To determine whether an artificial reef installation is feasible, there must be a thorough characterization of the habitat. An understanding of both small-scale and large-scale environmental processes is needed to determine factors that potentially will influence the reef. Large-scale processes include coastal circulation, wave climate, and sediment dynamics that take place over spatial scales of tens to hundreds of kilometers in the region of the reef. Small-scale processes include the physical characteristics in the immediate vicinity of the reef - the local current, wave and tide characteristics, temperature, salinity, and suspended and bottom sediments at a proposed reef site. The city of Port Richey, Florida, was considering installing an artificial reef of porcelain modules near Durney Key, a dredge spoil island just offshore. To assist in determining the feasibility of this proposal, I pursued three objectives: a) to characterize the oceanographic setting of Durney Key, including hydrodynamics, water quality and invertebrate biota; b) to investigate the potential for successful coral recruitment and growth in Durney Key waters; and c) to determine if porcelain is a suitable substrate for settlement of the larvae of coral species present in west central Florida. An array of Acoustic Doppler Current Profilers (ADCPs) were used to measure water velocity, water stage and temperature around Durney Key. ADCP data showed currents around Durney Key are tidally dominated with velocities increasing in winter due to frontal passages. Seasonal stage variation ranges from 0.29 m (11.4 in) to 0.64 m (2.1 ft) and seasonal temperature ranged from 10°C and 35°C for winter and summer, respectively. Atmospheric data from the Port Richey COMPS site showed average wind speeds were higher in winter (3.7 m/s or 12.4 ft/s) than summer (3.1 m/s or 10.2 ft/s), corresponding to increased average water velocities. Inorganic nutrients, salinity and pH were measured and compared to data from patch reefs in the Florida Keys to characterize the water quality and determine its suitability for coral recruitment and growth. Compared to Florida Keys patch reef waters, Durney Key water salinity averaged 12 parts per thousand (ppt) lower, pH was more variable with a lower minimum, and total phosphorus was much higher. Ceramic and porcelain recruitment tiles deployed to investigate larval recruitment were colonized by turf, coralline and macroalgae, with barnacles recruiting secondarily. Sediment cores revealed foraminiferal and molluscan assemblages characteristic of productive estuarine conditions. The Durney Key area was deemed not suitable for coral recruitment and growth on an inshore artificial substratum because of temperature extremes, potential for minimal water movement during summer, frequent occurrences of low salinity and pH, and high total organic phosphorus. Faunal studies demonstrated that the dominant recruitment reflects the common coastal/estuarine biota, which does not include reef-building corals.

This thesis describes the chemical investigations of several ascidian species collected from the Great Barrier Reef, Queensland, Australia. The thesis is divided into two separate components, Part A focuses on the isolation and structure elucidation of 11 previously undescribed ascidian metabolites. All structures were assigned using a combination of spectroscopic and/or chemical methods. Part B relates to the isolation and chemical conversion of a natural product to a combinatorial template. The natural product template was subsequently used in the generation of a solution-phase combinatorial chemistry library. A further two combinatorial libraries were generated from a synthesised model compound that was related to the natural product template. Part A. Investigation of Aplidium longithorax collected from the Swains Reefs resulted in the isolation of two new para-substituted cyclofarnesylated quinone derived compounds, longithorones J (30) and K (31). The former compound had its absolute stereochemistry determined by the advanced Mosher method. From an Aplidium longithorax collected from Heron Island, two new cyclofarnesylated hydroquinone compounds, longithorols C (46) and D (47) and a novel macrocyclic chromenol, longithorol E (48) were isolated. Longithorol C (46) had its absolute stereochemistry determined by the advanced Mosher method. Chemical investigation of the deep-purple colonial ascidian, Didemnum chartaceum collected from Swains Reefs led to the isolation of five new lamellarin alkaloids, which included the 20-sulfated derivatives of lamellarins B (94), C (95) and L (96), the 8-sulfated derivative of lamellarin G (97) and the non-sulfated compound, lamellarin Z (98). The known lamellarins A (63), B (80), C (64), E (65), G (67), and L (71) plus the triacetate derivatives of lamellarin D (82) and N (83) were also isolated. An aberration in the integration of signals in the 1H NMR spectra of the 20-sulfated derivatives (94-96) led to NMR relaxation studies. T1 values were calculated for all protons in the sulfated lamellarins (94-97) and their corresponding non-sulfated derivatives (80, 64, 71, 67). The protons ortho to the sulfate group in compounds (94-97) had T1 values up to five times larger than the corresponding protons in their non-sulfated derivatives (80, 64, 71, 67). A specimen of Eudistoma anaematum collected from Heron Island was shown to contain a new b-carboline alkaloid, eudistomin V (130), in addition to the two known metabolites, eudistomin H (105) and I (106). Part B. The known natural products, 1,3-diphenethylurea (29), 1,3-dimethylxanthine (30), 1,3-dimethylisoguanine (31) and the salts of tambjamine C (16), E (18) and F (19) were isolated from the ascidian, Sigillina signifera collected in Blue Lagoon, Lizard Island. Base hydrolysis on mixtures of the salts of tambjamine C (16), E (18) and F (19) resulted in the production of 4-methoxy-2,2-bipyrrole-5-carbaldehyde (26). This natural product template (26) was used in the generation of an enamine combinatorial chemistry library (98, 103-111) using solution-phase parallel synthesis. The biaryl compound, 4-(2-thienyl)-1H-pyrrole-2-carbaldehyde (59) was successfully synthesised using Suzuki-Miyaura coupling conditions and subsequently used as a template in the generation of an amine (67, 77, 80-87) and imine (78, 92-95) combinatorial library using solution-phase parallel synthesis.

The knowledge and understanding of sediment transport is essential for the development of effective management strategies for nutrient and sediment loading in estuarine systems. Estuarine suspended sediment (in high concentrations), has the ability to adversely impact upon surrounding ecosystems, such as the Great Barrier Reef, Australia. Due to a recent decline in water and sediment quality, it has recently been mandated that a number of tropical, coastal estuarine systems in Queensland, such as the Fitzroy River estuary, have their sediment loading reduced. In order to meet these requirements, a greater understanding of the sediment transport dynamics and driving processes (such as flocculation and settling velocity) needs to be achieved, and the accuracy of estimation improved. This research project was motivated by the need to improve the general accuracy of field measurements for estuarine suspended sediment transport and dynamics. Field-based measurements (especially settling velocity) are necessary for the parameterisation of sediment transport models. The difficulty in obtaining accurate, in situ data is well documented and is generally limited to methods that isolate a water sample from its natural environment, removing all influences of estuarine turbulence. Furthermore, the water samples are often extracted from points (Eulerian) where the history of the suspended particles is generally unknown. These sampling methods typically contain intrinsic errors as suspended sediment transport is essentially Lagrangian (i.e., flows with the net motion of flow-field) in nature. An investigation into different drogue systems conducted in parallel with a study into the tidal states of the Fitzroy River estuary led to the development of a novel Lagrangian drogue device, the LAD. Additionally, the water-tracking ability of the LAD was tested and found to accurately follow a parcel of estuarine water over a slack water period. Therefore the LAD was deployed in the Fitzroy River to assist in the further understanding of complex sediment transport processes such as flocculation and settling velocity in a natural estuarine flow field. The final device (the LAD - Lagrangian Acoustic Drogue) was developed, utilizing the principals of acoustic backscatter intensity-derived SSC measurements. The investigation of a series LAD deployments (during slack water) in the Fitzroy River estuary, revealed the dominant suspended sediment processes and also gave an insight into the prevailing flow-patterns. Results showed the presence of a settling lag mechanism between low and high tide, which can initiate a net sediment flow upstream with each flood tide. The bulk settling velocity showed comparable results at both low and high water. The LAD derived bulk settling velocity as a function of concentration (SSC), yielding a strong positive correlation (r2 = 0.73). Also the importance of flocculation in the bulk settling and clear up of the water column during periods of still water (high and low tide) was demonstrated as all in situ settling velocities (0.33 - 1.75 mm s-1) exceeded single grain approximations (0.47 mm s-1). This research demonstrates the potential for Lagrangian drogue studies as an effective measuring platform for the accurate quantification of estuarine suspended sediment dynamics. The application of the LAD in the Fitzroy River has lead to a significant improvement in the understanding of the system's real sediment transport processes. This research has provided an effective and accurate technique for measuring real settling velocities for input into numerical models or for the validation of existing model outputs. Furthermore, this technique shows great potential for application in other estuarine systems.

The objective of the research reported in this thesis was to develop a technique to monitor the dynamics of sediments and nutrients entering the coastal ocean with river plumes associated with high intensity low frequency events (e.g. floods), using ocean colour remote sensing. To achieve this objective, an inverse bio-optical model was developed, based on analytical and empirical relationships between concentrations of optically significant substances and remote sensing of water-leaving radiance. The model determines concentrations of water-colouring substances such as chlorophyll, suspended sediments, and coloured dissolved organic matter, as well as the values of optical parameters using water-leaving radiances derived from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS). To solve atmospheric correction in coastal waters, the aerosol type over clear waters is transferred to adjacent turbid water pixels. The vicinity of the Herbert River, central Great Barrier Reef zone, Australia, was used as a case study for the application of the algorithm developed. The satellite ocean colour technique was successfully validated using sea-truth measurements of water-colouring constituents acquired in the area during various seasons throughout 2002-2004. A high correlation between chlorophyll and dissolved organic matter was found in the coastal waters of the region, and when the bio-optical model was constrained to make chlorophyll a function of dissolved organic matter, the relationship between in situ and satellite-derived data was substantially improved. With reliable retrieval of the major water-colouring constituents, the technique was subsequently applied to study fluxes of particulate and dissolved organic and inorganic matter following a flood event in the Herbert River during the austral summer of 1999. Extensive field observations covering a seasonal flood in the Herbert River in February 2004 revealed high sediment and nutrient exports from the river to the adjacent coastal waters during the flood event. Due to rapid settling, the bulk of the sediment-rich influx was deposited close inshore, while the majority of nutrients exported from the river were consumed by phytoplankton in a relatively small area of the coastal ocean. With the help of ocean colour remote sensing, it was demonstrated that river-borne sediments and nutrients discharged by a typical flood in the Herbert River are mostly precipitated or consumed within the first 20 km from the coast and therefore are unlikely to reach and possibly affect the midshelf coral reefs of this section of the Great Barrier Reef lagoon.

Thesis (M.A.)--Ohio University, June, 2007. / Title from PDF t.p. Includes bibliographical references.

The seabed of the Southern Bight of the North Sea is mostly composed of sandy soft sediments. Natural hard substrates like pebbles are rare and only occur locally. Lost cargos or shipwrecks lie on the seabed as results of unintentional processes, but because of their inherent structure, they effectively act as artificial reefs deprived of an a priori defined set of functions. On Belgian waters, 231 shipwrecks and other artificial hard structures are dispersed on the continental shelf. Together with the sunken vessels of the neighbouring countries, they create a network of individually isolated hard substrates available for the colonization of the epifauna. The faunal diversity of these shipwrecks has never been studied before. This thesis analyzed the diversity as well as spatial and temporal variation in community structure of ten Belgian shipwreck sites. A total of 224 macrospecies have been identified, with at least 50 species new or rare for the Belgian fauna and Southern North Sea. All shipwrecks are strongly dominated by cnidarians in terms of biomass and by amphipods in terms of abundances. The artificial hard substrate communities isolate strongly from the surrounding soft sediment communities by sharing few species, being dominated by different faunal groups and having a distinct trophic organization. Looking at a cross-shore gradient of sites, three groups of shipwrecks could be determined. Metridium senile, a sea anemone, dominates a species poor community of the coastal sites. Channel water masses influence the offshore sites causing a more stable abiotic environment. The hydrozoan Tubularia indivisa dominates this community. Intermediate sites are also dominated by T. indivisa, but a higher biomass is here observed. It also appears that this T. indivisa is a key species allowing for the settlement of a large set of secondary epibionts. The shipwreck network is further discussed in the context of the regional diversity, dispersal of species and fisheries based applications

World-wide coral reefs are in a state of decline as a result of many local and regional factors. Recent global mass mortalities of reef corals due to record warm sea temperatures have led researchers to consider global warming as one of the most significant threats to the persistence of coral reef ecosystems over the next 100 years. It is well established that elevated sea surface temperatures (SSTs) cause widespread coral bleaching, yet confusion lingers as to what facet of extreme temperatures is most important. Utilizing long-term in situ datasets, nine thermal stress indices were calculated and their effectiveness at segregating bleaching years a posteriori for multiple reefs on the Florida Reef Tract was tested. Simple bleaching thresholds based on deviations above the climatological maximum monthly SST were just as effective at identifying bleaching years as complex thermal stress indices. Near real-time bleaching alerts issued by NOAA's Integrated Coral Observing Network (ICON) are now based upon a running 30-day average SST, such that alerts are only issued when the running 30-day average SST exceeds the estimated bleaching threshold for a particular site. In addition to three widespread, mass-coral bleaching events, the Florida Reef Tract was impacted by three tropical storms and 12 hurricanes from 1997-2005. Sea surface cooling associated with the high frequency of hurricanes that impacted Florida in 2005 likely acted to ameliorate the severity and duration of bleaching. Nonetheless, hurricane-associated cooling is not expected to nullify the proposed effects of climate change on coral reefs. The role of thermal stress in coral bleaching has been extensively studied for eastern tropical Pacific (ETP) coral reefs. However, the ETP presents a unique opportunity as this region has sub-optimal conditions for coral reef development because of upwelling of carbon dioxide-enriched deep water along the shallow thermocline. This upwelling results in a depressed aragonite saturation state which is likely an additional factor in the poor reef development throughout the ETP. The highest aragonite saturation documented in this study occur in the Gulf of Chiriquí, which corresponds with the greatest reef development of the entire ETP. Seasonal upwelling had a significant effect on the carbonate chemistry of surface waters in Pacific Panamá. This regionally-depressed aragonite saturation state of the ETP appears to result in corals with a less dense skeleton. Density values of poritid corals from the Galápagos, where aragonite saturation was the lowest documented in this study, were significantly less dense relative to those from Panamá and the Great Barrier Reef. The density of non-living pocilloporid framework components were no different across the ETP aragonite saturation gradients. This could be a result of the activity of boring sponges removing the primary carbonate material within the dead coral skeleton, thus lowering density, albeit physical-chemical dissolution cannot be ruled out. These studies provide real-world examples of the ramifications of global climate change upon coral reef ecosystems.

A single-beam acoustic seabed classification system was used to map coral reef environments in the upper Florida Keys, USA, and the Bahamas. The system consisted of two components, both produced by the Quester Tangent Corporation. A QTCView Series V, operating with a 50 kHz sounder, was used for data acquisition, and IMPACT software was used for data processing and classification. First, methodological aspects of system performance were evaluated. Second, the system was applied to the assessment of grouper and snapper habitat. Two methodological properties were explored: transferability (i.e. mapping the same classes at multiple sites) and reproducibility (i.e. surveying one site multiple times). The transferability results showed that a two-class scheme of hard bottom and sediment could be mapped at four sites with overall accuracy ranging from 73% to 86%. The locations of most misclassified echoes had one of two characteristics: a thin sediment veneer overlying hard bottom or within-footprint relief on the order of 0.5 m or greater. Reproducibility experiments showed that consistency of acoustic classes between repeat transects over the same area on different days varied, for the most part, between 50% and 65%. Consistency increased to between 78% and 92% when clustering was limited to two acoustic classes, to between approximately 70% and 100% when only echoes acquired within two degrees of nadir in the pitch direction were used, and to between 81% and 87% when a limited set of features was used for classification. The assessment of grouper and snapper habitat addressed the question whether areas of high fish abundance were associated with characteristic acoustic or geomorphological signatures. The results showed, first, that the hard bottom / sediment classification scheme was a useful first step for stratifying survey areas to increase efficiency of grouper census efforts. Second, an index of acoustic variability complemented the hard bottom / sediment classification by further targeting areas of potential grouper habitat. Finally, five grouper and snapper spawning aggregation sites were all found to have similar associations with drowned shelf edge reefs in the upper Florida Keys.

Sedimentary dikes at the Pipe Creek Junior Quarry were found to fill fractures formed by compaction and rotation of the reef flank beds and by regional stresses of less certain origin. A sequence of fracturing events has been established as well as a sequence for the emplacement of dike materials. Most of the carbonate dikes are found to be of Cayugan (Silurian) age, although some of the las carbonates are shown to be of Devonian age due to the presence of rounded detrital quartz grains within them. All of the quartz arenite dikes are found to be of Devonian age and are divided into two major groups: older white arenites and younger brown arenites. The two types of arenties have different characteristics and were deposited under different conditions.The arenites of Pipe Creek Junior Quarry were found to be similar to the arenites of the Bluffton Quarry which are also fracture fillings in Silurian reef rock. Other Devonian sand bodies are compared to the fracture filling and, although they are not identical, they show a similarity in materials and a pattern of environment and deposition that point to a northwestern source for all of the rounded quartz studied in this work. Environmental analysis of the quartz grains indicates a litoral mode of transport and sorting for most of the samples with an ecolian mode present in the sands outside the reef area and as a minor component for some of the younger sands within the reef area.A map of the glaciated quarry surface has been prepared for the purposes of this work and to preserve relationships that are constantly being removed by quarrying of the reef flank beds.

Over the last decade, coral reef remote sensing research has focused on habitat map development. Advances in field methods, spatial and spectral resolution of remote sensing data, and algorithm development have led to more detailed map categories and to heightened map accuracy. Studies have provided guidance for practitioners in areas such as imagery selection, algorithm application, and class selection methods, but the product has remained relatively unchanged – a habitat map showing the spatial distribution of a range of substrate classes, classified primarily on the basis of their spectral signature. However, the application of such a product in a management context has not been elaborated by the remote sensing community. The research described in this thesis addresses the challenge that the application of remotely-sensed coral reef information in a coral reef management environment elicits. In such an environment, the coral reef manager asks: "What can the map do to help me?", while the remote sensing scientist asks: "What type of information do you need?". The research described here aims to reconcile these two points of view, by answering the research question of this thesis: How can coral reef remotely-sensed information address stakeholder-specific coral reef management objectives? This question was answered through the development of a four-stage strategy. The strategy includes: 1) developing a traditional habitat map, 2) investigating stakeholder receptivity to the habitat map, 3) linking stakeholder interests with habitat data, and 4) illustrating the linked habitat data in what we term a management map. The strategy was applied on Bunaken Island, Indonesia, and involved the collection of both qualitative and quantitative data sets. The research was relevant to the communities on Bunaken Island, as they are directly responsible for the management of the coral reef resources surrounding Bunaken Island, and they are regularly planning and implementing coral reef management projects. The effectiveness of the four-stage strategy was evaluated in a framework that compares potential and actual uses of habitat maps and management maps in coral reef management projects. It was shown that management maps are superior to habitat maps for a wide range of management purposes. This research has provided two main contributions to the field of coral reef remote sensing and management. The first is the four-stage strategy that results in the development of management maps, and the second is the framework for evaluating the effectiveness of the management maps. This research seeks to traverse the gap between producers and users of coral reef remotely-sensed information. The recommendations made from this research addresses coral reef management procedures, action research, and cross-cultural communication. Each recommendation is founded on collaboration between scientist and manager. Such collaboration is crucial for successful application of remotely-sensed information to management.