A goal of the U.S. Environmental Protection Agency is to develop protocols applicable to coral reefs to distinguish between the effects of local water quality and those associated with regional to global environmental change. One test case is the current-dominated southeast coast of Florida where the Delray Outfall delivers 30 million gallons per day (114,000 cubic meters per day) of secondary-treated sewage into the ocean. Five study sites were established at depths between 15 and 18 m, and at distances between 1 and 18 km distance from the outfall, where the Stony Coral Rapid Bioassessment Protocol (RBP) was conducted to determine coral cover and selected other parameters. During sampling, 29 surface sediment samples were collected that I analyzed with respect to sediment texture, foraminiferal assemblages, and sediment constituents. Most samples were characterized by fine sands with <2% mud. A total of 77 genera of foraminifers were identified, averaging 28 genera per sample. Abundances of foraminiferal shells varied among samples by more than an order of magnitude (83 to 1010 shells per g sediment). The Foraminifera in Reef Assessment and Monitoring (FORAM) Index was calculated from the foraminiferal data, yielding values of 3 or more for all sites, with 26 of the 29 test sites yielding values >4, indicating that water quality should support coral growth. Sediment constituent analyses revealed that the sediments were overwhelmingly dominated by unidentifiable fragments (60%), with molluscan debris second (20%), and calcareous algae third (4.5%); larger foraminiferal shells and coral fragments together made up < 5.5%. The resulting sediment constituent (SEDCON) Index was consistently <2, indicating that erosional processes dominate over sediment production along the sampled shelf area. Results provided by the FORAM and SEDCON indices are consistent with results for stony coral based on the RBP. Stony coral cover was low at all sites, <2%, indicating that coral occurs in the area but neither dominates the benthos nor builds reefs. No relationship was observed between any parameter and distance from the Delray Outfall. However, both the RBP and FORAM Index indicated poorest conditions at the Horseshoe site, suggesting unidentified stressors in that vicinity.

Transplanted coral (Order: Scleractinia) colony condition was surveyed at five injury event sites, two coral nurseries, and one impact minimization location off the coast of Broward County, Florida, USA in 2012. Because stony corals are long-lived and slow growing, generally growing less than one centimeter in diameter per year, determining transplantation success requires long-term (greater than two years) monitoring. Long-term monitoring efforts, however, are rarely completed. This study is unique in that it examined stony coral transplantation success of several projects over a time period of 6-17 years. Control colonies were also surveyed in order to compare naturally growing coral colonies to the experimental (transplanted) colonies. Because the transplantation activities at the projects examined in this study occurred over a long time period (oldest population occurred 17 years prior to this study and the youngest occurred six years), colony percent partial mortality was used as a measure of success (colony condition). A successful effort should result in transplanted colonies experiencing partial morality similar to that of control colonies over extended periods of time. The control colonies used came from Broward County Annual Monitoring sites, and the M/V Firat and the C/V Hind ship grounding sites. The experimental colonies used came from five injury events (C/V Hind, Clipper Lasco, M/V Firat, and M/V Spar Orion ship grounding sites and Hillsboro Cable Drag location), two stony coral nurseries (DERM Modules and Warren Modules), and one impact minimization location (Broward County Mitigation Boulders). With all control colonies pooled and experimental colonies pooled, no significant differences in colony partial mortality were found between the experimental and control colonies. Once each experimental coral colony was reattached to the substrate, it generally appeared similar to the control colonies; the mean percent mortality for control colonies was 50% (2.95 ±SE) and the mean percent mortality for experimental colonies was 56% (1.24 ±SE). However, differences were found between stony coral species within each treatment (control and experimental). Colony mortality for identified control corals was greatest for Porites astreoides, Siderastrea siderea, and Montastrea annularis complex. For experimental colonies, S. siderea and P. astreoides had the most mortality. The least mortality of the control corals were found in Montastrea cavernosa, Solenastrea bournoni, and Meandrina meandrites. Of the experimental colonies, S. bournoni, M. meandrites, and Montastrea annularis complex had the least mortality. Resource managers need to consider colony transplantation location, coral species, and percent initial colony mortality when allocating efforts for injury and impact minimization events. Also, project initial restoration and final reports documenting transplantation locations and colony species, size and/or mortality should to be more detailed; this would be beneficial for future monitoring efforts.

Like coral reefs worldwide, the Florida Reef Tract has dramatically declined within the past two decades. Monitoring of 40 sites throughout the Florida Keys National Marine Sanctuary has undertaken a multiple-parameter approach to assess spatial and temporal changes in the status of the ecosystem. The objectives of the present study consist of the following: In chapter one, we review past coral reef studies; emphasis is placed on recent studies on the stony corals of reefs in the lower Florida Keys. We also review the economic impact of coral reefs on the state of Florida. In chapter two, we identify the underlying probability distribution function of the stony coral cover proportions and we obtain better estimates of the statistical properties of stony coral cover proportions. Furthermore, we improve present procedures in constructing confidence intervals of the true median and mean for the underlying probability distribution. In chapter three, we investigate the applicability of the normal probability distribution assumption made on the pseudovalues obtained from the jackknife procedure for the Shannon-Wiener diversity index used in previous studies. We investigate a new and more effective approach to estimating the Shannon-Wiener and Simpson's diversity index. In chapter four, we develop the best possible estimate of the probability distribution function of the jackknifing pseudovalues, obtained from the jackknife procedure for the Shannon-Wiener diversity index used in previous studies, using the xi nonparametric kernel density estimate method. This nonparametric procedure gives very effective estimates of the statistical measures for the jackknifing pseudovalues. Lastly, the present study develops a predictive statistical model for stony coral cover. In addition to identifying the attributable variables that influence the stony coral cover data of the lower Florida Keys, we investigate the possible interactions present. The final form of the developed statistical model gives good estimates of the stony coral cover given some information of the attributable variables. Our nonparametric and parametric approach to analyzing coral reef data provides a sound basis for developing efficient ecosystem models that estimate future trends in coral reef diversity. This will give the scientists and managers another tool to help monitor and maintain a healthy ecosystem.

The Veracruz Reef System (VRS) is located in the southwestern Gulf of Mexico. It is comprised of 28 coral reefs in various stages of development and conservation. They are protected under the Parque Nacional Sistema Arrecifal Veracruzano National Park created in 1992. There are many threats to the reefs of the VRS, including the Port and city of Veracruz, which hosts half a million inhabitants and Mexico’s oldest active port. The inhabitants of Veracruz have used reef resources for thousands of years, as evidenced in archaeological sites on Sacrificios island, and constructions throughout the city, most notably in the San Juan de Ulúa Fort which was built entirely of coral skeletons. Despite the usage and protection given under the National Park, there is relatively little known about the health and condition of the stony corals in the System. There has only been one large scale study of 21 reefs conducted in the VRS in the late 1980’s. Since then, the National Park was created and 28 reefs are now recognized. This study performed point-intercept transects on 24 of these reefs including five reefs added to the official list in 2012. Point-intercept transects were surveyed at 63 sites between 2007 and 2014. Percent cover was calculated for seven functional groups. Additionally, demographic data of a subset of individual stony coral colonies were assessed on each transect. The functional group with the greatest cover in the VRS was crustose coralline algae (mean ± S.E.: 28.9% ± 1.97), stony corals had the second highest cover (21.5% ± 1.24). The Jamapa river divides the VRS into two groups the Veracruz group to the North and the Anton Lizardo group to the south of the river mouth. The Veracruz group had lower crustose coralline algae cover (28.1% ± 2.71) and coral cover (17.8% ± 1.55) than the Anton Lizardo group (29.6% ± 2.87 CCA and 25.3% ± 1.86 coral cover). The highest average coral cover on a reef was recorded at Ahogado Chico (45.5% ± 5.58), and the highest cover recorded on a single transect was 70% at Santiaguillo reef. The lowest coral cover was recorded at the fringing reefs on the north of the VRS, Punta Gorda and Punta Brava which had less than 1% coral cover. Coral colonies averaged 69.1 cm ± 3.10 in length at the VRS, 56.8 cm ± 2.98 in the Veracruz group and 81.7 cm ± 5.11 in the Antón Lizardo group. Old partial mortality was 25% ± 1.05 overall and similar between groups, recent partial mortality was 1.2% ± 0.21 and 1% at both groups. Disease prevalence was 3.9% for the VRS, 2.9% ± 0.88 in the Veracruz group and 4.9% ± 1.11 in the Antón Lizardo group. Overall, these reefs are faring slightly better than other reefs in the Caribbean having higher coral cover and larger colonies. However, the great variability in the health and condition of these reefs demands added attention and clear management goals to ensure their persistence in the face of ever growing threats. It is important to decrease the sources of stress, such as construction and poor waste water management in the area, better regulate fishing and approach a watershed wide management plan which takes into account upstream effects from the rivers that discharge into the Veracruz Reef System.