Studies on morphological variation are important as it can depict the relationship with environmental factors clearly and convey an understanding of the manner, mechanism and factors influencing plant adaptation and evolution. Although many studies have been conducted on South African salt marsh plant physiology and phytosociology there are at present very few morphological studies on estuarine plants. The aim of this study was to compare the morphological variation of estuarine macrophytes in three different estuary types in the warm temperate biogeographic zone of South Africa and to compare characters used in the taxonomic descriptions of species with those measured in the field. Permanently open estuaries investigated were Ngqusi (WC), Kowie (KW) and Swartkops (SW) estuaries. The Knysna Estuary (KN) was the estuarine bay investigated and the temporarily open/ closed estuaries (TOCEs) were the East Kleinemonde (EK) and Great Brak (GB) estuaries. Macrophytes were morphologically different across different estuary types. This suggests that there were different factors operating between these estuary types that would directly influence the morphology of species. The variation of plant height with different estuary types can be attributed to the fact that smaller salt marshes also have smaller habitat ranges compared to larger ones. The variation in morphological characteristics such as plant height can also be attributed to biogeographical range. Most morphological characteristics measured in the field fall within previously published ranges, and so these characters are useful in delimiting species. There were significant relationships between phenotypic variables and multivariate environmental variables. The most important of these variables were soil electrical conductivity, soil organic content and soil water content. Specifically, plant height increased with water content and decreased with salinity, flower stalk length had strong significant positive correlations with moisture content, organic content and pH while there were strong significant correlations with redox potential and electrical conductivity. Salt marshes are considered ideal for studying variation of species due to the explicit environmental gradients and plants occurring in salt marshes are halophytes that exhibit a range of morphological traits that allows for growth and reproduction under the stressful and extreme conditions. Considering recent climate change predictions and the consequent effects on South African estuaries this study provides significant information with regard to the response of species to a changing environment. The study was also aimed at updating the existing botanical database for South African estuaries in terms of species occurrence in South African estuaries, taxonomic name changes of existing species, new species, common names and habitats. Species diversity indices were also calculated for different estuaries, estuary types and biogeographic zones and diagnostic descriptions of the dominant salt marsh species were developed. The objective of this was that these data should provide baseline information for determining habitat richness and plant species diversity of South African estuaries which in turn should be used in determining priority estuaries for conservation and management. The identification key, developed using the DELTA software, would also aid researchers, managers and laymen in identifying salt marsh species. Results showed that the total number of macrophyte species, including intraspecific taxa and macroalgae, was 242 in 53 estuaries that were updated . There was an increase in the number of taxa recorded in the database primarily due to 1) research focus and full taxonomic surveys on larger estuaries and the big research projects has led to the identification of more species, 2) the addition of species that are not characteristically known as estuarine species, 3) the addition of 50 macroalgal taxa and 4) minor changes due to taxonomic revisions of species and the addition of newly described species. The Shannon diversity index showed that greater species diversity was found in the Berg (Groot) Estuary (4.220) and the Uilkraals Estuary (4.025). The cool temperate bioregion was the most diverse in the number of taxa (58) with the highest Shannon index (4.736). Permanently open estuaries were the most diverse in the number of unique taxa (56) with the highest Shannon index (4.867). Estuarine managers need to be aware of the species diversity in different estuarine types as well as the associated impacts on them. Conservation planning must therefore include species. Diagnostic features of INTKEY indicated that all 57 taxa were distinguishable from each other. Contrary to expectations plant height and not floral morphology was the best diagnostic characteristic. Ecological information such as the estuarine habitat, where different life forms occur, was important in delimiting species.

The Bushmans Estuary is one of the few permanently open estuaries in the Eastern Cape that is characterized by large intertidal salt marshes. Freshwater inflow to the estuary has decreased as a result of abstraction by more than 30 weirs and farm dams in the catchment. The mean annual run-off is naturally low (38 x 106 m3 y-1) and thus abstraction and reduction of freshwater inflow to the estuary is expected to cause a number of changes. The aims of this study were to determine the current health/status of the estuary based on the macrophytes and microalgae and identify monitoring indicators for the East London Department of Water Affairs, River Health Programme. Changes in the estuary over time were determined from available historical data which were compared with present data. This analysis showed that under normal average conditions freshwater inflow to the estuary is very low, less that 0.02 m3 s-1 most of the time. Under these conditions the estuary is in a homogenous marine state. Vertical and horizontal salinity gradients only form when high rainfall and run-off occurs (> 5 m3.s-1). Salinity gradients from 30.1 PSU at the mouth to 2.2 PSU in the upper reaches were measured in 2006 after a high flow event. However the estuary quickly reverted back to its homogenous condition within weeks after this flood. This study showed that freshwater inflow increased nutrient input to the estuary. Total oxidised nitrogen (TOxN) and soluble reactive phosphorus (SRP) concentrations were higher in August 2006, after the flood, than during the other low flow sampling sessions. TOxN decreased from a mean concentration of 21.6 μM in 2006 to 1.93 μM in February 2009. SRP decreased from 55.3 μM to 0.2 μM respectively. With the increased nutrient availability, the response in the estuary was an increase in phytoplankton biomass. After the 2006 floods the average water column chlorophyll-a was 9.0 μg l-1, while in the low freshwater inflow years it ranged from 2.1 to 4.8 μg l-1. The composition of the phytoplankton community was always dominated by flagellates and then diatoms, with higher cell numbers in the nutrient-enriched 2006 period. Although the water column nutrient data indicated that the estuary was oligotrophic, benthic microalgal biomass (11.9-16.1 μg.g-1) in the intertidal zone was comparable with nutrient rich estuaries. Benthic species indicative of polluted conditions were found (Nitzschia frustulum, Navicula gregaria, Navicula cryptotenelloides). These benthic species were found at the sites where wastewater / sewage seepage had occurred. Benthic diatom species also indicated freshwater inflow. During the high flow period in 2006 the dominant diatoms were fresh to brackish species that were strongly associated with the high concentrations of TOxN and SRP (Tryblionella constricta, Diploneis smithii, Hippodonta cf. gremainii, and Navicula species). During the freshwater limited period of 2008 and 2009 the benthic diatom species shifted to a group responding to the high salinity, ammonium and silicate concentrations. The species in this group were Nitzschia flexa, Navicula tenneloides, Diploneis elliptica, Amphora subacutiuscula and Nitzschia coarctata. Ordination results showed that the epiphytic diatom species responded to different environmental variables in the different years. Most of the species in 2008/2009 were associated with high salinity, temperature, dissolved oxygen, ammonium and silicate concentrations while the response was towards TOxN and SRP in 2006. The dominant species were Cocconeis placentula v euglyphyta in 2006; Nitzschia frustulum in 2008; and Synedra spp in 2009. The average biomass of the epiphytes was significantly lower in May 2008 than in both August 2006 and February 2009; 88.0 + 17.7 mg.m-2, 1.7 + 0.8 mg.m-2, and 61.8 + 14.4 mg.m-2 respectively. GIS mapping of past and present aerial photographs showed that submerged macrophyte (Zostera capensis) cover in 1966 and 1973 was less than that mapped for 2004. Salt marsh also increased its cover over time, from 86.9 ha in 1966 to 126 ha in 2004, colonizing what were bare sandy areas. Long-term monitoring of the health of the Bushmans Estuary should focus on salinity (as an indicator of inflow or deprivation of freshwater), benthic diatom identification and macrophyte distribution and composition (for the detection of pollution input), and bathymetric surveys (for shallowing of the estuary due to sedimentation).

The Swartkops River and Sundays River Estuaries are different in terms of morphology and the level of human impact. Budget models of DIP and DIN were constructed for each estuary at different riverine flow rates, using the Land-Ocean Interactions in the Coastal Zone (LOICZ) protocol. Nutrient dynamics in the estuaries were investigated using nutrient data and the results of the models. The Swartkops River Estuary acted as a sink of DIP and DIN, while being net heterotrophic. The Sundays River Estuary acted as a source of DIP and DIN, while being net autotrophic. Both systems were net denitrifying. The Swartkops River Estuary shows greater anthropogenic impacts in terms of nutrient loads than the Sundays River Estuary. A shift in nutrient concentration trends and system properties occurred between conditions of low and high riverine flow rates. The Swartkops River and Sundays River Estuaries were shown to be ‘outwellers’ of DIN and DIP, while having an important influence on the ratio of DIN:DIP exported to the adjacent ocean. Comparisons with other estuaries suggested that riverine flow into estuaries in the Eastern Cape region may display natural DIN:DIP ratios which are lower than the global average for “pristine” systems. Such ratios would be decreased further by increased water extraction for human activities.

Estuaries are some of the most productive yet threatened ecosystems in the world. Despite their importance they face significant threats through changes to river flow, eutrophication, rapid population growth long the caost and harvesting of natural resources. A number of international studies have been conducted investigating the structure and functioning of an array of ecosystems using ecological network analysis. Energy flow networks have been contsructed for coastal, lagoonal, intertidial and, most notably, permantently open estuaries. Despite the valualble insights contributed by these and other studies, a lack of information on the majority of estuarine ecosystems exists.

Recent geomorphic and hydrologic environments of a mid-latitude alpine basin are investigated under the integrative theme of paleohydrology. The aims of this research are: 1) to characterize the response of selected biological and geophysical elements to recent climatic change; 2) to determine the resolution and length of paleoenvironmental records in the study area; and 3) to ascertain the significance of observed and inferred environmental change over the Little Ice Age interval. Bella Coola River drains 5050 km² of glacierized mountains along the central coast of British Columbia. Biological elements examined on a basin-wide scale included: tree-growth in temperature and moisture-stressed environments, damage to trees in glacial and fluvial settings, pollen variations in a variety of sedimentary deposits and soil development. Geophysical elements include primarily glacio-lacustrine and floodplain sediments, glacier deposits and river channel morphology. A retrospective strategy was adopted by testing initially for the nature of relationships between synoptic climate, basin hydrology and element response during the period of instrument record (1900 AD to present). Inferences about pre-instrument environments were then made using the proxy data. Events of several types are characteristically mixed in a response record. Variations in Douglas and subalpine fir growth, glacio-lacustrine sedimentation rates, glacier fluctuations and shifting of the Bella Coola River reflect a combination of persistent and episodically extreme behavior. Glaciers appear to respond by advancing or retreating after departures in winter precipitation persistent for several years. Extreme events, particularly high-magnitude autumn floods, are not exclusively linked to a particular set of mean climatic departures. This makes inferences from proxy data such as floodplain deposits and flood-damaged vegetation difficult. Periods of increased flood frequency are supposed to relate to an increase in floodplain sedimentation. Except in very favorable circumstances, paleoenvironmental methods do not have the resolution promised. Climatic information recoverable from tree-ring data and glacio-lacustrine sediments is of considerably lower than annual resolution. Statistically based climate models using proxy data as independent variables produce low levels of explained variance. Proxy data sources in the basin were largely restricted to the last 300 to 4OO years or Little Ice Age interval. Most glaciers in the basin reached Little Ice Age maxima in the middle of the 19th century in response to below average temperatures and above average precipitation between approximately 1800 and 1855 AD. Tree-ring data and equilibrium line altitudes on glaciers indicate that precipitation was on average 25 to 30% greater than the 1951-1980 mean. Inferred below average temperatures in the early l8th century probably signaled the beginning of the Little Ice Age along the central coast; however, there was not a major response in glaciers until persistent positive departures in precipitation occurred. Recession of glaciers from Little Ice Age maxima was slowed by cooler and wetter conditions between I885 and 1900 AD. The persistence of warmer and drier conditions in the first half of the 20th century was exceptional in comparison with inferred climate of the last 330 years. Major floods in 1805/06, 1826, 1885 and 1896 correspond to intervals of increased precipitation. / Arts, Faculty of / Geography, Department of / Graduate

Two problems in oceanic/atmospheric modelling are examined in this thesis. In the first problem the release of fresh water from a midlatitude estuary to the continental shelf is modelled numerically as a Rossby adjustment problem using a primitive equation model. As the initial salinity front is relaxed, a first baroclinic mode Kelvin wave propagates into the estuary, while along the continental shelf, the disturbance travels in the direction of coastally trapped waves but with a relatively slow propagation speed. When a submarine canyon extends offshore from the estuary, the joint effect of baroclinicity and bottom relief provides forcing for barotropic flow. The disturbance now propagates along the shelf at the first coastally trapped wave mode phase speed, and the shelf circulation is significantly more energetic and barotropic than in the case without the canyon. For both the experiments with and without a canyon an anticyclonic circulation is formed off the mouth of the estuary, generated by the surface outflow and deeper inflow over changing bottom topography. As the deeper inflow encounters shallower depth, the column of fluid is vertically compressed, thereby spinning up anticyclonically due to the conservation of potential vorticity. This feature is in qualitative agreement with the Tully eddy observed off Juan de Fuca Strait. A study of the reverse estuary (where the estuarine water is denser than the oceanic water) shows that this configuration has more potential energy available for conversion to kinetic energy than the normal estuary. Bass Strait may be considered as a possible reverse estuary source for the generation of coastally trapped waves. Model solutions are compared with field observations in the Bass Strait region and with the results of the Australian Coastal Experiment. The effects of a wider shelf and a wider estuary are examined by two more experiments. For the wider shelf, the resulting baroclinic flow is similar to that of the other runs, although the barotropic flow is weaker. The wide estuary model proves to be the most dynamic of all, with the intensified anticyclonic circulation now extending well into the estuary. In the second problem the effect of the horizontal structure of midlatitude oceanic heating on the stationary atmospheric response is examined by means of a continuously stratified model and a simple two level model, both in the quasigeostrophic β-plane approximation. Solutions are obtained for three non-periodic zonal heating structures (line source, segmented cosine, and segmented sine). Little difference is observed between the solutions for these two different models (continuously stratified and two level). There are two cases which emerge in obtaining analytic solutions. In case 1, for large meridional wavenumbers, there exists a large local response and a constant downstream response. In case 2, for small meridional wavenumbers, the far field response is now sinusoidal. A critical wavenumber separating these two cases is obtained. The effect of oceanic heating on the atmosphere over the Kuroshio region is examined in an attempt to explain the large correlations observed between winter Kuroshio oceanic heat flux anomalies, and the winter atmospheric surface pressure and 500 & 700 mb geopotential heights, both upstream and downstream of the heating region. In both models, the response is consistent with the observed correlations. When western North Pacific heating and eastern North Pacific cooling are introduced into the models, a large low pressure response is observed over the central North Pacific. This feature is in excellent agreement with the observed correlations. A time dependent, periodic, two level model (with and without surface friction) is also introduced in order to study the transient atmospheric response to oceanic heating. The height at which the thermodynamic equation is applied is found to be crucial in determining the response of this model. When the heating is entered into the model near to the surface, unstable modes are prevalent sooner than they would be when the heat forcing is applied at a higher level. As in the steady state models, two cases dependent on the meridional wavenumber ɭ emerge in the analysis. For small scale meridional heating structures (large ɭ), the response consists of an upper level high and a lower level low which propagate eastward with time. For large scale meridional heating structures (small ɭ) the response essentially consists of a wavenumber 3-4 perturbation superimposed on the solution for large ɭ. / Science, Faculty of / Mathematics, Department of / Graduate

The abundance and microspatial distribution of harpacticoid copepods were studied from Jan 1977 to Jan 1980 at two intertidal sites on the Fraser River Delta, B.C.: one (Sand) on the crest of a sand wave and the other (Mud) on the edge of its muddy trough. Eight species formed the communities at the two sites. The composition of the communities was studied by biweekly survey in 1978. Longer term changes in the organization of the sand community were followed by annual mid-winter surveys over four years. Factor analysis was used to group species with similar patterns of seasonal occurrence and macrohabitat distributions. Microspatial patterns in the two communities were compared by heterogeneity chi-square analysis from random core samples collected monthly. The distribution of species relative to small-scale hydraulic bedforms (sand ripples) was studied at the sand site. Distinct patterns of community organization were seen at the two sites. The mud community was characterized by high temporal overlap of species; the sand species showed a distinctive pattern of temporal segregation. Although species in both communities were segregated at small spatial scales, microspatial partitioning was stronger and seasonally more variable in the mud. Spatial patterns in the sand were related to the rippled bedforms. Biogenic structuring by macrobenthos and disturbance by predators were implicated as the causes of microspatial patterns observed in the mud community in summer. Although the two communities showed distinct features of organization they were not completely isolated. Two mud species, Scottolana canadensis and Tachidius triangularis, 'migrated' to the sand in summer. The role of biological interactions in structuring the communities was investigated. Predation by small tidepool fish, Clevelandia ios and Leptocottus armatus, was studied by gut analysis. Predation was species- and size-selective, with two epipelic species, S. canadensis and T. triangularis, occurring most frequently in fish gut samples. A morphometric basis for ontogenetic variation in predation by C. ios was proposed. Evidence to support the hypothesis that competitive interactions help to structure harpacticoid copepod communities was found in changing patterns of abundance, changing patterns of microhabitat use and morphometric character displacement over four years. Competitive interactions were highly dynamic and appeared to be part of the cause of both the temporal and microspatial segregation observed in the sand community in 1979. By 1980, the eight species present in the January sand community formed a displacement series in body sizes. Although each harpacticoid community is unique, numerous parallels exist between the structure and function of the Iona North assemblage and those from shallow water habitats, worldwide. It is clear, therefore, that the conclusions from this research have more than local significance. / Science, Faculty of / Zoology, Department of / Graduate

The Indian River Lagoon (IRL) FL, USA, is an Estuary of National Significance due to its economic and high biodiversity. Microbial populations are understudied in the IRL despite their numerous ecological services. A two-year, nineteen-site Lagoon-Wide Survey (LWS) was conducted to provide the first 16S rRNA amplicon sequencing data on the microbiome of the sediment in the IRL and determine how the microbiome changed in response to environmental and anthropogenic factors. The most influential variables that explained the variability between microbiomes were porewater salinity, total organic matter (TOM), and copper (Cu). These results correlated with some of the anthropogenic pressures the IRL faces such as freshwater discharges from St. Lucie Estuary (SLE), trace metal contamination, and the accumulation of fine-grained, highly organic sediment known as “IRL muck” (muck). Research then focused on determining the microbial differences between three sets of sample types: sediment from the IRL versus the SLE; sediment that had three muck characteristics versus those with zero; and high TOM sediment that had high Cu versus high TOM sediment that had low Cu. Differentially abundant prokaryotes between sample types were determined with novel indicator analysis techniques. One technique tested the effectiveness of an indicator list to separate samples based upon the product of the sensitivity and specificity of partitioning around medoids clustering in comparison to metadata classifications. The other technique allowed for the tracking of changes in the entire indicator microbiome. These new indicator analysis techniques were created using the original LWS data and tested to determine how sediment microbiomes responded during two opportunistic surveys: dredging of muck from an IRL tributary (Eau Gallie River) and Hurricane Irma. These studies have filled the knowledge gap regarding the unknown microbiome of the IRL and how sediment microbiomes respond to extreme events such as dredging and a hurricane. They also led to the development of new indicator analysis techniques that can be used by to track changes in the entire indicator microbiome. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2020. / FAU Electronic Theses and Dissertations Collection

Knowledge of geotechnical soil properties in the upper meter of the seabed is important for challenges such as scour around submerged structures, management of unexploded ordnances, and generally issues associated with active sediment transport and deposition. Portable free fall penetrometers have been previously used to provide initial information on sediment type, strength, and stratification, but challenges with the calibration of empirical parameters such as the cone factor and strain rate factor hampered the derivation of geotechnical design parameters such as undrained shear strength. This challenge applies particularly in areas of more rare seabed soil conditions such as very soft estuarine sediments. This study aims to advance the analysis procedure of portable free fall penetrometers (PFFP) in soft subaquatic fine-grained soils with natural water contents greater than the liquid limit by estimating the undrained shear strength (su). The logarithmic and power law methods for strain rate correction were investigated at sites in the York River Estuary and yielded a match to vane shear results at a logarithmic multiplier of k=0.1-0.3 and a power law rate exponent of β=0.01-0.03, indicating minimal strain rate effects. Resulting representative cone factors based on sediment strength and profile groupings ranged from 7 to 12 for logarithmic, power law, and no strain correction, and were tested at sites in the Potomac River with similar sediment properties. The PFFP su compared well with mini-vane shear measurements with differences of less than ± 0.5 kPa. Additionally, the PFFP su showed inappreciable differences in strength with or without strain rate application. Therefore, these high water content soils that exhibit little strain rate effects within a soil behavior context, can be better understood through rheological studies. Rheological studies were conducted, and the storage and loss modulus were observed to remain constant when the soil is tested over a range of frequencies. This indicates that the sediment strength is not affected by the rate of soil testing. The outcome of this study is the advanced the use of the PFFP by quantifying the strain rate effects and defining the applicable cone factors for use in estimating the undrained shear strength of soft estuarine marine soils. Furthermore, the understanding of soil behavior of these soils has been explored from rheological context. / Master of Science / Presence of unexploded munitions (UXO) in waterways and coastal environments poses a danger to the populace. UXOs located proud on the seabed can be moved by hydrodynamic forces such as waves and currents to habited areas. This has prompted the need to understand how UXOs interact with the seabed regarding erosion, burial, as well as sinking. Current methods used to detect munitions can lack accuracy from unknown seabed soil conditions. Portable free fall penetrometers (PFFP) are rapid and economical tools that are used to obtain soil information in the seabed. However, the interpretation of the penetrometer data needs to be advanced to get more accurate results of soil strength. In this research, physical soil samples were retrieved and tested in the laboratory. The laboratory results were used to calibrate the PFFP to improve the estimation of soil strength from PFFP. The estuarine soil tested exhibited high water contents raising the question of whether to describe its behavior rather as soil or suspension. Further tests were carried out to study how this soil deforms and flows when a load is applied. The results from this research enable the measuring of strength of the seabed more accurately and improves the understanding of very soft estuarine soil behavior.

Seagrass is a key stone component for the Indian River Lagoon (IRL) ecosystem, and therefore it is an important topic for many studies in the lagoon. This study focuses on the effects of seagrass beds on the hydrodynamics in the IRL. A hydrodynamic model based on the Delft3D modeling system has been developed for the southern IRL including the St. Lucie estuary, Ft. Pierce and St. Lucie Inlets, and adjacent coastal waters. The model is driven by freshwater inputs from the watershed, tides, meteorological forcing, and oceanic boundary forcing. The model has been systematically calibrated through a series of numerical experiments for key parameters, particularly the bottom roughness, and configuration including heat flux formulation and bottom bathymetry. The model skills were evaluated with quantitative metrics (point-to-point correlation, root-mean-square difference, and mean bias) to gauge the agreements between model and data for key variables including temperature, salinity, and currents. A three-year (2013-2015) simulation has been performed, and the results have been validated with available data including observations at HBOI Land-Ocean Biogeochemistry Observatory (LOBO) stations and in situ measurements from various sources. The validated model is then used to investigate the effects of 1) model vertical resolution (total number of model vertical layers), 2) spatial variability of surface winds, and 3) seagrass beds on the simulated hydrodynamics. The study focuses on the vicinity of Ft. Pierce Inlet, where significant seagrass coverage can be found. A series of numerical experiments were performed with a combination of different configurations. Overall, the experiment with 2-dimensional (2-D) winds, ten vertical layers and incorporating seagrass provided the most satisfactory outcomes. Overall, both vertical resolution and spatial variability of surface winds affect significantly the model results. In particular, increasing vertical resolution improves model prediction of temperature, salinity and currents. Similarly, the model with 2-D winds yields more realistic results than the model forced by 0-D winds. The seagrass beds have significant effects on the model results, particularly the tidal and sub-tidal currents. In general, model results show that both tidal and sub-tidal currents are much weaker due to increase bottom friction from seagrass. For tidal currents, the strongest impacts lie in the main channel (inter-coastal waterway) and western part of the lagoon, where strong tidal currents can be found. Inclusion of seagrass in the model also improves the simulation of sub-tidal currents. Seagrass beds also affect model temperature and salinity including strengthening vertical stratification. In general, seagrass effects vary over time, particularly tidal cycle with stronger effects seen in flood and ebb tides, and seasonal cycle with stronger effects in the summer than in winter. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2016. / FAU Electronic Theses and Dissertations Collection