Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 131-143). / Coral reefs are biodiverse ecosystems that are at risk of degradation as a result of environmental changes. Reefs are constantly in a state of flux: the resident species assemblages vary considerably in space and time. However, the drivers of this variability are poorly understood. Tracking these changes and studying how coral reefs respond to natural and anthropogenic disturbance can be challenging and costly, particularly for reefs that are located in remote areas. Because many reef animals produce and use sound, recording the ambient soundscape of a reef might be one way to efficiently study these habitats from afar. In this thesis, I develop and apply a suite of acoustics-based tools to characterize the biological and anthropogenic acoustic activity that largely comprises marine soundscapes. First, I investigate links between reef fauna and reef-specific acoustic signatures on coral reefs located in the U.S. Virgin Islands. Second, I compare those findings to a more expansive study that I conducted in Maui, Hawaii, in which the drivers of bioacoustic differences among reefs are explored. Third, I investigate the distances over which sounds of biological origin may travel away from the reef and consider the range within which these acoustic cues might be usable by pelagic larvae in search of a suitable adult habitat. Fourth, I assess the extent to which the presence of vessel noise in shallow-water habitats changes the ambient soundscape. Finally, I present the results of a modeling exercise that questions how ocean noise levels might change over the next two decades as a result of major projected increases in the number and size of and distance traveled by commercial ships. The acoustics-based tools presented here help provide insight into ecosystem function and the extent of human activity in a given habitat. Additionally, these tools can be used to inform an effective regulatory regime to improve coral reef ecosystem management. / by Maxwell Bernard Kaplan. / Ph. D.

Understanding how coral reefs have developed in the past is crucial for placing contemporary ecological and environmental change within appropriate reef-building timescales (i.e. centennial to millennial). On Australia’s Great Barrier Reef (GBR), coral reefs situated within nearshore settings on the inner continental shelf are a particular priority. This is due to their close proximity to river point sources, and therefore susceptibility to reduced water quality as the result of extensive modification of adjacent river catchments following European settlement in the region (ca. 1850 CE). However, the extent of water quality decline and its impact on the coral reefs of the GBR’s inner-shelf remains contentious and is confounded by a paucity of long-term (> decadal) datasets. Central to the on-going debate is uncertainty related to the impact of increased sediment loads, relative to the natural movement and resuspension of terrigenous sediments, which have accumulated on the inner-shelf over the last ~6,000 years. The main aim of this thesis was to characterise and investigate the vertical development of turbid nearshore coral reefs on the central GBR. This aim was achieved through the recovery of 21 reef cores (3 - 5 m in length) from five proximal turbid nearshore reefs, currently distributed across the spectrum of reef ‘geomorphological development’ within the Paluma Shoals reef complex (PSRC). The recovered reef cores were used to establish detailed depositional and palaeoecological records for the investigation of the (1) internal development and vertical accretionary history of the PSRC; and (2) compositional variation in turbid nearshore coral and benthic foraminiferal assemblages during vertical reef accretion towards sea level. Established chronostratigraphic and palaeoecological records were further used to assess the impact of post-European settlement associated water quality change in a turbid nearshore reef setting on the central GBR. Radiocarbon dating (n = 96 dates) revealed reef initiation within the PSRC to have occurred between ~2,000 and 1,000 calibrated years before present, with subsequent reef development occurring under the persistent influence of fine-grained (< 0.063 mm) terrigenous sediments. The internal development of the PSRC was characterised by discrete reef facies comprised of a loose coral framework with an unconsolidated siliciclastic-carbonate sediment matrix. A total of 29 genera of Scleractinian coral and 86 genera of benthic foraminifera were identified from the palaeoecological inventory of the PSRC. Both coral and benthic foraminiferal assemblages were characterised by distinct assemblages of taxa pre-adapted to sediment stress (i.e. low light availability and high sedimentation). At the genus level, no discernable evidence of compositional change in either coral or benthic foraminiferal assemblages was found, relative to European settlement. Instead, variations in assemblage composition were driven by intrinsic changes in prevailing abiotic conditions under vertical reef accretion towards sea level (e.g. hydrodynamic energy, light availability, and sedimentation rate). These findings therefore highlight the importance for considering reef ‘geomorphological development’ when interpreting contemporary reef ecological status. Furthermore, this research emphasises the robust nature of turbid nearshore reefs and suggests that they may be more resilient to changes in water quality than those associated with environmental settings where local background sedimentary conditions are less extreme (e.g. towards the inner/mid-shelf boundary). To this end, this thesis presents new baseline records with which to assess contemporary ecological and environmental change within turbid nearshore settings on the central GBR.

Parrotfish are a diverse and ubiquitous group found on coral reefs worldwide. They are categorised into three main feeding modes; the browsers, scrapers and excavators, which together perform a number of important functional roles on coral reefs. Scraper and excavator parrotfish are common on most Indo-Pacific coral reefs where their roles in bioerosion, sediment production, grazing pressure and sediment reworking have been shown to influence benthic community composition, reef growth potential and sediment supply to reef habitats and reef associated sedimentary landforms. However, despite the widely known importance of parrotfish on coral reefs, our understanding of how their roles in carbonate cycling vary among species and among whole parrotfish communities in different reef habitats remains limited. This thesis produces original contributions to knowledge in the areas of species specific bioerosion estimates for the central Indian Ocean, bottom-up controls of habitat type on parrotfish assemblages and how variations in parrotfish assemblages translate to contributions to carbonate cycling processes among different reef habitats. The study was carried out across eight habitats on an atoll-edge reef platform in the central Maldives, where it was found that parrotfish community composition was driven by reef structural complexity and substrate type. Parrotfish occurred in six of the eight habitats, comprising ~44% of the platform area. Among these habitats, overall grazing pressure, bioerosion rates, sediment reworking and sediment production varied markedly. These processes were also found to have different spatial patterns over the reef platform, showing that they are not necessarily tightly coupled. In addition, reef habitats can vary in their importance for both sediment supply, and the relative importance of reworked sediment. Parrotfish produced a wide range of sediment size fractions, from < 32 to 2000 μm and produced predominantly coral sands (>80%) between 125 and 1000 μm in diameter. This is comparable to the grain types found on local reef islands, and it is likely that the most significant supply of this material is from habitats on the atoll-edge side of the platform (which make up ~20% of the total platform area). Quantifying parrotfish functional roles and understanding the drivers behind these processes is important for informing future empirical and modelling studies, particularly as coral reefs undergo a time of dramatic environmental change.

Aquaculture is of growing importance in the global seafood production. The environmental impact of aquaculture will largely depend on the type of environment in which the aquaculture system is placed. Sometimes, due to the abiotic or biotic conditions of the seascape, certain aquaculture systems tend to be placed within or near specific ecosystems, a phenomenon that in this thesis is referred to as aquaculture system - ecosystem links. The exposed ecosystems can be more or less sensitive to the system specific impacts. Some links are known to be widespread and especially hazardous for the subjected ecosystem such as the one between the shrimp aquaculture and the mangrove forest ecosystem. The aim of this thesis was to identify and investigate causes and consequences of other spatial links between aquaculture and ecosystems in the tropical seascape. Two different aquaculture system - ecosystem links were identified by using high resolution satellite maps and coastal habitat maps; the link between sea cage aquaculture and coral reefs, and the one between seaweed farms and seagrass beds. This was followed by interviews with the sea cage- and seaweed farmers to find the drivers behind the farm site selection. Many seaweed farmers actively choose to establish their farms on sea grass beds but sea cage farmers did not consider coral reefs when choosing location for their farms. The investigated environmental consequences of the spatial link between sea cage aquaculture and coral reefs were considerable both on the local coral reef structure, and coral associated bacterial community. Furthermore, coral reef associated fish are used as seedlings and feed on the farms, which likely alter the coral food web and lower the ecosystem resilience. Unregulated use of last resort antibiotics in both fish- and lobster farms were also found to be a wide spread practice within the sea cage aquaculture system, suggesting a high risk for development of antibiotic resistant bacteria. The effects of seaweed farms on seagrass beds were not studied in this thesis but have earlier been shown to be rather substantial within the borders of the farm but less so outside the farm. Further, a nomenclature is presented to facilitate the discussion about production system - ecosystem links, which may also be used to be able to incorporate the landscape level within eco-certifying schemes or environmental risk assessments. Finally - increased awareness of the mechanisms that link specific aquaculture to specific habitats, would improve management practices and increase sustainability of an important and still growing food producing sector - the marine aquaculture. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript.</p>

nÃo hà / A pesca indiscriminada de lagostas vem causando a diminuiÃÃo dos estoques, minimizando a efetividade da pesca artesanal e reduzindo a renda de comunidades pesqueiras, estimulando a ainda mais a sobrepesca e a captura de indivÃduos juvenis. Como alternativa, vem sendo implantadas as marambaias, que sÃo estruturas para fixaÃÃo de microorganismos aquÃticos para a formaÃÃo de cadeia trÃfica, servindo como atrator para espÃcies de interesse comercial. Na praia de Ponta Grossa, IcapuÃ- CE, o uso de marambaias voltadas prioritariamente para a pesca de lagosta partiu de pescadores locais em 2002. Com o sucesso das primeiras pescarias, houve âbloomâ de marambaias instaladas e dificuldade de controle sobre o uso das mesmas. Sobre o litoral cearense ainda sÃo poucas as informaÃÃes sobre o efeito de marambaias para a atraÃÃo de lagostas. Visando dar subsÃdios ao ordenamento de uso dessas estruturas, urge a necessidade de se determinar a efetividade para o aumento da produtividade e avaliar os impactos socioeconÃmicos e ambientais. Marambaias para lagosta sÃo estruturas de madeira com 30 cm de altura da base e 6 m2 de Ãrea. O lanÃamento foi realizado pelos pescadores em profundidades entre 3 e 13 m. Participaram deste estudo 36 pescadores. Foram analisados dados de 484 pescarias nos anos de 2003 (Ano I) a 2005 (Ano III), sendo 280 em profundidades <5 m e 204 em profundidades >5 m. A escolha dos intervalos de profundidade foi arbitrÃria. Estes dados serviram para a determinaÃÃo da captura por unidade de esforÃo (CPUE), do tamanho mÃdio das lagostas e do percentual de lagostas com tamanho comercial. A avaliaÃÃo socioeconÃmica foi realizada pelo cÃlculo do rendimento das pescarias. A avaliaÃÃo do impacto ambiental foi realizada pelo mÃtodo G.U.T.. O comprimento mÃdio das lagostas (Panulirus argus) ficou abaixo do tamanho mÃnimo determinado por lei (13 cm). As CPUEÂs ficaram acima da mÃdia histÃrica do CearÃ, indicando a eficiÃncia destas estruturas para o aumento da produtividade, embora os valores de receita mÃdia por pescador tenham sofrido significativa queda na renda no segundo e terceiro anos, indicando que houve apenas concentraÃÃo do estoque nas pescarias no primeiro ano. No Ano I, os impactos negativos mais significantes foram a sobreexploraÃÃo do estoque e a incidÃncia de lagostas juvenis nas capturas. Os impactos positivos mais significantes foram o incremento da pesca local, a criaÃÃo de novos habitats, o desenvolvimento de tecnologias e o fomento a pesquisa cientÃfica. No Ano III, os impactos negativos mais significantes foram a incidÃncia de lagostas juvenis nas capturas, a reduÃÃo da biomassa de pescado, a sobreexploraÃÃo de estoques pesqueiros e a reduÃÃo da pesca local. Quanto aos impactos positivos, destacam-se a reduÃÃo das pescarias com rede de emalhar e o fomento a pesquisa cientÃfica. Concluise que as marambaias nÃo atuaram de forma sustentÃvel, pois funcionaram apenas como concentradoras de estoque. Recomenda-se que o uso de marambaias deve obedecer a um plano de manejo e respeitar as normativas de proibiÃÃo da captura de juvenis de lagosta. / The indiscriminate lobster fisheries has been causing stock reduction, minimizing the effectiveness of artesian fisheries and reducing the income of fishing communities, stimulating even more the overfisheries and the capture of undersized lobsters. As an alternative, the community has been implanting artificial reefs, which are structures where microorganisms settle forming a feeding chain, therefore serving as an attractor for commercial species. At Ponta Grossa community, Icapuà â CE, the use of artificial reefs exclusively for lobster fishing was an initiative taken by some of the local fishermen in 2002. With the successful result of the first fisheries at the artificial reefs, a fast increase on the number of artificial occurred, what made the control of their use very difficult. So far, there a very few information about the effects of artificial reefs on the lobster fishery at Cearà State. In order to provide information to organize the use of these structures there is an urgent need to determine the real effectiveness of the initiative in terms of increasing fisheries and to evaluate social, economic and environmental impacts. The artificial reefs for lobster are build of wood measuring 30 cm in height and 6 m2 of Ãrea. The launching of the structures was carried through by the fishing in depths between 3 and 13 m. A total of 36 fishermen took part in this study. Data from 484 fishing activities were analyzed during the years of 2003 (year I) to 2005 (year III), being 280 of them in shallow waters (less than 5 m of depth) and 204 in waters deeper than 5m. These depths intervals were chosen arbitrarily. The data were used to determine the amount of lobster captured in relation to the fishery effort (CPUE), the average lobsterâs size and the percentage of lobsters above the legal commercial size. The socio-economic analysis was performed using the profit earned by each fishing activity. The environmental impact was performed by G.U.T. method. The results showed that the average size of captured lobsters (Panulirus argus) was below legal minimum size (13 cm). The amount of lobster captured in relation to the fishery effort was above the historical average of Cearà State, showing the efficiency of these structures to increase productivity, however the values for the average profit per fisherman decreased significantly during the second and third years of the study, suggesting that in the first year occurred just a concentration of lobster stock in the same area. In the first year the most significant negative impacts were the over exploitation of the stocks and the occurrence of juvenile lobster on the catches. The most significant positive impacts were the increase of local fishery, the formation of new habitats, the development of new technologies and the possibility to develop scientific research. In Year III the most significant negative impacts were the presence of juvenile lobsters in the catches, the reduction of fisheries biomass, the over exploitation and the reduction on the amount of local fishery. In relation to positive impacts, the reduction of the fisheries using gill nets and the possibility for scientific research were the most evident. In conclusion, the artificial reefs have not played a sustainable role because the main result was just the concentration of stocks in the same area. The use of artificial reefs should follow a management plan and respect the law restriction on capturing juvenile lobsters.

Submitted by Sandra Pereira (srpereira@ufrrj.br) on 2017-04-04T11:10:45Z No. of bitstreams: 1 2013 - Vin?cius da Rocha Miranda.pdf: 4210864 bytes, checksum: 3c37254eedb367413a77718eae172a75 (MD5) / Made available in DSpace on 2017-04-04T11:10:45Z (GMT). No. of bitstreams: 1 2013 - Vin?cius da Rocha Miranda.pdf: 4210864 bytes, checksum: 3c37254eedb367413a77718eae172a75 (MD5) Previous issue date: 2013-06-26 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior - CAPES / Cold-water coral reefs are of great ecological importance, they can support a great diversity associated with. They can offer a sheltered, three-dimensional, micro-habitat to many species. Studies involving the Brazilian deep-sea coral reefs, and the fauna which composes it, are recent and still scarce. These reefs were studied only in terms of the species of coral which composes it and their distribution in our coast, as the benthic fauna which are associated with this environment. Two projects, CAP-BC and ECOPROF, coordinated by CENPES/PETROBRAS, surveyed the Campos Basin (located at the northeast of Rio de Janeiro) with the objective of studying this environment and the associated fauna. On each project samples of the reef-building corals were collected with a ROV, at depths from 245 to 1100m. Five species of coral were surveyed: Solenosmilia variabilis Duncan, 1873, Lophelia pertusa (Linnaeus, 1758), Enallopsammia rostrata (Portual?s, 1758), Madrepora oculata Linnaeus, 1758 and Errina sp.,and fixed in formalin 10% and sorted at the laboratory. Here in, we present the first, qualitative, results from the polychaetes found in association with the coral reefs in Campos BasinThe specie of Eunice prognatha McIntosh, 1885 were the most abundant, followed by Harmothoe gilchristi (Day, 1960) and Nicon maculata Kimberg, 1866. The majority of polychaetes were found associated to the coral S. variabilis, followed by E. profunda and L. pertusa, both M. oculata and Errina sp. were the corals with less associated polychaetes. Five new species of Polychaeta are reported: Harmothoe sp. (Polynoidae), Pholoides sp. (Sigalionidae), Leocratides sp. (Hesionidae), Euchone sp. (Sabellidae) and Ophryotrocha sp. (Dorvilleidae).Specimens identified as Glycerella magellanica (McIntosh, 1885), Harmothoe gilchristi (Day, 1960), Eunice gracilicirrata (Treadwell, 1922), Eunice prognatha McIntosh, 1885, Pionosyllis procera Hartman, 1965, Haplosyllis ohma (Imajima & Hartman, 1964) and Nicon maculata Kimberg, 1866, are new occurrence for the Brazilian coast. Two other species, Filogranula revizee Nogueira & Abbud, 2009 and Notopygos crinita Grube, 1855had their range of occurrence extended. This is the first study aiming on the polychaetes associated with deep sea corals in the Brazilian waters, further studies should be conducted to better understand the distribution of species described here in, as well as to better understand the polychaete assemblage associated with each species of coral. / Recifes de corais de profundidade possuem uma grande import?ncia ecol?gica, uma vez que podem abrigar uma grande diversidade de esp?cies associadas. Isso ? poss?vel gra?as ? sua conforma??o tridimensional que proporciona uma alta hetereogenidade espacial, criando um ambiente protegido para muitas esp?cies. No Brasil, estudos sobre corais. de profundidade, s?o escassos e recentes. Muitos destes se limitam a descrever as esp?cies de corais encontradas e a sua distribui??o pela costa brasileira assim como organismos bent?nicos associados a eles. Recentemente foram realizados dois projetos coordenados pela CENPES/PETROBRAS, CAP-BC e ECOPROF com objetivo de realizar um levantamento dos recifes de corais de profundidade, bem como das esp?cies associadas a estes, na regi?o da Bacia de Campos (noroeste do estado do Rio de Janeiro). Em cada um desses projetos foi utilizado um ROV para coletar amostras nas profundidades entre 300 e 1100 metros. Cinco esp?cies de corais formadores desse ecossistema foram coletadas: Solenosmilia variabilis Duncan, 1873, Lophelia pertusa (Linnaeus, 1758), Enallopsammia rostrata (Portual?s, 1758), Madrepora oculata Linnaeus, 1758 and Errina sp., cada amostra foi fixada em uma mistura tamponada de formalina (10%), para posterior triagem em laborat?rio. Aqui apresentamos o estudo dos poliquetas associados a estes corais na Bacia de Campos. A esp?cie Eunice prognatha McIntosh, 1885 foi a mais abundante, seguida por Harmothoe gilchristi (Day, 1960) e Nicon maculata Kimberg, 1866. O coral S. variabilis foi o que apresentou o maior n?mero de esp?cies associadas, seguida dos corais E. rostrata e L. pertusa, j? as esp?cies M. oculata e Errina sp. foram os corais com menos esp?cies de poliquetas encontrados. Foram reportadas cinco novas esp?cies de poliquetas Harmothoe sp. (Polynoidae), Pholoides sp. (Sigalionidae), Leocratides sp. (Hesionidae), Euchone sp. (Sabellidae), e Ophryotrocha sp. (Dorvilleidae). O total de oito esp?cies foram registradas pela primeira vez para a costa brasileira: Glycerella magellanica (McIntosh, 1885), Harmothoe gilchristi (Day, 1960), Eunice gracilicirrata (Treadwell, 1922), Eunice prognatha McIntosh, 1885, Pionosyllis procera Hartman, 1965, Haplosyllis ohma (Imajima & Hartman, 1964), e Nicon maculata Kimberg, 1866. Duas outras esp?cies, viii Filogranula revizee Nogueira & Abbud, 2009 e Notopygos crinita Grube, 1855, tiveram suas ?reas de ocorr?ncia ampliadas. Este ? o primeiro estudo focando nos poliquetas associados aos corais de profundidade da costa brasileira. Novos estudos devem ser realizados para melhor compreender a distribui??o das esp?cies descritas neste trabalho, assim como entender as poss?veis associa??es destas com as esp?cies de coral desse ecossistema

This study examined patterns of coral reproduction and recruitment on lagoonal reefs adjacent to Mombasa in Kenya, at latitude 4ºS. Very little detailed research has been done on the reproductive patterns of scleractinian corals on equatorial reefs, where it has been suggested that seasonality and spawning synchrony may break down due to the weak environmental cues that are thought to govern the onset and timing of reproduction. Gametogenic data were collected for three faviid (Echinopora gemmacea, Platygyra daedalea and Leptoria phrygia) and three Acropora species (A. tenuis, A. valida and Acropora sp.1) in the Mombasa Marine National Park and Reserve between April 2003 – May 2005. A further 20 species of Acropora were identified (9 species represented range extensions) and marked to examine intra- and inter-specific spawning synchrony within this genus. In comparison to other regions, the overall pattern of coral reproduction in Kenya was found to be asynchronous, with spawning occurring over 9 months of the year from August – April, with some level of ‘temporal reproductive isolation’ occurring between species in relation to the main lunar month and lunar quarter when spawning occurred. Proximate cues governing the timing of reproduction could not be clearly discerned in Kenya with spawning occurring during both rising and maximum temperatures, during both neap and spring tides and across all lunar phases. Acropora species spawned over a 7-month period between October – April and faviid species over a 5-month period from December - April. The timing of reproduction in Acropora varied both within and among species, with the main release of gametes occurring from January – March when sea surface temperatures were at their summer maximum. Individual species released gametes over 2-5 months. The greatest overlap in spawning Acropora species occurred in February, which coincided with the spawning months of P. daedalea and E. gemmacea and suggests that some degree of multispecific spawning is a characteristic of Kenyan reefs. Within the main spawning period individual Acropora species had their main spawning in different lunar months. Acropora species released gametes in all lunar quarters, with the highest number of colonies and species spawning in the 3rd lunar quarter (i.e. in the 7 nights after full moon). Spawning in the faviids was more synchronised than Acropora species with the majority of faviid corals spawning in the 3rd lunar quarter. Single annual cycles of gametogenesis were recorded in E. gemmacea, A. tenuis, L.phrygia, most colonies of A. valida and Acropora sp.1, and in 84% of P. daedalea colonies. Biannual cycles of gametogenesis were recorded in 16% of P.daedalea colonies, which included two morphotypes identified in the Mombasa lagoon through morphometric and genetic studies. The presence of different oocyte sizes in L.phrygia during gametogenesis suggested that in some colonies there were two slightly overlapping oogenic cycles, which terminated in spawning within 1-2 months of each other. Overlapping oogenic cycles have not previously been recorded in hermaphroditic broadcast spawning corals in the tropics. The findings from Kenya support the hypothesis of protracted breeding seasons and a breakdown of spawning synchrony nearer the equator. It is hypothesised that the high fecundities recorded in faviid and Acropora species in Kenya compared to other regions, may allow reef corals to stagger their reproduction over 2-5 months, without incurring a significant reduction in fertilisation rates. Spat from the Family Pocilloporidae dominated settlement tiles in the Marine National Park and Reserve comprising 93.7% of spat, which contrasts with other tropical reefs where Acroporidae spat dominate. Patterns of settlement of Acroporidae spat generally coincided with the timing and extended spawning season in Acropora species in Kenya. The density and relative composition of coral recruits and juvenile corals on natural substrata recorded during this study were similar to those recorded before the 1997-98 bleaching event. There is no evidence to suggest that Kenya’s reefs have undergone a phase-shift in community structure, and reef recovery is occurring post-bleaching with mean percent hard coral cover currently at 25%. The slow rate of recovery of Kenya’s reefs is likely to reflect the scale of the mortality, source and availability of coral larvae as well as post-settlement processes operating at individual sites. In the medium-term, the recovery of Kenya’s reefs appears to be more strongly dependent on larvae from local reefs.

The present study explored the spatial and temporal demographic trends in oyster population dynamics and their relationships to freshwater inflows and the pathogen Dermo (Perkinsus marinus) on three reefs (Shell, Mad Island, and Sammy?s) in West Matagorda Bay, Texas. The objectives were to design and link three population models that simulate oyster population dynamics and integrate the environmental factors that influence growth, reproduction and settlement of larvae among these three reefs. The following variables were evaluated: relative abundance of oyster spat, submarket- and market-size oysters, average weighted incidence of Dermo and percent Dermo infection (prevalence) in submarket- and market-size oysters and their relationships to environmental variables of salinity, temperature, flow and distance from freshwater sources. Using a 30-month continuous dataset, environmental variables accounted for 36% of the variation in Dermo-related variables among the three reefs, and were also positively correlated with distance from freshwater sources. The relative abundance of spat and dead oysters was related to peaks in freshwater inflows occurring 30 days prior to larval settlement. Using these spatial and temporal relationships among biological and environmental variables, and data from five years of monitoring three reefs in Matagorda Bay, an integrated Stella model was developed that simulated oyster population responses to stochastic environmental changes over a 50-year period. Although the geological and structural complexity of each reef appeared to be similar, the model showed the relationship of growth, spawning and spat set were related to hydrologic variation between different reefs and time periods. The model revealed that up-estuary reefs relied on the distribution of larvae from down-estuary reefs following mortality related to freshwater inflow. The model also indicated that loss of freshwater inflows to down-estuary reefs resulted in higher sustained Dermo infections, thus loss of spawning potential and subsequent distribution of larvae to up-estuary reefs. The three oyster populations in West Matagorda Bay provide spawning connectivity and function as an integrated resource for sustaining all oyster reef populations in this bay system. The model presented in this research provides a basis for understanding the population dynamics of WMB as well as a better understanding of the interaction among the reefs that sustain these populations. The model developed in this investigation provides a basis for developing oyster population models for other bay systems and for future research regarding hydrologic influences on oyster population dynamics.

The purpose of this investigation was to integrate the knowledge and techniques of marine geotechnical engineering, underwater acoustic and optical observation into studying the engineering problems of artificial reefs off south-western coast of Taiwan (Fang-Liau ,Lin-Yang, Yung-An artificial reefs etc.) and the destruction of mooring system on farming cages caused by the interaction of wave-current system. The ultimate goal of this investigation was to understand the scouring activities of loosely and closely spaced artificial reefs; as well as, to evaluate the feasibility of using artificial reefs as deadweight anchoring devices for farming cages at Fang-Liau reef site. The results of this research were as follows: Fang-Liau artificial reef site: The maximum scouring depth can reach as deep as 2.2m around closely distributed reefs at this site. Only a few loosely deployed reefs were buried there, and the scouring depressions around these buried reefs had been filled up completely. To sum up, the behavior of scouring produced by the action of wave, current and typhoon around this site, merely limited to loosely distributed reefs, and the rim of closely distributed reefs. With the scouring time increasing, there were no obvious evidences for the burial of artificial reefs at this site. Lin-Yang artificial reef site: The scouring depressions around part of loosely deployed reefs expand as typhoons attacking at this site. The horizontal range of the scouring depressions can reach 92.3m in length, and parts of the reefs were buried during the process of scouring. Besides, as time went on, part of closely distributed reefs illustrated periodic variations of being buried by sediments with ripple marks, then shown up with evident height, and then buried again. To sum up, the behavior of scouring produced by the action of wave, current and typhoon around this site could cause the complete burial of the reefs. The possible procedures for the burial of reefs in the scouring depression were the actions of backfill of sandy sediments at this site. Yung-An artificial reef site: During summer time, especially with typhoons passed by, surficial sediments at this site were evident with mega ripple marks. The effects of scouring at this site were prominent than those at Fang-Liau reef site. The textures of surficial sediments were the major factor which induced this difference. Based on the considerations of safety of sliding, bearing capacity and overturning, the usage of artificial reefs as anchoring devices for farming cages could not satisfy the basic engineering requirements under the action of extreme wave and current. This research suggested the usage of cubical concrete block with shear keys for anchoring devices on farming cages. The minimum buoyant weight of this block should reach 28.8 to 38.7ton. The problem regarding construction and deployment techniques of this block need further considerations.

The present study explored the spatial and temporal demographic trends in oyster population dynamics and their relationships to freshwater inflows and the pathogen Dermo (Perkinsus marinus) on three reefs (Shell, Mad Island, and Sammy?s) in West Matagorda Bay, Texas. The objectives were to design and link three population models that simulate oyster population dynamics and integrate the environmental factors that influence growth, reproduction and settlement of larvae among these three reefs. The following variables were evaluated: relative abundance of oyster spat, submarket- and market-size oysters, average weighted incidence of Dermo and percent Dermo infection (prevalence) in submarket- and market-size oysters and their relationships to environmental variables of salinity, temperature, flow and distance from freshwater sources. Using a 30-month continuous dataset, environmental variables accounted for 36% of the variation in Dermo-related variables among the three reefs, and were also positively correlated with distance from freshwater sources. The relative abundance of spat and dead oysters was related to peaks in freshwater inflows occurring 30 days prior to larval settlement. Using these spatial and temporal relationships among biological and environmental variables, and data from five years of monitoring three reefs in Matagorda Bay, an integrated Stella model was developed that simulated oyster population responses to stochastic environmental changes over a 50-year period. Although the geological and structural complexity of each reef appeared to be similar, the model showed the relationship of growth, spawning and spat set were related to hydrologic variation between different reefs and time periods. The model revealed that up-estuary reefs relied on the distribution of larvae from down-estuary reefs following mortality related to freshwater inflow. The model also indicated that loss of freshwater inflows to down-estuary reefs resulted in higher sustained Dermo infections, thus loss of spawning potential and subsequent distribution of larvae to up-estuary reefs. The three oyster populations in West Matagorda Bay provide spawning connectivity and function as an integrated resource for sustaining all oyster reef populations in this bay system. The model presented in this research provides a basis for understanding the population dynamics of WMB as well as a better understanding of the interaction among the reefs that sustain these populations. The model developed in this investigation provides a basis for developing oyster population models for other bay systems and for future research regarding hydrologic influences on oyster population dynamics.