Marine sponges were examined from shallow waters of southeast Florida and the Florida Keys to determine species composition and distribution of commensal amphipod crustaceans from shallow reef, mangrove, and seagrass habitats. Twenty sponge species were investigated during this study, sixteen of which housed amphipods in the families Colomastigidae and/or Leucothoidae. Six species of commensal amphipods were identified. Leucothoe spinicarpa (Abildgaard) species "complex" was the most dominant amphipod commensal, representing 63% of the total amphipods collected. The L. spinicarpa "complex" contains four local morphotypes, which are diagnosed and briefly described. Common sponge hosts included Callyspongia vaginalis, Mycale sp., and Myriastra kallitetilla.

Coastal waters in the Fort Lauderdale area of Florida host a series of relatively small colonial formations of the hermatypic coral Acropora cervicornis. Until recently, the extent and distribution of these colonies in nearshore marine waters was largely unknown. This study identified a number of occurrences of this scleractinian coral located between Hillsboro Inlet and Port Everglades Inlet, no further than 1.5 miles offshore. A diver was towed to locate the corals. A series of surveys were conducted and the results were used to classify the occurrences into different growth forms; thicket formations, isolated occurrences, and remnant colonies. Thicket formations were subsequently sub-divided into three groupings; small, medium, and large. The classification system is species and site specific for this study area. This system allows rapid assessment of colonies and provides a basis for long term monitoring of the progression and regression of A. cervicornis in the study area.

Chapter 1: The great white shark, Carcharodon carcharias, is the most widely protected elasmobranch in the world, and is classified as Vulnerable by the IUCN and listed on Appendix III of CITES. Monitoring of trade in white shark products and enforcement of harvest and trade prohibitions is problematic, however, in large part due to difficulties in identifying marketed shark parts (e.g., dried fins, meat and processed carcasses) to species level. To address these conservation and management problems, I have developed a rapid, molecular diagnostic assay based on species-specific PCR primer design for accurate identification of white shark body parts. The assay is novel in several respects: It employs a multiplex PCR assay utilizing both nuclear (ribosomal internal transcribed spacer 2) and mitochondrial (cytochrome b) loci simultaneously to achieve a highly robust measure of diagnostic accuracy; it is very sensitive, detecting the presence of white shark DNA in a mixture of genomic DNAs from up to ten different commercially fished shark species pooled together in a single PCR tube; and it successfully identifies white shark DNA from globally distributed animals. In addition to its utility for white shark trade monitoring and conservation applications, this highly streamlined, bi-organelle, multiplex PCR assay may prove useful as a general model for the design of genetic assays aimed at detecting body parts from other protected and threatened species. Chapter 2: Sharks and their relatives (Class Chondrichthyes) were the among the first vertebrates to evolve internal fertilization, yet our understanding of mating and parentage in this ancient group lags far behind many other animal groups. This is especially surprising because many shark populations worldwide are experiencing severe declines in abundance, and conservation planners are in dire need of basic information on their reproductive natural history. Based on a few genetic and field observational studies, current speculation is that polyandrous mating and multiple paternity may be as common in sharks as they are in most other vertebrate groups. Here, I examine this idea by genetically analyzing paternity in the hammerhead, Sphyrna tiburo (bonnethead), from the west coast of Florida, using the largest and most geographically widespread sample of shark litters analyzed to date. Contrary to expectations based on results from a few other shark species, the ability of female bonnetheads to store sperm and observations of their social behavior, I found that over 80% of females produced litters sired by a single male (genetic monogamy). This is the first record of this genetic mating system in this ancient class of fishes. When multiple paternity does occur in S. tiburo, I found no evidence for the involvement of any more than one additional male, no consistent pattern of paternity skew between fathers and an overrepresentation of multiple paternity in bigger litters with larger mothers. My results suggest that sharks and their relatives may exhibit diverse mating strategies and, as a result, some species may have a reduced capacity to maintain genetic variation in the face of large-scale depletion or changes in sex-ratio.

The inshore environment of Broward County, Florida consists of three coral reef/hard bottom reef tracts, separated by sand substrate, running parallel to the coast in sequentially deeper water. My study was an extensive inventory of the fishes associated with these reef tracts. At quarter nautical mile intervals, for an eighteen nautical-mile coastline section, fishes were censused at western, eastern edges and crests of each of the three reef tracts. On SCUBA, using the Bohnsack-Bannerot point count method, fish abundance, species richness, sizes (TL), and general habitat characteristics were recorded within an imaginary cylinder 15m in diameter extending to the surface. The position of each count site location was recorded by DOPS after each census. During a 4-year period, August 1998 to November 2002, 667 count sites were censused. A total of 86,463 fish belonging to 211 species (S2 families) were recorded. Significant differences (p<0.05, ANOVA, SNK) in total abundance, species richness and biomass were noted among the three reef tracts. There were significantly greater species richness and fish abundance on the offshore reef tract than on the middle tract, which, in turn, had greater richness and abundance than the inshore reef tract (p<0.05, ANOVA, SNK). The offshore reef tract had significantly higher biomass than the inshore reef tract, which, in turn, had significantly higher biomass than the middle reef tract (p<0.05, ANOVA, SNK). These tract-dependent differences may be due to a variety of variables, such as depth, current, refuge, food availability, or other habitat preferences. Differences were also found based on the site (edges or crest) on the reef and location of the reefs (north or south) relative to Port Everglades and Hillsboro Inlet. The count sites within 5 miles south of Port Everglades had lower total abundance and species richness (p<0.05, ANOVA) than the same number of count sites north of the port. Also, south of Port Everglades, the western edge of the reef tracts had greater abundance and richness values than the eastern edge or the crest (p<0.05, ANOVA). North of Port Everglades, the eastern edge predominated in both abundance and richness (p<0.05, ANOVA). The reason(s) for these differences may be linked to topographic variables. In general, at count sites north of Port Everglades, the eastern edges of the reef tracts have a higher amount of vertical relief, and attendant refuge, than at southern count sites. Likewise, although in general the regressions were weak, bottom cover, rugosity and depth were regressed, to some extent, with differences in species richness and abundance. Hillsboro Inlet had similar findings. Count sites within 3.75 miles south of the inlet had lower abundance and species richness (p<0.05, ANOVA) than the same number of sites north of the inlet. This may be due to the effects of effluent transport by the predominantly north-bound current parallel to the coast of Broward County. Juvenile grunts, an important forage base, were significantly higher on the inshore and middle reefs, which did not differ significantly from each other, than the offshore reef. Of immediate management interest, my findings include a surprising scarcity of legal size groupers (2) and snappers (198) over the entire survey area.

Carapace lengths and widths of nesting loggerhead sea turtles (Caretta caretta) were measured at Pompano Beach and Fort Lauderdale, Florida to determine if plastron and/or track crawl widths were predictive of carapace size. Straight and curved carapace measurements were taken. Plastron and track crawl width were measured at four points on each crawl: 1) emerging at the tide line; 2) mid-way to the nest; 3) mid-way returning to the surf; and 4) at the tide line returning to the surf. All four measurements were significantly different from each other (P < 0.005) along each crawl. Crawl width was the most variable factor in all comparisons. Maximum straight carapace length correlated with emergent track crawl width at the tide mark (r = 0.8464, P < 0.001), indicating that track width was predictive of straight carapace length (+/- 3.95 cm standard error of estimate). Clutch size correlated with notch-to-tip straight carapace length (r = 0.6635, P < 0.0005) and with emergent track crawl width measured mid-way to the nest (r = 0.5735, P < 0.005). Carapace and crawl width measurements were predictive of clutch size (+/- 21 eggs and 23 eggs standard error of estimate, respectively).

Artificial reefs have been constructed of many different materials including concrete, tires and limestone quarry rock. Few studies have compared the suitability of different construction materials in terms of their efficacy in acquiring diverse faunal assemblages. This study compares the fishes and macroinvertebrates associated with twelve collocated reefs constructed of gravel-concrete aggregate, tire-concrete aggregate, and limestone quarry boulders (four of each treatment) in 7m of water, 200m offshore Miami Beach, FL. All twelve reefs were deployed the same day in two lines of six, 100m apart. The four quarry stone reefs consist of a pile of 50 boulders. Four reefs were constructed of concrete with gravel aggregate and four of concrete with tire aggregate. These eight reefs, produced by CSR Rinker under license agreement with Stability Reefs Inc., contain 25, 1.5 m edge and 25, 1.2 m edge modules. Fish species, abundance, size (TL) and macroinvertebrate presence/absence from all reefs were recorded every two months by SCUBA divers. Data were analyzed with non-parametric two-way analysis of variance using Statistical Analysis Systems (SAS) software. After 18 months, fish abundance and species richness on each treatment exhibited a significant (p0.05). Species richness on the quarry stone reefs was significantly greater than on gravel-concrete aggregate and tire-concrete aggregate tetrahedron reefs (which did not differ). However, further statistical tests on species richness showed no difference between substrate types. Examination of the invertebrate data indicated no obvious differences in invertebrate reef preferences, excepting hard corals, which were more abundant on the quarry stone reefs.

The suitability of eight species of marine phytoplankton as feed were tested for: the marine rotifers Brachionus plicatilis and Brachionus rotundiformis, larval stage penaeid shrimp Litopenaeus vannamei, and larval stage sea urchin Lytechinus variegatus. The species selected were Dunaliella sp., Isochrysis sp., Micromonas pusilla, Nannochloris sp., Nannochloropsis salina, Pavlova pinguis, Porphyridium cruentum, or Rhodomonas lens. These species were selected as genera or representatives of classes (divisions) rarely or never used in aquaculture but which have unique and/or abundant fatty acids, polysaccharides, and vitamins. Three experiments were designed to test these algal diets: 1. Algal feed trials for the marine rotifers Brachionus rotundiformis and Brachionus plicatilis. Brachionus plicatilis had the greatest increase in population (729%) when fed M. pusilla than with the other seven species. The replicates fed R. lens decreased to only 16% of their initial concentration, this indicates that this algal species is not suitable for cultivation of B. plicatilis. Growth of the replicates fed the other six algal species ranged from 127% (P. pinguis) to >300%. Brachionus rotundiformis had the greatest increase in population (1441%) fed M. pusilla than with the other seven species. The replicates fed P. cruentum and P. pinguis had negative population growth (24% and 6% respective). Growth of the replicates fed the other five algal species ranged from 177% (R. lens) to >275%. 2. Algal feed trials for Litopenaeus vannamei. In the initial (single algal species) feed trial, Litopenaeus vannamei larvae (nauplii IV and V, protozoea I, II, and Ill, and mysis I) fed the algal species P. cruentum and P. pinguis produced the highest larval survival of ~100% and 85% respective, and therefore may be suitable for penaeid larviculture. The larvae fed Dunaliella sp., Nannochloris sp., and N. salina all died before the end of the nine day feed trial period. The larvae fed R. lens and Isochrysis sp. had survival rates of 47% and 20% respective. The larvae fed M. pusilla had the lowest rate of survival (12%). For the second feed trial, a dual algal combination was fed to L. vannamei larvae (nauplii IV and V, protozoea I, II, and III, and mysis I). Each combination included either P. pinguis or Isochrysis sp. and one of the other algal species that had supported survival in larval feed trial one (M. pusilla, P. cruentum, and R. lens) for a total of six combinations and a seventh combination of both P. pinguis and Isochrysis sp. The dual algal combination of P. pinguis + M. pusilla had a significantly greater percentage of survival (53%) and rate of larval development (30% to mysis I) than the other combination algal diets. A somewhat lower percentage of survival was achieved with the combinations of Isochrysis sp. + P. cruentum and Isochrysis sp. + M. pusilla (34% and 33% respectively). The four remaining combinations had limited success (P. pinguis + P. cruentum 16%) (P. pinguis + Isochrysis sp. 8%) (P. pinguis + R. lens 7%) (Isochrysis sp. + R. lens 5%). 3. Initial feed trial for Lytechinus variegatus. This feed trial examined the potential of four of the algal species i.e., Micromonas pusilla, Pavlova pinguis, Porphyridium cruentum, and Rhodomonas lens in sea urchin culture. The sea urchin Lytechinus variegatus was chosen as a representative of the Echinodermata to establish protocols for future research of this and other classes of Echinoderms with similar larval stages and with potential commercial viability for the marine ornamental and sea urchin roe industries. Beginning one day after fertilization the sea urchin larvae were fed one of the four algal species until termination of the experiment at day nine. At the algal concentrations used in this research R. lens produced the best results, with larvae having either fully developed rudiments or had settled as juveniles. Larvae fed P. pinguis had reached the fully developed pluteus stage. Those fed P. cruentum were slightly less developed, but had reached the eight-arm pluteus stage. Larvae fed M. pusilla were approximately evenly divided between the six-arm and early eight-arm stages. These results indicate that, of the algal species tested: Micromonas pusilla is a superior algal species for the production of the marine rotifers Brachionus rotundiformis and Brachionus plicatilis. Pavlova pinguis is a superior algal feed for the larval survival and development of the penaeid shrimp Litopenaeus vannamei, either singularly or in combination. Rhodomonas lens is a superior algal species for the larval development of the sea urchin Lytechinus variegatus.

Traditionally, the hygienic quality of beaches has been determined by monitoring the water for microbial indicators of fecal pollution. Beach sand, which may also be an important medium for the transmission of fecal borne pathogens, has rarely been examined. The aims of this study where to examine the prevalence of fecal indicator organisms in tidally affected beach sand and in dryer upper beach sand, relative to water; identify the potential sources of indicator organisms in beach sand; examine the prevalence of selected eukaryotic microbes at sandy beaches; and investigate the potential health risks related to beach use. Three south Florida Beaches (Ft. Lauderdale Beach, Hollywood Beach, Hobe Beach) were sampled bimonthly for a I year period. Significantly, enterococci, fecal coliform, and E. coli levels were consistently present at higher concentrations in beach sand compared to the seawater at all 3 study beaches. Levels of somatic and F-specific coliphages were also present at higher concentrations in beach sand. Microbial- source tracking analysis by carbon utilization profiling suggested that the predominate sources of enterococci in beach sand were seagulls, and transiently replicating indigenous populations. Acanthamoeba spp. was the most commonly isolated free-living naked amoeba in this study and molecular analysis revealed that 19 of the 20 beach sand clones were genotype T4, the Acanthamoeba keratitis-associated genotype. With respect to salinity, the growth characteristics of beach sand Acanthamoeba isolates were similar to Acanthamoeba isolated from corneal scrapings. Results from the beach survey indicated that beach goers may have an increased risk for acquiring contact related ailments at Hobe Beach. Accordingly, bacterial and viral fecal indicator microbes were detected at the highest frequency and greatest average concentrations from Robe Beach. Reports of enteric and respiratory related symptoms were not higher in beach goers compared to the control cohort.

Several health problems such as gastroenteritis, upper respiratory infections and skin, eye, and ear infections can be associated with swimming in polluted waters. In order to assess potential health risks, authorities regularly monitor the quality of recreational waters by analyzing for indicator organisms. Total coliforms, fecal coliforms, enterococci and E. coli, naturally found in the intestinal flora of warmblooded animals, are amongst the most frequently used bacterial indicators for sewage pollution. These organisms are thought to be representative of more virulent pathogens and their densities in the water are indicative of the amount of sewage contamination present. Current guidelines for beaches in the United States recommend routine testing of beach water samples, but risks associated with bacterial numbers in the sand have never been considered. This is surprising because many beachgoers spend most of their time around the sand. As part of an EPA-funded study to investigate microorganisms on the beach, levels of E. coli in the sand and the water were recorded over a lO-month period at two different beaches in South Florida. Densities were consistently higher in the dry sand relative to the wet sand and sand had more bacteria than water. Mesocosm experiments conducted in the laboratory showed that, regardless of conditions, E. coli levels significantly increased within 24 h to 48 h in sterile sand but died when added to sterile seawater. Because of the high sand counts, the potential for bacteria to wash out of sand was studied at Hollywood Beach. Results showed that beach bacteria that grow in situ and wash out into the water influence the densities of E. coli in the water. This has consequences for water managers assessing beach quality. Future protocols for sampling might include water samples collected well away from the swash zone. Attempts were made to isolate a eukaryotic pathogen, Entamoeba histolytica, from wet sand because previous work had shown that sand samples were occasionally positive for E. histolytica using a commercially available test kit. Even although Entamoeba-like organisms were present, ELISA test revealed that these were not E. histolytica. Preliminary experiments were conducted using alternative methods for assessing fecal pollution. The levels of two types of coliphage, somatic and F-specific phage, were determined during the monthly samplings. The numbers did not generally correlate with the levels of E. coli or enterococci. Polymerase Chain Reaction, targeting pathogenic genes of E. coli, was used to screen E. coli colonies from wet sand, dry sand and sewage. Because of the surprisingly high numbers of positive results in the dry sand, further investigation will be needed to determine the significance of the results.

The purpose of this research was to evaluate the overall effectiveness of the pollution control measures in place at the South Dade Landfill, located in Miami, Florida. Pollution control measures in place at the landfill include the lining and capping of landfill cells, a landfill wetland retention basin and a groundwater remediation interceptor trench (GWRIT). This study was performed over a ten (10) month span beginning in October, 2002 and ending in July, 2003. This study dealt specifically with the effectiveness of the GWRIT and landfill wetlands in reducing the amount of un-ionized ammonia (NH3) in the landfill leachate. Through the analysis of surface water and groundwater surrounding the landfill, it was concluded that the pollution control measures reduced levels of un-ionized ammonia by 98% of the concentration of NH3 found in the landfill's leachate.