. capensis to determine the precise physiological response that water deprivation and SO2 pollution had under controlled growth conditions. Potted plants were exposed to water deprivation or SO2 fumigation in the light or dark. Besides chlorophyll a fluorescence, photosynthetic gas exchange and Rubisco activity were also measured. Changes in fast fluorescence rise kinetics observed under field conditions suggest considerable modulation of photosystem II function by rainfall with concomitant involvement of a heat stress component as well. In both the field and laboratory experiments, one of the JIP-test parameters, the so-called performance index (PIABS), was identified as a very sensitive indicator of the physiological status of the test plants. Moreover, under laboratory conditions, a good correlation existed between the water deprivation-induced decline in CO2 assimilation rates and the decline in PIABS values. The JIP-test in general, and the PIABS in particular, shows considerable potential for application in the investigation of water availability influences on desert ecosystems. In the laboratory experiments, water deprivation caused stomatal closure but also a slight elevation in intercellular C02 concentration and inhibition of Rubisco activity, suggesting that mesophyll limitation was the dominant factor contributing to the decrease in C02 assimilation rates. Following re-watering, A. capensis showed remarkable recovery capacity. Fumigation of A. capensis with 1.2 ppm SO2 in the dark or light revealed relatively small effects on C02 assimilation. The inhibitory effects on photosynthesis were also fully reversible, indicating no permanent metabolic/structural damage. The effects on photosynthesis were more pronounced when fumigation occurred in the dark. This phenomenon might be related to diurnal differences in cellular capacity for SO2 detoxification. When long-term moderate water deprivation was combined with simultaneous SO2 fumigation, there was no additional inhibitory effect on photosynthesis. These findings suggest that water deprivation do not increase sensitivity towards SO2 pollution in A. capensis. Fumigation with SO2, singly or in combination with water deprivation also had no major effect on chloroplast ultrastructure. It appears that A. capensis is remarkably resistant to SO2 pollution even in the presence of low water availability, which is a common phenomenon in desert ecosystems. Since A, capensis seems to be highly tolerant to S02, its suitability as an indicator species for the detection of SO2 pollution effects at Skorpion Zinc mine is questionable. Because water availability dominates the physiological/biochemical response in this species, subtle SO2 pollution effects might be difficult to detect against this dominant background. The high water content of A. capensis and similar succulents might act as a substantial sink for SO2 and could convey considerable tolerance against this form of air pollution. / Thesis (M.Sc. (Botany))--North-West University, Potchefstroom Campus, 2006.

Species diversity may simultaneously be a cause and a consequence of variability in population, community and ecosystem properties. Ecology has traditionally focused on elucidating the causes of biodiversity. However, in the last decade and a half ecologists have asked the opposite question: What are the consequences of species diversity? The majority of these studies elucidated the effects of species diversity within single trophic levels. Incorporating trophic complexity is the next step in this research program. In this dissertation I investigated the causes of resource species diversity, as well as the impacts that resource diversity has on rates of consumption and the stability of population, community and ecosystem properties over time in planktonic food webs. The high diversity of phytoplankton found in nature appears to defy the competitive exclusion principle, and elucidating the mechanisms which maintain this diversity continues to be a challenge. In general, variability in limiting factors is required to maintain non-neutral species diversity, but this variability can be generated by forces outside of the competitive community (i.e. exogenous), or may be the outcome of competitive interactions themselves (i.e. endogenous). Using microcosm experiments, I showed that endogenously generated variability in limiting factors was more effective at maintaining phytoplankton species diversity over the long-term, although the strength of this effect depended on the composition of the phytoplankton community. Existing resource diversity has been proposed to generally weaken consumer-resource interaction strengths and limit consumer control of resource biomass. This is because more diverse resource communities are more likely to contain inedible, unpalatable, toxic or non-nutritious species. However, when resource communities contain multiple palatable species, diversity may also accelerate consumption. Using grazing experiments with multiple zooplankton consumer species, I found that the mechanism, direction and magnitude of modulation of consumption depended on the feeding selectivity of the consumer and the composition of the resource community. By altering consumer-resource interaction strengths in the short-term, resource species diversity may impact the stability of consumer-resource dynamics in the long-term. In separate microcosm experiments, I investigated the influence of resource species diversity, community composition and consumer feeding selectivity on population, community, and ecosystem properties over time. Diversity had positive effects on phytoplankton population biomass, resource community biomass, the rate of photosynthesis, the standing stock of particulate nutrients, and the generalist consumer’s population density. It also stabilized resource community biomass and the stocks of particulate nutrients over time. Unexpectedly, diversity did not stabilize either of the consumer populations, regardless of feeding selectivity. This suggests that effects of diversity on resource community properties do not impact consumer dynamics linearly. Resource community composition was generally more important than resource species diversity in determining food web properties. The importance of community composition in determining both the causes and consequences of resource diversity in these experiments points to the importance of species’ traits and the outcomes of their interactions. I suggest that the use of complex adaptive systems theory and trait-based approaches in the future will allow a consideration of the feedbacks between the causes and consequences of species diversity in food webs. / Graduate

The work presented in this thesis was aimed to investigate the structure-function relationship of several photosynthetic Light-Harvesting Complexes (LHCs) including Chlorophyll Protein 29 (CP29) and Light-Harvesting Complex II (LHCII) of green plants, and Fenna-Matthews-Olson (FMO) complex of green sulfur bacterium Chlorobium tepidum. Based on the exciton calculations, a model was proposed to the electronic excited states (EES) of both CP29 and LHCII complexes by incorporating a considerable part of the current information offered by structure determination, mutagenesis analysis and spectroscopy in the modeling. The essential parameters for characterizing the excited states, Qy dipole orientations and site energies were assigned by suggesting a model that can explain both the key features of the linear (polarized) absorption spectra and the time scales of the energy transfer processes in CP29 and LHCII. The idea of offering structural information through setting connection between the spectroscopy and the spectral simulations were supported by the presented results on CP29 and LHCII. New spectroscopic measurements (absorption, linear dichroism (LD) and circular dichroism), carried out at 4 K on the FMO complex were presented, and also the LD spectrum was corrected for the degree of orientation of the sample, in order to provide comparison of not only the shape but also the size of the simulated and experimental spectra. The EES structure of the FMO complex was studied by simulating the measured optical spectra with more realistic model than the previously applied models. Simulations have been carried out with a computer program based on exciton model, which includes inhomogeneous, homogeneous and lifetime broadenings explicitly.

EPR spectroscopy and isotopic substitution were used to gain increased knowledge about the proton-coupled electron transfer (PCET) mechanism for the reduction of the tyrosine D radical (YD*) in photosystem II. pL dependence (where pL is either pH or pD) of both the rate constant and kinetic isotope effect (KIE) was examined for YD* reduction. Second, the manner in which protons are transferred during the rate-limiting step for YD* reduction at alkaline pL was determined. Finally, high field electron paramagnetic resonance (EPR) spectroscopy was used to study the effect of pH on the environment surrounding both the tyrosine D radical and the tyrosine Z radical (YZ*). At alkaline pL, it was determined that the proton and electron are both transferred in the rate-limiting step of YD* reduction. At acidic pL, the proton transfer occurs first followed by electron transfer. Proton inventory experiments indicate that there is more than one proton donation pathway available to YD* during PCET reduction at alkaline pL. Additionally, the proton inventory experiments indicate that at least one of those pathways is multiproton. High field EPR experiments indicate that both YD* and YZ* are hydrogen bonded to neutral species. The EPR gx component for YD* is invariant with respect to pH. Analysis of the EPR gx component for Yz* indicates that its environment becomes more electropositive as the pH is increased. This is most likely due to changes in the hydrogen bond strength

Processes where a molecule absorbs visible light and then converts the solar energy into chemical energy are important in many biological systems, such as photosynthesis and also in many technical applications e.g. photovoltaics. This thesis describes a part of a multidisciplinary project, aiming at a functional mimic of the natural photosynthesis, with the overall goal of production of a renewable fuel from sun and water. More specific, the thesis is focused on design and photophysical characterization of new photosensitizers, i.e. light absorbers that should be capable of transferring electrons to an acceptor and be suitable building blocks for supramolecular rod-like donor-photosensitizer-acceptor arrays. The excited state lifetime, the excited state energy and the geometry are important properties for a photosensitizer. The work presented here describes a new strategy to obtain longer excited state lifetimes of the geometrically favorable Ru(II)-bistridentate type complexes, without a concomitant substantial decrease in excited state energy. The basic idea is that a more octahedral coordination around the Ru will lead to longer excited state lifetimes. In the first generation of new photosensitizers a 50-fold increase of the excited state lifetime was observed, going from 0.25 ns for the model complex to 15 ns for the best photosensitizer. The second generation goes another step forward, to an excited state lifetime of 810 ns. Furthermore, the third generation of new photosensitizers show excited state lifetimes in the 0.45 - 5.5 microsecond region at room temperature, a significant improvement. In addition, the third generation of photosensitizers are suitable for further symmetric attachment of electron donor and acceptor motifs, and it is shown that the favorable properties are maintained upon the attachment of anchoring groups. The reactivity of the excited state towards light-induced reactions is proved and the photostability is sufficient so the new design strategy has proven successful.