Thesis (M.S.)--University of Puerto Rico, Mayaguez Campus, 2006. / Includes bibliographical references.

The production of an economic good derived from a renewable natural resource base involves the extraction of ecosystem function values as represented by the contribution made to production by the originating ecosystem. The artisanal fisheries of Jamaica is used as a case study in the examination of the characteristics of economic production processes and the development of a biophysically-based index to account for captured ecosystem values. The following is provided: (i) a description of the fisheries of Jamaica and derivation of economic production function models; (ii) a description of the socio-economic condition of the fisheries of Montego Bay Marine Park (Montego Bay, Jamaica) which serves to further illustrate the nature of artisanal fisheries in Jamaica, as well as a more traditional economic approach to resource valuation; and, (iii) the development of an index which as a proxy measure captures the biophysical values of the contributions of the natural biotic environment (the “embodied ecosystem values”) to the fisheries, and an examination of the extent to which those values are proportionately reflected in monetary exchange values. In addition, contributions are made concerning: (i) the development of an economic data collection and analysis programme for Jamaica (also more widely applicable to countries of the developing tropics) which will allow for more informed decisions concerning the management of coral reef fisheries; (ii) general principles concerning the development of biophysical indices, such as indices of biodiversity, which will ultimately be used to inform government policy and management decisions; (iii) the validity of indices derived from ecosystem statistics; and, (iv) the potential for the further development of models which explicitly incorporate the contributions of ecosystems to economic production processes. Cobb-Douglas and translog models of fishing effort are derived from catch and effort data for the years 1996 and 1997 to describe the relationships between catch and firm-level inputs as they vary by fishery within Jamaica. Data on the total catch, crew size, gear soak time, and quantity of gear used yield separate functions of effort for the use of China net, trap, hand line, palanca, speargun, and troll fishing technologies. By further accounting for the month and fishing location (i.e. north coast versus south coast), the seasonal and regional influences on catch rates are explored. Patterns of production include reduced catch rates associated with fishing the north coast shelf and a seasonal peak in catch levels during the late summer and fall. The use of production function models of effort are found to provide informative descriptions of fishery production processes, yet avoid many of the technical difficulties associated with more traditional bioeconomic approaches. The Index of Captured Ecosystem Value (ICEV) is developed from a basis in information theory relevant to an analysis of network flows in ecosystems. Technical coefficients, describing the production relationship between ICEV values and market values of catches associated with individual fishing efforts, revealed that captured ecosystem function associated with fisheries using distinct technologies (i.e. China net, trap, hand line, palanca, and speargun) were valued differently by the market. This “surplus value” appears to be rooted in the observation that certain fisheries target species which are more connected within the coral reef food web than those species typically captured by other fisheries. Consideration of the biophysical contributions of coral reef ecosystems to fisheries production reveals distortions between market and supply-side values, indicating that the role of ecosystems is not being consistently treated. / Graduate

The Hudson Bay Basin is the largest intracratonic basin in North America, but remains a frontier area for our knowledge of its stratigraphy and sedimentology and its hydrocarbon potential. Large domal reefs (up to 10 m thick and 500 m wide) in the Upper Ordovician Red Head Rapids Formation on Southampton Island developed on the margin of this shallow-marine evaporitic basin in which physical and chemical seawater parameters were distinct from the open ocean and in which a diverse community of reef-building and dwelling metazoans was unable to flourish. The main reef facies comprise boundstone and cementstone composed of various proportions of early-calcified sponge tissues, microbial encrusters, synsedimentary cement and small colonial metazoans. The accretionary mechanisms of the Red Head Rapids reefs were mainly the result of framebuilding by early-calcified sponges and small colonial corals and binding by calcimicrobial elements for the boundstone facies, and of massive aragonitic cement precipitation near the seafloor for the cementstone facies. These Upper Ordovician reefs, in which microbialites dominate but coexist with metazoans, were more widespread in the Early Ordovician immediately prior to the Middle to Late Ordovician expansion of skeletal-dominant reefs. The Upper Ordovician reefs on Southampton Island, porous and locally bitumen impregnated, underwent early marine, near-surface and progressive burial diagenesis; reducing its primary porosity but significantly increasing its secondary porosity. They represent one of the major untested petroleum play types identified in the Hudson Bay Basin.

Tropical coral reefs are highly productive ecosystems thriving in oligotrophic waters, a phenomenon facilitated by efficient but delicate biogeochemical cycling within reef communities. Global climate change and local stressors are driving phase shifts from coral- to non-calcifier-dominated states in reefs worldwide, substantially altering reef biogeochemical functioning. While major benthic players such as coral and macroalgae have been investigated in detail regarding carbon and nutrient dynamics, the less conspicuous “reef cryptobiome” (sensu Carvalho et al., 2019) – comprising most of reef diversity – has only recently gained attention. Autonomous Reef Monitoring Structures (ARMS) have recently been developed to sample coral reef cryptobenthic communities in a non-destructive and standardised way, allowing exploration of these often overlooked biota. Here, 16 ARMS were deployed for seven months in four distinct habitats dominated by different benthic players (i.e., four units per habitat) in a nearshore Red Sea coral reef to investigate the cryptobiome associated with proxies of varying benthic states. Two of these habitats were coral-dominated, and one each dominated by turf algae or coral rubble. To assess the biogeochemical fluxes of pioneering cryptobenthic communities, ARMS were incubated in situ prior to retrieval using customised chambers. Subsequently, 16S rRNA gene amplicon and shotgun metagenomic sequencing of the ARMS sessile (i.e., encrusting) fractions were performed to link observed fluxes with prokaryotic taxonomic and functional profiles, particularly regarding nitrogen cycling. The results show that the pioneering cryptobiome represents a significant source of inorganic nutrients and that its associated microbial communities facilitate the mineralisation and assimilation of organic matter and provide crucial genetic functional pathways for nitrogen cycling. Functional similarities among habitats suggested functional redundancy despite variation in bacterial community composition. Hence, the reef cryptobiome can be considered an important biogeochemical player in coral reefs, actively shaping the abiotic conditions within niches of the reef framework and driving the recruitment and persistence of crytobenthic and other reef organisms. As communities associated with the algae-dominated reef habitat were most distinct compositionally and biogeochemically, and as non-calcifiers are becoming more dominant in many reefs, this has implications for intensifying phase shifts in coral reefs worldwide. Future ARMS studies will also benefit from adjustment of sample processing and molecular protocols, resulting in higher sample throughput and lower costs in times of increased application of ARMS.

No description available.

Yeung, Chung Wing. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 143-156). / Abstracts in English and Chinese. / Acknowledgements --- p.i / Abstract (English) --- p.iii / Abstract (Chinese) --- p.vi / Contents --- p.vii / List of Tables --- p.xii / List of Figures --- p.xii / Chapter Chapter 1 --- Introduction / Chapter 1.1 --- Ecological and economic importance of coral reef habitats --- p.1 / Chapter 1.2 --- D egradation of coral reefs --- p.2 / Chapter 1.2.1 --- Natural recovery --- p.3 / Chapter 1.2.2 --- Restoration of disturbed reefs --- p.3 / Chapter 1.2.2.1 --- Whole colony transplantation --- p.4 / Chapter 1.2.2.2 --- Fragment transplantation --- p.4 / Chapter 1.2.2.3 --- Coral nursery --- p.5 / Chapter 1.3 --- Studies on octocorals --- p.6 / Chapter 1.3.1 --- Functional ecology of octocorals --- p.7 / Chapter 1.3.2 --- Biodiversity of octocorals in Hong Kong --- p.9 / Chapter 1.3.3 --- Threats on octocorals in Hong Kong --- p.10 / Chapter 1.4 --- The focus and significance of the present study --- p.12 / Chapter 1.4.1 --- "Lobophytum sarcophytoides, the study organism" --- p.14 / Chapter 1.4.2 --- Objectives --- p.15 / Chapter 1.5 --- Thesis Outline --- p.16 / Chapter Chapter 2 --- Seasonal Variation and Size-dependent Eco-physiological Performances of the Soft Coral Lobophytum sarcophytoides / Chapter 2.1 --- Introduction --- p.19 / Chapter 2.1.1 --- Damage recovery --- p.20 / Chapter 2.1.2 --- Photosynthetic activity --- p.21 / Chapter 2.1.3 --- Reproductive biology --- p.22 / Chapter 2.1.4 --- Growth rate --- p.23 / Chapter 2.1.5 --- Significance and objectives --- p.23 / Chapter 2.2 --- Study Sites --- p.24 / Chapter 2.2.1 --- Lan Guo Shui (LGS) --- p.24 / Chapter 2.2.2 --- Tolo Harbour (MSL) --- p.25 / Chapter 2.3 --- Methodologies --- p.27 / Chapter 2.3.1 --- Sample collection --- p.27 / Chapter 2.3.2 --- Treatment of samples --- p.27 / Chapter 2.3.3 --- Health condition --- p.28 / Chapter 2.3.4 --- Damage recovery --- p.29 / Chapter 2.3.5 --- Growth rate --- p.29 / Chapter 2.3.6 --- Photosynthetic activity --- p.30 / Chapter 2.3.7 --- Reproductive biology --- p.30 / Chapter 2.3.8 --- Statistical Analysis --- p.31 / Chapter 2.4 --- Results --- p.32 / Chapter 2.4.1 --- Acclimation of transplanted corals --- p.32 / Chapter 2.4.2 --- Health condition --- p.33 / Chapter 2.4.3 --- Growth rate --- p.34 / Chapter 2.4.4 --- Photosynthetic activity --- p.38 / Chapter 2.4.5 --- Damage recovery --- p.39 / Chapter 2.4.6 --- Reproductive biology --- p.40 / Chapter 2.5 --- Discussion --- p.41 / Chapter 2.5.1 --- Diurnal expansion and contraction of colonies --- p.41 / Chapter 2.5.2 --- Size fluctuation of the colonies --- p.42 / Chapter 2.5.3 --- Possible factors for the high initial mortality of corals --- p.43 / Chapter 2.5.4 --- Causes of bleaching and the harmful effects --- p.44 / Chapter 2.5.5 --- Energy allocation between reproduction and growth --- p.47 / Chapter 2.5.6 --- Quick healing of cut fragments and its ecological implication --- p.48 / Chapter 2.5.7 --- Choice of suitable fragment size for nursery use --- p.49 / Chapter 2.5.8 --- Suitable season for conducting the experiment --- p.50 / Chapter 2.6 --- Summary --- p.51 / Chapter Chapter 3 --- Effects of Temperature on the Health Condition and Photosytnthetic Activity of the Soft Coral Lobophytum sarcophytoides / Chapter 3.1 --- Introduction --- p.69 / Chapter 3.2 --- Methodologies --- p.73 / Chapter 3.2.1 --- Sample collection --- p.73 / Chapter 3.2.2 --- Experimental set-up of aquaria for growing corals --- p.73 / Chapter 3.2.2.1 --- Temperature experiment I --- p.74 / Chapter 3.2.2.2 --- Temperature experiment II --- p.74 / Chapter 3.2.2.3 --- Temperature experiment III --- p.76 / Chapter 3.2.3 --- Health condition --- p.76 / Chapter 3.2.4 --- Photosynthetic activity --- p.77 / Chapter 3.2.5 --- Statistical analysis --- p.78 / Chapter 3.3 --- Results --- p.79 / Chapter 3.3.1 --- Temperature experiment I --- p.79 / Chapter 3.3.1.1 --- Health condition --- p.79 / Chapter 3.3.1.2 --- Photosynthetic activity --- p.80 / Chapter 3.3.2 --- Temperature experiment IIA --- p.81 / Chapter 3.3.2.1 --- Health condition --- p.81 / Chapter 3.3.2.2 --- Photosynthetic activity --- p.83 / Chapter 3.3.3 --- Temperature experiment IIB --- p.84 / Chapter 3.3.3.1 --- Health condition --- p.84 / Chapter 3.3.3.2 --- Photosynthetic activity --- p.85 / Chapter 3.3.4 --- Temperature experiment III --- p.85 / Chapter 3.3.4.1 --- Health condition --- p.85 / Chapter 3.3.4.2 --- Photosynthetic activity --- p.86 / Chapter 3.4 --- Discussion --- p.87 / Chapter 3.4.1 --- The effect of acclimation --- p.87 / Chapter 3.4.2 --- Temperature tolerance range of L. sarcophytoides --- p.90 / Chapter 3.4.3 --- Indicators of coral health --- p.92 / Chapter 3.4.3.1 --- Photosynthetic activity --- p.92 / Chapter 3.4.3.2 --- Colony contraction --- p.94 / Chapter 3.4.3.3 --- Bleaching --- p.95 / Chapter 3.4.3.4 --- Algal overgrowth --- p.97 / Chapter 3.4.3.5 --- Attachment of transplanted corals --- p.99 / Chapter 3.5 --- Summary --- p.100 / Chapter Chapter 4 --- Reproductive Biology of Lobophytum sarcophytoides / Chapter 4.1 --- Introduction --- p.114 / Chapter 4.2 --- Methodologies --- p.117 / Chapter 4.2.1 --- Study site --- p.117 / Chapter 4.2.2 --- Sample collection and treatments --- p.117 / Chapter 4.3 --- Results --- p.119 / Chapter 4.3.1 --- Gametogenic development: Size changes --- p.119 / Chapter 4.3.2 --- Gametogenic development: Developmental stages --- p.120 / Chapter 4.3.2.1 --- Oogenesis --- p.120 / Chapter 4.3.2.2 --- Spermatogenesis --- p.121 / Chapter 4.4 --- Discussion --- p.122 / Chapter 4.4.1 --- Unusual oogenic development pattern in L sarcophytoides --- p.122 / Chapter 4.4.2 --- Possible effect of lack of a temperature cue on gametogenic development --- p.123 / Chapter 4.4.3 --- Alternative explanation: Energy allocation --- p.126 / Chapter 4.5 --- Summary --- p.128 / Chapter Chapter 5 --- Summary and Perspectives --- p.137 / References --- p.143

The first detailed investigation of Maldivian rim island development and reef-to-island connectivity is presented. Study sites were selected on windward and leeward rim aspects of Huvadhu Atoll, and analyses were undertaken at a millennial, contemporary and near-future temporal scales. At millennial temporal scales, contrasting models of island development were presented for the windward and leeward sites. Marked between-site differences were found in the timings of island initiation (2,800-2,000 cal. yr. B.P. and 4,200-3,600 cal. yr. B.P. at the windward and leeward sites respectively). Hence, sea-level does not represent the sole control upon island formation. The period of island initiation and heightened mobility occurred during the mid-Holocene sea-level highstand. Future sea-level rise may thus reactivate the process regime responsible for reef island initiation, potentially inducing further island building and/or heightened island mobilisation. Contemporary analyses highlighted the homogeneity of the sediment reservoir across marine, beach and island sediments. Specifically, sand-grade coral was dominant across all samples within both sites (>50%). The most likely source of sand-grade coral is excavator parrotfish, which was consistent with ecological survey-based estimates of sediment production (excavator parrotfish accounted for 72.8% and 68.2% of sediment production at the windward and leeward sites). The highest sediment production rates were found within the lagoonward environments (59.4% and 75.4% at the windward and leeward sites), which is consistent with the more recent lateral lagoonward mode of island building. With regard to near-future analyses, the apparent recent areal expansion of seagrass beds demonstrated the capacity of ecological changes to cause shifts in sediment production budgets (contributing an additional ~243 tonnes yr-1 of sediment on the leeward rim platform). In addition, significant increases in benthic sediment mobility were found at both study sites under sea-level rise scenarios. Increases in mobility were markedly larger in magnitude at the leeward site than at the windward site. A challenge for the adaptive capacity of atoll nations is thus to acknowledge this atoll-scale diversity in future management strategies.

No description available.

Scleractinian corals increasingly are studied as geochemical archives of modern- and palaeoclimate, but microsampling for geochemical data is complicated by: 1) the microstructural complexity and spatial variability in skeletal growth in different coral genera; and 2) the rapidity and scale of diagenetic alteration that occurs in living coralla. Geochemical sampling techniques now have spatial resolution into the sub-micrometer to tens of micrometers range, and it is hoped that the spatial resolution can be translated to temporal resolution. This study investigated the effects on geochemical analyses imposed by microstructure and diagenesis in different live-collected coral genera representing somewhat different depositional environments. Suites of samples of four reef-building genera (Acropora, Pocillopora, Goniastrea and Porites) were collected from three adjacent environments in intertidal and subtidal positions near the reef edge at Heron Reef, Great Barrier Reef and studied by means of optical and scanning electron microscopy, combined with vibrational and energy dispersive spectroscopy. The first section of this study compares and documents the microstructure of the four coral genera. Each genus was found to have very different three-dimensional arrangements of microstructural elements, and a new general growth model was proposed for Acropora, to take into account differences in the timing of precipitation of trabeculae and thickening deposits. The results highlight the complexity and spatial variability of skeletal growth in different coral genera. Because microstructural patterns vary in different genera, direct observation of microstructural elements and growth lines are necessary to allow geochemical microsamples to be placed into series that represent temporal sequences with known degrees of time averaging. Coral growth rates (i.e., rates of extension) are discussed to determine the range of temporal relationships that exist between closely spaced skeletal microstructural elements. Such data are necessary in order for coral skeletogenesis to be understood and are critical for constraining microsampling strategies aimed at developing true time series geochemical data at very fine spatial and temporal scales. The second part of the study focused on early diagenetic alteration of the corals, which is an equally important concern for geochemical analysis. Early marine diagenesis was documented in the same live-collected samples of the four common reef-building coral genera. Samples show extensive early marine diagenesis where parts of the coralla less than three years old contain abundant macro- and microborings (sponges, algae, cyanobacteria and fungi) and significant amounts of aragonite, high-Mg calcite, low-Mg calcite and brucite [Mg(OH)2] cements. Many of the cements are associated with microendoliths and endobionts that inhabit recently abandoned parts of the skeleton. The cements are problematic for palaeoclimate reconstruction because geochemical proxies used for paleoclimate studies are meant to reflect ambient seawater chemistry and conditions, but the occurrence of brucite and low-Mg calcite demonstrates how far fluid chemistry in microenvironments within the corals has evolved from ambient seawater. Some Porites lobata specimens have had as much as 60% of the most recently deposited skeletal aragonite (i.e., the part of the skeleton that projects into the layer of living polyps) bored and replaced by low-Mg calcite cement. The low-Mg calcite cement has significantly different trace element ratios (Sr/Ca(mmol/mol) = 6.3 ± 1.4; Mg/Ca(mmol/mol) = 12.0 ± 5.1) than the host coral skeletal aragonite (Sr/Ca(mmol/mol) = 9.9 ± 1.3; Mg/Ca(mmol/mol) = 4.5 ± 2.3), thus providing a serious challenge for Sr/Ca or Mg/Ca based sea surface temperature calculations. This study illustrates that many diagenetic changes that can radically alter important geochemical characteristics of coral skeleton occur very early on the sea floor (i.e., while corals are still alive). Documented cements altered trace element inventories (e.g., Sr and Mg), thus, interfering with the use of those elements in palaeotemperature calculations. Hence, significant diagenetic changes that jeopardise palaeoclimate data do not require long-term diagenesis or meteoric exposure. Some of the diagenetic changes (e.g., calcite filled borings) occur at scales that are very difficult to detect short of visual inspection using SEM. Hence, vetting of coral samples with SEM is required before any sample is subjected to geochemical analysis.

Trajectories of decline have been described in coral reefs throughout the Indo-Pacific region, with long-term losses of abundance, diversity and habitat structure. Since European settlement of the Queensland coastline in the mid-18th century, widespread changes in land use have occurred within Great Barrier Reef (GBR) catchments (e.g. extensive land clearing, agriculture and grazing). Despite direct and indirect evidence indicating decline of inshore reefs, it has proven difficult to ascertain links between land use changes, terrestrial discharge, water quality and the decline of coral reefs at regional scales, and the contributions of anthropogenic influences to the disturbance regimes of inshore reefs remains highly controversial. This thesis uses palaeoecological reconstruction of coral assemblages and high-precision U-Series dating to examine changes in community structure of inshore coral reefs in the Palm Islands region across decadal and centennial scales. Comparisons of modern and historical coral assemblages provide evidence of a collapse of Acropora coral communities at Pelorus Reef in the early 20th Century. Fossil assemblages in an adjacent site at Pelorus provide further evidence of an extrinsic shift from historical Acropora assemblages to more sediment-tolerant corals in modern assemblages, a change without precedence in 800 years of record. Sediment cores (2-5m length) were extracted from Pandora and Havannah reefs to determine long-term rates of reef growth throughout the late Holocene. Computer Axial Tomography (CAT) scans of cores revealed a framework dominated by coral fragments, and U-Series dating of corals revealed rapid and continuous reef growth at both reefs throughout the last 1000 yrs. Comparisons of reef accretion (m ka-1) from cores with published accretion rates from early-mid Holocene inshore GBR reefs show that reef slope environments are now accreting at rates equal to and exceeding those of the last 8000 years. This result contradicts assumptions that inshore reefs are undergoing or have undergone natural trajectories of geomorphic decline. A bayesian approach to determine stability of coral communities from the Pandora and Havannah cores indicates that those coral communities have existed in stable states for upwards of 400yrs, punctuated by periods of instability. Contrary to some paradigms of biodiversity, the high diversity communities were unstable on centennial scales, 4 yet the low diversity assemblages did not necessarily confer stability to these assemblages. Growth rates of inshore reefs were independent of diversity or community structure. From a management perspective, these results provide a longer-term (decades to centuries) understanding of coral community dynamics on inshore reefs of the GBR that provides a basis for detecting and understanding changes following European settlement, and a baseline for the management and potential restoration of coral communities at local and regional scales.