A bioeconomic simulation model of the middle Atlantic surf clam (Spisula solidissima) fishery has been developed from a survey of biological and econometric relationships. While identifying the biological input parameters available in the literature, the economic submodel of the fishery has been developed with price and landings time series data, and with data obtained through the use of survey questionnaires and interviews with surf clam fishermen and processors. Alternative management scenarios in the fishery have been evaluated from industry costs in both the harvesting and processing sectors and analysis of the demand for raw product confronting surf clam fishermen. Multiple regression analysis of time series data indicates that surf clam ex-vessel prices may be negatively related to surf clam landings whereas hard clam prices are positively related to ex-vessel ocean quahog prices and ex-vessel oyster prices. The strength of this relationship confirms the status of ocean quahogs as very close substitutes for surf clams. The results of case studies using the model suggest that the Mid-Atlantic Fishery Management Council has followed a prudent course of action in managing the surf clam fishery. The model also projects that, (1) larger yield quotas may be possible in the immediate future without jeopardizing surf clam population stability, (2) overcapitalization in the fishery appears to remain a problem, and (3) the economic outlook for the operators of small vessels remains relatively bleak.

The logistical difficulties of research in extremely low temperatures and lack of access to the Arctic have meant that there is a historic dearth of knowledge of coastal Arctic biogeochemistry, especially during winter when sea ice is present. Recent observations, however, indicate that the Arctic is changing rapidly. Changes include increased temperatures, decreased extent and volume of sea ice, and increased freshwater inputs. How these changes influence biogeochemical cycles is an open question, especially in the highly productive coastal regions of the Chukchi Sea. Here I present nitrogen (N) uptake and regeneration rates for phytoplankton and bacteria measured in the shallow waters and landfast sea ice near Barrow, Alaska. Experiments were performed using tracer-level incubations of stable isotope (15N) ammonium, nitrate, urea, and amino acids during January, April, and August over two successive years (2010 --- 2012). Autotrophic versus heterotrophic N uptake was measured with traditional size fractionation. In brief, I found that outside of the spring phytoplankton bloom period, ammonium and amino acids were the preferred N substrates assimilated. Regeneration of N and nitrification were especially high during winter. A high-speed cell sorting flow cytometer was used to distinguish bacterial sub-populations and their uptake rates. Low nucleic acid populations were active in taking up N compounds, although not at quite the same rate as high nucleic acid cells. The difference was less pronounced during winter compared to summer. Additional experiments were designed to artificially warm the samples to demonstrate that ammonium uptake rates increased with temperature and substrate availability, whereas nitrification rates did not. Uptake and regeneration of ammonium and nitrate along with nitrification was also measured in landfast sea ice. This is the first report of N uptake from within the sea ice matrix in the Chukchi Sea. Given the paucity of information on N cycling in the Arctic Ocean, these data can inform modeling efforts to predict future changes in the system and also provide a baseline by which to compare future observations.

Studies were carried out to quantify abundance, mortality, and variability in these parameters, during settlement and recruitment of bivalve mollusks, using the oyster, Crassostrea virginica, as a primary model species. Most work was undertaken in the York River, Chesapeake Bay, Virginia, with additional work in the Indian River, Florida. The period chosen, in the bivalve early life history, was from the late planktonic larva to the early benthic juvenile. Studies were designed to specifically examine (a) abundance of late-stage larvae in the plankton, (b) the relationship between larval abundance and settlement, and (c) mortality immediately following settlement. Variability in abundance or mortality was also examined at each of these stages. It was found that, of larvae in the plankton with the morphological characteristics of competency-to-settle, about 80% would settle within 24 hours, under laboratory conditions. Temporal variation in abundance of planktonic larvae was high and apparently random, but separate species covaried in observed abundance. Time of day and tidal phase had little or no effect on larval distribution, but late stage larvae showed a consistent depth preference, which varied depending on species. Crassostrea late larvae tended to be most abundant near the benthos, both at the Virginia site and at the Florida site. The relationship between planktonic abundance and settlement density of Crassostrea was weak, within one order of magnitude of variation in larval abundance, although the same relationship for a sympatric species in Florida, Ostrea equestris, was significant. Settlement onto a natural oyster reef was more variable but not significantly lower than settlement onto adjacent defaunated shell substrate. The increased variability could not be accounted for by coverage by dominant fouling macroorganisms. Mortality of newly-settled juvenile Crassostrea was high, with near 100% mortality within 28 days on a natural oyster reef, with high but significantly lower (about 96%) mortality on previously defaunated shell substrate over the same time.

Mesozooplankton function as microbial microhabitats and can support concentrations of bacteria orders of magnitude higher than in the surrounding water. These zooplankton-associated bacteria can have much higher production rates than their free-living counterparts. Portions of the zooplankton microhabitat may also be anoxic and provide refuge for anaerobic bacteria and their associated processes within the oxygenated water column. Despite their common presence in the marine environment, zooplankton-associated bacteria are largely ignored by microbial ecologists and zooplankton ecologists alike. Consequently, factors which influence zooplanktonassociated bacterial abundance, community composition and function, and how zooplankton-associated bacteria compare to free-living bacteria are not well known. The goal of my research was to investigate which environmental parameters and zooplanktonspecific characteristics influenced the zooplankton-associated bacterial abundance, community composition and function. During a year-long field study in the York River, VA, free-living bacteria concentration peaked in the summer, while zooplanktonassociated bacteria concentration peaked in both summer and winter. There were no relationships between number of bacteria per individual zooplankter and zooplankter size. Ambient ammonium concentration was the one environmental parameter that correlated with all zooplankton-associated bacterial concentrations. In laboratory experiments, copepods raised in high ammonium concentration had high concentrations of loosely attached bacteria, while copepods raised in low ammonium concentration supported fewer, firmly attached bacteria, suggesting greater exchange between free-living and zooplankton-associated bacterial communities in nutrient rich systems. Zooplankton-associated bacterial communities were genetically distinct from free-living bacterial communities and utilized a wider array of carbon substrates. Changes in ambient environmental conditions played a larger role than zooplankton-characteristics in shaping zooplankton-associated bacterial community composition and function. Additionally, the potential importance of zooplankton guts as anoxic microhabitats was evaluated by comparing carbon substrate usage by the total bacterial (epibiotic + gut) and gut bacterial communities of the calanoid copepod Acartia tonsa under aerobic and anaerobic conditions. Gut bacteria were responsible for a large portion of the microbial activity associated with the copepod under both aerobic and anaerobic conditions. A larger variety of substrate subsets were used by zooplankton-associated bacteria than free-living bacteria under anaerobic conditions, suggesting that each zooplankton group selects for a specific combination of bacteria. In fact, some zooplankton-associated bacteria were not detected in the surrounding water and utilized substrates not used by free-living bacteria. These results highlight that zooplankton act as micro bial hotspots and zooplankton-associated bacteria are an important part of the total bacterial abundance, diversity and functionality in aquatic systems.

The spot (Leiostomus xanthurus) is an important commercial and recreational species in Virginia. Recruitment of juveniles to the Bay is characterized by large interannual fluctuations, that can be explained by the sequence and direction of wind during various phases of the early life history. An environmentally-modified Ricker stock-recruitment curve was developed incorporating the southeasterly winds in November-December, the southerly winds in January-March, and the westerly winds in April-May. This model explained 81% of the variation and closely paralleled the VIMS Juvenile Spot Index. Spot from the Chesapeake Bay migrate south in fall to spawn near or south of Cape Hatteras. Larvae were distributed over the shelf south of Oregon Inlet in February and early March, with the youngest larvae found over the outer shelf off Cape Hatteras. By late March, spot were distributed over the inner shelf north of Oregon Inlet to the mouth of the Chesapeake Bay. Age and size of larvae increased in a northward and shoreward direction. The persistence of larvae over the inner shelf north of Oregon Inlet suggests that a mechanism for northward transport occurs in this area. Northward transport over the inner shelf in the southern MAB is possible with multiple southerly wind events. Spot larvae would not have to be transported the entire distance to the Chesapeake Bay entrance, but only to where the bottom layers of the water column are moving toward the Bay. Recruitment to the Chesapeake Bay began in February or March of 1990 and in April of 1989 and lasted for two months. Spot entering the Bay were approximately 84 days old and 14.0 mm SL. The birthdates of spot collected offshore in the southern MAB and those at the Bay mouth were very similar, suggesting that recruits to the Bay were from the same pool of larvae collected earlier in the season and providing further support for a spawning location south of Cape Hatteras and not off the Chesapeake Bay as previously reported.

Approximately 40% of the bottom of Chesapeake Bay is less than 2.0 m in depth and many of these broad shoal environments are bordered by wetlands. The vegetated and nonvegetated subtidal and intertidal environment is a dynamic mosaic of highly productive estuarine habitats linked by the exchange of waterborne materials. This study developed simulation models of primary production and material exchange for four littoral zone habitats of the Goodwin Islands National Estuarine Research Reserve (NERR) in lower Chesapeake Bay. Field studies were conducted to determine the sediment biogeochemical and biomass characteristics of sandy shoal, seagrass, silt-mud, and marsh habitats. Ecological models were developed for each habitat based upon their position and ecological characteristics. The models simulate the dynamics of phytoplankton, particulate and dissolved organic carbon, dissolved inorganic nitrogen, sediment microalgae, Zostera marina, and Spartina alterniflora. Following sensitivity analysis and validation the models were used to estimate annual primary production, nitrogen processes, and material exchange. The net annual rate of phytoplankton production was 66.0, sediment microalgae ranged 101-169, Zostera marina community production was approximately 350 gC m&\sp{lcub}-2{rcub}& yr&\sp{lcub}-1{rcub}&, and Spartina alterniflora shoots and root-rhizomes produced 1150 gC m&\sp{lcub}-2{rcub}& yr&\sp{lcub}-1{rcub}& (gC m&\sp{lcub}-2{rcub}& yr&\sp{lcub}-1{rcub}&). Nitrogen uptake was in excess of demand in phytoplankton while the reverse was true for the macrophytes. The marsh habitat accounted for 43% of the total annual primary production for the ecosystem despite being the smallest habitat while the largest habitat (nonvegetated subtidal) required 52% of the total ecosystem nitrogen demand. All four habitats imported phytoplankton, particulate organic carbon, and dissolved inorganic nitrogen annually. While the intertidal habitats imported dissolved organic carbon the subtidal habitats showed net annual export. These models were developed to assess ecosystem structure, function, and change in the littoral zone of Chesapeake Bay. Ecosystem structure was assessed through field research and model development. Ecosystem function was assessed by using the model to generate annual producer, habitat, and ecosystem carbon and nitrogen budgets. The model is currently being used to investigate the interactive effects of water quality, primary production, and habitat composition in order to assess potential change in the estuary.

Traditional coral reef monitoring efforts lack assessment of coral health at tissue and cellular levels. This thesis investigated tissue, cellular, and gross morphological responses of the Caribbean staghorn coral, Acropora cervicornis, to elevated sedimentation and phosphate using state-of-the-art histological techniques. Branch fragments of A. cervicornis were collected offshore Broward County, FL, acclimated for 12 weeks, subjected to a 4-week experimental period, and given a 1-week recovery period in laboratory aquaria. Treatments consisted of high doses (200 mg cm-2 day-1) of sedimentation (S), phosphate (4 μM) (P), and a combination of these two (S + P), in addition to control conditions (C). Specimens were observed and photographed for gross morphological appearance. One specimen per tank was sacrificed for histological purposes weekly. Specimens were also sacrificed in the field and during acclimation for baseline comparison. The following gross morphological changes were more common in treatments relative to acclimated and control specimens: polyp retraction, discoloration (including palor and/or bleaching), excess mucus, and loss of white apical tips. For sanded treatments, sediment-clearing rates declined from ≤ 2 hours to up to 24 hours after four weeks of daily exposure. After the recovery period, all remaining specimens showed slight improvement in gross morphological appearance. Degenerative histopathological changes in the epidermis included attenuation, decreased abundance and atrophy of mucocytes, and loss of cellular architecture. In the gastrodermis, attenuation, mucocyte swelling followed by atrophy, compromised integrity and reduced densities of zooxanthellae, and necrosis were observed. In the calicoblastic epidermis, mucocyte swelling (S, S + P only) and an increase in eosinophilic granules were noted. In the mesenteries, changes included loss of gonad development, loss of basophilia, dissociation and/or necrosis of filaments and cnidoglandular bands. Quantitative histological measurements in the oral epidermis revealed significantly different decreases in mucocyte abundance with exposure to treatments and additive or synergistic effects of sand and phosphate. Semi-quantitative results were obtained by separately ranking 16 histologic parameters within major coral tissue types. Ranks of each parameter were combined to give a histopathologic condition score for each specimen. Median condition scores for each treatment increased during Weeks 1 to 4, and significant differences were found between treatments in Weeks 1 to 3. Highest scores consistently appeared in S and/or S + P treatments throughout Weeks 1 to 4. Histopathological responses and severity of changes were similar for all treatments, without a clear additive or synergistic effect in the S + P treatment. During the recovery period, the P treatment continued to decline in overall tissue condition, while S and S + P treatments showed signs of tissue recovery. Acclimated and control corals also exhibited similar, yet less severe, patterns of gross morphologic and histopathologic alterations, indicating tank effects. Changes described at organismal, tissue, and cellular levels in this study were indicative of compromised health of coral specimens and may aid future health assessment and monitoring of critical populations of A. cervicornis in Florida and the greater Caribbean, with additional applications to the fields of coral stress and disease.

No description available.

Chapter 1 Producing thematic coral reef benthic habitat maps from single-beam acoustic backscatter has been hindered by uncertainties in interpreting the acoustic energy parameters E1 (~roughness) and E2 (~hardness), typically limiting such maps to sediment classification schemes. In this study acoustic interpretation was guided by high-resolution LIDAR (Light Detection And Ranging) bathymetry. Each acoustic record, acquired from a BioSonics DT-X echosounder and multiplexed 38 and 418 kHz transducers, was paired with a spatially-coincident value of a LIDAR-derived proxy for topographic complexity (Reef-Volume) and its membership to one of eight LIDAR-delineated benthic habitat classes. The discriminatory capabilities of the 38 and 418 kHz signals were generally similar. Individually, the E1 and E2 parameters of both frequencies differentiated between levels of LIDAR Reef-Volume and most benthic habitat classes, but could not unambiguously delineate benthic habitats. Plotted in E1:E2 Cartesian space, both frequencies formed two main groupings: uncolonized sand habitats and colonized reefal habitats. E1 and E2 were significantly correlated at both frequencies; positively over the sand habitats and negatively over the reefal habitats, where the scattering influence of epibenthic biota strengthened the E1:E2 interdependence. However, sufficient independence existed between E1 and E2 to clearly delineate habitats using the multi-echo E1/E2 Bottom Ratio method. The point-by-point calibration provided by the LIDAR data was essential for resolving the uncertainties surrounding the factors informing the acoustic parameters in a large, survey-scale dataset. The findings of this study indicate that properly interpreted single-beam acoustic data can be used to thematically categorize coral reef benthic habitats. Chapter 2 A large-scale acoustic survey was conducted in Apr-May 2008, with the objective of quantifying the abundance and distribution of seasonal drift macroalgae (DMA) in the Indian River Lagoon. Indian River was surveyed from the Sebastian Inlet to its northernmost extent in the Titusville area. Banana River was surveyed from its convergence with the Indian River northward to the Federal Manatee Zone near Cape Canaveral. The survey vessel was navigated along pre-planned lines running east-west and spaced 200 m apart. The river edges were surveyed to a minimum depth of approximately 1.3 m. Hydroacoustic data were collected with a BioSonics DT-X echosounder and two multi-plexed digital transducers operating at 38 and 418 kHz. The 38 and 418 kHz hydroacoustic data were processed with BioSonics Visual Bottom Typer (VBT) seabed classification software to obtain values of E1’ (time integral of the squared amplitude of the 1st part of the 1st echo waveform), E1 (2nd part of 1st echo), E2 (complete 2nd echo), and FD (fractal dimension characterizing the shape of the 1st echo). Following quality analysis, a training dataset was compiled from 131 hydroacoustic + video samples collected across the extent of the study area. The 38 and 418 kHz E1’, E1, E2, and FD datasets were merged and submitted to a series of three discriminant analyses (DA) to refine the training samples into three pure end-member categories; bare substrate, short SAV (typically Caluerpa prolifera, ~10cm or less), and DMA. The Fisher’s linear discriminant functions from the third and final descriptive DA were used to classify each of the 480,000+ hydroacoustic survey records as either bare, short SAV, or DMA. The classified survey records were then used to calculate the biomass of DMA as the product of average DMA cover for a block of ten records times the wet weight of DMA. The DMA biomass was found to be 69,859 metric tons (wet weight) within the 293.1 km2 study area. The acoustically-predicted mean percent cover of DMA was (i) significantly greater within the navigation channels (18.3%) than outside (12.2%), and (ii) significantly greater in the Indian River (12.9%) than in the Banana River (9.3%). The overall predictive accuracy of total SAV (i.e. short SAV plus DMA) was 78.9% (n=246) at three levels of cover (0-33, 33-66, and 66-100%). The Tau coefficient, a measure of the improvement of the classification scheme over random assignment, was 0.683 ± 0.076 (95% CI), i.e. the rate of misclassifications was 68.3% less than would be expected from random assignment of hydroacoustic records to total SAV cover. The incorporation of multi-plexed digital transducers in conjunction with new post-processing techniques realized the goal of establishing an accurate, efficient, and temporally consistent method for acoustically mapping DMA biomass. Chapter 3 This chapter presents the results of a large-scale hydroacoustic survey conducted in April-May 2008. The objective of this study was to map the distribution and vertical extent of muck in the Indian River Lagoon, utilizing the data collected during a seasonal drift macroalgae survey. Indian River was surveyed from the Sebastian Inlet to its northernmost extent in the Titusville area. Banana River was surveyed from its convergence with the Indian River northward to the Federal Manatee Zone near Cape Canaveral. The survey vessel was navigated along pre-planned lines running east-west and spaced 200 m apart, except for when muck was indicated by the oscilloscope display, at which point a meandering path was adopted to demarcate the horizontal extent of muck. Hydroacoustic data were collected with a BioSonics DT-X echosounder and two multi-plexed digital transducers operating at 38 and 420 kHz. The vertical extent of muck was derived from the 38 kHz hydroacoustic signal, which was processed with Visual Analyzer, a fish-finding software package produced by BioSonics Inc. The software was adapted to integrate echo energy below the water-sediment interface, and a set of post-processing algorithms were developed to translate the sub-bottom echo energy profile into continuous scale estimates of muck thickness. In this manner 500,000+ 38 kHz pings were translated into 88,927 geo-located estimates of muck layer thickness, down to a minimum bottom depth of 1 m. Ground-truthing was conducted in July 2008 at twenty sites within the Indian River. The predictions of muck layer thickness were found to be accurate over the ground-truthed range of 0-3m (r2 = 0.882, SE=0.52m). The vertical distribution of acoustically-predicted muck demonstrated the tendency for muck to accumulate in deeper areas of the lagoon. For the case of Indian River (excluding navigation channels), muck was not detected in depths shallower than 1.4m and rare in the range of 1.4-2.2 m (only 3.6% of records had a predicted muck thickness greater than 0.5 m). The frequency of muck plateaued between 2.2-3.4 m (9.6%) before making a sharp rise to 82% in the range of 4-5 m. As expected, the mean muck layer thickness was significantly greater within the navigation channels (0.56 m) than outside of them (0.08 m). A significant latitudinal trend of muck thickness was detected within the Indian River navigation channels. The mean muck thickness decreased from 1.38 m at its northernmost origins to 0.83 m in the Titusville area before plateauing at approximately 0.4 m for the remainder of segments. Outside of the main ICW channels, 23 individual muck deposits were identified; 22 in the Indian River and 1 in the Banana River. Factors in descending order of co-occurrence were proximity to causeways or jetties, riverbed depressions, and proximity to shore and drainage channels. In conclusion, this study establishes that a single-beam acoustic survey is a cost-effective and accurate alternative for mapping the distribution and vertical extent of muck deposits in the shallow-water environment of the Indian River Lagoon. Moreover, the temporal consistency afforded by a digital transducer allows for direct and meaningful comparisons between successive surveys. Chapter 4 A thematic map of benthic habitat was produced for a coral reef in the Republic of Palau, utilizing hydroacoustic data acquired with a BioSonics DT-X echosounder and a single-beam 418 kHz digital transducer. This paper describes and assesses a supervised classification scheme that used a series of three discriminant analyses (DA) to refine training samples into end-member structural and biological elements, utilizing E1′ (leading edge of 1st echo), E1 (trailing edge of 1st echo), E2 (complete 2nd echo), fractal dimension (1st echo shape), and depth as predictor variables. Hydroacoustic training samples were assigned to one of six predefined groups based on the plurality of benthic elements (sand, sparse SAV, rubble, pavement, rugose hardbottom, branching coral), visually estimated from spatially co-located ground-truthing videos. Records that classified incorrectly or failed to exceed a minimum probability of group membership were removed from the training dataset until only ‘pure’ end-member records remained. This refinement of ‘mixed’ training samples circumvented the dilemma typically imposed by the benthic heterogeneity of coral reefs, i.e. to either train the acoustic ground discrimination system (AGDS) on homogeneous benthos and leave the heterogeneous benthos un-classified, or attempt to capture the many ‘mixed’ classes and overwhelm the discriminatory capability of the AGDS. This was made possible by a conjunction of narrow beamwidth (6.4o) and shallow depth (1.2 to 17.5 m), which produced a sonar footprint small enough to resolve most of the microscale features used to define benthic groups. Survey data classified from the 3rd-Pass training DA were found to (i) conform to visually-apparent contours of satellite imagery, (ii) agree with the structural and biological delineations of a benthic habitat map created from visual interpretation of 2004 IKONOS imagery, and (iii) yield values of benthic cover that agreed closely with independent, contemporaneous video transects. The methodology was proven on a coral reef environment for which high quality satellite imagery existed, as an example of the potential for single-beam systems to thematically map coral reefs in deep or turbid settings where optical methods are unsatisfactory. Chapter 5 Beginning In the winter of 2003-2004, several episodes of red drift macroalgae blooms resulted in massive amounts of macroalgae washing ashore the beaches of Sanibel Island, Bonita Springs, and Ft Meyer Florida. A study conducted after the first event supported a link to increasing land-based nutrient enrichment. A large-scale program was initiated in May 2008, with the primary goal of further defining the possible roles and sources of nutrient enrichment with respect to nuisance macroalgae blooms. This study reports the results of the hydroacoustic mapping component of this program. The goal of this study was to identify areas of substrate suitable for supporting a macroalgae bloom. Areas within San Carlos Bay and offshore Sanibel Island, FL were hydroacoustically surveyed from nearshore to about 11 km offshore during the periods of October 6-10, 2008 and May 10-22, 2009. The hydroacoustic data was acquired with a BioSonics DT-X echosounder and a multiplexed single-beam digital transducers operating at 38 and 418 kHz. Eleven acoustic parameters derived from the 38 and 418 kHz signals were utilized to classify the survey data into 5 ascending categories of visually-apparent seabed roughness. Classes 1 and 2 were both primarily constituted of unconsolidated silt and sand-sized sediments, unsuitable for a bloom. Class 3 is a marginal substrate for a bloom, consisting of packed sand and large intact shell debris. Classes 4 and 5 offer the best attachment sites for a bloom, consisting of consolidated shell hash, live hardbottom, and submerged aquatic vegetation. The majority (~ 80%) of acoustic classifications were of soft bottom sediments (classes 1-2), but there were two significant expanses of rough seabed suitable for macroalgae attachment. These two areas covered a total of 19 km2, within which ~ 56% of the hydroacoustic records classified as “rough” (classes 3-5). The first was a large area of seagrass beds and live hardbottom in the mouth of San Carlos Bay, where large amounts of macroalgae were variably present during the April-May 2009 surveys. The second was offshore Lighthouse Point, near the mouth of San Carlos Bay, situated near a large sand spit that extended from the beach to approximately 6 km offshore. Along the west side of the sand spit there were substantial areas of moderate to high bottom roughness, mostly in the form of consolidated shell hash. The average depths of these two acoustically-rough areas were only 5.0 and 4.0 m, so sufficient irradiance to initiate a bloom could be assumed. These textured and shallow areas on or near the mouth of San Carlos Bay are presumably potential sources for macroalgae attachment and growth, which could easily be transported onto the beaches under some storm conditions given the close proximity to the shoreline. In contrast, the areas in open Gulf of Mexico waters were classified predominantly as soft sediments with low bottom roughness. The site offshore Redfish Pass had a moderate (~22%) proportion of “rough” classifications out to 5km offshore, but from 5-10km offshore the bottom classified as >95% soft sediments. The other two Gulf of Mexico sites classified as >95% soft sediments from nearshore to 11 km offshore. Independent, concurrent video transects indicated there were small areas with large amounts of shell and live hard bottom that occurred sporadically greater than 10km offshore, but all things considered the open Gulf waters around Sanibel Island may not be a major source of drift macroalgae. Chapter 6 This study presents the results of methods developed for acoustic remote sensing of Acropora cervicornis, a threatened species of scleractinian sporadically occurring on the nearshore hardbottom of Southeast Florida. The objective was to develop techniques for mapping isolated Acropora patches on a scale larger than what is feasible using on-the-ground methods. A time-series of A. cervicornis cover could inform resource managers about the fate of such patches, e.g. do they appear and vanish, creep by extension from a central point, or leap by colony fragmentation. The main challenge to acoustically mapping A. cervicornis was distinguishing it from gorgonians occupying the same habitat. Hydroacoustic surveys were conducted in October 2009 at two nearshore sites in Broward County, FL utilizing a BioSonics DT-X echosounder and multiplexed single-beam digital transducers operating at frequencies of 38 and 418 kHz. NCRI scientists have monitored the spatial extent and percent cover of A. cervicornis within these sites, providing an ideal background against which to calibrate the hydroacoustic predictions. Two approaches were evaluated. The first approach utilized BioSonics EcoSAV post-processing software, designed to predict areal cover and canopy height of submerged aquatic vegetation using a series of heuristic pattern-recognition algorithms. Anchored over A. cervicornis, the 38 and 418 kHz signals performed similarly well. Anchored over gorgonians, the 38 kHz signal detected the canopy roughly half as frequently as the 418 kHz signal. Undifferentiated 418 kHz EcoSAV cover was allocated to either A. cervicornis or gorgonians exploiting this frequency-dependent detection. The second approach utilized the acoustic energy (E0, E1′, E1, and E2) and shape (fractal dimension) parameters obtained from BioSonics Visual Bottom Typer software. A dual-frequency training dataset was used to classify records as sand, bare pavement, gorgonians, or A. cervicornis. Both approaches yielded promising results, based on a number of metrics, unambiguously demonstrating that single-beam AGDS are capable of reliably detecting A. cervicornis and gorgonians under controlled conditions.

The ocean surgeon, Acanthurus bahianus, is a coral reef fish inhabiting the tropical and subtropical waters of the western Atlantic, including southeastern Florida. This study was a 23-month analysis of the reproductive cycle correlated with the annual build up and depletion of fat reserves in the fish. In addition, an age and growth analysis of this species was conducted. A total of 507 fish were analyzed for length, weight, gonad weight and fat body weight. 478 were aged by microscopic examination of the transverse section of the sagittae otolith. The von Bertalannfy growth equation was used to determine length at age. The calculated maximum age for A. bahianus at this site was 17.86 (the oldest fish collected was an 18 year old male). The male and female gonadosomatic index increased from October to reach their highest levels in February and regressed to the lowest levels in June. The fat bodies held an inverse relationship with the gonadal growth. The fat body somatic index was the highest in August and September preceeding the gonadal recrudescence and reached the lowest levels in March. There was a correlation between fat bodies and mean sea surface temperatures at the study site but it is not clear if this is a casual relationship. This study is the first to report an in depth analysis of the fat and reproductive tissue cycles of A. bahianus and adds to knowledge of age and growth of this species.