In the eutrophic waters of the Indian River Lagoon (IRL), decreases in overall shellfish size have been reported, which may be related to coastal acidification. To understand the relationship between acidification and eutrophication, water samples from 20 sites spanning the IRL were collected and analyzed for dissolved nutrients and omega values in spring (dry season) and fall (wet season), 2016-2017. Additionally, three sites were sampled weekly to observe temporal variability of nutrients and omega values. For the IRL-Wide sampling, sites with higher dissolved nutrient concentrations showed lower omega values with significant negative relationships. Both sampling programs showed an overall positive linear relationship between salinity and omega values. This work suggests that salinity and dissolved nutrients have implications for acidification in the IRL and must be considered for future water quality, shellfish and coral reef restoration. / Includes bibliography. / Thesis (M.F.A.)--Florida Atlantic University, 2018. / FAU Electronic Theses and Dissertations Collection

Seagrasses are important foundation species in coastal ecosystems. Genetic diversity of seagrasses can influence a number of ecological factors including, but not limited to, disturbance resistance and resilience. Seagrasses in the Indian River Lagoon (IRL), Florida are considered to be highly disturbed due to frequent events, like algal blooms, that impair water quality, reducing available light for seagrass growth. Halodule wrightii is a dominant seagrass throughout the IRL, but its genetic diversity has only been quantified in a few Gulf of Mexico and Florida Bay populations and little is known about its potential ecological consequences. I quantified the genetic variation of H. wrightii using microsatellite markers in the southern IRL to determine: (i) how disturbance history influenced genetic diversity, (ii) if morphology of clones was, in part, genetically controlled and related to disturbance history, and (iii) if genotypes showed phenotypic plasticity in response to disturbances. In the IRL, H. wrightii populations exhibited moderate genetic diversity that varied with disturbance history. The disturbance history of a population was classified by the variance in the percent occurrence of H. wrightii over a 16-year period. Genotypic richness and clonal diversity of H. wrightii increased with increasing disturbance histories. Other genetic diversity measures (e.g., allelic richness, observed heterozygosity) did not change with disturbance history. These findings suggest that impacts to seagrass coverage over time can change the genotypic composition of populations. When different genotypes of H. wrightii were grown in a common garden, differences in leaf characteristics among genotypes provided evidence that morphological trait variation is, in part, explained by genetic variance. The disturbance history of genotypes did not directly affect morphological traits. However, significant genotype x site (within disturbance history) interactions found greater variation in shoot density and below ground traits of H. wrightii genotypes from sites of intermediate disturbance history. Traits of H. wrightii were shown to be phenotypically plastic. Significant genotype x environment interactions for shoot density and height demonstrated that genotypes responded differently by increasing, decreasing, and not changing sizes in response to light reduction. Genetic diversity of H. wrightii has strong implications for ecological function in coastal communities. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2016. / FAU Electronic Theses and Dissertations Collection

The goal of this study was to develop an alternative approach to typical seagrass transplantation techniques that damage the donor bed. Floating individuals of Halodule wrightii were collected in the Indian River Lagoon (IRL), Florida, during fall of 2013 and spring of 2014, with the fall collection planted in outdoor tanks. Only 25% of individuals collected in the fall survived the winter in the tanks. Individuals from both collections were deployed onto biodegradable mats in a capped dredge hole in the IRL in March, 2014. Approximately 66% of the mats survived the six-month experiment, and the area covered by seagrass quadrupled. Growth in shoot count, average height, horizontal spread, and biomass was similar for both fall and spring treatments. Thus, time and effort of overwintering had no benefit over spring harvesting. The use of floating individuals can provide a more practical, environmentally friendly alternative to traditional transplanting for seagrass re storation. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2015. / FAU Electronic Theses and Dissertations Collection

The environmental history of Longneck Lagoon was reconstructed by analysing 15 sediment cores collected between 22 April, 1992 and 29 August, 1995. Longneck Lagoon is a shallow, man-modified lake situated in the north-western part of Sydney in New South Wales, Australia, in the Hawkesbury River floodplain. It has undergone a considerable change over recent years and at the end of the study was reported to have turbid water and no floating leaved plants or submerged aquatic plants. The hypothesis of this study was that vertical patterns in sediment characteristics can be related to biological, physical or chemical changes that have taken place within Longneck Lagoon and its catchment area. Assessment of inter-core variation within one area of the lagoon and between different areas was carried out and is highly recommended to others who may wish to conduct similar studies elsewhere. Restoration/regeneration of the previous diverse aquatic plant flora, associated with variable water depth in the pre-weir condition, would require the removal/modification of the weir, possibly reduction in the nutrient income to the lake, and, potentially, addressing mobilisation and internal cycling of accumulated nutrients which have accreted within the system. / Doctor of Philosophy (PhD)

Many coral reefs around the world were damaged during the 1998 mass bleaching event. The acroporids in the lagoon of Dongsha Atoll were eliminated during massive bleaching, and they are still not recovered. Three hypotheses were proposed to explain how the lagoon of Dongsha Atoll has not recovered during the past twelve years¡G1. the lack of recruitment, 2. the persistent interfering on newly recruiting acroporids by hot water, 3.the interfering on those acroporids by predators. Four types of habitats, i.e., reef tops, reef slopes, reef bases, and inter-patch-reefs were surveyed on their coral communities, densities of juvenile corals, growth rates, pests and diseases of corals. The tissue samples were collected to assess reproductive status of corals. Moreover, Acropora muricata branches were transplanted from north coast of Dongsha Island to 3 m and 9 m depths in the lagoon of Dongsha Atoll for testing suitability of the environment. The acroporids were mature, and they spawned between March and May in 2010. Live coral coverage was 16% on average; small coral densities were 1.5/m2, much lower than other lagoons. Besides, acroporid represented 8% of coral coverage and 4% of juvenile corals which are lower than those of other lagoon. Water temperatures were higher in 2010 than 2009. However, coral skeletal extension rates do not show any reign of reduction. In addition, most acroporids survived 2010 summer¡]sea water temperature exceeded 30¢J¡G40-64%¡^ in the transplantation experiment. During two years of survey, only 6 individuals Acanthaster planci. So the lack of recruits might be the bottleneck to the recovery of acroporid in Dongsha lagoon.

Dapeng Bay is located in the southwest coast of Taiwan. It is a cystic shaped shallow lagoon, which has only one entry for exchanging lagoon water with the coastal current. The water quality is depending on the refreshing rate and the mixing level in the lagoon. In order to understand the circulation pattern monthly measurements using an ADP are carried out. Three water quality monitoring stations are constructed for regular online observation of the water quality in the lagoon. The flows are on the west-northwest direction during the flood and toward the west during ebb. Strong currents are observed in the tidal inlet channel. The general circulation patterns are mainly dominated by tide though wind effects can observed from the measurements. This study established a three-dimensional hydrodynamic modeling system using the FVCOM model developed at the U.S. Marine Ecosystem Dynamics Modeling Laboratory for the simulation of Dapeng Bay currents. The study includes the comparison of the recent circulation and the flow fields after broaden of the inlet navigation channel. This will change not only the shape but also dredge the channel deeper. These variations may differ the circulation patterns and the exchange quantities as well. The model results are first compared with the observations for the present situation as calibration. The simulation results for the studies of the changing of the inlet channel will be discussed.

Tapeng Bay is the second largest lagoon in Taiwan. The biological and ecological environments are an autotrophic system and are influenced by seasonal variability, terrestrial pollutant inputs and the exchange rates with seawater. There¡¦re intense oyster culture and fish farming activities in the bay before July, 2002. The oyster was the most important spineless member in the lagoon. They would filtrate microplankton and detritus; they would also excrete nutrient and consume dissolved oxygen. Therefore, oyster played a very crucial role in the Tapeng Bay. This study combines the biological responses of the oysters with the complicated interaction among microplankton, nutrient, detritus and dissolved oxygen to establish the relationship of dynamical mechanisms between variables by applying the system dynamics simulation software STELLA. Model results clearly reveal that the oysters are the main species of filtration. The factors which affect the biomass of oysters include microplankton concentration, temperature and individual mass; the connection between oysters and other biological variables is closely tied. The study has also shown that the removing of oysters may cause significant increases of plankton and detritus during the eutrophication condition. Although the simulated water quality variables show higher than those obtained from sampling experiments in the literatures, the trend corresponds well with the relative studies. Despite the fact that oysters excrete much nutrient and nutrient is mostly taken up by microplankton, the condition of nutrient limitation has never happened, which is in correspondence with the result. In the sensitivity analysis, the parameters of oyster filtration rate and the autotroph nitrogen to carbon ratio are important factors which have influence on oysters biomass, and the concentration of microplankton and ammonium. Oyster excretion rate and the proportion of oyster feces and pseudofeces also have significant influences on the concentration of ammonium. The oyster culture racks in the Bay have already been torn down, but the Bay is still eutrophic. This is a clear indication of the importance of the oysters in the lagoon. Properly culture some oysters in the area where exist high concentrations of microplankton or organic input. By applying the oyster abundant filtration, planktons and suspended solids, mostly detritus and organic matters, can probably be controlled and the water quality in the bay can thus be improved. Although the STELLA has its limitation on broader applications, the model developed by this study can be combined with the features of social or economic fields. A decision supporting system can be developed for the management of ecological environment policies.

Coastal wetlands and rivermouth lagoons are dynamic systems, which respond rapidly to sea-level, tectonic, meteorological, anthropogenic and other synergistic drivers. This research used a multi-disciplinary approach to investigate two representative West Coast lagoon systems (Totara Lagoon and the Shearer Swamp-Waikoriri Lagoon Complex) in order to document their present-day geomorphology and determine the development and processes acting on these systems over historical time. This information was then used to predict their future under varying climate, development and management pressures. In addition to adding to the West Coast knowledge base, the findings of this research are applicable to similar systems elsewhere in New Zealand and internationally. This investigation used a multidisciplinary approach to investigate the dynamics, structure, development and active processes in the two study systems. Techniques to document current hydrology and topography included hydrological records of water level, temperature and conductivity, and Global Navigation Satellite Surveys (GNSS). Outlet dynamics over a decadal scale were investigated through temporal aerial photograph analysis, and sediment core analyses showed changes occurring over longer timescales. Significant differences in morphology and dynamics were observed between Totara Lagoon and Waikoriri Lagoon, with the former being much larger, more stable, and less dynamic in terms of dune morphology and outlet migratory patterns. Hydrologically, Totara Lagoon is currently in an estuarine phase, and experiences significant tidal inflows, which demonstrates the connectivity between definitions of coastal lagoons and estuaries. Waikoriri Lagoon is freshwater, and can be described as a hapua-type system, but exhibits very different river flow and barrier composition to East Coast examples. Sediment core analyses from Shearer Swamp and northern Totara Lagoon showed little change over a decadal to centennial scale, but evidence of a change in margin dynamics in response to farming and stabilisation of adjacent dune ridges was observed in Shearer Swamp. Results suggest landward migration of the southern end of Totara Lagoon occurred over this timeframe. The future of these systems depends on the interaction between climate and anthropogenic (including management) factors. A conceptual model of process and response suggests three possible resultant scenarios: lagoon loss, natural lagoon, or artificially modified lagoon. A significant finding of this research is the recognition that some systems exist on a continuum between a hapua and an estuary, switching hydrological states through time while maintaining consistent morphology. In addition, the importance of barrier permeability in hapua formation is highlighted, and the term ‘sandy hapua’ introduced to distinguish these low-flow systems with low barrier permeability from the typical mixed sand and gravel examples documented on the East Coast. These findings enhance scientific understanding of rivermouth lagoon systems, and demonstrate the wide spectrum of conditions under which they may form. This process-based understanding is important from a coastal management perspective as concerns of human induced climate change and accelerated sea level rise grow.

Hapua are complex and dynamic systems, and are especially vulnerable due of their location at the end of river catchments. The Hurunui River hapua is currently under pressure from the intensification of irrigation and agriculture, and a number of dam proposals in its catchment. The purpose of this research was to investigate the current conditions in the Hurunui River hapua, how they respond to the observed range of contemporary catchment and coastal processes, and to examine of the longer-term behaviour and vulnerability of the hapua. This information was then used to make predictions on how the hapua could be impacted if dams were to be built in the catchment, or if significant changes in the catchment occur. A multidisciplinary approach was used to investigate the short-term baseline conditions, and the long-term geomorphology of the Hurunui River hapua. Water characteristics were investigated over a falling tide, in different areas of the hapua, and in different energy conditions. The short-term behaviour of the hapua was investigated using hourly images from a time-lapse camera. The long-term vulnerability over decadal time scales was analysed using aerial photographs. This study showed that the flow of the river, the shape of the hapua, and the position of the outlet has a major control over the characteristics of the water. The surface area, the position of the barrier, and the width of the barrier of the Hurunui River hapua have been variable historically. From this research, it is predicted that the greatest impact on the Hurunui hapua would result if there is a dam related change the shape and outlet of the hapua to a state that reduces water residence time and decreases water quality. It is also predicted that if the outlet is maintained at the northern end of the hapua, and no ponded areas are present, that there would be the least problems with water quality. The findings of this research have improved the understanding of the water characteristics and processes of the Hurunui River hapua, and how they respond to change.

Thesis (Ph.D.) -- University of Western Sydney, 2000. / "October 2000" Bibliography: leaves 168-88.