Brian Dzwonkowski

Development and application of a neural network based ocean colour algorithm in coastal waters

An algorithm for determining chlorophyll‐a concentrations in shallow, case II waters has been developed and applied to nearly six years of Sea‐viewing Wide Field‐of‐view Sensor (SeaWiFS) data in order to observe the general chlorophyll‐a patterns in a coastal estuarine environment. Due to the fact that the current empirical chlorophyll‐a algorithm (OC4) used to process SeaWiFS data breaks down in coastal waters, a neural network based algorithm was developed. The neural network in the study uses SeaWiFS remote sensing reflectance data paired with in situ chlorophyll‐a data in the Delaware Bay and its adjacent coastal zone (DBAC) from a number of different days and seasons in an effort to overcome the limitations of single day algorithms and simulated dataset algorithms. Although the neural network model (NN) in this study displayed some difficulty representing high chlorophyll‐a values, it showed significant improvement over the OC4 algorithm. The performance parameters of the NN were an r 2 of 0.79, a root mean square (RMS) error of 3.69 mg m−3 and a relative RMS error of 0.77. The NN was used to reprocess approximately six years of cloud free imagery of the DBAC from which the spatial and temporal variability of the chlorophyll‐a distributions in the DBAC were analysed. Time series of absolute chlorophyll‐a values for five stations along the central axis of the Delaware Bay were analysed using Fourier analysis techniques, from which chlorophyll‐a patterns were found to have a quasi‐annual period. Furthermore, the spatial distributions of the chlorophyll‐a patterns were analysed using a general climatology and monthly climatologies of normalized chlorophyll‐a values. The climatologies generally agreed with spatial distributions determined from historic ship‐based data. The study found that summer blooms in the mid‐estuary of the Delaware Bay may be more important than previously observed. This suggests that more frequent and synoptic measurements via satellite can reveal important new information about even well studied regions.

Seasonal differences in wind‐driven across‐shelf forcing and response relationships in the shelf surface layer of the central Mid‐Atlantic Bight

National Atmospheric and Oceanographic Administration [NA17EC2449]; NASA-Space [NNG05GO92H]; NOAA-SG [NA09OAR4170070]; NASA [NNG05GO92H, NNX08AW02A, NNX09AF33G]

Subtidal across-shelf velocity structure and surface transport effectiveness on the Alabama shelf of the northeastern Gulf of Mexico

[1] A 3.33 year time series of velocity and hydrographic data from a mooring site on the 20 m isobath of the Alabama shelf in the northeastern Gulf of Mexico are used to examine across‐shelf circulation. The flow structure and surface transport are determined on this wide shallow shelf system, in which wind stress is a primary forcing mechanism, over a wide range of environmental conditions. The relatively long data set allows the along‐ and across‐shelf wind stress responses to be separated so that their individual contributions to the flow structure can be analyzed. This study finds that both along‐ and across‐shelf wind stress play a role in the across‐shelf circulation. While the along‐shelf wind is correlated with the currents during all seasons, the across‐shelf shelf wind is most clearly correlated with the currents during fall and winter when the water column is least stratified and the across‐shelf wind stress is strongest. In addition, wind stress magnitude, mid‐depth vertical shear of the horizontal velocity, and stratification all show significant relationships with across‐shelf transport effectiveness to varying degrees. The wide range of stratification conditions provides new insight on the influence of stratification on transport effectiveness and across‐shelf wind stress forcing. Under very low stratification conditions, there is no apparent relationship between stratification and transport effectiveness, and across‐shelf wind stress can generate a significant forcing contribution. As stratification increases, across‐shelf wind stress becomes less important and the transport effectiveness increases to a point, above which, there is again no clear relationship with stratification.

Development of a Low-Cost Arduino-Based Sonde for Coastal Applications

This project addresses the need for an expansion in the monitoring of marine environments by providing a detailed description of a low cost, robust, user friendly sonde, built on Arduino Mega 2560 (Mega) and Arduino Uno (Uno) platforms. The sonde can be made without specialized tools or training and can be easily modified to meet individual application requirements. The platform allows for internal logging of multiple parameters of which conductivity, temperature, and GPS position are demonstrated. Two design configurations for different coastal hydrographic applications are highlighted to show the robust and versatile nature of this sensor platform. The initial sonde design was intended for use on a Lagrangian style surface drifter that recorded measurements of temperature; salinity; and position for a deployment duration of less than 24 h. Functional testing of the sensor consisted of a 55 h comparison with a regularly maintained water quality sensor (i.e., YSI 6600 sonde) in Mobile Bay, AL. The temperature and salinity data were highly correlated and had acceptable RMS errors of 0.154 °C and 1.35 psu for the environmental conditions. A second application using the sonde platform was designed for longer duration (~3–4 weeks); subsurface (1.5–4.0 m depths) deployment, moored to permanent structures. Design alterations reflected an emphasis on minimizing power consumption, which included the elimination of the GPS capabilities, increased battery capacity, and power-saving software modifications. The sonde designs presented serve as templates that will expand the hydrographic measurement capabilities of ocean scientists, students, and teachers.

Multiscale analysis of factors that affect the distribution of sharks throughout the northern Gulf of Mexico

Identification of the spatial scale at which marine communities are organized is critical to proper management, yet this is particularly difficult to determine for highly migratory species like sharks. We used shark catch data collected during 2006–09 from fishery-independent bottom-longline surveys, as well as biotic and abiotic explanatory data to identify the factors that affect the distribution of coastal sharks at 2 spatial scales in the northern Gulf of Mexico. Centered principal component analyses (PCAs) were used to visualize the patterns that characterize shark distributions at small (Alabama and Mississippi coast) and large (northern Gulf of Mexico) spatial scales. Environmental data on temperature, salinity, dissolved oxygen (DO), depth, fish and crustacean biomass, and chlorophyll-a (chl-a) concentration were analyzed with normed PCAs at both spatial scales. The relationships between values of shark catch per unit of effort (CPUE) and environmental factors were then analyzed at each scale with co-inertia analysis (COIA). Results from COIA indicated that the degree of agreement between the structure of the environmental and shark data sets was relatively higher at the small spatial scale than at the large one. CPUE of Blacktip Shark (Carcharhinus limbatus) was related positively with crustacean biomass at both spatial scales. Similarly, CPUE of Atlantic Sharpnose Shark (Rhizoprionodon terraenovae) was related positively with chl-a concentration and negatively with DO at both spatial scales. Conversely, distribution of Blacknose Shark (C. acronotus) displayed a contrasting relationship with depth at the 2 scales considered. Our results indicate that the factors influencing the distribution of sharks in the northern Gulf of Mexico are species specific but generally transcend the spatial boundaries used in our analyses.

Environmental Influences on Juvenile Fish Abundances in a River-Dominated Coastal System

Abstract We investigated the influence of climatic and environmental factors on interannual variations in juvenile abundances of marine fishes in a river-dominated coastal system of the north-central Gulf of Mexico, where an elevated primary productivity sustains fisheries of high economic importance. Fish were collected monthly with an otter trawl at three stations near Mobile Bay from 1982 to 2007. Fish sizes were used to isolate juvenile stages within the data set, and monthly patterns in juvenile fish abundance and size were then used to identify seasonal peaks for each species. The average numbers of juvenile fish collected during these seasonal peaks in each year were used as indices of annual juvenile abundances and were related to corresponding seasonal averages of selected environmental factors via a combination of principal components analysis and co-inertia analysis. Factors contributing the most to explain interannual variations in juvenile fish abundances were river discharge and water temperature during early spring—early summer, wind speed and North Atlantic Oscillation index during late fall—winter, and atmospheric pressure and wind speed during summer—fall. For example, juvenile abundances of southern kingfish Menticirrhus americanus during summer—fall were positively associated with atmospheric pressure and negatively associated with wind speed during this period. Southern kingfish juvenile abundances during late fall—winter were also negatively associated with wind speed during the same period and were positively associated with river discharge during early spring—early summer. Juvenile abundances of the Atlantic croaker Micropogonias undulatus during early spring—early summer were negatively associated with river discharge and North Atlantic Oscillation during late fall—winter. Overall, the importance of river discharge for many of the species examined emphasizes the major role of watershed processes for marine fisheries production in coastal waters of the north-central Gulf of Mexico.

The coupled estuarine‐shelf response of a river‐dominated system during the transition from low to high discharge

Opportunistic observations captured the coupled estuarine-shelf interactions as the Alabama coastal region transitioned from a period of low to flood river discharge conditions. The period of focus was 18 February to 10 April 2011 during which time a combination of in situ (water level, salinity and velocity) and remote sensing (ocean color) data provided information on the estuarine and shelf environment prior to, during, and post a major river discharge event that captured a relatively rare spatially synoptic view of the structural evolution of a discharge plume in response to changing forcing conditions. The discharge event generated major changes in the hydrographic conditions and forcing responses within the estuary and on the shelf. The resulting surface advected plume was observed for approximately two weeks, during which time the observed differences in shelf circulation were directly linked to the discharge plume and a plume bulge with anticyclonic circulation was identified at times throughout the event. The plume was exposed to a range of wind conditions which modulated the surface structure: downwelling winds elongated the plume structure and upwelling winds reversed and widened the plume. The influence of wind forcing, even during very low wind (<3.75 m s−1) and large outflow (∼7000 m3 s−1) conditions, was apparent, as a result of the shallow and wide characteristics of the plume. Anticyclonic bulge regions have only been identified in a few systems and the occurrence of this feature on the Alabama shelf has significant implications on transport and fate of river discharge in this region.

Water Level and Velocity Characteristics of a Salt Marsh Channel in the Murderkill Estuary, Delaware

ABSTRACT Dzwonkowski, B.; Wong, K.-C., and Ullman, W.J., 2014. Water level and velocity characteristics of a salt marsh channel in the Murderkill estuary, Delaware. High-frequency observations of water level and velocity over one year in Murderkill estuary, a tributary estuary of Delaware Bay, are used to examine changes in tidal and subtidal flow characteristics as water propagates from the mouth of the estuary (Bowers site) into a minor channel that connects to a contiguous salt marsh (channel site), a setting where long-term continuous data sets are uncommon. These data provide insight into the flow behavior in marsh channels, the driving mechanisms of water exchange, and the potential for particle and solute exchange between tidal marshes and their adjacent estuaries. At both sites, tidal forcing is normally the dominant driving mechanism in water level and velocity signals with remote wind forcing having a limited contribution. As the tidal signal propagates from the Bowers site into the salt marsh, however, the progressive-type mixed wave is transformed into a standing wave with minor velocity distortions resulting from a reduction in the M2 tidal constituent as well as an amplification of the M4 overtide. The variability at both sites is typically well explained as a linear superposition of high-frequency tidal constituents and remotely forced wind-driven subtidal fluctuations. During storm events at intermediate to spring tides, however, both tidal and subtidal velocity characteristics in the channel are more nonlinear compared to both typical channel conditions and those at the Bowers site. During these events, in response to remote winds, tidal flow in the channel becomes progressive in form and flood dominant, while subtidal velocities are ebbward and nearly an order of magnitude stronger than typical conditions.

Inflow of shelf waters into the Mississippi Sound and Mobile Bay estuaries in October 2015

Abstract. The exchange of coastal waters between the Mississippi Sound (MSS), Mobile Bay, and Mississippi Bight is an important pathway for oil and pollutants into coastal ecosystems. This study investigated an event of strong and persistent inflow of shelf waters into MSS and Mobile Bay during October 2015 by combining in situ measurements, satellite ocean color data, and ocean model predictions. Navy Coastal Ocean Model predicted high-salinity shelf waters continuously flowing into the estuarine system and forecasted low-salinity waters trapped inside the estuaries which did not flush out until the passage of tropical cyclone Patricia’s remnants in late October. The October 2015 chlorophyll-a anomaly was significantly low inside and outside the MSS for the 2003 to 2015 time series. Similar low-chlorophyll-a anomalies were only seen in 2003. The October 2015 mean in situ salinities were up to 8 psu higher than mean from 2007 to 2015, and some estuarine stations showed persistent salinities above 30 psu for almost a month in agreement with model predictions. October 2015 was associated with low fall seasonal discharge, typical of fall season, and wind which was persistently out of the east to southeast [45–180]°. These persistent wind conditions were linked to the observed anomalous conditions.

Data processing for a small‐scale long‐term coastal ocean observing system near Mobile Bay, Alabama

The oceanographic community routinely collects time series data of hydrography, water current velocity, and other basic physical, chemical, and biological properties of the marine environment. Such data are essential for establishing baseline characteristics of marine and estuarine ecosystems. However, the task of taking the raw data files as downloaded from a variety of instruments from multiple manufacturers, and converting them into file formats that can be used to address specific research questions, can be highly complex and time consuming. To illustrate some of these complexities, we have thoroughly documented the data processing steps for a small coastal ocean observing system near Mobile Bay, Alabama, that has been in operation since 2004. Our goals were to produce documentation and data provenance in sufficient detail for full science reproducibility of all studies that use data from this system, provide a template for other ocean observation operations, and highlight a need for better recognition of the significant amount of time and expertise often required to do both the data processing and the documentation for long-term observational systems.