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Blooms of toxic algae are increasing in magnitude and frequency around the globe, causing extensive economic and environmental impacts. On the west coast of Florida, blooms of the toxic dinoflagellate Karenia brevis (Davis) have been documented annually for the last 30 years causing respiratory irritation in humans, fish kills, and toxin bioaccumulation in shellfish beds. As a result, methods need to be established to monitor and predict bloom formation and transport to mitigate their harmful effects on the surrounding ecosystems and local communities. In the past, monitoring and mitigation efforts have relied on visual confirmation of water discoloration, fish kills, and laborious cell counts, but recently satellite remote sensing has been used to track harmful algal blooms (HABs) along the Florida coast. Unfortunately satellite ocean color is limited by cloud cover, lack of detection below one optical depth, and revisit frequency, all of which can lead to extended periods without data. To address these shortcomings, an optical phytoplankton discriminator (OPD) was developed to detect K. brevis cells in mixed phytoplankton assemblages. The OPD was integrated into autonomous underwater vehicle (AUV) platforms to gather spatially and temporally relevant data that can be used in collaboration with satellite imagery to provide a 3D picture of bloom dynamics over time. In January 2005, a Remote Environmental Monitoring UnitS (REMUS) AUV with an OPD payload was deployed on the west coast of Florida to retrieve a similarity index (SI), which indicates when K. brevis dominates the phytoplankton community. SI was used to monitor a K. brevis bloom in relation to temperature, salinity, chlorophyll, and ocean currents. Current speed, SI, temperature, salinity, and chlorophyll a from the AUV were used to quantify a 1 km displacement of the K. brevis bloom front that was observed over the deployment period. The ability to monitor short term bloom movement will improve monitoring and predictive efforts that are used to provide warnings for local tourism and fishing industries. In addition, understanding the fine scale environmental conditions associated with bloom formation will increase our ability to predict the location and timing of K. brevis bloom formation. This study demonstrates the use of one autonomous platform and provides evidence that a nested array of AUVs and moorings equipped with new sensors, combined with remote sensing, can provide an early warning and monitoring system to reduce the impact of HABs.

In oceanography, there has been a growing emphasis on coastal regions, partially because of their inherent complexity, as well as the increasing acknowledgment of anthropogenic impacts. To improve understanding and characterization of coastal dynamics, there has been significant effort devoted to the development of autonomous systems that sample the ocean on relevant scales. Autonomous underwater vehicles (AUVs) are especially well suited for studies of the coastal ocean because they are able to provide near-synoptic spatial observations. These sampling platforms are beginning to transition from the engineering groups that developed and continue to improve them to the science user. With this transition comes novel applications of these vehicles to address new questions in coastal oceanography. Here, the relatively mature Remote Environmental Monitoring Units (REMUS) AUV system is described and assessed. Analysis of data, based on 37 missions and nearly 800 km of in-water operation, shows that the vehicle’s navigational error estimates were consistently less than 10 m, and error estimates of mission duration, distance, velocity, and power usage, once the vehicle was properly ballasted, were below 10%. An example of the transition to science is demonstrated in an experiment conducted in 2002 in Monterey Bay, California, where the vehicle was used to quantify critical horizontal length scales of variability. Length scales on the order of tens to hundreds of meters were found for the region within 25 km of the coastline, which has significant implications for designing proper sampling approaches and parameterizing model domains. Results also demonstrate the overall utility of the REMUS vehicle for use by coastal oceanographers.

The focus of this paper is on the development of methodology for short-term (1–3 days) oceanic bioluminescence (BL) predictions and the optimization of spatial and temporal bioluminescence sampling strategies. The approach is based on predictions of bioluminescence with an advection–diffusion–reaction (tracer) model with velocities and diffusivities from a circulation model. In previous research, it was shown that short-term changes in some of the salient features in coastal bioluminescence can be explained and predicted by using this approach. At the same time, it was demonstrated that optimization of bioluminescence sampling prior to the forecast is critical for successful short-term BL predictions with the tracer model. In the present paper, the adjoint to the tracer model is used to study the sensitivity of the modeled bioluminescence distributions to the sampling strategies for BL. The locations and times of bioluminescence sampling prior to the forecast are determined by using the adjoint-based sensitivity maps. The approach is tested with bioluminescence observations collected during August 2000 and 2003 in the Monterey Bay, California, area. During August 2000, BL surveys were collected during a strong wind relaxation event, while in August 2003, BL surveys were conducted during an extended (longer than a week) upwelling-favorable event. The numerical bioluminescence predictability experiments demonstrated a close agreement between observed and model-predicted short-term spatial and temporal changes of the coastal bioluminescence.

Although bioluminescence (BL) in the open ocean has been extensively studied, coastal BL remains poorly understood due, in large degree, to a lack of BL instrumentation appropriate to measure the fine-scale biological and physical complexity of the coastal regime. As a contribution toward understanding coastal BL, we developed the Multipurpose Bioluminescence Bathyphotometer (MBBP). This compact, self-contained bathyphotometer (BP) was designed to function in a variety of deployment modes, including conventional shipboard profilers, towed platforms, autonomous underwater vehicles (AUVs), and profiling moorings. In all configurations, the instrument preserves signal structure at centimeter to meter scale resolution, the scale at which higher-flow instruments might disturb thin layers and other fine-scale water column features. In the MBBP, seawater is conveyed with minimal premeasurement excitation into a light-baffled stimulation and measurement chamber at a continuously measured flow rate of 350 to 400 mL s−1. A photomultiplier tube (PMT) records light from bioluminescent organisms after they are mechanically stimulated at the chamber entrance by a high-velocity impeller. Calibration and test protocols were developed to determine BL stimulation efficiency and MBBP measurement characteristics. To illustrate the capabilities of the MBBP to resolve the fine-scale structure of the BL community, measurements from two coastal environments are presented.

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A large database of in situ bio-optical measurements was collected at the Long-term Ecosystem Observatory off the southern coast of New Jersey, USA. In part, the research effort focused on reconciling in situ estimates with satellite-derived estimates of the inherent optical properties (IOP). At 442 nm, in situ absorption values ranged from less than 0.2 to over 1.5 inverse metres. Satellite estimates of backscatter ranged from 0.002 to 0.03 inverse metres at 442 nm and showed significant variability in time and space during July 1999, reflecting the recurrent high frequency events that characterize the region—wind-mixing, storms and coastal upwelling. Despite this variability, there was good qualitative agreement between the satellite derived IOP estimates and in situ IOP measurements. Both absorption and backscatter values increased near-shore, reflecting enhanced concentrations of phytoplankton, sediments and dissolved organic matter.

Published version. Source at http://doi.org/10.1016/j.pocean.2015.08.005. Several recent lines of evidence indicate that the polar night is key to understanding Arctic marine ecosystems. First, the polar night is not a period void of biological activity even though primary production is close to zero, but is rather characterized by a number of processes and interactions yet to be fully understood, including unanticipated high levels of feeding and reproduction in a wide range of taxa and habitats. Second, as more knowledge emerges, it is evident that a coupled physical and biological perspective of the ecosystem will redefine seasonality beyond the ‘‘calendar perspective”. Third, it appears that many organisms may exhibit endogenous rhythms that trigger fitness-maximizing activities in the absence of light-based cues. Indeed a common adaptation appears to be the ability to utilize the dark season for reproduction. This and other processes are most likely adaptations to current environmental conditions and community and trophic structures of the ecosystem, and may have implications for how Arctic ecosystems can change under continued climatic warming.

The light regime is an ecologically important factor in pelagic habitats, influencing a range of biological processes. However, the availability and importance of light to these processes in high Arctic zooplankton communities during periods of 'complete' darkness (polar night) are poorly studied. Here we characterized the ambient light regime throughout the diel cycle during the high Arctic polar night, and ask whether visual systems of Arctic zooplankton can detect the low levels of irradiance available at this time. To this end, light measurements with a purpose-built irradiance sensor and coupled all-sky digital photographs were used to characterize diel skylight irradiance patterns over 24 hours at 79°N in January 2014 and 2015. Subsequent skylight spectral irradiance and in-water optical property measurements were used to model the underwater light field as a function of depth, which was then weighted by the electrophysiologically determined visual spectral sensitivity of a dominant high Arctic zooplankter, Thysanoessa inermis. Irradiance in air ranged between 1–1.5 x 10-5 μmol photons m-2 s-1 (400–700 nm) in clear weather conditions at noon and with the moon below the horizon, hence values reflect only solar illumination. Radiative transfer modelling generated underwater light fields with peak transmission at blue-green wavelengths, with a 465 nm transmission maximum in shallow water shifting to 485 nm with depth. To the eye of a zooplankter, light from the surface to 75 m exhibits a maximum at 485 nm, with longer wavelengths (>600 nm) being of little visual significance. Our data are the first quantitative characterisation, including absolute intensities, spectral composition and photoperiod of biologically relevant solar ambient light in the high Arctic during the polar night, and indicate that some species of Arctic zooplankton are able to detect and utilize ambient light down to 20–30m depth during the Arctic polar night. This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

An integrated ocean observatory has been developed and operated in the coastal waters off the central coast of New Jersey, USA. One major goal for the Long-term Ecosystem Observatory (LEO) is to develop a real-time capability for rapid environmental assessment and physical/biological forecasting in coastal waters. To this end, observational data are collected from satellites, aircrafts, ships, fixed/relocatable moorings and autonomous underwater vehicles. The majority of the data are available in real-time allowing for adaptive sampling of episodic events and are assimilated into ocean forecast models. In this observationally rich environment, model forecast errors are dominated by uncertainties in the model physics or future boundary conditions rather than initial conditions. Therefore, ensemble forecasts with differing model parameterizations provide a unique opportunity for model refinement and validation. The system has been operated during three annual coastal predictive skill experiments from 1998 through 2000. To illustrate the capabilities of the system, case studies on coastal upwelling and small-scale biological slicks are discussed. This observatory is one part of the expanding network of ocean observatories that will form the basis of a national observation network.

Developing optical detection techniques for discriminating particular phytoplankon species in mixed assemblages has long been a goal of aquatic scientists. Previously, a processing algorithm for phytoplankton absorption spectra was reported that suggested detection of the red tide dinoflagellate Gymnodinium breve was possible. The algorithm evaluated the fourth derivative of the particulate absorption spectrum of an unknown sample and compared it to a standard fourth derivative spectrum for G. breve using a similarity index. We report here the first-time application of this technique to the detection of G. breve in natural, mixed phytoplankton communities. Pigment and spectral absorption data were collected from natural blooms of G. breve in the eastern Gulf of Mexico. This dinoflagellate is the only species of phytoplankton in the Eastern Gulf of Mexico observed to contain the pigment gyroxanthin-diester, and it appears in constant proportion to cellular chlorophyll a (Chl a) in G. breve. The in vitro absorption spectrum of gyroxanthin-diester is nearly identical to other xanthophylls (including diadinoxanthin, lutein, and 199-hexanoyloxyfucoxanthin) and is not singularly responsible for imparting a unique absorption signature. Quantifying gyroxanthin-diester and Chl a allowed us to estimate the fraction of the biomass in mixed populations associated with G. breve. Subsequent regression of the G. breve similarity indexes to the G. breve biomass fractions yielded a significant linear correlation. Finally, the liquid waveguide capillary cell appears to be a promising technology for automating this technique.

Our objective was to quantify the potential variability in remotely sensed chlorophyll a (Chl a) and primary productivity in coastal waters of the Southern Ocean. From data collected throughout the springs/summers of 1991–1994, we calculated the proportion of water column Chl a and primary productivity within the upper optical attenuation length (K −1par) and the satellite-weighted depth. The temporal variability was resolved every 2–3 days and was observed to be greater within years than between years. Three-year averages (n=223) revealed that 10.2 ± 3.6% of total Chl a and 14.8 ± 6.5% of production occurred within satellite-weighted depth in predominantly Case I waters. The average values were twice as high within K −1par, 24.1 ± 8% of total Chl a and 34 ± 9% of production respectively. Masked in these long-term averages are very large changes occurring on short time scales of seasonal blooms. We observed that the patterns of Chl a vertical distribution within blooms are also subject to taxonomic influence and dependent upon the physiological state of the phytoplankton. Highest proportions of water column Chl a in the first optical depth were measured during the rapid onset of surface cryptophyte blooms each year, i.e. 50% within K −1par and 30% above the satellite-weighted depth. Lowest fractions, 6% and 2% of biomass within K −1par and satellite-weighted depth respectively, were associated with peak bloom conditions independent of taxonomy. Our analyses suggest that satellite-dependent models of Chl a and subsequent chlorophyll-dependent primary production will be challenging to develop for the near-shore Southern Ocean, especially given the potentially high natural variability in the vertical distribution of Chl a driven by physical forcing, the photoadaptive abilities of polar phytoplankton, and taxonomic influences.

Monitoring programs for harmful algal blooms (HABs) are currently reactive and provide little or no means for advance warning. Given this, the development of algal forecasting systems would be of great use because they could guide traditional monitoring programs and provide a proactive means for responding to HABs. Forecasting systems will require near real-time observational capabilities and hydrodynamic/biological models designed to run in the forecast mode. These observational networks must detect and forecast over ecologically relevant spatial/ temporal scales. One solution is to incorporate a multiplatform optical approach utilizing remote sensing and in situ moored technologies. Recent advances in instrumentation and data-assimilative modeling may provide the components necessary for building an algal forecasting system. This review will outline the utility and hurdles of optical approaches in HAB detection and monitoring. In all the approaches, the desired HAB information must be isolated and extracted from the measured bulk optical signals. Examples of strengths and weaknesses of the current approaches to deconvolve the bulk optical properties are illustrated. After the phytoplankton signal has been isolated, species-recognition algorithms will be required, and we demonstrate one approach developed for Gymnodinium breve Davis. Pattern-recognition algorithms will be species-specific, reflecting the acclimation state of the HAB species of interest.Field data will provide inputs to optically based ecosystem models, which are fused to the observational networks through data-assimilation methods. Potential model structure and data-assimilation methods are reviewed.

Eight hundred photosynthesis-irradiance relationships were determined in the shelf waters adjacent to Palmer Station, Antarctica during the spring/summer periods of 1991–94. Biomass specific maximum photosynthetic rate, PBmax, and the light limited photosynthetic efficiency, αB, were poorly correlated to the physical forcing and nutrient regimes at the sampling stations. The two photosynthetic parameters, however, did strongly covary indicating the minimum irradiance required to saturate photosynthesis, Ik, was relatively constant in this highly variable environment. The variability in Ik could partially be attributed to both depth in the water column and time of the year, with the highest values occurring for surface samples during the summer period of peak incident irradiance. Given this and the significant dependence of Pmax on phytoplankton biomass, a simple empirical model for primary productivity was developed. An independent test of the model was performed on data collected in a mesoscale offshore grid and predicted primary production was found to be within 13% of measured values. Although there are limitations to this approach (i.e. exclusion of diel periodicity in photosynthetic response), these results provide relatively robust estimates of daily primary production for the Southern Ocean.

The raio of the xanthophylll pigments diadinoxanthin and diatoxanthin to chlorophyll a [(DD+DT}:Chl a] was used as a photoadaptive index during the development of a large Antarctic diatom bloom. This index was found to track fluctuations in the incident solar irradiance and the in situ light field over a 3 order magnitude change in the water column biomass. Depth profiles of the (DD+DT}:Chl a ratio showed that the upper mixed layer, assessed by physical data, was in fact stable over the course of the month. Diel experiments conducted over the same period showed a delayed (5–8 h) response of the DD+DT pool to the instantaneous Qpar (400–700 nm) irradiance. These time series results illustrate the potential use of xanthophyll pigmnents in assessing phytoplankton light histories and the degree of water column stability.

This study assessed the impact of temperature on the photosynthetic activity in the dino- flagellate Alexandrium fundyense (Ca28) for cultures grown at 75 umol photons rrr2 s~' over a range of temperatures. Increasing light intensity under static temperatures caused a S-fold decrease in the maximum quantum yield for photosystem II (PSII) (FJFm). Carbon fixation rates mirrored high-light depressions in FJFm. Cells in the presence of streptomycin showed an 83% recovery in FJFm; therefore, only a minor proportion of the decline in FJFm was attributable to PSII damage by bright light. For cells transferred to higher temperatures, FJFm was less sensitive to high light, decreasing only 20-40% compared to the 80-90% decrease observed for cells incubated at their ambient growth temperature. For cells shifted to higher temperatures, the rapid recovery phase of FJFm was not present; therefore, cells did not initiate downregulation of PSII. Higher capacity to maintain electron transport, as indicated by the quantum yields, was confirmed by enhanced carbon fixation. Shifts to lower temperatures significantly increased PSII sensitivity to high light. Overall, these relationships reflect the synergy between photosynthetic light and dark reactions which are differentially impacted by changes in temperature.

The impact on downwelling irradiance of phytoplankton, cromophoric dissolved organic matter (CDOM) and particulate inorganic carbon (PIC) in the form of coccoliths, is described using a radiative transfer model and field data from the Barents Sea (BS). While annual Emiliania huxleyi blooms in the BS have been detected with satellite remote sensing, this is the first bio-optical field study on E. huxleyi from this area. Bio-optical variables were measured in August 2007 along a transect through the Polar Front from Arctic Water (ArW) into an E. huxleyi bloom in Atlantic Water (AW). The depth of the euphotic zone was on average 52m in ArW, 45m in frontal mixed water (FMW) and 21m in AW. At the 10% irradiance depth in AW, phytoplankton had attenuated 40%, CDOM 17% and PIC 18% of the irradiance from 400 to 700nm. Numbers from ArW were 36%, 26% and pot) in AW was 1.8× higher than in ArW, and PIC had reduced PP pot in AW by 20-40% at stations with ~100-130mg PIC m -3. A novel approach for estimating PIC based on a theoretical relationship between diffuse attenuation and irradiance reflectance is also described.

Our goal was to provide a high-resolution temporal data base for modeling primary production in shelf waters adjacent to Palmer Station, Antarctica. Here, the resulting 1991/1992 data base is used to: (1) determine in situ productivity over a range of seasonal to subseasonal time scales; (2) identify time scales of significant variability in marine productivity during the peak growing season; (3) identify environmental, experimental and analytical factors that can significantly impact the accuracy of daily, weekly and seasonal productivity estimates; and (4) integrate our findings with previous studies of Antarctic coastal primary pro- duction. Data were gathered every 2–3 days during a 3-month period in the austral spring/summer of 1991/1992. Photosynthesis-irradiance (P-I) relationships were determined throughout the euphotic zone and P-I parameters, combined with knowledge of the in-water light field, were used to derive instantaneous rates of in situ primary production. Additionally, weekly samples were collected from surface and chlorophyll a maxima for characterization of the patterns of diel periodicity in P-I parameters. Seven diel patterns were discerned over the season and used to time-correct instantaneous measurements and derive noontime, daily, monthly and seasonally integrated estimates of production. During the season, a large bloom was responsible for some of the highest daily produc- tivity rates reported for the Southern Ocean (0.8 g C m-3 d-1, 6.3 g C m-2 d-1). Significant variation in daily integrated rates occurred generally on time scales less than a week. Peak timing and magnitude of daytime periodicities in photosynthesis varied widely over the season, closely coupled to changes in phytoplankton community composition. Instantaneous measurements of primary production, if uncorrected or improperly corrected for daytime periodicities in carbon fixation, were unreliable predictors of production on longer time scales even if the water column was sampled every few days. High frequency sampling and consideration of diel periodicity may be requirements when attempting to discern differences between short time-scale variability and long-term trends in Antarctic primary production.

This paper presents a system of multiple coordinating autonomous underwater vehicles (AUV) that can localize and track a shark tagged with an acoustic transmitter. Each AUV is equipped with a stereo-hydrophone system that provides measurements of the relative bearing to the transmitter, as well as an acoustic modem that allows for inter-AUV communication and hence cooperative shark state estimation and decentralized tracking control. Online state estimation of the shark's state is performed using a Particle Filter in which measurements are shared between AUVs. The decentralized control system enables the AUVs to circumnavigate a dynamic target, (i.e. the estimated shark location). Each AUV circles the target by tracking circles of different radii and at different phase angles with respect to the target so as to obtain simultaneous sensor vantage points and minimize chance of AUV collision. A series of experiments using two AUVs were conducted in Big Fisherman's Cove in Santa Catalina Island, CA and demonstrated the ability to track a tagged leopard shark (Triakis semifasciata). The performance of the tracking was compared to standard manual tracking performed using an directional hydrophone operated by a researcher in a boat. In an additional experiment, the AUVs tracked an acoustic tag attached to the tracking boat to quantify the error of the state estimation of the system.

This chapter presents aspects of underwater hyperspectral imaging (UHI) techniques aimed at mapping biogeochemical objects of interest (OOI) on the seafloor. Case examples of instrument-carrying platforms and biogeochemical applications are given. We discuss how to create high resolution, georeferenced, optically corrected digital underwater maps of different habitats, minerals, substrates, and organisms. Corrections for platform speed and direction, inherent optical properties (IOP), optical path length, dynamic positioning, and pitch/roll/yaw are discussed in the context of using UHI-based optical fingerprints (i.e. spectral reflectance in visible wavelengths) of different targets to create maps that can help discriminate, identify, and quantify OOI, and provide statistical information on relevant seafloor features.

Penguin foraging and breeding success depend on broad-scale environmental and local-scale hydrographic features of their habitat. We investigated the effect of local tidal currents on a population of Adélie penguins on Humble Is., Antarctica. We used satellite-tagged penguins, an autonomous underwater vehicle, and historical tidal records to model of penguin foraging locations over ten seasons. The bearing of tidal currents did not oscillate daily, but rather between diurnal and semidiurnal tidal regimes. Adélie penguins foraging locations changed in response to tidal regime switching, and not to daily tidal patterns. The hydrography and foraging patterns of Adélie penguins during these switching tidal regimes suggest that they are responding to changing prey availability, as they are concentrated and dispersed in nearby Palmer Deep by variable tidal forcing on weekly timescales, providing a link between local currents and the ecology of this predator.

Ocean observatories are collections of networks of sensors that are deployed to sample the ocean physics, chemistry, and biology. The goal of these networks is to overcome chronic undersampling of the oceans by providing sustained measurements in space and time. The data collected by these networks are used to address a range of basic and applied research questions, hindered by a lack of data. The ocean observatories represent collections of platforms capable of collecting data over a range of scales. The platforms include ships, satellites, radars, and a range of Lagrangian systems. Data from the individual platforms are aggregated by sophisticated cyberinfrastructure software systems, which when combined with global communications allow for two-way communication between the shoreside personnel and the networks that can be deployed anywhere in the world. This two-way communication allows the networks to be adaptively configured to improve sampling of specific processes. The maturation of these systems comes at a fortuitous time as the oceans are increasingly showing evidence of changes in the physics, chemistry, and biology over the last few decades. Understanding those changes will require the data collected by the ocean observatories.

The development and implementation of a three-dimensional ocean modeling system for the Prince William Sound (PWS) is described. The system consists of a regional ocean model component (ROMS) forced by output from a regional atmospheric model component (the Weather Research and Forecasting Model, WRF). The ROMS ocean model component has a horizontal resolution of 1 km within PWS and utilizes a recently-developed multi-scale 3DVAR data assimilation methodology along with freshwater runoff from land obtained via real-time execution of a digital elevation model. During the Sound Predictions Field Experiment (July 19–August 3, 2009) the system was run in real-time to support operations and incorporated all available real-time streams of data. Nowcasts were produced every 6 h and a 48-h forecast was performed once a day. In addition, a sixteen-member ensemble of forecasts was executed on most days. All results were published at a web portal ( http://ourocean.jpl.nasa.gov/PWS ) in real time to support decision making. The performance of the system during Sound Predictions 2009 is evaluated. The ROMS results are first compared with the assimilated data as a consistency check. RMS differences of about 0.7 °C were found between the ROMS temperatures and the observed vertical profiles of temperature that are assimilated. The ROMS salinities show greater discrepancies, tending to be too salty near the surface. The overall circulation patterns observed throughout the Sound are qualitatively reproduced, including the following evolution in time. During the first week of the experiment, the weather was quite stormy with strong southeasterly winds. This resulted in strong north to northwestward surface flow in much of the central PWS. Both the observed drifter trajectories and the ROMS nowcasts showed strong surface inflow into the Sound through the Hinchinbrook Entrance and strong generally northward to northwestward flow in the central Sound that was exiting through the Knight Island Passage and Montague Strait entrance. During the latter part of the second week when surface winds were light and southwesterly, the mean surface flow at the Hinchinbrook Entrance reversed to weak outflow and a cyclonic eddy formed in the central Sound. Overall, RMS differences between ROMS surface currents and observed HF radar surface currents in the central Sound were generally between 5 and 10 cm/s, about 20–40% of the time mean current speeds. The ROMS reanalysis is then validated against independent observations. A comparison of the ROMS currents with observed vertical current profiles from moored ADCPs in the Hinchinbrook Entrance and Montague Strait shows good qualitative agreement and confirms the evolution of the near surface inflow/outflow at these locations described above. A comparison of the ROMS surface currents with drifter trajectories provided additional confirmation that the evolution of the surface flow described above was realistic. Forecasts of drifter locations had RMS errors of less than 10 km for up to 36 h. One and two-day forecasts of surface temperature, salinity and current fields were more skillful than persistence forecasts. In addition, ensemble mean forecasts were found to be slightly more skillful than single forecasts. Two case studies demonstrated the system’s qualitative skill in predicting subsurface changes within the mixed layer measured by ships and autonomous underwater vehicles. In summary, the system is capable of producing a realistic evolution of the near-surface circulation within PWS including forecasts of up to two days of this evolution. Use of the products provided by the system during the experiment as part of the asset deployment decision making process demonstrated the value of accurate regional ocean forecasts in support of field experiments.

From his expertise in biosonar, Whitlow Au brought a wealth of ideas on sonar use, design, and context to the study of wild cetaceans, resulting in great contributions to our understanding of odontocete foraging ecology. This contribution follows that foundation, using an integrated approach comprising echosounders deployed in a deep-diving autonomous underwater vehicle, ship based acoustics, visual observations, direct prey sampling, and animal-borne tags to explore the behavior of Risso’s dolphins foraging in scattering layers off California. Active acoustic measurements demonstrated that Risso’s dolphins dove to discrete prey layers throughout the day and night. Using acoustic data collected from the AUV, we found layers made up of distinct, small patches of animals of similar size and taxonomy adjacent to contrasting patches. Prey formed particularly tight aggregations when Risso’s dolphins were present. Squid made up over 70% of the patches in which dolphins were found and more than 95% of those at t...

The general objective of the work underway is to develop a baseline characterization of the spatial and temporal variability in optical/acoustical water properties for tropical island environments in response to variations in physical forcing.

Presented is a method for estimating the 2D planar position, velocity, and orientation states of a tagged shark. The method is designed for implementation on an Autonomous Underwater Vehicle (AUV) equipped with a stereo-hydrophone and receiver system that detects acoustic signals transmitted by a tag. The particular hydrophone system used here provides a measurement of relative bearing angle to the tag, but does not provide the sign (+ or -) of the bearing angle. A Particle Filter was used for fusing these measurements over time to produce a state estimate of the tag location. The Particle Filter combined with an active control system allowed the system to overcome the ambiguity in the sign of the bearing angle. This state estimator was validated by tracking both a stationary tag and moving tag with known positions. These experiments revealed state estimate errors were on par with those obtained by manually driven boat based tracking systems, the current method used for tracking fish and sharks over long distances. Final experiments involved the catching, releasing, and an autonomous AUV tracking of a 1 meter Leopard Shark (Triakis semifasciata) in SeaPlane Lagoon, Los Angeles, California.

With collaborated research efforts in the regional coastal ocean observing systems (SCCOOS, CeNCOOS, and NANOOS) off the U.S. West Coast (USWC), the nearly completed high-frequency radar (HFR) network provides an unprecedented capability to monitor and understand coastal ocean dynamics and phenomenology through hourly surface current measurements at up to 1 km resolution. The dynamics of the surface currents off the USWC are governed by tides, winds, Coriolis force, low-frequency pressure gradients (less than 0.4 cycles per day (cpd)), and nonlinear interactions of those forces. The HFR surface currents resolve coastal surface ocean variability continuously across scales from sub-mesoscale to mesoscale (O(1) km to O(1000) km). Their spectra decay with k-2 at high wave number (less than 100 km) in agreement with theoretical sub-mesoscale spectra below the observational limits of present-day satellite altimeters.

[1] Autonomous underwater vehicles (AUVs) can map water conditions at high spatial (horizontal and vertical) and temporal resolution, including under cloudy conditions when satellite and airborne remote sensing are not feasible. As part of the RADYO program, we deployed a passive radiometer on an AUV in the Santa Barbara Channel and off the coast of Hawaii to apply existing bio-optical algorithms for characterizing the optical constituents of coastal seawater (i.e., dissolved organic material, algal biomass, and other particles). The spectral differences between attenuation coefficients were computed from ratios of downwelling irradiance measured at depth and used to provide estimates of the in-water optical constituents. There was generally good agreement between derived values of absorption and concurrent measurements of this inherent optical property in Santa Barbara Channel. Wave focusing, cloud cover, and low attenuation coefficients influenced results off the coast of Hawaii and are used to evaluate the larger-scale application of these methods in the near surface coastal oceans.

[1] Extensive AUVs surveys showed that during the development of upwelling, bioluminescent dinoflagellates from the northern part of the Monterey Bay, California (called the upwelling shadow area), were able to avoid advection by southward flowing currents along the entrance to the Bay, while non-bioluminescent phytoplankton were advected by currents. It is known that vertical swimming of dinoflagellates to deeper layers helps them avoid losses due to advection. In the present paper, we investigate if modeling dinoflagellates' vertical swimming can explain the observed dinoflagellates' ability to avoid advection during the upwelling development. The dynamics of a dinoflagellate population is modeled with the tracer model with introduced vertical swimming velocity. Three swimming behaviors are considered: sinking, swimming to the target depth and diel vertical migration. Velocities in all swimming cases are considered in the ranges of documented velocities for the observed dinoflagellates species during the upwelling development in the Monterey Bay. Our modeling confirmed that observed bioluminescent dinoflagellates' avoidance of advection during the upwelling development can be explained by their vertical swimming ability. In the case of swimming with 20 m/day (which is half of observed maximum swimming velocity), around 40% of dinoflagellates population from the northern part of the Bay were advected along the entrance to the Bay in comparison to the case without swimming. This is in agreement with the ratio of around 45% of observed mean bioluminescence intensity at the entrance to the Bay to the observed mean intensity in the northern part of the Bay. This mechanism also helps explain the general persistence of dinoflagellates in this part of the coastline.

Introduction The absorption of light by algal pigments determines the cellular absorption of phytoplankton and thus contributes to the in situ optical signatures of coastal and offshore waters. This is the basis of a range of bio-optical approaches used for monitoring phytoplankton distribution (taxa and biomass) and is the focus of this chapter. Details regarding bio-optical signatures of phytoplankton and their spectral absorption, scattering and fluorescence characteristics are covered in Chapter 13, this volume. Details of how phytoplankton adjust their pigments in response to variation in light climate are reviewed in Chapter 11, this volume. Phytoplankton blooms cover spatial scales that vary from patches of 1 m 2 to large blooms covering more than 1 × 10 6 km 2 (Franks, 1997; Smyth et al ., 2004; Schofield et al ., 2008). Related to the spatial scale is the temporal variability of these blooms (from minutes to years), depending on the physical and biological processes at a given location. The development of techniques for monitoring phytoplankton blooms at different geographical and temporal scales has evolved rapidly in recent years (Kahru and Brown, 1997; Schofield et al ., 1999; Babin et al ., 2008). Because of the wide range in scale, different methods and approaches (different sensors and corresponding platforms) are needed for monitoring water masses and associated phytoplankton blooms as a function of environmental change (i.e. temperature, salinity, circulation and light regime), biogeochemical cycling, eutrophication, ocean acidification and pollution. Globally, monitoring of phytoplankton bloom dynamics is important to estimate changes in primary productivity affecting carbon and nutrient cycling in the world oceans.

Optical Phytoplankton Discriminator (OPD, a.k.a. BreveBuster) determines colored dissolved organic material (CDOM) absorption spectra and particulate light absorbance spectra. The CDOM absorption spectra and correlation coefficients (referred to as 'similarity indexes') between the particulate absorbance spectra and known phytoplankton classes are available in real-time. Post-deployment processing calculates the best fit of multiple absorbance spectra from known phytoplankton taxonomic classes. Through this process the OPD provides an estimate of the phytoplankton community chlorophyll distribution among the classes included in the fit process. The major components of the OPD include: a liquid-waveguide capillary cell (LWCC), a fiber-optic spectrometer, a tungsten-deuterium fiber-optic light and a 0.2 micrometer pore cross-flow filter. In-water operation of the OPD began in May 2003. Since that date 25 of these instruments have been deployed on a variety of autonomous underwater vehicles, buoys, piers, channel markers and boats and ships. It has been utilized in CDOM studies off the New Jersey coast, in HAB monitoring efforts in the Gulf of Mexico and the Great Lakes, and in phytoplankton community structure studies in the Galapagos Islands and the Mediterranean Sea. Most recently, it has been deployed to Veracruz, Mexico for HAB monitoring. Presently, several OPD's operating on Slocum gliders and coastal buoys make up a local HAB observatory south of Tampa Bay, Florida, partially supported by the NOAA/IOOS through GCOOS. This presentation will detail the OPD's capabilities and report results from several of the deployments listed above. The ongoing effort to effectively visualize 4-D phytoplankton community structure will be discussed.

signals with phase speeds of O(10) and O(100 to 300) km day −1 and time scales of 2 to 3 weeks. The signals with slow phase speed are only observed in southern California. It is hypothesized that they are scattered and reflected by shoreline curvature and bathymetry change and do not penetrate north of Point Conception. The seasonal transition of alongshore surfacecirculationforcedbyupwelling‐favorablewindsandtheirrelaxationiscapturedinfine detail.Submesoscaleeddies,identifiedusingflowgeometry,haveRossbynumbersof0.1to3, diameters in the range of 10 to 60 km, and persistence for 2 to 12 days. The HFR surface currents resolve coastal surface ocean variability continuously across scales from

[1] During spring and summer time, coastal upwelling influences circulation and ecosystem dynamics of the Monterey Bay, California, which is recognized as a National Marine Sanctuary. Observations of physical, bio-optical properties (including bioluminescence) together with results from dynamical biochemical and bioluminescence models are used to interpret the development of the upwelling event during August 2003 in Monterey Bay, California. Observations and the biochemical model show the development of a phytoplankton bloom in the southern portion of Monterey Bay. Model results show an increase of nutrients in the southern portion of the bay, where nutrient-rich water masses are brought in by the southward flow and cyclonic circulation inside the bay. This increase in nutrients together with the sluggish circulation in the southern portion of the bay provides favorable conditions for phytoplankton growth. Our observations and models suggest that with the development of upwelling the offshore water masses with the subsurface layer of bioluminescent zooplankton were replaced by water masses advected from the northern coast of the bay with a relatively high presence of mostly nonbioluminescent phytoplankton. Inshore observations from autonomous underwater vehicles (AUVs) show consistent coincidence of chlorophyll, backscatter, and bioluminescence maxima during upwelling development. Offshore AUV observations (taken at the entrance to the bay) show a deeper bioluminescence maximum below the surface layers of high chlorophyll and backscatter values during the earlier stages of upwelling development. Later, the observed deep offshore bioluminescence maximum disappeared and became a shallower and much weaker signal, coinciding with high chlorophyll and backscatter values offshore. Based on the biochemical and bioluminescence models, a methodology for estimating the nighttime water-leaving radiance due to stimulated bioluminescence is demonstrated and evaluated.

Autonomous buoyancy-driven gliders are becoming an increasingly important platform for the Navy for semi-continuous oceanographic observations. These observations are central to enhancing ocean model forecasting, underwater communications, underwater imaging, and a host of other applications. In order to provide these functions, it is critical that the flight characteristics be maintained for duration, spatial coverage and navigation. Currently, a number of the glider systems in use suffer in flight performance from biofouling, and this problem is exacerbated if the vehicle spends more time near coastlines or near the surface where there is enhanced biological activity. Here, we propose to leverage an existing ONR biofouling program (Code 34) to examine and evaluate the coatings of the 3 glider types currently in use. These evaluations will be compared to each other as well as the nontoxic coatings being evaluated under the biofouling program. These results have the potential to significantly increase the endurance and performance of gliders with direct benefits to the Navy.

We propose to continue our work coupling Unmanned Underwater Vehicle (UUV) and other coastal observations with a 3D hydrodynamic model (DELFT-3D FLOW) to investigate circulation and transport of coastal source material. While coastal areas near riverine discharge have traditionally been difficult to sample, UUVs with advanced sensor technology afford the opportunity to systematically study the dynamic components of these systems. Highly resolved measurements of circulation patterns, in water components, bottom topography and characterization will be coupled with the modeling effort. This combination will allow UUV guidance and improve model performance. It is hoped that the integration of mobile systems for localized modeling will be a "system" that is portable to other systems to help advance our understanding of circulation patterns and mechanisms for change in bottom topography and morphology.

Climate change will alter marine ecosystems; however, the complexity of the food webs, combined with chronic undersampling, constrains efforts to predict their future and to optimally manage and protect marine resources. Sustained observations at the West Antarctic Peninsula show that in this region, rapid environmental change has coincided with shifts in the food web, from its base up to apex predators. New strategies will be required to gain further insight into how the marine climate system has influenced such changes and how it will do so in the future. Robotic networks, satellites, ships, and instruments mounted on animals and ice will collect data needed to improve numerical models that can then be used to study the future of polar ecosystems as climate change progresses.

Mature striped bass (Morone saxatilis) were collected from the spawning reaches of the Choptank River, Maryland for the purpose of evaluating stress effects associated with capture. Two commonly used capture devices were evaluated—gillnetting and electrofishing. Results indicated that stress, as measured by changes in plasma corticosteroid and chloride concentrations, was significantly lower and recovery time quicker in those fish captured by electrofishing compared to gillnetting. By the end of the study period (48 h), those fish captured by electrofishing had recovered from the initial capture shock as evidenced by corticosteroid levels returning to near baseline levels. Conversely, at 48 h post-capture, those fish captured by gillnetting exhibited severe hypochloremia and elevated corticosteroid levels approaching that of the initial stress associated with capture.

To investigate the connectivity between central California marine protected areas (MPAs), back-projections were calculated using the network of high-frequency (HF) radar ocean surface current mapping stations operated along the California coast by the member institutions of the Coastal Ocean Currents Monitoring Program with funding provided by California voters through Propositions 40 & 50 and administered by the State Coastal Conservancy. Trajectories of 1 km resolution grids of water particles were back-projected from ten MPAs each hour, out through 40 days in the past, from each day in 2008, producing a map of where surface waters travel over a 40-day period to reach the MPAs — and visualizations of the length of time the waters travel along these paths. By comparing the travel times of those back-projected track-points that crossed between MPA regions, the connection time between MPAs along the State's central coast was assessed. Repeating these calculations resulted in a connectivity matrix between the MPAs in the region, and may be useful for assessing connectivity for the important invertebrate and fish larvae that are restricted to the surface ocean during a fraction of their lifecycle.

The Underwater Bioluminescence Assessment Tool (U-BAT) is a small, lightweight, platform-adaptable, bioluminescence sensor for use in coastal and open ocean environments. As part of the Office of Naval Research sponsored Small-business Technology Transfer (STTR) program, WET Labs developed a commercially available bioluminescence sensor, evolved from the Multipurpose Bioluminescence Bathyphotometer third generation (MBBP-G3) technology developed at the University of California, Santa Barbara (UCSB). UBAT provides a scalable, reliable, and accurate measure of mechanically stimulated bioluminescence potential in units of photons Γ1 capable of measuring less than 1 m fine-scale vertical resolution. The objectives of this work are: 1) to highlight the importance of long-term bioluminescence measurements and show that bioluminescence, in conjunction with other inherent optical properties (IOPs) can provide a more complete picture of spatial and temporal variability of biogeochemical complexity of coastal and ocean ecosystems, and 2) to provide the potential user with general knowledge of the effect of biofouling on the measurement of bioluminescence and 3) to describe general maintenance and service requirements necessary to maintain bioluminescence data quality over long deployment periods. A commercial UBAT prototype built by WET Labs, Inc., has been deployed since 2007 on an autonomous profiling system located at the California Polytechnic State University (Cal Poly) research facility in Avila Beach, CA. The pier is an excellent test facility and is constructed of concrete and steel and extends over 1 km into San Luis Obispo Bay. The pier is 10 meters above the water where the depth of the water is 12–14 m. Sea water quality is high and provides a rich biota for research. This region is well known for its dynamic seasonal bioluminescence community which is composed of both bioluminescent Zooplankton and phytoplankton species. Vertical profiles of bioluminescence were collected every half hour along with chlorophyll fluorescence, turbidity, beam-C, conductivity, temperature, and salinity measurements. Over the deployment period, intense blooms of bioluminescence were observed and at times bioluminescence was inversely correlated with chlorophyll fluorescence and turbidity. Thus, bioluminescence, in conjunction with other IOPs, can provide a more complete picture of spatial and temporal variability of biogeochemical complexity of coastal and ocean ecosystems, particularly for the response of the planktonic community to environmental fluctuations. By broadening the use of bioluminescence measurements the UBAT will significantly increase general understanding of the roles of bioluminescence in oceanic biodynamics. Long-term deployments necessary for ecosystem monitoring require frequent system maintenance to ensure high-quality data. Prior to leaving the factory, UBAT bioluminescence light detection system and flow rate are calibrated with NIST traceable standards. Over a deployment period, increased bio-fouling typically decreases the signal accuracy. To track changes in the quality of measured bioluminescence, a validation light source is provided with each UBAT that is powered and controlled by the UBAT. The effect of biofouling on the quality of measured bioluminescence and flow rate are compared for two UBATs deployed in coastal regions, under different deployment regimes. In Avila Beach, CA, UBAT is deployed on an autonomous profiler package that is maintained outside of the water and automatically rinsed with fresh water between profiles which reduces biological growth on the sensors and the effect of biofouling on the data quality. In Yaquina Bay, OR, UBAT is deployed at a WET Labs test facility and maintained in the water during a period of peak biological growth. Yaquina Bay is a small drowned river estuary draining a 658 square km watershed located along the central Oregon coast that is very productive and also has dynamic seasonal periods for biological growth. Design changes applied to the UBAT in Yaquina Bay, OR, compared to the earlier model at Avila Beach, CA are intended to reduce the effect of biofouling. The composition of the material used for the detection chamber walls is the primary difference between the UBATs. The detection chamber of the UBAT deployed in Avila Beach, CA is composed of virgin Teflon, whereas the UBAT deployed in Yaquina Bay, OR is molded polyurethane loaded with 20% titanium dioxide. We expect that the titanium dioxide has improved anti-biofouling properties. A secondary design change was to the light baffle at the sensor exhaust. The exhaust baffle of the UBAT deployed in Avila Beach, CA is more restricted whereas the exhaust baffle of the UBAT deployed in Yaquina Bay has a 3-turn helical baffled with a copper exhaust cover. Recommendations for the frequency and method of maintenance, techniques to improve data quality and analysis of the employed anti-biofouling techniques will be discussed.

The development and implementation of a real-time ocean forecast system based on the Regional Ocean Modeling System (ROMS) off the coast of central California are described. The ROMS configuration consists of three nested modeling domains with increasing spatial resolutions: the US West coastal ocean at 15-km resolution, the central California coastal ocean at 5 km, and the Monterey Bay region at 1.5 km. All three nested models have 32 vertical sigma (or terrain-following) layers and were integrated in conj. unction with a three-dimensional variational data assimilation algorithm (3DVAR) to produce snapshots of the ocean state every 6 h (the reanalysis) and 48-h forecasts once a day. This ROMS forecast system was operated in real time during the field experiment known as the Autonomous Ocean Sampling Network (AOSN-II) in August 2003. After the field experiment, a number of improvements were made to the ROMS forecast system: more data were added in the reanalysis with more careful quality control procedures, improvements were made in the data assimilation scheme, as well as model surface and side boundary conditions. The results from the ROMS reanalysis are presented here. The ROMS reanalysis is first compared with the assimilated data as a consistency check. An evaluation of the ROMS reanalysis against the independent measurements that are not assimilated into the model is then presented. This evaluation shows the mean differences in temperature and salinity between reanalysis and observations to be less than 1 degrees C and 0.2 psu (practical salinity unit), respectively, with root-mean-square (RMS) differences of less than 1.5 degrees C and 0.25 psu. Qualitative agreement is found between independent current measurements and the ROMS reanalysis. The agreement is particularly good for the vertically integrated current along the offshore glider tracks: the ROMS reanalysis can realistically reproduce the poleward California Undercurrent. Reasonably good agreement is found in the spatial patterns of the surface current as measured by high-frequency (HF) radars. Preliminary results concerning the ROMS forecast skill and predictability are also presented. Future plans to improve the ROMS forecast system with a particular focus on assimilation of HF radar current measurements are discussed. Jet Propulsion Laboratory, California Institute of Technology, under contract with the National Aeronautics and Space Administration (NASA) Office of Naval Research (ONR) through a subcontract from MBARI to Raytheon ONR’s program element 0601153N for J. Doyle Computational resources for COAMPS were supported in part by the FNMOC.

The long-term objective is to contribute to the development of the components of limited area, open boundary, coastal nowcast/forecast systems that will resolve the time and length scales of the relevant physical-biological dynamics in shallow coastal environments.

We propose to continue our work coupling Unmanned Underwater Vehicle (UUV) observations with a 3D hydrodynamic model (Delft3d-FLOW) to investigate circulation in a tidally dominated system. While these areas have traditionally been difficult to sample, UUVs with advanced sensor technology afford the opportunity to systematically study the dynamic components of these systems. Highly resolved measurements of circulation patterns, in water components, bottom topography and characterization will be coupled with the modeling effort. This combination will allow UUV guidance and improve model performance. It is hoped that the integration of mobile systems for localized modeling will be a "system" that is portable to other systems to help advance our understanding of circulation patterns and mechanisms for change in bottom topography and morphology.

One of the challenges for model prediction and validation is providing them with data of appropriate spatial and temporal resolution. The maturation and increased application of autonomous underwater vehicles (AUVs) in aquatic environments allows systematic data collection on these model-relevant scales. The goal of this study was to apply a fine-scale circulation and transport model (Delft3D) to improve AUV mission planning and use data collected by the AUV to evaluate and improve model performance. A dye release was conducted in a tidally dominated embayment, and a planning phase model based on the best available data was used as a baseline for evaluation and for AUV mission planning (forecast). The planning phase model correctly predicted the general shape and direction of the dye plume and allowed for successful mission planning. Subsequently, bathymetry data collected by the AUV was incorporated into the model (hindcast), with temperature and salinity collected before the experiment. Comparisons with fluorometer measurements from the AUV indicate that the model effectively predicted the edges of the plume and centerline location. The location was also confirmed by remote sensing from an aircraft. Thermal stratification was found to be an important fate mechanism in the final model, and the results demonstrate the integration of observational data sets for small, short-duration surface-contaminant releases. This study highlights the strength of a phased, iterative approach with observation platforms and may serve as a guide toward improving the performance and evaluation of future coastal hydrodynamic and transport modeling efforts. [References: 29]

Polar regions have experienced significant warming in recent decades. Warming has been most pronounced across the Arctic Ocean Basin and along the Antarctic Peninsula, with significant decreases in the extent and seasonal duration of sea ice. Rapid retreat of glaciers and disintegration of ice sheets have also been documented. The rate of warming is increasing and is predicted to continue well into the current century, with continued impacts on ice dynamics. Climate-mediated changes in ice dynamics are a concern as ice serves as primary habitat for marine organisms central to the food webs of these regions. Changes in the timing and extent of sea ice impose temporal asynchronies and spatial separations between energy requirements and food availability for many higher trophic levels. These mismatches lead to decreased reproductive success, lower abundances, and changes in distribution. In addition to these direct impacts of ice loss, climate-induced changes also facilitate indirect effects through changes in hydrography, which include introduction of species from lower latitudes and altered assemblages of primary producers. Here, we review recent changes and trends in ice dynamics and the responses of marine ecosystems. Specifically, we provide examples of ice-dependent organisms and associated species from the Arctic and Antarctic to illustrate the impacts of the temporal and spatial changes in ice dynamics.

[1] Nighttime water-leaving radiance is a function of the depth-dependent distribution of both the in situ bioluminescence emissions and the absorption and scattering properties of the water. The vertical distributions of these parameters were used as inputs for a modified one-dimensional radiative transfer model to solve for spectral bioluminescence water-leaving radiance from prescribed depths of the water column. Variation in the water-leaving radiance was consistent with local episodic physical forcing events, with tidal forcing, terrestrial runoff, particulate accumulation, and biological responses influencing the shorter timescale dynamics. There was a >90 nm shift in the peak water-leaving radiance from blue (∼474 nm) to green as light propagated to the surface. In addition to clues in ecosystem responses to physical forcing, the temporal dynamics in intensity and spectral quality of water-leaving radiance provide suitable ranges for assessing detection. This may provide the information needed to estimate the depth of internal light sources in the ocean, which is discussed in part 2 of this paper.

[1] Many bioluminescence observations are made from the ocean's surface. However, the depth of the bioluminescent source is difficult to estimate on the basis of surface observations alone, given the variable light attenuation of unknown concentrations of water column constituents such as phytoplankton, colored dissolved organic matter, and detritus. Part 1 of this paper showed that bioluminescent water-leaving radiance signals are detectable, even in extremely turbid and dynamic coastal waters. Here, in part 2 of this paper, we analyze the water-leaving radiance patterns of bioluminescence modeled by HydroLight 4.2 to determine if the depth of the bioluminescent source can be estimated from its spectral signature. We find that the depth of the bioluminescent source is contained within the spectral signal and can be elucidated by simple neural networks. These networks can predict the depth of a bioluminescent layer with great accuracy, solely on the basis of the spectral shape of bioluminescent water-leaving radiance in a variety of water column and bottom type conditions. In addition, we found that as little as three wavelengths from the spectrum of water-leaving radiance are sufficient for an accurate determination of the depth of the bioluminescent source.

We propose to continue our Unmanned Underwater Vehicle (UUV) work to investigate circulation and bottom morphology in tidal flats and surrounding environments. While these areas have traditionally been difficult to sample, UUVs with advanced sensor technology afford the opportunity to systematically study the dynamic components of these systems. Our deployments of the REMUS UUV in coastal waters of the Pacific, Atlantic and Gulf of Mexico demonstrate the ability of this platform to operate routinely in VSW environments, including harbors, estuaries, and the near shore/surf zone transition. Highly resolved measurements of circulation patterns, in water components, bottom topography and characterization will be taken in the specific study sites chosen for this DRI. These data will support the general goals of this DRI in identifying and advancing our understanding of mechanisms for morphologic change in tidal mud flats.