The ubiquitous, free-living naked amoeba, Acanthamoeba, is an opportunistic pathogen that can cause the painful eye disease Acanthamoeba keratitis (AK), and, in immunocompromised individuals, the fatal disease granulomatous amebic encephalitis (GAE). Acanthamoeba keratitis is a rare corneal disease that effects contact lens wearers more than non-contact lens wearers, though up to 10-15% of cases do occur in non-contact lens wearers (Radford et al., 2002; Walochnik et al., 2000). The aims of this work were fourfold: 1) to determine if there were differences in the tolerance of several strains of acanthamoebae to three commonly used multipurpose lens cleaning solutions, 2) to determine whether acanthamoebae were present in domestic water in south Florida; tapwater has been implicated as a route of infection, 3) to determine if a previously designed set of Polymerase Chain Reaction (PCR) primers would be useful in distinguishing possible pathogenic acanthamoebae from environmental strains, and 4) to determine if acanthamoebae cysts would be a suitable surrogate for dinoflagellate cysts during the testing of ballast water treatment systems. These supposedly disparate studies are linked. There is great interest in understanding what makes some strains invasive and others benign. Thus a wide range of strains were examined from various environmental sources (including the beach) and from clinical samples. It was reasoned that tolerance differences might be related to pathogenicity. Since the strains were from known sources, the robustness of the molecular screening method could be tested. Finally, the resilience of cysts and the fact that different strains showed different responses to stressors implied that strains of some cysts might be good mimics of dinoflagellate cysts for verifying the effectiveness of ballast water treatment systems. The industry is most concerned about these problem cysts that must be inactivated before water is released. Unfortunately, it is impossible to grow large numbers of dinoflagellate cysts for testing. Fourteen acanthamoebae isolates from both clinical and environmental sources were tested for their susceptibility to the three most effective (against bacteria) contact lens multi-purpose cleaning solutions (MPS). These toxicity tests showed that different strains responded differently to the effects of the cleaning solutions. Surprisingly, the pathogenic strains were not universally the most tolerant. However, in all cases cysts were more resistant than trophic amoebae and no MPS was 100 % effective at killing acanthamoebae. Over a 2 year period, 283 water samples were obtained from south Florida and scored for the presence of naked amoebae including Acanthamoeba. Over 19% of domestic water samples tested positive for amoebae, although only 2.8% were positive for Acanthamoeba. The two sets of primers, reportedly capable of distinguishing pathogenic amoebae, were tested with pathogenic and environmental isolates. One set of primers held promise since it correctly identified a 195 bp band (the marker for pathogenic strains) in 50% of pathogenic strains. Moreover, this band was absent in 78% of the non-pathogenic strains. With Acanthamoeba’s resilience and its ease of culture, it was hypothesized to be an ideal candidate for use as a surrogate test organism for the verification of ballast water treatment systems. Experiments conducted in this thesis compared the sensitivity of acanthamoebae cysts to 6 other heterotrophic protist species. Finally, throughout the entire study, additional physiological clues were sought that might shed light on why some strains are capable of invading the eye. These included genotyping isolates (the T4 genotype is most frequently found in keratitis infections), determining the temperature tolerance of strains, and comparing the capacity of some strains to burrow into agar (possibly seeking out areas of low oxygen tension).

In 1988, offshore dredging for a beach renourishment project in Miami-Dade County, Florida caused extensive damage to the second reef tract off of Sunny Isles Beach. In an effort to restore and mitigate for the damage to the reef, the Sunny Isles Reef Restoration Project (SIRR) began in August of 1991. Three different types of artificial reef modules—Dome modules (D), CSA2 Module Designs (M), and Reef Replacement modules (R)—were placed on the edge of second reef where the damaged occurred. The colonization development of the benthic assemblages on the modules was monitored for the initial four years following deployment by G.M. Selby and Associates. This study sought to examine the same modules previously studied in order to determine the changes in species diversity and density as well as the level of similarity among the different module types and between the modules and the surrounding natural reef. Over time the diversity and density of benthic organisms has increased on the modules. The similarity among the modules has increased as well since the original monitoring. All three modules types share some similarities with the surrounding reef with the D and R modules being the most similar. Determining whether the similarity between the benthos on the modules and natural reef has leveled off or if an increased level of similarity is still attainable requires future research and monitoring efforts.

Four ocean models are used to investigate the response of the coastal ocean to strong offshore winds: a linear 11/2-layer model, a linear 21/2-layer model, a nonlinear 11/2-layer model and a nonlinear 21/2-layer model. The nonlinear models include thermodynamics and entrainment, the latter allowing cool lower-layer water to move into the upper layer. The models are forced by wind stress fields similar in structure to the intense winter-time, mountain-pass jets (~20 dyne/cm2) that appear in the Gulfs of Tehuantepec and Papagayo and blow directly offshore for periods of 3 - 10 days. Analytic and numerical solutions are arranged in a hierarchy of increasing dynamical complexity in order to illustrate the important physical processes. They compare favorably with observations in several ways, including the large sea-level drop at the coast and the fast westward propagation speeds of anticyclones. While the wind strengthens there is an ageostrophic current (not Ekman drift) that is directed offshore. This offshore drift forces coastal upwelling, thereby lowering the local sea level and sea surface temperature (SST). Although the drop in sea level at the coast can be large and rapid, none of this signal propagates poleward as an upwelling-favorable coastally trapped wave. While the wind weakens the ageostrophic current is directed onshore, and consequently the coastal ocean readjusts toward its initial state. Throughout the wind event, cyclonic and anticyclonic gyres spin up offshore on either side of the jet axis due to Ekman pumping. Entrainment cools SST offshore on and to the right (looking onshore) of the jet axis, and virtually eliminates the cyclonic gyre. The advection terms intensify the anticyclonic gyre and give it a more circular shape. After a wind event, the anticyclonic gyre propagates westward due to β. In all the 11/2-layer solutions, its propagation speed is less than observed values. In the 21/2-layer solutions, however, the Tehuantepec gyre moves westward and southward at a speed of 7.5 km/day and Papagayo gyre propagates westward at 12.8 km/day, both close to observed speeds. The coastal sea-level drop is enhanced by several factors: horizontal mixing, advection of the upper-layer thickness field h, enhanced forcing, coastal geometry, and the existence of a second active layer in the 21/2-layer model. Horizontal mixing enhances the sea-level drop because the coastal boundary layer is actually narrower with mixing; consequently, the interface below the upper-layer must rise farther to balance the volume of water that is displaced offshore. Advection of h intensifies upwelling by carrying regions of shallow h offshore. The forcing τ/h is enhanced near the coast where h is thin. When the coastal geometry includes a bay, the wind has an alongshore component that intensifies upwelling at the apex of the bay. Finally, in analytic solutions to the 21/2-layer model the presence of two baroclinic modes increases the sea-level drop to some degree; in numerical solutions the maximum sea-level drop also increases because it is not as severely limited as it is in the 11/2-layer model. Of these factors the strengthened forcing τ/h has by far the largest effect on the magnitude of the drop, and when all of them are included the resulting maximum drop is -30.0 cm, close to observed values. To investigate the processes that influence the propagation speeds of anticyclones, several test wind-forced calculations as well as additional numerical experiments with isolated eddies were carried out. Solutions to dynamically simpler versions of the 11/2-layer model show that the speed is increased both by β-induced self-advection and by larger h at the center of the gyre, both factors measuring the strength of the gyre circulation. Solutions to the 21/2-layer model indicate that the lower-layer flow field advects the gyres westward and southward, significantly increasing their propagation speed. Solutions with isolated eddies confirm that self-advection enhances the propagation speed of 11/2-layer anticyclones, and indicate that it is advection by a wind-forced background circulation that increases the speed of 21/2-layer anticyclones.

Sedimentation parameters, turbidity, extension (linear) growth, bleaching and polyp expansion were examined prior to, during, and after the dredge and fill activities associated with the first renourishment of Hollywood and Hallandale beaches, 1991. During the project, approximately 1.1 million cubic yards of beach compatible material was taken from two offshore borrow areas and placed on 5.3 miles of beach. Treatment stations were at offshore (adjacent to the borrow area) and nearshore (adjacent to fill area) locations. Control stations were placed at least 3km north, offshore of John U. Lloyd Beach State Recreation Area. Two coral species abundant in this area, Solenastrea bournoni and Dichocoenia stokesii, were monitored monthly on each reef for signs of bleaching and polyp expansion, indicators of stress and surface clearing ability respectively. After dredging was completed, the corals were collected for growth analysis (linear extension) by the Alizarin stain method. At treatment stations, associated with dredging, a significant decrease in extension growth rate in S. bournoni but not D. stokesii occurred. A decrease in fossa length of D. stokesii suggested that dredging effects caused a change in columella shape. Bleaching occurred in many of the colonies but may have been caused by an unknown factor. Polyp expansion, a means of sediment rejection, did not correlate with the proximity to dredging. The corals may be relying on other means of sediment removal. This study suggests that the effects of dredging on stony corals are species specific.

This dissertation consists of three chapters, two of which are presented in manuscript form. Chapter One is an introduction and review of the measurement of phytoplankton chlorophyll a carbon-specific growth rates. Chapter Two consists of the manuscript ASPECTS OF CHLOROPHYLL a CARBONSPECIFIC GROWTH RATE IN THE EASTERN NORTH ATLANTIC OCEAN. It has been formatted in accordance with the specifications of the oceanographic journal Marine Ecology Progress Series. In Chapter Two, an evaluation of the short-term kinetics of the labeling time of natural phytoplankton populations in different oceanic regions showed that chI a labeling varied in relation to both environmental conditions and latitude. At subtropical stations rapid short-term increases in the activity of chI a were coincident with large (> 38%) increases in total photosynthetically available radiation. The rapid short-term increases resulted in overestimates of the growth rate. Overall though, a strong correlation between chI a carbon-specific growth rates and independently-derived assimilation numbers was evident. This strong correlation, particularly with end-of-day samples suggests that the chI a labeling technique for phytoplankton carbon-specific growth rate determination is applicable in different oceanic regions under broadly varying environmental conditions. Chapter Three consists of the manuscript DISTRIBUTIONS OF CHLOROPHYLL AND PRIMARY PRODUCTIVITY IN RELATION TO WATER COLUMN STRUCTURE IN THE EASTERN NORTH ATLANTIC OCEAN. Chapter Three has been formatted in accordance with specifications of the Journal of Global Biogeochemical Cycles. Chapter Three has been submitted under the co-authorship of G. Berberian for review by the Journal of Biogeochemical Cycles. In Chapter Three latitudinal variations in the megascale (103 km) distribution of biological properties were observed in relation to the water column structure between 60°N and 7°N in the Eastern Atlantic Ocean. High chI a concentrations in the northern latitudes were associated with a shoaling of the pycnocline. A secondary region of high chI a at 7°N was associated with a lens of low salinity Amazon River water. Productivity maxima were located south of Iceland, in the vicinity of the Azores Front, and at the Amazon River water feature. The research described in Chapters Two and Three was performed during the Eastern North Atlantic section of the 1988 National Oceanic and Atmospheric Administration (NOAA) Global Change Expedition. Two appendices are included in the dissertation which contain pertinent Global Change Expedition data used in the manuscripts. Appendix One contains data relevant to Chapter Two, while Appendix Two contains data relevant to Chapter Three. A NOAA Data Report (Frazel, Berberian and Hitchcock 1989) containing complete data for the Global Change Cruise is also available. Reference lists are included at the end of Chapters Two and Three, while a master reference list is given at the end of the dissertation. Chapter Three has been formatted in accordance with specifications of the Journal of Global Biogeochemical Cycles. Chapter Three has been submitted under the co-authorship of G. Berberian for review by the Journal of Biogeochemical Cycles. In Chapter Three latitudinal variations in the macroscale (103 km) distribution of biological properties were observed in relation to the water column structure between 60°N and 7°N in the Eastern Atlantic Ocean. High chl a concentrations in the northern latitudes were associated with a shoaling of the pycnocline. A secondary region of high chI a at 7°N was associated with a lens of low salinity Amazon River water. Productivity maxima were located south of Iceland, in the vicinity of the Azores Front, and at the Amazon River water feature. The research described in Chapters Two and Three was performed during the Eastern North Atlantic section of the 1988 National Oceanic and Atmospheric Administration (NOAA) Global Change Expedition. Two appendices are included in the dissertation which contain pertinent Global Change Expedition data used in the manuscripts. Appendix One contains data relevant to Chapter Two, while Appendix Two contains data relevant to Chapter Three. A NOAA Data Report (Frazel, Berberian and Hitchcock 1989) containing complete data for the Global Change Cruise is also available. Reference lists are included at the end of Chapters Two and Three, while a Master Reference List is given at the end of the dissertation.

The purpose of this study was to assess whether phagotrophy may be proportionally more important to coral nutrition with decreasing light intensity. An animal carotenoid pigment, possibly astaxanthin, isolated from Montastrea annularis was used as an indicator of phagotrophy. This carotenoid was measured in corals collected over a depth transect in the field and in corals exposed to varying amounts of food and light in laboratory experiments. In the field, multiple cores of the same and different coral heads were collected at each of four depths, 4.6, 7.6, 18.3 and 22.9 m. In the laboratory, cores from the same coral head were maintained at three light intensities (0.024, 24 and 90 μE m-2s-l) with three feeding schedules at each intensity (no Artemia, 2-3 Artemia/ml, and 8-10 Artemia/ml). The pigments from the corals' symbiotic algae, zooxanthellae, and from the coral polyp were acetoneextracted and quantitatively isolated by reverse-phase, high performance liquid chromatography (HPLC). Parametric statistics were used to determine whether carotenoid concentrations in corals varied significantly with depth along the transect in the field, or with light intensity or particulate food concentration in the laboratory. In the field, mean concentrations of the animal carotenoid increased significantly between 7.6 and 18.3 m over a depth range from 4.6 to 22.9 m. A significant increase in animal carotenoid concentration was also found when 4.6 and 7.6 m data were pooled and compared with pooled data from 18.3 and 22.9 m. This suggests the possibility of two populations. In the laboratory, animal carotenoid concentrations increased significantly with decreasing irradiance. However, at each individual light intensity the absolute concentrations of animal carotenoid were similar no matter what the feeding regime. Between the light intensities of 24 and 0.024 μE m-2s-l animal carotenoid content increased in corals fed 8-10 Artemia/ml and in un-fed corals. That no difference was found between light intensities in corals fed 2-3 Artemia/ml may be because of the high variability observed in animal carotenoid content for this group. The animal carotenoid content from combined field and laboratory data varied proportionally with the natural logarithm of light. It appeared that below approximately 200-400 μE m-2s-l (10% and 20% PAR) the rate of change in carotenoid content increased with respect to light. The animal carotenoid:peridinin ratio may reflect the relative importance of phagotrophy to coral nutrition. The ratio increased with depth with one exception. In conclusion, the carotenoid isolated from the coral polyp increased with decreasing irradiance. This increase may result from a carotenoid-rich diet. Such an increase may reflect an increase in phagotrophy.

On the morning of June 19, 1991, approximately 3, 790 L (1,000 gallons) of heavy fuel oil were spilled into the waters of Port Everglades, Florida. The oil impacted one of several mitigation sites located in John U. Lloyd State Park (JUL). These sites were planted with Rhizophora mangle and Spartina alterniflora prior to the spill. Laguncularia racemosa and Avicennia germinans had also established themselves through natural recruitment. After the spill, these seedlings were coated with oil in varying amounts depending upon their location relative to the intervening oil slick and their elevation within the intertidal zone. To assess the impacts of the oil on the mitigation site, measurements were taken on the three species of mangroves. These measurements included: survival, growth rate, development of leaves, foliation, branches, and roots. Results indicated that L. Racemosa seedlings were less tolerant to oil contamination than A. germinans and R. mangle seedlings. In addition, there were some cases where growth stimulations were found in the exposed seedlings. The results from this investigation may aid in the selection of appropriate mangrove species that are to be utilized for wetland restoration sites located near ports, terminals, or refineries which are at high risk for oil pollution.

Analysis of samples collected bimonthly between summer 2001 and spring 2002 showed that the numbers of enterococci on three South Florida beaches were significantly higher in 'dry' sand compared to wet sand. Moreover, the wet and dry sand samples showed higher levels of fecal organisms than present in seawater. Other fecal bacteria (E. coli and total coliforms) showed similar trends. These interesting results suggest that the sand is acting as a filter and is concentrating fecal bacteria from the water column. This idea was supported by quantitative laboratory and field experiments showing that sand does actively filter fecal organisms out of the water column. However, this does not satisfactorily explain how high numbers of fecal bacteria are being amassed in the upper beach sand (='dry' sand), which is above the high water mark. The possibility that high numbers of fecal organisms were being transported in the air was tested using an Anderson Type impactor air sampler. A total of 45,000 liters of air were filtered but no airborne enterococci were detected. A more likely explanation is that there W8 increased survival of sand-trapped enteric bacteria in beach sand although the degree of survival must fluctuate given the wide range of different physical and chemical parameters from the water line to the top of the beach. Mesocosm experiments were conducted in a controlled laboratory environment, using sterile seawater and sterile beach sand seeded with a known number of E. coli and enterococci. Parameters of interest included temperature, moisture content, salinity, particle size, and nutrient status. Generally, these mesocosm experiments showed that fecal bacteria can grow (and reproduce) in sand but slowly die in seawater alone. Additional mesocosm experiments conducted using natural seawater and beach sand containing indigenous microbiota suggested that predation had a dramatic effect on the fate of fecal bacteria in the beach environment. A series of palatability studies added additional information by showing that micropredators were capable of consuming fecal indicator bacteria in the beach environment.

No description available.

More than 500 species of higher marine fungi in over 300 genera have been described. Many marine fungi are highly specialized for marine environments relative to their terrestrial counterparts, having appendaged ascospores and conidia to aid in buoyancy, entrapment, and adherence to substrates. They have been reported to inhabit a wide variety of substrates including decaying wood, leaves, calcareous and chitinous substrates, seaweeds, and seagrasses. Most early studies on marine fungi were carried out in temperate regions. Investigations have now shifted to tropical locations in order to better evaluate the abundance and diversity of marine fungi on a global basis. Many surveys have focused on mangrove habitats in the Pacific and Atlantic Oceans, resulting in the discovery of many new taxa. The purpose of this study was to examine the distribution and seasonal occurrence of higher marine fungi along a salinity gradient in a marine estuary, Henderson Creek in Rookery Bay Reserve Naples, Florida. Parameters including temperature and salinity were measured. Three stations were established along Henderson Creek. Mean salinity ranged from 5 ppt at the low salinity station Visitor Center to 36ppt at the high salinity station Field Station. Substrates used for fungal collections were wood panels of a hardwood Oak (Quercus sp.) and a softwood Pine (Pinus sp.). Four panels were submerged at each station and removed in 3 month increments over the course of one year. One-hundred-and-sixteen species of filamentous higher marine fungi were identified over the course of this study, including seventy-one Ascomycetes, three Basidiomycetes, and forty-one Deuteromycetes. There was no clear pattern of seasonality in the species composition. Total species diversity and richness decreased in each 3month period following the first 3 month period. Changes in salinity appeared to alter the ratio of Ascomycetes to Fungi Imperfecti observed at each station. Marine fungi in this collection were compared with previous reports on the east coast of Florida (Adams, 2003a; Kukich, 2005; Vogel, Schatz, Laubach, & Rogerson, 2008). A higher total species number as well as greater diversity was observed in this study when compared with reports from mangroves in southeast Florida. Marine fungi are active decomposers in mangrove environments and contribute to total dissolved organic matter in estuarine and near shore ecosystems. While most studies focused on the taxonomy of marine fungi, few have looked at their ecology. Further studies will have to be conducted to better determine the role of filamentous marine fungi in near shore and estuarine environments.