Thesis (MTech (Oceanography))--Cape Peninsula University of Technology, 2009 / A collaborative study between Marine and Coastal Management (MCM) and the Oceanographic Research Institute (ORI) was initiated in March 2001 to investigate the physical oceanography of Sodwana Bay, South Africa, and the affects on coral communities resident to the area. A bottom-mounted Acoustic Doppler Current Profiler (ADCP) and three Underwater Temperature Recorders (UTR) were deployed to complement the long-term monitoring UTR deployed on Nine-Mile Reef (NMR) in 1994. The study was terminated after 30 months, whereby all instruments were removed except for the long-term monitoring UTR.

O objetivo deste trabalho foi caracterizar os hábitats bênticos do Banco de Abrolhos e comparar dois tipos de recife no local: rasos e mesofóticos. Foram feitas filmagens com um ROV em 20 estações ao redor do Banco para um estudo em mesoescala. Para a comparação dos recifes, foram feitas filmagens nos recifes rasos de Sebastião Gomes e Parcel dos Abrolhos e na área mesofótica de Itacolomis. As imagens foram analisadas através do programa CPCe®. Foram calculadas a abundância total das espécies por área e por estação e os índices de diversidade e equitabilidade. As estações foram comparadas através do cálculo da similaridade de Bray Curtis e de uma análise fatorial de correspondência (AFC). Nas estações ao redor do Banco foi constatado uma extensa área de rodolitos na parte externa e áreas de fundo inconsolidado na região mais interna. Os bancos de rodolito ocorreram sempre em profundidades maiores que 30 metros. Nos recifes rasos houve uma dominância de macroalgas (ca. 23%), octocorais (ca. 16%) e zoantídeos (ca. 14%), sendo sempre mais diversos que os bancos de rodolitos. O recife mesofótico de Itacolomis teve cobertura predominantemente rodolítica (ca. 48%). Dentre os outros organismos encontrados, os mais abundantes foram macroalgas (ca. 17%) e esponjas (ca. 4%). Abrolhos é o ecossistema mais rico do Atlântico Sul e se encontra severamente ameaçado. Pouco se conhece ainda sobre seu funcionamento e sobre suas áreas mais profundas. Estudos como este são necessários para entender e conservar o Banco de Abrolhos. / The benthic habitats of Abrolhos Bank were characterized and two kind of reefs were compared: shallow and mesophotic. Video footage was taken in 20 sites on the Bank using an ROV. Other footages were taken on the shallow reefs Sebastião Gomes and Parcel dos Abrolhos and at the mesophotic Itacolomis to make the comparison. Still images from videos were analyzed using the CPCe® program. We calculated the total abundance, diversity and equitability of epibenthic species. We also compared the sites using the similarity index of Bray Curtis and a correspondence analysis (CFA). Large rhodolith beds were found on the Bank edges, with inner sites composed mainly by soft bottoms. Rhodolith beds were always found at depths greater than 30 meters. At the shallow reefs macroalgae (ca. 23%), octocorals (ca. 16%) and zoanthids (ca. 14%) dominated. These sites presented higher epibenthic diversity than rhodolith beds. Rhodoliths dominated in the mesophotic area of Itacolomis reef with ca. 48% coverage. Other abundant organisms were macroalgae (ca. 17%) and sponges (ca. 4%). Abrolhos is the richest ecosystem in the South Atlantic ocean and it is severely threatened. There is still little information available, specially for the deeper zone. More researches like the one presented herein are very important and necessary to understand and conserve Abrolhos Bank.

O objetivo deste trabalho foi caracterizar os hábitats bênticos do Banco de Abrolhos e comparar dois tipos de recife no local: rasos e mesofóticos. Foram feitas filmagens com um ROV em 20 estações ao redor do Banco para um estudo em mesoescala. Para a comparação dos recifes, foram feitas filmagens nos recifes rasos de Sebastião Gomes e Parcel dos Abrolhos e na área mesofótica de Itacolomis. As imagens foram analisadas através do programa CPCe®. Foram calculadas a abundância total das espécies por área e por estação e os índices de diversidade e equitabilidade. As estações foram comparadas através do cálculo da similaridade de Bray Curtis e de uma análise fatorial de correspondência (AFC). Nas estações ao redor do Banco foi constatado uma extensa área de rodolitos na parte externa e áreas de fundo inconsolidado na região mais interna. Os bancos de rodolito ocorreram sempre em profundidades maiores que 30 metros. Nos recifes rasos houve uma dominância de macroalgas (ca. 23%), octocorais (ca. 16%) e zoantídeos (ca. 14%), sendo sempre mais diversos que os bancos de rodolitos. O recife mesofótico de Itacolomis teve cobertura predominantemente rodolítica (ca. 48%). Dentre os outros organismos encontrados, os mais abundantes foram macroalgas (ca. 17%) e esponjas (ca. 4%). Abrolhos é o ecossistema mais rico do Atlântico Sul e se encontra severamente ameaçado. Pouco se conhece ainda sobre seu funcionamento e sobre suas áreas mais profundas. Estudos como este são necessários para entender e conservar o Banco de Abrolhos. / The benthic habitats of Abrolhos Bank were characterized and two kind of reefs were compared: shallow and mesophotic. Video footage was taken in 20 sites on the Bank using an ROV. Other footages were taken on the shallow reefs Sebastião Gomes and Parcel dos Abrolhos and at the mesophotic Itacolomis to make the comparison. Still images from videos were analyzed using the CPCe® program. We calculated the total abundance, diversity and equitability of epibenthic species. We also compared the sites using the similarity index of Bray Curtis and a correspondence analysis (CFA). Large rhodolith beds were found on the Bank edges, with inner sites composed mainly by soft bottoms. Rhodolith beds were always found at depths greater than 30 meters. At the shallow reefs macroalgae (ca. 23%), octocorals (ca. 16%) and zoanthids (ca. 14%) dominated. These sites presented higher epibenthic diversity than rhodolith beds. Rhodoliths dominated in the mesophotic area of Itacolomis reef with ca. 48% coverage. Other abundant organisms were macroalgae (ca. 17%) and sponges (ca. 4%). Abrolhos is the richest ecosystem in the South Atlantic ocean and it is severely threatened. There is still little information available, specially for the deeper zone. More researches like the one presented herein are very important and necessary to understand and conserve Abrolhos Bank.

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>

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

Thesis (Ph.D)--Physics, Georgia Institute of Technology, 2009. / Committee Chair: Weiss, Howard; Committee Member: Cvitanovic , Predrag; Committee Member: Goldman, Daniel; Committee Member: Schatz, Michael; Committee Member: Wiesenfeld, Kurt. Part of the SMARTech Electronic Thesis and Dissertation Collection.

Thesis (Ph. D.)--University of Texas at Austin, 2001. / Vita. Includes bibliographical references (leaves 173-201). Available also in a digital version from Dissertation Abstracts.

Coral reefs are greatly impacted by the physical characteristics of the water surrounding them. Incidence and severity of mass coral bleaching and mortality events are increasing worldwide due primarily to increased water temperature, but also in response to other stressors. This decline in reef health demands clearer understanding of the compounding effects of multiple stressors, as well as widespread assessment of coral reef health in near-real time. Satellites offer a means by which some of the physical stressors on coral reefs can be measured. The synoptic spatial coverage and high repeat sampling frequency of such instruments allow for a quantity of data unattainable by in situ measurements. Unfortunately, errors in cloudmasking algorithms contaminate satellite derived sea surface temperature (SST) measurements, especially during anomalously cold events. Similarly, benthic interference of satellite-derived reflectance signals has resulted in large errors in derivations of water quality or clarity in coral reef environments. This work provides solutions to these issues for the coral reef environments of the Florida Keys. Specifically, improved SST cloudmasking algorithms were developed for both Advanced Very High Resolution Radiometer (AVHRR; Appendix A) and Moderate Resolution Imaging Spectroradiometer (MODIS) data (Appendix B). Both of these improved algorithms were used to reveal the extent and severity of a January 2010 cold event that resulted in widespread mortality of Florida Keys corals. Applied to SST data from 2010, the improved MODIS cloudmasking algorithm also showed improved quantity of SST retrievals with minimal sacrifice in data quality. Two separate algorithms to derive water clarity from MODIS measurements of optically shallow waters were developed and validated, one focusing on the diffuse downwelling attenuation coefficient (Kd, m-1) in visible bands (Appendix C), the other on Kd in the ultraviolet (Appendix D). The former utilized a semi-analytical approach to remove bottom influence, modified from an existing algorithm. The latter relied on empirical relationships between an extensive in situ training dataset and variations in MODIS-derived spectral shape, determined using a stepwise principal components regression. Both of these algorithms showed satisfactory validation statistics, and were used to elucidate spatiotemporal patterns of water clarity in the Florida Keys. Finally, an approach was developed to use Landsat data to detect concurrent MODIS-derived reflectance anomalies with over 90% accuracy (Appendix E). Application of this approach to historical Landsat data allowed for long-term, synoptic assessment of the water environment of the Florida Keys ecosystem. Using this approach, shifts in seagrass density, turbidity increases, black water events, and phytoplankton blooms were detected using Landsat data and corroborated with known environmental events. Many of these satellite data products were combined with in situ reports of coral bleaching to determine the specific environmental parameters individually and synergistically contributing to coral bleaching. As such, SST and visible light penetration were found to be parsimoniously explaining variance in bleaching intensity, as were the interactions between SST, wind and UV penetration. These relationships were subsequently used to create a predictive model for coral bleaching via canonical analysis of principal coordinates. Leave-one-out-cross-validation indicated that this model predicted `severe bleaching' and `no bleaching' conditions with 64% and 60% classification success, respectively, nearly 3 times greater than that predicted by chance. This model also showed improvement over similar models created using only temperature data, further indicating that satellite assessment of coral bleaching based only on SST data can be improved with other environmental data. Future work should further supplement the environmental parameters considered in this research with databases of other coral stressors, as well as improved quantification of the temperature at the depth of corals, in order to gain a more complete understanding of coral bleaching in response to environmental stress. Overall, this dissertation presents five new algorithms to the field of satellite oceanography research. Although validated primarily in the Florida Keys region, most of these algorithms should be directly applicable for use in other coastal environments. Identification of the specific environmental factors contributing to coral bleaching enhances understanding of the interplay between multiple causes of reef decline, while the predictive model for coral bleaching may provide researchers and managers with widespread, near real-time assessments of coral reef health.

The tropical seascape is herein defined as a landscape made up of five ecosystems: coastal terrestrial forests, mangrove forests, seagrass beds, coral reefs and the deep sea. Previous studies have shown that men and women use the tropical seascape in different ways. If the seascape was to change as a result of anthropogenic climate change, then men and women could potentially be affected differently by those changes. The seascape is particularly vulnerable to the predicted rise in sea-level and ocean warming, but the coastal terrestrial forests and mangrove forests are in addition vulnerable to the increased storms and hurricanes a warmer climate is predicted to lead to. While men and women utilizes these ecosystems in many different ways, this study found, based on the literature reviewed, that in a worst-case scenario all parts of the seascape could potentially be destroyed and none of the activities performed there today could be performed in the future. The deep sea would not be destroyed, but the fish living there would move to higher latitudes and deeper waters, effectively ending the fishing practices in the tropical waters. To save the tropical seascape anthropogenic climate change would have to stop on a global scale, since the problem cannot be solved on a local or regional level.