Due to the continuing anthropogenic degradation of coral reefs worldwide, there is the need for effective, experimentally-tested, reef restoration methodologies. Much effort and energy has been spent on scleractinian (stony) coral transplantation. However, less attention has been directed towards effective restoration techniques for gorgonian (Coelenterata: Octocorallia) transplantation. While most primary restoration activities involve the salvaging and transplantation of loose or fragmented coral colonies following a disturbance, this study used clippings from healthy adult gorgonian donor colonies as transplants to test the effectiveness of different gorgonian attachment techniques. Two abundant local gorgonian species were targeted as donor colonies for this study, Pseudopterogorgia acerosa (Pallas, 1776) and Plexaura flexuosa (Lamouroux, 1821). In April 2007, 160 clippings (80, 25 cm clippings from each species) were transplanted at a large vessel grounding site offshore Broward County, southeast Florida. Two attachment materials, Portland cement and Aquamend® underwater epoxy, were compared for attachment success. Of the 80 total clippings for each species, 40 had 10 cm of their base tissue removed from around the proteinaceous axis, while the remaining 40 clippings did not undergo the base stripping treatment. Within a month, all clip wounds on the donor colonies were completely healed. After 1 year, the highest percent attachment and survival (100%) was observed for the P. flexuosa clippings that underwent the base stripping treatment and were attached with epoxy. The least successful treatment, with the highest percent missing and lowest survival (30%), was the P. acerosa non-stripped base treatment attached with cement. For cemented P. acerosa clippings, tissue that had not been stripped became necrotic and sloughed off, resulting in a loose attachment, preventing the clipping from forming its own independent attachment. Pseudopterogorgia acerosa had lower survival than P. flexuosa due to heavy predation by Hermodice, Cyphoma and Simnia species. For both species, the epoxy treatments had the highest percent survival. Cemented colonies had lower survival due to colonies breaking near their base, likely a result of the caustic and abrasive nature of cement. Growth of the transplants differed, showing species-specific variation, while the growth rates for the donors fell between rates published within literature for both species. Both species of transplanted clippings formed new holdfasts, where actual gorgonin had been deposited over the attachment material, the greatest holdfast formation being observed in the epoxy treatments.

Acanthamoeba are common in all environments and are the cause of Acanthamoeba keratitis. Acanthamoeba keratitis is a sight threatening infection of the cornea commonly found in association with contact lens wear. Acanthamoeba isolates tested grew at temperatures up to 35°C. They were also shown to be capable of growth at low oxygen conditions. Comparison between known pathogenic isolates and environmental isolates showed no clear difference in ability to grow in these conditions. Five isolates, three pathogenic, NSU05023, NSU05012, and NSU06001; and two environmental ones BP and MS26 grew faster to 400 trophozoites in low oxygen conditions than in ambient air. This ability would allow the isolates to grow between the contact lens and the cornea. Five contact lens multi-purpose solutions (Clear Care®, Opti-Free®, Complete®, Renu®, and Aquify®) were tested against four isolates; two pathogenic isolates NSU06004 and P120 and two environmental isolates HK17P191 and FLA22. Results showed that the hydrogen peroxide solution (Clear Care®) was more effective against all strains at 78.75% and the remaining four MPS solutions were below 35%. Acanthamoeba are very common in all environments and are capable of infecting the eye. The currently available contact lens disinfecting solutions are not very effective in preventing Acanthamoeba growth.

Light pollution is any excessive or obtrusive man made light source which disrupts the natural environment. Hatchling marine turtles are adversely affected by light pollution and therefore unlit nesting beaches are essential habitats for all marine turtle species. In Broward County, the most significant conservation issue facing nesting and hatchling marine turtles is the amount of light pollution present on urban sea turtle nesting beaches. The reduction of hatchling mortality from light pollution is an ongoing conservation goal of the State of Florida, Broward County, and the Broward County Sea Turtle Conservation Project (BCSTCP). Conservation techniques and policies intended to reduce hatchling mortality due to light pollution in Broward County have included: mass nest relocation using restraining and self release hatcheries, limited individual relocation of nests, and lighting ordnances in coastal municipalities. Until the 2006 sea turtle nesting season the BCSTCP utilized a mass relocation scheme which removed nests from unsafe and well lighted beach areas to other hatching areas which were not as severely impacted by light pollution. In 2006 the use of hatcheries was phased out and only limited relocation continued. Along with limited relocation, municipalities were strongly encouraged to reduce light pollution. Comparisons will be made based on the 2003-2008 nesting seasons determine which policies and conservation tools were the most effective at reducing hatchling mortality due to light pollution. This study tested the following hypotheses: (1) there has been no significant decrease in light pollution in Broward County, (2) there has been no significant decrease in disoriented hatchlings on Broward County beaches, (3) recent changes to relocation techniques have not improved hatchling production with in Broward County. Results showed that the despite efforts by municipalities no overall reduction in light pollution has occurred. Initially hatchling disorientation events and the number of disoriented hatchlings increased after the policy change but have decreased during the most recent nesting season. Limited relocation yields a higher hatchling success rate then mass relocation. Although some improvements have been made light pollution control and reduction is still needed in order to reduce the accidental deaths of hatchlings due to disorientation.

The widespread decline of Acroporid corals throughout the Western Atlantic and Caribbean has been well documented over the last several decades. Acropora cervicornis and Acropora palmata were listed as threatened on the US Endangered Species Act in May of 2006. Major contributors to Acropora species mortality include disease, predation, sedimentation, nutrient loading, thermal stress and storm damage. These stressors, combined with the species dependence on asexual reproduction and limited potential for larval recruitment, make the full recovery of populations uncertain. Several Acropora cervicornis patches have been documented offshore southeast Florida, despite the substantial impact of both natural and anthropogenic disturbances nearshore Broward County, FL. Some investigation has been done on the distribution, abundance and ecological structure of some of these patches, but limited information exists on abundance and distribution outside of these dense patch boundaries. Acquiring such data requires thorough investigations throughout the near-shore habitat of southeast Florida. The first goal of this study was to investigate the current Acropora cervicornis distribution in this near-shore habitat to utilizing a recent large-scale data set and determine if they are spatially uniform or clustered. The second goal was to investigate the effects of key habitat characteristics on locations of high densities of A. cervicornis, in the form of large-scale topographic metrics through the use of GIS and high resolution bathymetry data. The third goal was to compare several characteristics of colonies and fragments inhabiting the near-shore habitats over the course of a year to investigate the existence of any habitat specialization. These characteristics included size, mortality, condition (presence of recent mortality due to disease or predation), morphology, attachment success and persistence. The Getis-Ord Gi* statistic and Anselin Local Moran’s I spatial cluster analysis of abundance showed significant clustering at several locations within the research area which was supported by the inverse distance weighted surface model (IDW). Topographic metrics with a significant influence in predicting Acropora cervicornis presence were substrate type, proximity to shore and to a ridge. There were no significant differences in colony size, percent mortality or condition between colonies on pavement and rubble. Probability for colony sustainability was significantly greater on pavement than rubble. There was no significant difference in branching angles or diameters on colonies inhabiting rubble or pavement. However, colonies growing in rubble had significantly more branching than colonies growing on pavement. Several significant differences between the measures of plot composition (abundances of attached colonies, loose fragments and incidences of disease and predation within a defined area) between pavement and rubble were observed. There were more colonies and loose fragments on rubble sites than pavement sites throughout the duration of the study. There were significantly higher percentages of diseased masses on rubble than on pavement. Significant differences were found in 3-dimensionality and attachment success of fragments between those monitored on pavement and rubble. Fragment movement was not significantly different between substrates. This research supports NOAA’s designation of the southeast Florida near-shore environment as critical habitat for Acropora cervicornis. Acropora cervicornis is a sessile invertebrate, but its life history strategies allow for considerable mobility. This study showed that A. cervicornis inhabits the whole depth range and all substrates present within the near-shore study area. Protective seafloor topography is likely to influence where aggregations are found but the appropriate combination of factors to predict where these locations are, has yet to be determined. Limited evidence of habitat specialization by means of substrate was observed but more needs to be acquired to confidently claim it is occurring. Acropora cervicornis displays similar growth, mortality and condition characteristics on both pavement and rubble; however observed differences in morphology may hold the key to understanding where sexual reproduction is most successful. More information on the morphological responses of A. cervicornis to various forms of injury is required. The results of this research enables proactive management for conservation of the threatened coral, Acropora cervicornis, through the production of a distribution map, better understanding of local habitat associations, and providing a baseline for future monitoring and research on population dynamics.

It has been well established that a connection exists between oceanographic controls and shallow water carbonate production. To date, however, no investigations into these bio-trophic interactions have been performed for the Galápagos Archipelago. In this study, carbonate sediment samples, collected form a host of settings along the geographical extent of the Galápagos are compared with remotely sensed temperature and chlorophyll-a data for each collection site. The Galápagos Archipelago is a volcanic island chain which emerges between 1º40’N-1 °25’S and 89 °15’W-92 º00’W, off the west coast of Ecuador. Though the archipelago lies in proximity to the equator, a unique interaction of environmental conditions results in the Galápagos being situated at the convergence point of 26-29°C currents from the north, 20-22°C currents from the south and nutrient rich and cool upwelling water from the west. This puts the Galápagos in a warm-temperate environment more typical for higher latitudinal settings. In the current study, by comparing sediments from varying environments to the available oceanographic parameter data, a preliminary assessment of the response of carbonate producing organism of the Galápagos Archipelago to their local oceanographic controls was ascertained. The findings from this study add to growing evidence, which stresses the importance that variations in oceanographic parameters play in determining the biogenic makeup of shallow water carbonates (on latitudinal gradients). Furthermore, the results buttress the argument that detailed catalogues of the biogenic components of shallow water carbonates, as well as a cross reference of these sediments with their oceanographic controls, should be compiled if we are going to have a more complete understanding of the complex interactions between these physical and biological realms.

Shark populations worldwide are suspected to be in severe decline due to domestic and international markets for trade in shark products, especially dried fins in Asian markets, and as a result of bycatch mortality in multi-species fisheries. The management of sharks on a species-specific basis has become imperative for shark conservation, particularly in regions where numerous species are heavily fished, because sharks with differing life-history characteristics respond differently to exploitation. However, many commercially exploited sharks are morphologically similar and not easily identifiable to the species level. This problem is exacerbated when it comes to identifying detached fins, processed carcasses (logs), and filets or steaks at the dock or in trade. To address these species-identification problems and make available an accurate but practical, DNA-based forensic method for use in conservation and management of sharks, I have developed a highly streamlined genetic assay based on multiplex polymerase chain reaction (PCR) and species-specific primers derived from interspecific DNA sequence differences in the nuclear ribosomal internal transcribed spacer 2 (ITS2) locus of sharks. This forensic assay allows accurate identification of body parts from ten shark species commonly exploited worldwide for their meat and/or fins. In this thesis, I report on the development and use of this assay in the form of two separate suites of species-specific PCR primers that can be used in a high-density multiplex format to achieve rapid and accurate species identification. Chapter 1 of this thesis describes a suite of species-specific primers and multiplex PCR assay that simultaneously distinguishes among seven pelagic shark species: four species of mackerel sharks: shortfin mako (Isurus oxyrinchus), longfin mako (Isurus paucus), porbeagle (Lamna nasus) and salmon (Lamna ditropis); and the three species of alopiid (thresher) sharks: common thresher (Alopias vulpinus), bigeye thresher (Alopias superciliosus) and pelagic thresher (Alopias pelagicus). The second species-specific primer suite, described in chapter 2, simultaneously identifies the three globally distributed and most commercially important species of hammerheads: the great hammerhead (Sphyrna mokarran), scalloped hammerhead (Sphyna lewini) and the smooth hammerhead (Sphyrna zygaena). The species-specific PCR primers and forensic approach described here provide an efficient, straightforward technique that can be used in conservation and management relevant contexts where large volumes of samples need to be screened quickly. Preliminary testing of dried fins from the Hong Kong market and confiscated fins from U.S. and South African law enforcement activities suggests that this genetic technique will be useful for large-scale survey applications, such as monitoring the species composition of the fin trade as well as improving fisheries law enforcement capabilities. The efficient nature of the general forensic approach reported here may also make it useful as a model applicable to monitoring trade in other wildlife products on a global scale.

This study addresses the topical issue of ballast water discharge. There is a need for best management practices to minimize the release of non-indigenous (or exotic) organisms contained in ballast tanks. The release of such biota originating from foreign ports has been shown to have significant health, ecological and economic impacts on receiving waters. One hope for the future is to develop effective treatment systems to disinfect the water prior to discharge. A preliminary study of cruise ship ballast water was conducted to assess the concentrations of in situ microorganisms (bacteria and protists) and macroinvertebrates contained in a typical ballast tank. Chemical and physical parameters were also monitored as part of this investigation. This was the first reported study of the constituents of ballast water from a cruise ship and provided valuable baseline information about the scale of treatment that would be required to reduce the number of organisms to acceptable discharge levels. A local company (Marine Environmental Partners [MEP] Inc., Florida) embarked on the development of a novel ballast water treatment system. Research reported here focused on assessing the effectiveness (in terms of biotic kill or inactivation) of various configurations of treatment components. In this way, the company was guided towards the most effective full-scale system. Treatment options investigated included chlorination/bromination, gas ionization, filtration and coagulation in either a closed, recycling system, or via a one-pass system. The bacterial and protistan (algae and protozoa) counts in both control and treated water samples were routinely monitored by laboratory enrichment cultivation methods. Techniques appropriate for viruses and macroinvertebrates were also investigated. Since these enumeration methods are all time consuming, indirect counting methods were also investigated in an attempt to identify useful rapid detection methods for ballast treatment assessment. Methods evaluated included ATP analysis, Biological Oxygen Demand studies and epifluorescence microscopy using a commercially available fluorescent stains to distinguish live from dead bacteria. After laboratory trials identified the most promising combination of system components, a pilot ballast water treatment system was constructed (by MEP) and installed on-board a Carnival Cruise ship, the Elation. Using enumeration methods similar to those used in the laboratory experiments, the efficacy of this novel treatment system was assessed. These shipboard tests, which were conducted over a 5 d period, showed that the complete system was capable of killing or inactivating around 95% of the indigenous bacteria in a ballast tank and slightly less of the protists (90%). Perhaps more importantly, this testing highlighted the difficulties of assessing treatment systems on board a ship. Accurate assessment of treatment technologies may require land-based testing, and discussion of this option is included.

Stony coral coverage data was compared from three different methodologies: diver colony length x width measurements (DLW), image colony length x width measurements (ILW), and image colony tracing (ITA). An archival data set consisting of diver measurements (DLW) and 30m2 belt transect photographs from 28 sites was used to compare image measurement (ILW) and traced area (ITA) coral coverage data. All image measurement and tracing were done using Coral Point Count with Excel extensions V3.3 (CPCe). Using diver measurements (DLW) as the standard for comparison, hypothesis testing, mathematical quantification, and error analysis was used to compare the data obtained from each methodology. Diver visual acuity is superior to image resolution, but diver measurement proved to be highly variable. Conversely, image-based techniques proved to be very precise monitoring tools, but lacked the sensitivity of the human eye. On average, image measurements (ILW) reported 85.1±10.6% and traced areas (ITA) reported 55.6±7.7% of diver measurement (DLW) reported coral coverage (p. 32). Tracing precision (ITA) was greatest, followed by image measurements (ILW), reporting ≈14.7x and ≈4.6x more precision than diver measurements (DLW), respectively (p. 29). Additionally, an in depth-study was done on image colony tracing (ITA) to explore its potential as a monitoring tool. The detailed nature of tracing was highly susceptible to the effects of wide-angle photography. Using in situ images, traced area precision was 1.0-4.6% at the image center where lens distortion is minimized. Accuracy was greatly affected at the quadrat periphery where lens distortion caused a negative bias of 26.7%, however, objects centered in the quadrat resulted in a slight positive bias of 3%. Effects of image scaling and calibration associated with image tracing proved to affect estimated coral coverage less than 0.01%. Initially this study was conducted under the premise that diver measurements were water-intensive and not necessarily efficient. Provided either image-based technique was able to approximate diver reported coral coverage, they could be efficient and economical alternatives for resource managers. The results of this study suggest that each of the three methodologies were not exact replacements for the other. Each could be substituted, but not without consequence. Since no single methodology will suit every monitoring or financial situation, selection should always involve the technique yielding the most statistically sensitive data. More importantly, the implementation of complementary, rather than exclusive monitoring methodologies, may prove to be the most reasonable solution.

The City of Miami has placed 12 artificial reefs approximately 100m offshore in two parallel transects. The reason for this deployment was to tum a barren seabed into a productive environment for aquatic organisms. The reefs were placed close to the shoreline to allow easy access for snorkellers, divers, and fisherman. Three different types of reef materials were used in constructing the artificial reefs: boulders composed of limestone, concrete shaped as tetrahedrons, and concrete mixed with tire aggregate shaped as tetrahedrons. This study consisted of two separate assessments: I) a survey from two of each of the different reef types that were assessed bimonthly for one year to observe coral recruitment and 2) a survey of all 12 artificial reefs once at the end of the study to observe coral recruitment. In the year-long study, the results indicated that the number of coral recruits were highest on the boulder reefs (0.05>p>0.025, n=2), a significant difference. However, there was no significant difference in the area of corals on each substrata (0.10>p>0.05, n=2). In the final assessment of all 12 artificial reefs the greatest number of corals and area of corals on average were on the boulder reefs. However, there was no significant difference in either the number of coral recruits (0.50>p>0.25, n=4) or coral area (0.25>p>0.10, n=4). An explanation for this non-significance was the low coral recruitment of boulder reef two (B2). When B2 was treated as an outlier there was significance in both the number and the area of corals (0.025>p>0.01, n=3).

The culture of sea turtles provides a means for reestablishing depleted natural populations through restocking and, at the same time, alleviates pressures of over-exploitation on existing populations. A major problem in the rearing of sea turtles is disease control, particularly skin-disease. Necrotic skin lesions develop within the initial months of raising hatchlings and usually result in death, if not treated. Unfortunately, most treatments for controlling skin diseases in sea turtles have proven to be ineffective and labor intensive. The primary objective of this study was to determine the effectiveness of an iodophor compound (Vanodine™) and standard treatment (KMnO4) in the prevention and treatment of developing skin lesion disease observed in sea turtle aquaculture. Samples of skin lesions encountered in the culture of sea turtles were described and identified. Bacteria associated with these skin lesions were isolated, cultured, and identified. To test the prophylaxis of the treatments three study groups (N=35) of Caretta caretta (loggerhead sea turtles) were randomly selected from a mixed group of hatchlings, from six egg clutches. One group served as a “control" and remained untreated. The other two groups were treated with (1) Vanodine at a final concentration of 1:10,000 (100 ppm) and (2) Potassium permanganate (KMnO4) at a concentration of 1:1,000 (1,000 ppm). In both treatment groups, chemicals were added directly to the water of the holding tanks and maintained for 8-10 hour intervals. To confirm the prophylactic effect, the initially untreated and KMnO4 treated groups were switched to Vanodine treatment on the seventh week of the study and the turtles in the initially Vanodine treated group were removed from treatment. This cross-over experiment followed the same experimental protocol as the initial phase of the prophlactic study. In order to determine the effectiveness of Vanodine on already established skin lesions, untreated loggerhead sea turtles of approximately 4 months of age were ramdomly divided into two groups. One group remained untreated and another group was treated with Vanodine at a final concentration of 1:10,000 (100 ppm) for 8 to 10 hours daily. This procedure continued for seven weeks, at which time the untreated group was treated with Vanodine and treatment in the initially Vanodine treated group was terminated. This cross-over experiment was identical in procedure and duration to the initial treatment study. The susceptibility for natural skin lesion development in hatchling loggerhead sea turtles had been reported to occur during the third to fourth month after hatching. In this study, skin lesions developed in the Vanodine and untreated groups during the fifth week of life: however, skin lesions occurred during the second week on the turtles exposed to KMnO4. Vanodine inhibited skin and scute lesion development in sea turtle hatchlings. Turtles which had previously developed skin lesion disease were successfully treated with Vanodine. It is important to note that Vanodine did not inhibit all lesions but was significant in reducing lesions when compared to the untreated and KMnO4 treated groups. More and larger skin lesions occurred in the KMnO4 group than in the untreated group. KMnO4 had been used as a standard treatment for skin lesion disease in sea turtles and is effective on some skin lesion types, if administered topically. In this study, the addition of KMnO4 to the water of the holding tank was not successful in the prevention of skin and scute lesions in newly hatched loggerhead sea turtles when compared to the untreated group of turtles. Switching the KMnO4 group to Vanodine (week 7) resulted in a highy significant (P>0.9995) decreasing trend in skin lesion number and area. After the KMnO4 turtles were exposed to Vanodine, lesion number first increased for initial two weeks of treatment, but then declined at a substantial rate thereafter. Skin lesion area decreased throughout the study period. Visible KMnO4 staining and matting of necrotic tissue around established lesions persisted for about two weeks after treatment was switched. The flushing of residual KMnO4 in conjunction with regeneration of stain damaged tissue appeared to be required before Vanodine could effectively treat existing skin lesions. Scute lesions, especially those associated with Salmonella sp., were eliminated by the exposure to Vanodine. Number and area of scute lesions in the prophylactic study, became significantly (p>0.9995) lower in the Vanodine treated group compared to the untreated group after six weeks of treatment and remained significantly different throughout the cross-over experiment. Scute lesion number and area were greater in the KMnO4 group compared to the untreated group, with the difference becoming highly significant (P>0.9995) by week six. KMnO4 was not effective in controlling scute lesions when compared to the untreated and Vanodine treated groups. Vanodine seems to have two important roles in controlling skin lesion disease in sea turtle culture. First, the biocidal properties of the iodophor cause a possible reduction in the microbial load infiltrating the lesions. Second, Vanodine treatment of the water in the holding facility permits sufficient time for lesion healing by inhibiting the invasion of “opportunistic” pathogens. It appears that “opportunistic” pathogens which invade the already open lesion cause the high morbidity and mortality associated with skin lesion diseases in hatchling sea turtles. The procedure developed in this study for treating an entire group of sea turtles by administering the iodophor directly 'into the water of the holding facility is very efficient when compared to the labor intensive practice, utilized by many previous methods, in which turtles were treated individually. Vanodine's application to raising sea turtles affords a one-step procedure for administering the iodophor to the entire stock, and enhancing the hatchling survival rate.