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Coastal and ocean acidification can alter ocean biogeochemistry, with ecological consequences that may result in economic and cultural losses. Yet few time series and high resolution spatial and temporal measurements exist to track the existence and movement of water low in pH and/or carbonate saturation. Past acidification monitoring efforts have either low spatial resolution (mooring) or high cost and low temporal and spatial resolution (research cruises). We developed the first integrated glider platform and sensor system for sampling pH throughout the water column of the coastal ocean. A deep ISFET (Ion Sensitive Field Effect Transistor)-based pH sensor system was modified and integrated into a Slocum glider, tank tested in natural seawater to determine sensor conditioning time under different scenarios, and validated in situ during deployments in the U.S. Northeast Shelf (NES). Comparative results between glider pH and pH measured spectrophotometrically from discrete seawater samples indicate that the glider pH sensor is capable of accuracy of 0.011 pH units or better for several weeks throughout the water column in the coastal ocean, with a precision of 0.005 pH units or better. Furthermore, simultaneous measurements from multiple sensors on the same glider enabled salinity-based estimates of total alkalinity (AT) and aragonite saturation state (ΩArag). During the Spring 2018 Mid-Atlantic deployment, glider pH and derived AT/ ΩArag data along the cross-shelf transect revealed higher pH and ΩArag associated with the depth of chlorophyll and oxygen maxima and a warmer, saltier water mass. Lowest pH and ΩArag occurred in bottom waters of the middle shelf and slope, and nearshore following a period of heavy precipitation. Biofouling was revealed to be the primary limitation of this sensor during a summer deployment, whereby offsets in pH and AT increased dramatically. Advances in anti-fouling coatings and the ability to routinely clean and swap out sensors can address this challenge. The data presented here demonstrate the ability for gliders to routinely provide high resolution water column data on regional scales that can be applied to acidification monitoring efforts in other coastal regions.

With our marine ecosystems under threat from climate change, there is an urgent need to continuously monitor marine conditions. One key indicator is the dissolved oxygen level, but existing sensors are limited by size and costs that preclude widespread non-intrusive monitoring. This work reports a new dual-gate design based on organic electrochemical transistors (OECTs) to track dissolved oxygen concentration in seawater, a highly challenging matrix owing to its high ionic strength and multitude of chemical interferents. We present the novel operating principle, by deriving the channel conductance with respect to potentials on the two gates. The sensor achieved a detection limit of 0.5 ppm dissolved oxygen concentration in seawater. The device demonstrated reliable operation over five days and was capable of monitoring oxygenation changes arising from the photosynthesis cycles of saltwater macro-algae.

Coastal and ocean acidification can alter ocean biogeochemistry, with ecological consequences that may result in economic and cultural losses. Yet few time series and high-resolution measurements exist to track the existence and movement of water low in pH and/or carbonate saturation. Past acidification monitoring efforts have either low spatial resolution (mooring) or high cost and low temporal and spatial resolution (research cruises). Therefore, there is a critical need to deploy new, cost-effective technologies that can routinely provide high resolution water column data on regional scales in our coastal ocean. We developed the first integrated glider platform and sensor system for sampling pH in the water column of the coastal ocean. A Deep-Sea ISFET (Ion Sensitive Field Effect Transistor) pH sensor system was modified and integrated into a Slocum G2 glider and tested during a deployment in the Mid-Atlantic Bight. Measurements of pH exhibited a time lag that shifted during the deployment, but shifts were applied to correct pH. Glider pH and spectrophotometric pH measured in discrete water samples were in good agreement for some comparisons but not others, and those offsets were likely the result of delayed or incomplete conditioning (at deployment start) or mismatches due to water sampling techniques. Glider pH data along the cross-shelf transect revealed higher pH associated with the depth of chlorophyll and oxygen maximums and a warmer, saltier water mass. Lower pH occurred in bottom waters of the middle shelf and slope, and nearshore following a period of heavy precipitation. These results demonstrate the application of glider-based acidification monitoring in other coastal regions, providing the foundation of what could become a national acidification monitoring network.

The biodiversity and high productivity of coastal terrestrial and aquatic habitats are the foundation for important benefits to human societies around the world. These globally distributed habitats need frequent and broad systematic assessments, but field surveys only cover a small fraction of these areas. Satellite-based sensors can repeatedly record the visible and near-infrared reflectance spectra that contain the absorption, scattering, and fluorescence signatures of functional phytoplankton groups, colored dissolved matter, and particulate matter near the surface ocean, and of biologically structured habitats (floating and emergent vegetation, benthic habitats like coral, seagrass, and algae). These measures can be incorporated into Essential Biodiversity Variables (EBVs), including the distribution, abundance, and traits of groups of species populations, and used to evaluate habitat fragmentation. However, current and planned satellites are not designed to observe the EBVs that change rapidly with extreme tides, salinity, temperatures, storms, pollution, or physical habitat destruction over scales relevant to human activity. Making these observations requires a new generation of satellite sensors able to sample with these combined characteristics: (1) spatial resolution on the order of 30 to 100-m pixels or smaller; (2) spectral resolution on the order of 5 nm in the visible and 10 nm in the short-wave infrared spectrum (or at least two or more bands at 1,030, 1,240, 1,630, 2,125, and/or 2,260 nm) for atmospheric correction and aquatic and vegetation assessments; (3) radiometric quality with signal to noise ratios (SNR) above 800 (relative to signal levels typical of the open ocean), 14-bit digitization, absolute radiometric calibration temporal resolution of hours to days. We refer to these combined specifications as H4 imaging. Enabling H4 imaging is vital for the conservation and management of global biodiversity and ecosystem services, including food provisioning and water security. An agile satellite in a 3-d repeat low-Earth orbit could sample 30-km swath images of several hundred coastal habitats daily. Nine H4 satellites would provide weekly coverage of global coastal zones. Such satellite constellations are now feasible and are used in various applications.

Requirements for understanding the relationships between ocean color and suspended and dissolved materials within the water column, and a rapidly emerging photonics and materials technology base for performing optical based analytical techniques have generated a diverse offering of commercial sensors and research prototypes that perform optical measurements in water. Through inversion, these tools are now being used to determine a diverse set of related biogeochemical and physical parameters. Techniques engaged include measurement of the solar radiance distribution, absorption, scattering, stimulated fluorescence, flow cytometry, and various spectroscopy methods. Selective membranes and other techniques for material isolation further enhance specificity, leading to sensors for measurement of dissolved oxygen, methane, carbon dioxide, common nutrients and a variety of other parameters. Scientists are using these measurements to infer information related to an increasing set of parameters and wide range of applications over relevant scales in space and time.

The pigment absorption peak in the red waveband observed in phytoplankton and particulate absorption spectra is primarily associated with chlorophyll- a and exhibits much lower pigment packaging compared to the blue peak. The minor contributions to the signature by accessory pigments can be largely removed by computing the line height absorption at 676 nm above a linear background between approximately 650 nm and 715 nm. The line height determination is also effective in removing the contributions to total or particulate absorption by colored dissolved organic matter and non-algal particles, and is relatively independent of the effects of biofouling. The line height absorption is shown to be significantly related to the extracted chlorophyll concentration over a large range of natural optical regimes and diverse phytoplankton cultures. Unlike the in situ fluorometric method for estimating chlorophyll, the absorption line height is not sensitive to incident irradiance, in particular non-photochemical quenching. The combination of the two methods provides a combination of robust phytoplankton biomass estimates, pigment based taxonomic information and a means to estimate the photosynthetic parameter, E K , the irradiance at which photosynthesis transitions from light limitation to light saturation.

Schistosomiasis affects millions of people in developing countries and is responsible for more than 200,000 deaths annually. Because of toxicity and limited spectrum of activity of alternatives, there is effectively only one drug, praziquantel, available for its treatment. Recent data suggest that drug resistance could soon be a problem. There is therefore the need to identify new drug targets and develop drugs for the treatment of schistosomiasis. Analysis of the Schistosoma mansoni genome sequence for proteins involved in detoxification processes found that it encodes a single cytochrome P450 (CYP450) gene. Here we report that the 1452 bp open reading frame has a characteristic heme-binding region in its catalytic domain with a conserved heme ligating cysteine, a hydrophobic leader sequence present as the membrane interacting region, and overall structural conservation. The highest sequence identity to human CYP450s is 22%. Double stranded RNA (dsRNA) silencing of S. mansoni (Sm)CYP450 in schistosomula results in worm death. Treating larval or adult worms with antifungal azole CYP450 inhibitors results in worm death at low micromolar concentrations. In addition, combinations of SmCYP450-specific dsRNA and miconazole show additive schistosomicidal effects supporting the hypothesis that SmCYP450 is the target of miconazole. Treatment of developing S. mansoni eggs with miconazole results in a dose dependent arrest in embryonic development. Our results indicate that SmCYP450 is essential for worm survival and egg development and validates it as a novel drug target. Preliminary structure-activity relationship suggests that the 1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethan-1-ol moiety of miconazole is necessary for activity and that miconazole activity and selectivity could be improved by rational drug design., Author Summary Over 600 million people in endemic countries are at risk of contracting schistosomiasis, which results in over 200,000 deaths each year and significant illness to most people that are infected. There are concerns that the drug widely used for the treatment of schistosomiasis, praziquantel, may be losing efficacy due to evolution of drug resistant worms. Since the disease mainly affects the poor in developing countries, pharmaceutical companies have little interest in developing new drugs and none are currently being tested. In this paper we focus on a novel parasite protein, cytochrome P450, which we propose to be a new drug target. Worms are unusual in having only one cytochrome P450 gene; humans have 57 cytochrome P450 genes. By using reverse genetic and chemical approaches we found that the schistosome cytochrome P450 is essential for worm survival and egg development and, therefore, is an essential and druggable target. Drugs that target fungal cytochrome P450s and are already in use for treating several human diseases were identified as potential hits for further development for schistosomiasis treatment.

The biological and physical processes contributing to planktonic thin layer dynamics were examined in a multidisciplinary study conducted in East Sound, Washington, USA between June 10 and June 25, 1998. The temporal and spatial scales characteristic of thin layers were determined using a nested sampling strategy utilizing 4 major types of platforms: (1) an array of 3 moored acoustical instrument packages and 2 moored optical instrument packages that recorded distributions and inten- sities of thin layers; (2) additional stationary instrumentation deployed outside the array comprised of meteorological stations, wave-tide gauges, and thermistor chains; (3) a research vessel anchored 150 m outside the western edge of the array; (4) 2 mobile vessels performing basin-wide surveys to define the spatial extent of thin layers and the physical hydrography of the Sound. We observed numerous occur- rences of thin layers that contained locally enhanced concentrations of material; many of the layers per- sisted for intervals of several hours to a few days. More than one persistent thin layer may be present at any one time, and these spatially distinct thin layers often contain distinct plankton assemblages. The results suggest that the species or populations comprising each distinct thin layer have responded to different sets of biological and/or physical processes. The existence and persistence of planktonic thin layers generates extensive biological heterogeneity in the water column and may be important in maintaining species diversity and overall community structure.

A model based on Mie theory is described that estimates bulk participate refractive index n¯p from in situ optical measurements alone. Bulk refractive index is described in terms of the backscattering ratio and the hyperbolic slope of the particle size distribution (PSD). The PSD slope ξ is estimated from the hyperbolic slope of the particulate attenuation spectrum γ according to the relationship γ ≈ ξ − 3, verified with Mie theory. Thus the required in situ measurements are the particulate backscattering coefficient, the total particulate scattering coefficient, and the particulate attenuation coefficient. These parameters can be measured with commercially available instrumentation with rapid sampling rates and real-time data return. Application of the model to data from the Gulf of California yielded results that agreed with expectations, e.g., predicted n¯p was 1.04–1.05 in the chlorophyll maximum and 1.14–1.18 near sediments. Below the chlorophyll maximum in case I type waters, predicted n¯p values were between 1.10 and 1.12, suggesting the presence of a significant inorganic mineral component in the background or detrital organic particles with low water content.

Spectral attenuation and absorption coefficients of particulate matter and colocated hydrographic measurements were obtained in the Mid-Atlantic Bight during the fall of 1996 and the spring of 1997 as part of the Coastal Mixing and Optics experiment. Within the bottom boundary layer (BBL) the magnitude of the beam attenuation decreased and its spectral shape became steeper with distance from the bottom. Concurrently, the slope of the particulate size distribution (PSD) was found to increase with distance from the bottom. Changes in the PSD shape and the magnitude of the beam attenuation as functions of distance from the bottom in the BBL are consistent with particle resuspension and settling in the BBL, two processes that are dependent on particle size and density. For particles of similar density, resuspension and settling would result in a flattening of the PSD and an increase in the beam attenuation toward the bottom. In both fall and spring the magnitude of the particle attenuation coefficient correlates with its spectral shape, with a flatter shape associated with higher values of the attenuation. This observation is consistent with idealized optical theory for polydispersed nonabsorbing spheres. According to this theory, changes in the steepness of the particle size distribution (particle concentration as a function of size) will be associated with changes in the steepness of the attenuation spectra as a function of wavelength; a flatter particle size distribution will be associated with a flatter attenuation spectrum. In addition, the observed ranges of the beam attenuation spectral slope and the PSD exponent are found to be consistent with this theory.

Optical properties of dissolved (colored dissolved organic material (CDOM)) and particulate matter and hydrographic measurements were obtained at the Mid-Atlantic Bight during the fall of 1996 and the spring of 1997 as part of the Coastal Mixing and Optics experiment. To assess the temporal and spatial variability, time series were obtained at one location and cross-shelf transects were carried out. On short timescales, variability in the vertical distribution of the dissolved fraction was mostly due to high- frequency internal waves. This variability was conservative, resulting in no changes on isopycnals. Over longer periods and episodically, CDOM variability was dominated by storms. The storms were associated with sediment resuspension events and were accompanied by an increase in the absorption by the dissolved materials. Data from spatial transects show that near the bottom, over the shelf, and in both spring and fall, increased particulate absorption and increased CDOM absorption co-occur. These data support the hypothesis that bottom sediments can act as a source of dissolved organic carbon during sediment resuspension events.

We have collected data during eight separate research cruises from open ocean to estuarine oceanic environments. Inherent optical property data collected during these cruises were incorporated into a large database totaling 1914 vertical samples. The range of each inherent optical property within this database spans over 2 orders of magnitude. Using this database, we examine the spectral relationships of each of the inherent optical properties based on the measurements made at 488 nm. The results of this study show that there are dependencies in the individual inherent optical properties (IOP) spectra that are linearly related. The information from the regression models is used to explain the linear dependencies observed in the global data set. A separate data set collected from a recent cruise is used to compare regional relationships with the global. The implication of this research is that over a diversity of oceanic regimes, there are fundamental, first-order relationships in the individual IOP spectra. These relationships can provide an estimate of the individual IOP spectral relationships when no information about the IOP is available, as is often the case in ocean color remote sensing. More detailed models, however, may be necessary in order to more accurately predict the IOP spectral relationships on regional scales where the expected range of variability is small.

The project research addresses our long-term goal to develop an analytical suite of the Advanced Laser Fluorescence (ALF) methods and instruments to improve our capacity for characterization of aquatic environments. The ALF technique uniquely combines spectrally and temporally resolved measurements of the laser-stimulated emission (LSE) to provide assessments of key variables, including chlorophyll a (Chl a), chromophoric dissolved organic matter (CDOM), and phycobiliprotein-containing phytoplankton and cyanobacteria. The pump-during-probe measurements of variable fluorescence, Fv/Fm, yield assessments of phytoplankton photophysiological status. An extensive series of ALF measurements in diverse water types has demonstrated ALF utility as an integrated tool for aquatic research and observations. The specific goal of the project is to develop the next generation, commercial ALF sensors for oceanographic research, validation of satellite ocean color data, and environmental monitoring. The objectives are: 1. To develop the Aquatic Laser Fluorescence Analyzer (ALFA) for laboratory and field applications, including discrete sample analysis and underway shipboard measurements. 2. To develop the ALF In Situ (ALFIS) fiber-probe sensor. 3. To integrate, test and deploy the ALFA and ALFIS sensors on the solar-powered AUVs and research cruises. 4. To initiate operational use of the new ALF instruments for ecological and biogeochemical measurements, and validation of ocean color remote sensing.

Coastal waters represent the commingling of offshore marine and terrestrial surface source waters and therefore are naturally complex and variable. Our long term goal is to establish observational and modeling approaches to predict sources and scales of variability in the source waters, particularly those related to land use activities in upstream watersheds, from observations and measurements in the coastal waters. Hydrologic optics provides an approach to characterizing physical and biogeochemical processes in aquatic systems over a range of time and space scales. The linkage between observations of the inherent optical properties (IOPs; absorption, scattering and fluorescence) and the geophysical properties lie in the establishment of robust optical proxies and the quantification of the temporal and spatial scales over which these proxies remain conservative in their properties. Our objectives are to identify and quantify specific optical and chemical characteristics of the colored particulate and dissolved fractions originating in the Penobscot River system that are associated with defined land use activities (land use proxies), and to determine the scales of variability over which these proxies can be detected both temporally (i.e. seasonal and episodic events) and spatially (from the source into coastal waters).

Remote sensing of reflected sunlight from the upper ocean is a tremendous tool for studying biological, chemical, geological, and physical processes over a broad range of time and space scales. Global biogeochemical phenomena spanning seasonal (e.g., spring bloom), multi-year (e.g., the El Nino Southern Oscillation), to decadal (e.g., climatic variability) time scales can be resolved by an orbiting satellite imager. Reflected light in the visible domain (wavelengths of ~400 to 700 nm) is particularly useful in the study of upper ocean processes, as many important biogeochemical components of seawater absorb and scatter light effectively in this spectral range (the term “ocean color” specifically relates to the spectral character of this water-leaving visible light). These dissolved and particulate seawater components play key roles in the cycling of carbon in the ocean and serve as indicators of ecosystem health. Down-looking, passive remote sensors in air and space measure sunlight that is reflected upward into the sensor; in addition to the atmospherically scattered photons, a portion of the measured radiance results from photons that have exited the ocean and passed back through the atmosphere to the sensor in orbit. This portion is termed spectral upwelled water-leaving radiance, Lu (W m nm sr) and primarily consists of light scattered in the backward direction off the particles and molecules of seawater (for a complete discussion, refer to Chapter 1). Sunlight incident at the ocean surface is represented as spectral downwelling surface irradiance, Ed (W m nm), and the socalled remote sensing reflectance, Rrs, is derived from Lu/Ed, with Lu strictly defined in the nadir direction (normal to the plane of the ocean surface). Although Lu consists of primarily backscattered light, equally important in terms of its information content is the component of incident sunlight missing in the upwelled light. This is light that has been absorbed (or filtered) by the constituents of seawater in the upper ocean. The dependence of Rrs on these optical processes of backscattering and absorption just below the ocean surface (represented as 0) can be simply written (Morel and Prieur 1977)

Coastal waters represent the commingling of offshore marine and terrestrial surface source waters and therefore are naturally complex and variable. Our long term goal is to establish observational and modeling approaches to predict sources and scales of variability in the source waters, particularly those related to land use activities in upstream watersheds, from observations and measurements in the coastal waters. Hydrologic optics provides an approach to characterizing physical and biogeochemical processes in aquatic systems over a range of time and space scales. The linkage between observations of the inherent optical properties (IOPs; absorption, scattering and fluorescence) and the geophysical properties lie in the establishment of robust optical proxies and the quantification of the temporal and spatial scales over which these proxies remain conservative in their properties. Our objectives are to identify and quantify specific optical and chemical characteristics of the colored particulate and dissolved fractions originating in the Penobscot River system that are associated with defined land use activities (land use proxies), and to determine the scales of variability over which these proxies can be detected both temporally (i.e. seasonal and episodic events) and spatially (from the source into coastal waters).

In this final technical report we have provided results of initial analyses into the design of a light-weight, autonomous, modular, bottom-up vertical profiling system named Mini AMP. The results of these analyses were used to produce a set of mechanical and electrical specifications and designs for the Mini AMP that emphasizes operational reliability, ease of use, and configuration flexibility. We believe that the results of this Phase I research effort demonstrate the feasibility of developing a Mini AMP system, positioning us to take this project to Phase II. We present a development pathway that will lead to the successful implementation and construction of the Mini AMP system. Our goal is to develop a multi-parameter, reliable, long-term vertical profiling capability that promise to significantly advance observational science and monitoring of coastal waters. The Mini AMP system will provide a reliable, easy to maintain, and rapidly deployable/recoverable solution to obtaining long term, high vertical resolution profiles of important physical and bio-optical properties in coastal regions.

Apply a newly developed ocean-color inversion algorithm to measurements made in the west Florida Shelf and off the California coast, we derived the particle backscattering coefficient and the total absorption coefficient. From the derived total absorption coefficient, we calculated the absorption coefficients of the phytoplankton pigments and that of the gelbstoff (Colored Dissolved Organic Matter). From the derived pigment absorption coefficients, we further calculated the chlorophyll-a concentrations. These derived values were compared with those measured from water samples. It is found that the derived values are very consistent with those measured ones, suggesting that the inversio nmethods work very well for these coastal waters, and can be applied to satellite data for wide observations.

The new Aquatic Laser Fluorescence Analyzer (ALFA) provides spectral and temporal measurements of laser-stimulated emission (LSE) for assessment of phytoplankton pigments, community structure, photochemical efficiency (PY), and chromophoric dissolved organic matter (CDOM). The instrument was deployed in the Northern Gulf of Mexico to evaluate the ALFA analytical capabilities across the estuarine-marine gradient. The robust relationships between the pigment fluorescence and independent pigment measurements were used to validate the ALFA analytical algorithms and calibrate the instrument. The maximal PY magnitudes, PYm = PY(1-1.35·10−4PAR)−1, were estimated using the underway measurements of PY and photosynthetically active radiation (PAR). The chlorophyll (Chl) spatial patterns were calculated using the ratio of Chl fluorescence to PY to eliminate the effect of non-photochemical quenching on the underway Chl assessments. These measurements have provided rich information about spatial distributions of Chl, PYm, CDOM, and phytoplankton community structure, and demonstrated the utility of the ALFA instrument for oceanographic studies and bio-environmental surveys. The data suggest that the fluorescence measurements with 514 nm excitation can provide informative data for characterization of the CDOM-rich fresh, estuarine, and coastal aquatic environments.

percent light levels, absorption coefficient, optical depth, downwelling irradiance.

A model is presented that allows the prediction of percent photosynthetically available radiation (PAR) levels from measured profiles of the absorption coefficient at 490 nm in the Gulf of California. Percent PAR levels depend on the diffuse attenuation coefficients of the wavelengths that make up PAR, which in turn depend on the absorption coefficient. The emphasis is on developing a simple but robust model that can be used by researchers to plan deployments of photosynthesis experiments in the Gulf of California.

In order to be able to invert optical remote sensing data, it is necessary to understand the absorption, scattering and attenuation spectra. In this paper we present a study of the vertical distribution and spectra of the inherent optical properties by the particulate and dissolved materials in the Gulf of California. Most of the optical properties in the gulf are dominated by phytoplankton and their by-products (Case I waters). Only in the extreme northwestern region of the gulf were the optical properties dominated by inorganic materials. Typical spectra for the various components are presented. The distribution of the components and their relative contribution to the total optical properties are discussed.

A model is presented which predicts the diffuse attenuation coefficient of downwelling irradiance as a function of depth and the depth of the euphotic zone as based on the one percent level of photosynthetically active radiation from vertical profiles of spectral absorption and attenuation. The model is tested using data obtained in the Gulf of California. The modeled diffuse attenuation coefficients and PAR levels ar shown to have average errors of less than five percent when compared to the measured values.

Empirically-based satellite estimates of chlorophyll a [Chl] (e.g. OC3) are an important indicator of phytoplankton biomass. To correctly interpret [Chl] variability, estimates must be accurate and sources of algorithm errors known. While the underlying assumptions of band ratio algorithms such as OC3 have been tacitly hypothesized (i.e. CDOM and phytoplankton absorption covary), the influence of component absorption and scattering on the shape of the algorithm and estimated [Chl] error has yet to be explicitly revealed. We utilized the NOMAD bio-optical data set to examine variations between satellite estimated [Chl] and in situ values. We partitioned the variability into (a) signal contamination and (b) natural phytoplankton variability (variability in chlorophyll-specific phytoplankton absorption). Not surprisingly, the OC3 best-fit curve resulted from a balance between these two different sources of variation confirming the bias by detrital absorption on global scale. Unlike previous descriptions of empirical [Chl] algorithms, our study (a) quantified the mean detrital:phytoplankton absorption as ~1:1in the global NOMAD data set, and (b) removed detrital (CDOM + non-algal particle) absorption in radiative transfer models directly showing that the scale of the remaining variability in the band ratio algorithm was dominated by phytoplankton absorption cross section.

An optical dataset was collected on a mooring in the Santa Barbara Channel. Radiative transfer modeling and statistical analyses were employed to investigate sources of variability of in situ remote sensing reflectance [r(rs)(lambda,4 m)] and the f/Q ratio. It was found that the variability of inherent optical properties and the slope of the particle size distribution (xi) were strongly related to the variability of r(rs)(lambda,4 m). The variability of f/Q was strongly affected by particle type characteristics. A semianalytical radiative transfer model was applied and effects of variable particle characteristics on optical closure were evaluated. Closure was best achieved in waters composed of a mixture of biogenic and minerogenic particles.

The temperature and salt dependencies of absorption by liquid water (H2O) and heavy water (D2O) were determined using a hyperspectral absorption and attenuation meter (WET Labs, AC-S). Sodium chloride (NaCl) was used as a proxy for seawater salts. There was no significant temperature (PsiT) or salt (PsiS) dependency of absorption at wavelengths550 nm. At wavelengths550 nm, PsiT exhibited peaks at approximately 604, 662, and 740 nm. A small negative trough in PsiS occurred at approximately 590 nm, followed by a small positive peak approximately 620 nm, a larger negative trough at approximately 720 nm, and a strong positive peak at approximately 755 nm. The salt dependency of absorption by heavy water, Psis(H), exhibited a negative power-law shape with very low Psis(H), at wavelengths550 nm. Our experiments with NaCl, clean open ocean seawater, and artificial seawater support the hypothesis that salts modify the absorption spectra of seawater by modifying the molecular matrix and vibrations of pure water.

Relationships and variability of bio-optical properties in coastal waters are investigated. Optical proxies indicate that these coastal waters are optically complex and highly variable and are categorized as follows: (1) relatively clear and dominated by high index of refraction, biogenic particles, (2) more turbid, consisting of mostly inorganic particles and little phytoplankton, (3) extremely turbid with high concentrations of inorganic particles, and (4) more turbid and dominated by biogenic particles. We present a method, alternative to traditional remote-sensing algorithms, of classifying coastal waters [the Spectral Angle Mapper (SAM)] and utilize the SAM to successfully isolate plume conditions in time series of downwelling irradiance and total absorption coefficient. We conclude with a discussion of the use of the SAM for coastal management operations.

The dependence of the reflectance at the surface on the vertical structure of optical parameters is derived from first principles. It is shown that the depth dependence is a function of the derivative of the round trip attenuation of the downwelling and backscattered light. Previously the depth dependence was usually modeled as being dependent on the round trip attenuation. Using the new relationship one can calculate the contribution of the mixed layer to the overall reflectance at the surface. This allows one to determine whether or not to ignore the vertical structure at greater depth. It is shown that the important parameter to average is the ratio of the backscattering and absorption coefficients. The surface reflectance is related to the weighted average of this parameter, not the ratio of the weighted average of the backscattering and the weighted average of the absorption. Only in the special case of "optical homogeneity" where the ratio of the backscattering and absorption coefficients does not vary with depth, can the vertical structure be ignored. Other special cases including constant backscattering and variable absorption are also investigated.

A new algorithm has been developed for simultaneous retrieval of aerosol optical properties and chlorophyll concentrations in case I waters. This algorithm is based on an improved complete model for the inherent optical properties and accurate simulations of the radiative transfer process in the coupled atmosphere-ocean system. It has been tested against synthetic radiances generated for the Sea-Viewing Wide Field-of-View Sensor (SeaWiFS) channels and has been shown to be robust and accurate. A unique feature of this algorithm is that it uses the measured radiances in both near-IR and visible channels to find that combination of chlorophyll concentration and aerosol optical properties that minimizes the error across the spectrum. Thus the error in the retrieved quantities can be quantified.

We tested closure between in situ radiometric and absorption coefficient measurements by using a nearly backscattering-independent remote-sensing reflectance model that employs the remote-sensing reflectance at three wavelengths. We show that only a small error is introduced into the closure model when the proper functional relationships of f/Q and the backscattering is taken to be a constant when using the sea-viewing wide field-of-view sensor wavelengths 443, 490, and 555 nm. A method of inverting the model to obtain the absorption coefficient by use of simple linear spectral relationships of the absorption coefficient is provided. The results of the model show that the independent measurements of reflectance and absorption obtain closure with a high degree of accuracy.

Classical radiative transfer programs are based on the plane-parallel assumption. We show that the Gershun equation is valid if the irradiance is averaged over a sufficiently large area. We show that the equation is invalid for horizontal areas of the order of tens of meters in which horizontal gradients of irradiance in the presence of waves are much larger than vertical gradients. We calculate the distribution of irradiance beneath modeled two-dimensional surface waves. We show that many of the features typically observed in irradiance profiles can be explained by use of such models. We derive a method for determination of the diffuse attenuation coefficient that is based on the upward integration of the irradiance field beneath waves, starting at a depth at which the irradiance profile is affected only weakly by waves.