Thesis (M.S.) in Oceanography--University of Maine, 2004. / Includes vita. Includes bibliographical references (leaves 35-39).

Five line transect surveys for marine mammals were conducted offshore of mainland Ecuador and the Galápagos Islands from 2008-2011. These data were used in conjunction with MODIS (Moderate Resolution Imaging Spectroradiometer) observations of ocean color and sea surface temperature (SST) to assess spatial and temporal relationships between surface oceanographic features and cetacean distribution within the Eastern Equatorial Pacific (EEP). Results from this study indicated that oceanographic processes affected cetacean distribution on inter-annual, seasonal, and weekly to monthly time scales. The spatial scales on which these processes affect cetacean distribution are small, the smallest associations being found at 4 km2 bin sizes, as well as 9 km2 and 36 km2 bin sizes. By utilizing ocean color and SST data from the MODIS instrument and analyzing variability of these parameters in addition to average concentration, cetacean distribution within the region was related to the locations of frontal boundaries. Cetaceans were grouped into two categories based on the trophic level and relative depths at which they forage. Cetaceans feeding nearer the ocean surface and lower on the trophic scale were generally found in cooler waters of higher average chlorophyll concentration and elevated variability. Those cetaceans feeding higher on the trophic scale and lower in the water column (mesopelagic and bathypelagic depths) were sighted within relatively warmer waters of reduced temperature variability near areas of high chlorophyll variability (though less variable and lower in average chlorophyll than surface feeding cetaceans), with little spatial and temporal lag between peak surface chlorophyll concentration and cetacean presence. The EEP is a biologically productive region with many competing economic and environmental interests. Ecuador is home to one of the largest artisenal fishing fleets in South America, and entanglement of various cetacean species has been a known issue for several decades (Félix and Haase, 2006; Castro and Rosero, 2010). Seismic exploration, shipping, and tourism are also found on the busy waterways surrounding both mainland Ecuador and the archipelago. The results of this study provide additional insight into the mesoscale processes affecting the distribution and habitat use of cetaceans within the EEP and South American waters and to support ongoing ecosystem management efforts.

Thesis (Ph. D.)--University of Rhode Island, 2006. / Typescript. Includes bibliographical references (leaves 213-226).

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Accurate retrieval of water-leaving reflectance from satellite-sensed signal is decisive for ocean color applications, because water-leaving radiance only account for less than 10% of satellite-sensed radiance. The standard atmospheric correction algorithm relies on black pixel assumption, which assumes negligible water-radiance reflectance at the near-infrared (NIR) bands. The standard NIR-based algorithm generally works well for waters where the NIR water-leaving radiance is negligible or can be properly accounted for. However, the black pixel assumption does not hold over turbid waters, which results in biased retrievals of remote sensing reflectance (Rrs). Therefore, this study aimed to improve atmospheric correction over turbid waters. Based on Sentinel-3, two ways to cope with nonzero NIR water-leaving reflectance were explored. First, this study proposed to use artificial neural networks to estimate and correct NIR water-leaving reflectance at TOA (ANN-NIR algorithm). The rationale of it is that hydrosol optical properties are much simpler at NIR spectral region, where pure water absorptions are the dominant factor. The proposed algorithm outperformed the standard NIR-based algorithm over highly turbid waters. Considering results demonstrated in this study, ANN-NIR algorithm should be useful for ocean color sensors with less than two SWIR bands. Second, this study adapted the SWIR-based algorithm for atmospheric correction of Sentinel-3 OLCI by coupling with the two SWIR bands of SLSTR. Three SWIR band combinations were tested: 1020 and 1613, 1020 and 2256, and 1613 and 2256 nm. The SWIR-based algorithm obviously performed better than NIR-based algorithm over highly turbid waters, while the NIR-based is still preferred for clear to moderately turbid waters. The SWIR band of 1020 nm combined with either SWIR band of 1613 or 2256 nm is recommended for the SWIR-based algorithm except for extremely turbid waters, because the band of 1020 nm has better radiometric performance. Over extremely turbid waters, the band combination of 1613 and 2256 nm should be used, since the water-leaving reflectance is still non-negligible at the band of 1020 nm over these waters. Considering atmospheric correction performance obtained by the NIR- and SWIR-based algorithms, the NIR-based and SWIR-based algorithm are practically applied over clear and turbid waters, respectively. This study revisited the effectiveness of the turbidity index for the current NIR-SWIR switching scheme. The turbidity index calculated from aerosol reflectance varies from 0.7 to 2.2, which is not close to one as expected. In addition to water-leaving reflectance, its value also depends on the spectral shape of aerosol reflectance, which varies with aerosol size distributions, aerosol optical thickness, relative humidity and observing geometries. To address this problem, this study proposed a framework to determine switching threshold for the NIR-SWIR algorithm. An Rrs threshold was determined for each MODIS land band centered at 469, 555, 645 and 859 nm, respectively. Their thresholds are 0.009, 0.016, 0.009 and 0.0006 sr-1, respectively. However, Rrs(469) tends to select SWIR-based algorithm wrongly for clear waters, while NIR-SWIR switching based on Rrs(859) tends to produce patchy patterns. By contrast, NIR-SWIR switching based on Rrs(555) with a threshold of 0.016 sr-1 and Rrs(645) with a threshold of 0.009 sr-1 produced reasonable results. Considering the contrasted estuarine and coastal waters, combined applications of NIR- and SWIR-based algorithm with the switching scheme should be useful for these waters. This study will contribute to better ocean color atmospheric corrections over turbid waters. Atmospheric correction algorithms based on black pixel assumption have been implemented and tested in this study, while combined applications of NIR-based and SWIR-based algorithms are recommended over contrasted transitional waters. However, further studies would still be required to further improve and validate atmospheric correction algorithms over turbid waters.

In situ measurements were used to study the bio-optical properties of marine waters within the Gulf of Paria (GOP, Venezuela) and in the Southeastern Caribbean Sea (SEC) as they are affected by the seasonal discharge of the Orinoco River plume. The main purpose of this study was to determine the impact of colored dissolved organic matter (CDOM) (also known as Gelbstoff), phytoplankton, and total suspended matter (TSM) in the color of the Orinoco River plume. This information is essential for regional ocean color algorithms development. Salinity and silica values indicate that the GOP and SEC waters were under the influence of the Orinoco River plume during both seasons. This riverine influence resulted in high values of Gelbstoff absorption, αg(λ), which contributed to up to 90% of the total absorption at 440 nm in both the GOP and SEC regardless of the season. Phytoplankton absorption contributions were normally around 5%, but during the dry season these values reached 20% in the SEC. Ratios of αg(440) to αph(440) were extremely large, with most of the values ranging from 10 to 50. Due to the strong absorption by Gelbstoff, light at the blue wavelengths (412 nm, 440 nm and 490 nm) was attenuated to 1% of the subsurface irradiance in the first 5 m of the water column within the GOP, and in the first 10 m of the water column in the SEC. Furthermore, the absorption by Gelbstoff significantly decreased the water leaving radiance (Lw(λ)) in the blue wavelengths along the Orinoco River plume. As αg(λ) relatively decreased from the GOP to the SEC (X≈1.6 m-1 and X≈ 0.9 m-1, respectively), a shift in the maximum peak of Rrs(λ) spectra (Rrsmax(λ)), towards shorter wavelengths (from ~ 580 nm to ~500 nm) was observed. Similar to Gelbstoff, concentrations of TSM normally decreased from the stations near the Delta to the stations in the SEC. The impact of TSM on the color of the Orinoco plume was represented by a reduction in the magnitude of Rrsmax(λ) of ~50% going from the waters near the Orinoco delta to the SEC, indistinctively of the season.

As human populations increase along coastal watersheds, the understanding and monitoring of Harmful Algal Blooms (or red tides) is an increasingly important issue. A consistent method for accurately detecting red tides using satellite measurements would bring tremendous societal benefits to resource managers, the scientific community and to the public as well. In the West Florida Shelf, blooms of the toxic dinoflagelate Karenia brevis are responsible for massive red tides causing fish kills, massive die-offs of marine mammals, shellfish poisoning, and acute respiratory irritation in humans. In this work, for the first time a long-term dataset (2002~2006) the MODerate Resolution Imaging Spectroradiometer (MODIS) is compared (i.e., matched-up) to an extensive data set of in situ cell counts of K. brevis; provided by the Florida Fish and Wildlife Conservation Commission's Fish and Wildlife Research Institute. The pairing of remote sensing data with near-coincident field measurements of cell abundance was successfully used to derive the basis for the development of an alternative ocean color based algorithm for detecting the optical signatures associated with blooms of K. brevis in waters of the West coast of Florida. Conclusions are geographically limited to the Central West Florida Shelf during the boreal Summer-Fall (i.e., the K. brevis blooming season). The new simpler Empirical approach is compared with other two more complicated published techniques. Their potential is verified and uncertainties involved in the identification of blooms of K. brevis are presented. The results shown here indicate that the operational NOAA method for detecting red tides in the Gulf of Mexico (Stumpf et al., 2003; Tomlinson et al., 2004) performs less accurately than the other two algorithms at identifying K. brevis blooms. The sensitivity and specificity of the Bio-optical (Cannizzaro, 2004; Cannizzaro et al., 2008) and Empirical algorithms are simultaneously maximized with an optimization procedure. The combined use of these two optimized algorithms in sequence provides another new monitoring tool with improved accuracy at detecting K. brevis of blooms. The ability of this Hybrid scheme ranges about 80% for both sensitivity and specificity; and the capability at predicting a correct red tides is 70%, and ~85% for non-blooms conditions. The spatial and temporal knowledge of K. brevis blooms can improve the direction of field monitoring to areas that should receive special attention, allowing better understanding of the red tide phenomenon by the scientific community. The relevant agencies can also develop more appropriate mitigation action plans, and public health guidance can be improved with the enhancement of sustainable costal management strategies.

SeaWiFS was collecting ocean color data since 1997. This means chlorophyll-a data for more than ten years. Since, SeaWiFS Chl-a data is validated for Black Sea this data set can be used for analysis. Nevertheless, the data is not gap free due to cloud effect. One of the main objectives of this work is to obtain a gap free, complete Chl-a data set for the Black Sea. For this purpose DINEOF method will be used.

The variability of water-column absorption due to colored dissolved organic matter (CDOM) and phytoplankton in coral reef regions is the focus of this study. Hydrographic and CDOM absorption measurements made on the Bahamas Banks and in Exuma Sound during the spring of 1999 and 2000 showed that values of salinity and CDOM absorption at 440nm were higher on the banks (37.18 psu, 0.06 m^-1), compared to Exuma Sound (37.04 psu, 0.03 m^-1). Spatial patterns of CDOM absorption in Exuma Sound revealed that plumes of CDOM-rich water flow into Exuma Sound from the surrounding banks. To examine absorption variability in reef regions throughout the world, a thirteen-year time series of satellite-derived estimates of water-column absorption due to CDOM and phytoplankton were created from Sea-viewing Wide Field-of-view Sensor (SeaWiFS) and Moderate Resolution Imaging Spectroradiometer (MODIS) data. Time series data extracted adjacent to coral reef regions showed that variability in absorption depends on oceanographic conditions such as circulation patterns and winds as well as proximity to sources of light-absorbing materials that enter the water column, such as from terrestrial runoff. Waters near reef regions are generally clear, exhibiting a lower "baseline" level of CDOM absorption of approximately 0.01 m^-1 at 443nm. The main differences between regions lie in the periods during the year when increased levels of absorption are observed, which can be triggered by inputs of terrestrially-derived material, as in the Great Barrier Reef lagoon, or wind-driven upwelling as in the Andaman Sea and eastern Pacific Ocean near Panama. The lowest CDOM absorption levels found were approximately 0.003 m^-1 at 443nm near the islands of Palau and Yap, which are removed from sources of colored materials. The highest absorption levels near reefs were associated with wind-driven upwelling during the northeast monsoon on the Andaman coast of Thailand where values of CDOM absorption at 443nm reached 0.7 m^-1. Simulations of the underwater light field based on satellite-derived absorption values revealed that changes in absorption have a strong influence on light levels to which corals are exposed, particularly in the ultraviolet region of the spectrum, where CDOM is the primary absorber of light. Episodes of coral bleaching during 1998 and 2002 were found to be associated with elevated seawater temperatures as well as decreased levels of CDOM absorption, indicating that corals were exposed to light stress along with thermal stress during periods of bleaching.