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The goal of this thesis was to examine submerged macrophoe biomass, distribution, and ecosystem effects at scales large enough to incorporate the littoral zone into models of whole lake structure and function. Submerged macrophyte biomass and distribution was shown to be highly variable between growing seasons and primarily dependant upon air temperature and the timing of the onset of the growing season. Within a growing season, a mass balance study showed an undisturbed macrophyte bed to markedly lower phytoplankton biomass: total phosphorus ratios, although the net effect of the bed on the growing season phosphorus budget was minimal. The weedbed preferentially retained phytoplankton biomass while being a source of bacterial production to the open water. These findings were mirrored at the among lake scale, as planktonic respiration and bacterial production were higher in macrophyte dominated lakes than would be expected based on phytoplankton biomass alone. Further, phytoplankton biomass was lower than would be expected based on epilimnetic phosphorus levels, showing that the classical view of pelagic interactions that proposes phosphorus determines phytoplankton abundance, which in turn determines bacterial abundance through the production of organic carbon, becomes less relevant as macrophyte cover increases. Long term phosphorus accumulation in the littoral zone was shown to be linked to macrophyte biomass, and on average almost an order of magnitude higher than calculated from the growing season (June--October) phosphorus budget, suggesting that the bulk of phosphorus accumulation in weedbeds occurs outside of the growing season. Finally, sediment core data showed that while submerged weedbeds accumulate up to four times as much bulk sediment compared to the profundal zone, phosphorus accumulation in weedbeds is much less than observed in the profundal zone. These results strongly indicating that submerged macrophyte beds play a central role in trapping ep

[Truncated abstract] This study focussed on how isolation and environmental heterogeneity in salt lakes has influenced intraspecific variation in the calanoid copepod Calamoecia clitellata. Calamoecia clitellata relies on passive vectors for dispersal, and this, coupled with the insular nature of salt lakes, may promote genetic divergence at a molecular level. When contrasting environments are involved, genetic divergence may also occur at the life history level, possibly due to local adaptation. I examined the distribution of genetic variation among 14 populations in Western Australia using molecular genetic markers, and examined variation in life history traits among contrasting environments. To ascertain how isolation had influenced molecular genetic variation, I determined population genetic structure and used a phylogeographic approach to infer the impact of historical events. Environmentally induced variation was also evident in the field, with a switch from subitaneous egg production to resting egg production coinciding with changing environmental conditions. It is proposed that plasticity in life history traits has evolved in response to temporal environmental heterogeneity … It can be concluded that isolation in salt lakes in Western Australia has influenced molecular and phenotypic variation in C. clitellata in contrasting ways. At the molecular level, contemporary and historical isolation have promoted genetic divergence of populations, yet when coupled with environmental heterogeneity, marked phenotype plasticity has arisen. This study raises questions as to whether phenotype plasticity is a widespread phenomena in zooplankton found in temporary saline waters and an adaptive strategy to tolerate marked temporal environmental heterogeneity

Macrophytes are an integral component of lake littoral zones and play an irreplaceable role in maintaining the ecological balance of wetlands. Recent research has highlighted the role of lake-scale environmental factors (or “filters”) and catchment- and/or landscape-scale processes in explaining variation in macrophyte communities across different scales. In this work, the effects of land-use and connectivity on macrophyte communities were explored at two contrasting spatial scales (i.e. local catchment scale and topographic catchment scale). At the local catchment scale, the results revealed strong scale-dependency. The effects of land use on macrophyte richness were most apparent at fine spatial scales (within 0.5 to 1 km) and significantly outweighed the importance of hydrology. In terms of growth form composition, the effects of hydrological connectivity were stronger than those of land use, with the greatest effect observed at an intermediate distance (~ 5 km) from the lake. The study on the hydrologically-connected lake pairs indicated that environmental filters were more influential in explaining species turnover than lake connectivity. Interestingly, geographical connectivity explained more of the variability in species turnover than hydrological connectivity. Moreover, the relative importance of environmental filters and lake connectivity to species turnover was very sensitive to the degree of human disturbance. The multi-scale interaction analyses indicated the effect of lake alkalinity on macrophyte composition is strongly influenced by catchment scale variables including hydrological features and land use intensity. The turnover in macrophyte composition in response to variability in alkalinity was stronger in catchments with low lake and stream density and weaker in catchments with a more highly developed hydrological network. Lake abiotic variables were found to have more influence on macrophyte composition in lowland catchments with a higher intensity of human disturbance. Moreover, the catchment-scale factors promoting the establishment of different communities were found to vary between catchments depending on lake type, the degree of environmental heterogeneity and hydrological connectivity.

Lake St Lucia in northern KwaZulu-Natal, South Africa, experiences severe ecological stress during dry periods largely as a result of diminishing freshwater supplies and conditions of hypersalinity. Possible intervention involves diverting the Mfolozi River to the St Lucia Lake system. However, due to high sediment loading, water from the Mfolozi river requires considerable filtration before a link can be established. A suggested option considered in this study is to restore the existing sugarcane farmlands on the Mfolozi Floodplain (~20 800 ha) to previous wetland conditions to reinstate a sediment removal function amongst other benefits. Proposed restoration will have a direct impact on the industries currently supported by the iSimangaliso Wetland Park and the Mfolozi Floodplain (tourism, sugar, conservation). to understand a measure of such impacts, ecosystem services for both Lake St Lucia and the Mfolozi Floodplain were analysed (flood alleviation, water provision, water purification, sediment regulation, tourism, fisheries, vegetation for harvest, existence, cultural and research). Annual economic values for each ecosystem service were determined by means of valuation methods that included benefit transfer and replacement cost. Results showed a current annual minimum value of the Mfolozi Floodplain and Lake St Lucia as greater than R21 million and R1.1 billion respectively. Partial restoration of the floodplain (~6 000 ha) is expected to increase the sum of all ecosystem services values by approximately 26% for the Mfolozi Floodplain and by 23% for the St Lucia System. Full restoration (~20 800 ha) increases the total ecosystem services value by 88% and 50% for the Mfolozi Floodplain and St Lucia System respectively. Results showed that economic values for existence, fisheries, tourism and water provision increase by the greatest percentage for the St Lucia System under both restoration scenarios. Partial and full restoration of the floodplain will result in the greatest increases in economic value for the services existence, tourism, fisheries and the harvesting of vegetation on the Mfolozi Floodplain.

Using Coachella Valley's Salton Sea ecosystem as a model, several multidisciplinary wetland activities for grades three to six were developed. A resource guide for educators is included.

Freshwater lakes are among the most important ecosystems for both human and other biological communities. They account for about 87% of surface freshwater in the planet, thus constituting a major source of drinking water. They also provide a wide range of ecosystem services that go from the sustenance of a rich biodiversity to the regulation of hydrological extremes; from the provision of a means for recreation to the support of local economies, e.g., through tourism and fisheries, just to cite a few. Lakes are now also widely recognised as natural early warning systems, their responses potentially being effective indicators of local, regional and global scale phenomena such as acidification and climate change, respectively. This is because of their high sensitivity to environmental factors of the most diverse nature that can rapidly alter the course of their evolution. Examples of this are the observed abrupt shifts between alternative stable states in shallow lakes, which led them to become the archetype, go-to example in alternative stable state theory. Therefore, attaining a good scientific understanding of the many processes that take place within these ecosystems is fundamental for their adequate management. Among the tools that serve this purpose, ecological models are particularly powerful ones. Since their introduction in the 1960s, the development of mechanistic ecological models has been driven by their wide spectrum of potential applications. Nevertheless, these models often fall into one of the two following categories: overly simplistic representations of isolated processes, with limited potential to explain real-world observations as they fail to see the bigger picture; or overly complex and over-parameterised models that can hardly improve scientific understanding, their results being too difficult to analyse in terms of fundamental processes and controls. Moreover, it is now well known that an increased complexity in the mechanistic description of ecological processes, does not necessarily improve model accuracy, predictive capability or overall simulation results. To the contrary, a simpler representation allows for the inclusion of more links between model components, feedbacks which are usually overlooked in highly-complex models that partially couple a hydro-thermodynamic module to a biogeochemical one. However, ecological processes are now known to have the potential to significantly alter the physical response of aquatic ecosystems to environmental forcing. For example, steadily increasing concentrations of coloured dissolved organic carbon, a process known as brownification (also browning), as well as the intense phytoplankton blooms that characterise lakes undergoing severe nutrient enrichment, a process known as eutrophication, have been shown to have the potential to alter the duration of the stratified period, thermal structure and mixing regime of some lakes. In this thesis, with the aim of addressing the limitation of partially-coupled models to account for such feedbacks, we further develop a process-based model previously reported in scientific literature. Subsequent studies have already built upon this model in the last few years. In Chapter 2, we do so too by integrating hydro-thermodynamics and biogeochemistry in a reduced complexity framework, i.e., customising the model so that each version only includes the fundamental processes that, brought together, sufficiently describe the studied phenomena. Two case studies served the purpose of testing the adaptability and applicability of the developed model under different configurations and requirements. Limnological data for these two studies were measured at high spatial and temporal resolutions by means of an automated profiling system and recorded as part of two large-scale mesocosm experiments conducted in 2015 and 2016 at the IGB LakeLab in Lake Stechlin, Brandenburg, Germany. Meteorological datasets were also made available to us for both periods by the German Federal Environment Agency. The scope of the first experiment, which we describe in Chapter 3, was that of detecting any changes attributable to eutrophication and browning, in the competition for nutrients and light between four different groups of lake primary producers. These four groups are phytoplankton, periphyton, epiphyton and macrophytes. The model version for this study, therefore, includes equations for all four groups. By tailoring the model to these very specific needs with relative ease, we demonstrate its versatility and hint at its potential. The second experiment, described in Chapter 4, sought to shed light on the largely unknown effects of an increase in the diffuse luminance of the night sky that is due to artificial light at night (artificial skyglow) on lake metabolic rates, i.e., gross primary productivity, ecosystem respiration and net ecosystem productivity (the difference between the first two). For this purpose, an empirical equation for dissolved oxygen concentration was included, the parameters of which were estimated by means of a Markov Chain Monte Carlo sampling method within a Bayesian statistical framework, showing the compatibility, with these statistical methods, of our otherwise fully deterministic model. In Chapter 5, we present a theoretical study on the ecological controls of light and thermal patterns in lake ecosystems. A series of simulations were performed to determine in which cases ecological processes such as eutrophication and brownification may have an observable effect on the physical response of lakes to environmental forcing, which we assessed along a latitudinal gradient. Results show that, in general, across all examined latitudes, and consistent with previous studies, accounting for phytoplankton biomass results in higher surface temperatures during the warm-up phase, slightly lower water temperatures during the cool-down phase, and a shallower thermocline throughout the entire stratified period. This effect is relatively more important in eutrophic lakes where intense blooms are likely. This importance, however, decreases as lakes get browner. Finally, in line with the overall scope of the SMART EMJD, in Chapter 6 we illustrate the case of Ypacaraí Lake, the most important lake in landlocked Paraguay, hoping to provide an example of how interdisciplinary research and international intersectoral collaboration can help bridge the gap between science and management of freshwater ecosystems. This lake presents very special hydro-ecological conditions, such as very high turbidity that can impair phytoplankton growth despite its nutrient-based trophic state indices having consistently fallen within the hyper-eutrophic range in recent years. A strong interest in its complex functioning, through modelling, was taken early on. This led to a collaborative research line being established among several public and private institutions in Italy, Germany and Paraguay. Results so far include: • three concluded UniTN Master theses in Environmental Engineering, partly developed in Paraguay, the first two in collaboration with the “Nuestra Señora de la Asunción” Catholic University (UCNSA) and the third one with the National University of Asunción (UNA); • a collaborative UCNSA-UniTN research proposal submitted for consideration to receive funding through the PROCIENCIA Programme of the National Council of Science and Technology of Paraguay (CONACYT); and • the first multidisciplinary review that has ever been published about the case of Ypacaraí Lake, which highlights the importance of such a collaborative and integrative approach to further advance scientific knowledge and effectively manage this ecosystem.

Thesis (MEng)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: The Swartvlei estuary and lake system is situated on the southern coast of the Western Cape Province of South Africa and forms part of the core conservation area of the Wilderness National Park. The Swartvlei system comprises two interlinked water bodies, namely Swartvlei Lake and Swartvlei estuary. SANParks have been monitoring this estuary closely over the past two decades, due to its importance to the ecology and to tourism. There are also low-lying properties on the perimeter of the Swartvlei estuary which run the risk of occasional flooding. Two of the major monitoring issues in this estuary system are the water level required for successful mouth breaching, and the influence of the water level on the low-lying properties. This study presents a preliminary analysis of the sediment budget across the Swartvlei estuary mouth. The objective of this study was to identify the various sediment contributory factors and to estimate the quantities that each individually contributed towards the defined sediment budget. / AFRIKAANSE OPSOMMING: Die Swartvlei meer en see monding is geleë aan die kaapse suidkus van Suid- Afrika. Dit vorm deel van die kern bewarings area van die Wilderness Nationale Park. Die Swartvlei sisteem bestaan uit twee verbinde, kern dele nl: Swartvlei meer en estuarium. Vir die afgelope twee dekades is hierdie area onder die noue toesig van SANParke as gevolg van die belangrikheid van die area met betrekking tot toerisme en ekologie. Daar is ook menigde laag liggende eiendomme aan die oewers, wat baie sensitief is vir watervlak stygings. Die optimum water vlakke benodig vir die uitskuring van die gety monding het ook implikasies vir die laag liggende eiendome en vereis noukeurige monitering. ‘n Voorlopige analise van die sediment begroting rondom die gety monding word deur hierdie studie voorgelê.