I investigated the emergence of marine benthic harpacticoid and cyclopoid copepods from subtidal sediment into the bottom water. Previous field studies with traps found that copepods emerge from the sediment within 2 h of dusk. I examined emergence in 20-min periods from 1200 h to 0100 h (13 h) in a laboratory flume under conditions of constant flow velocity and in-situ salinity and temperature. Light intensity was adjusted to field conditions every 20 min. I observed the largest peak in benthiccopepod emergence during the 20-min sampling period corresponding to the onset of darkness. This result will help set the stage for studies of emergence cues. The synchronicity of emergence observed in our study may be an antipredation strategy to swamp potential predators, reducing the probability of any one individual being consumed. / A Thesis Submitted to the Department of Oceanography in Partial Fulfillment of the Requirements for the Degree of Master of Science. / Fall Semester, 2003. / July 31, 2003. / Laboratory Study, Flume, Copepod, Benthic / Includes bibliographical references. / David Thistle, Professor Directing Thesis; Joel Kostka, Committee Member; Nancy Marcus, Committee Member.

Naturally-occurring radioisotopes are ubiquitous in nature, and as such, there are many opportunities for researchers to use them as environmental tracers. Their associated radioactive decay rates provide an inherent time clock that often makes these radioisotopes more effective chemical tracers than other substances, since they can help assess the temporal component of a particular process. Radioisotopes were employed in this study to examine different coastal oceanographic processes that have far reaching consequences. A review of various measurement methods for assessing Ra-226 concentrations, a valuable tracer employed throughout most of this dissertation, is presented. This is followed by applying natural radioisotopes to study various oceanographic processes in China, Hawaii, and a river system in the southeastern United States. Acrylic fibers impregnated with manganese-dioxide ('Mn-fiber') have become a valuable tool for concentrating dissolved radium for oceanographic applications. Several techniques have been outlined in the literature describing the measurement of Ra-226 on Mn-fiber via its gaseous daughter, Rn-222. We describe procedures for three radon-based non-destructive measurement techniques for Ra-226 on Mn-fiber (via RAD7, RaDeCC, and Rn emanation line systems) and perform an intercomparison among them, using the standard technique of gamma-spectrometry as a reference. We find that all methods agree in terms of the measured activity, with the respective correlation coefficients (r) between any two different methods ranging from 0.78 to 0.93. The methods vary in their advantages, with the Rn emanation line and RaDeCC techniques offering the best measurement uncertainties and lowest minimum detection activities, while the RAD7 method is the least operator-demanding technique. In the reported field activities, radium isotopes were mapped around the mouth of the Yellow River in China to examine the transport rates of Yellow River water through the estuary and into the Bohai Sea during three different field excursions, covering a large range in the discharge patterns of the river. Using radium isotope ratios, horizontal transport rates ranging from 1.4 to 4.7 cm/s were found throughout the delta and apply over most of the discharge range of the river while exhibiting no seasonal variability. Time series analyses of radium isotopes and Rn-222 were also used near the Yellow River delta to assess submarine groundwater discharge (SGD) rates. Modeled vertical SGD rates in this area varied between 4 and 20 cm/day during the sampling periods, thus delivering significant volumes of groundwater containing elevated concentrations of nutrients to the coastal zone. We combine these results to show that the dissolved freshwater nitrate inputs (riverine and SGD) around the Yellow River delta cannot be directly transported to the central Bohai Sea (where increasing nitrate levels have been documented) before being biologically or otherwise removed. Rn-222 was the main tracer employed to examine groundwater discharge along the leeward coast of the Big Island of Hawaii. Here, geological formations act to direct coastal aquifer waters to point-source discharges, forming buoyant plumes of freshwater extending out into the coastal waters. A box model was created using mass balance of radon, salt, and water to assess the discharge rates of these plumes. The point-source inputs were found to discharge thousands of cubic meters of brackish water to the coastal zone each day, ranging from 1100 m3/day to 12,000 m3/day of total water fluxes. The purely freshwater components of these discharges varied from 630 m3/day to 8600 m3/day. Considering possible sources of nutrient and industrial contamination in this area, these discharges can significantly affect the local reefs and ecosystems along this coast. A particle tracing project was performed in the Apalachicola-Chattahoochee-Flint River system in the southeastern United States. The river system empties into Apalachicola Bay in northwest Florida, a biodiverse and economically valuable ecosystem to the state of Florida. We applied various naturally-occurring radionuclides as tracers to reveal suspended particle transport behavior under both base flow (June 2006) and high discharge conditions (February 2007). Potassium-40 activities are used to assess the lithogenic/crustal fractions of each suspended sediment sample (ranging from 4-60%), whereas the organic fraction ranges from 4 to 32% by mass. Particulate radium isotopes (namely Ra-226 and Ra-228) were employed to trace the origin of the suspended particle flux to Apalachicola Bay. During low discharge, the Flint River dominates the particulate flux to Apalachicola Bay (70%), whereas the Chattahoochee River contributes 30% of the flux and the Apalachicola River is net depositional. During high discharge, the Chattahoochee River contributes the majority of the suspended particles (56%), with the Apalachicola River contributing 30% and the Flint River only providing 14% of the particulate flux. The Be-7/Pb-210 activity ratios were used to assess the residence time of suspended particles in upstream reservoirs (5.2 days in Lake Blackshear and 60 days in West Point Lake), and also to examine open channel transport velocities (~ 13 cm/sec in the lower Flint River) during high discharge. / A Dissertation Submitted to the Department of Oceanography in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy. / Spring Semester, 2009. / January 30, 2009. / Radioisotopes, Radium, Radon, Submarine Groundwater Discharge / Includes bibliographical references. / William C. Burnett, Professor Directing Dissertation; Joseph F. Donoghue, Outside Committee Member; Jeffrey P. Chanton, Committee Member; Philip N. Froelich, Committee Member; Kevin G. Speer, Committee Member; Stephen Opsahl, Committee Member.

I examined the acoustic ecology of coastal bottlenose dolphins (Tursiops truncatus) in the Big Bend region of Florida and compared it to other populations of dolphins found in similar habitats. This region is one of the most acoustically pristine coastal environments in Florida, marked by little human activity. Historically this region's dolphin population has not been studied, leaving a gap in our knowledge of these animals. Acoustic recordings were collected as part of photo-identification and habitat-use surveys, and then categorized into fall, winter, spring, and summer seasons. Whistle rates were highest in spring, even when normalized for group size. Echolocation rates were not different between seasons over both years, but individual years had differences. Interestingly, burst pulse sounds and pops rarely occurred. Bottlenose dolphins are not the only source of noise in their marine habitat, so to understand the acoustic environment of these animals, human- and fish-produced sounds were also considered. Remote autonomous acoustic recorders were deployed at eight sites in the Big Bend region and each location was found to have a unique soundscape with respect to dolphin, fish, snapping shrimp, and human-produced sound. Toadfish (Opsanus beta), sea catfish (Arius felis), and silver perch (Bairdiella chrysoura) were the only identifiable fish species to produce sound and caused notable increases in sound levels at low frequencies where they vocalized. There were twelve unidentifiable biological sounds; all exhibit properties of fish or invertebrate produced sounds. Locations exhibited different temporal peaks in fish sound production. Overall, human-produced noise was uncommon and only found in the form of boat noise, but when present it greatly increased sound levels, especially in low frequencies. Dolphin vocalizations were not found at all locations, however, the lack of dolphin vocalizations does not necessarily mean that dolphins were not present in these regions. This study confirmed that the region is relatively acoustically pristine. / A Thesis Submitted to the Department of Oceanography in Partial Fulfillment of the Requirements for the Degree of Master of Science. / Spring Semester, 2007. / March 22, 2007. / Marine Mammal, Bottlenose Dolphin, Acoustics / Includes bibliographical references. / Douglas Nowacek, Professor Directing Thesis; David Mann, Committee Member; Louis St. Laurent, Committee Member.

Bacteria serve as traditional indicators of water quality. In the past decade, methods have been developed to explore the use of more human specific indicators. One of these suggested indicators is caffeine. Caffeine is widely consumed in populated areas and has already been proven as a successful indicator in freshwater systems. This project aimed to modify the caffeine extraction method to obtain ng/L detection limits and prove its usefulness as a tracer in marine systems. Optimal extractions were performed with solid phase extraction using traditional C-18 sorbent columns. Extracts were then run on a GC/MS. Freshwater samples were examined in this project to determine a background level of caffeine in relatively isolated areas. Analysis of samples from creeks in southwest Georgia did not detect caffeine. An isolated wetland sample did contain caffeine and led to the identification of a natural local source of caffeine, the Yaupon Holly. Samples were also collected along the Ochlockonee river system. Some of its tributaries known to have treated wastewater effluent were also sampled. Samples from these tributaries contained measurable caffeine, but caffeine was not found in the main stem. The marine system sampled was Sarasota Bay, Florida. There was no interference of salts in marine samples to compromise the method. Caffeine concentrations were found to be highest along the mainland side of the bay, where septic systems were suspected sources of contamination. Caffeine had an inverse relationship with salinity and conductivity and positive correlations with nutrient concentrations. Fecal coliforms correlated well with caffeine, but not with the more resilient enterococcus bacterium. Samples of groundwater were analyzed and proved a definite source of caffeine to this system. A degradation experiment found that in a natural sample of marine water exposed to sunlight, caffeine has a half-life of approximately 30 days. However, for samples kept in the dark the half-life increases to 71 days, and samples refrigerated at a constant 4oC and in the dark have a half-life of 178 days. / A Thesis Submitted to the Department of Oceanography in Partial Fulfillment of the Requirements for the Degree of Masters of Science. / Fall Semester, 2004. / October 20, 2004. / solid phase extraction, GC/MS, natural sources, degradation, source indicator, caffeine, Ochlockonee River, Sarasota Bay, groundwater seepage / Includes bibliographical references. / Jeffrey Chanton, Professor Co-Directing Thesis; Steven Opsahl, Professor Co-Directing Thesis; William Burnett, Committee Member.

The Field Research Center (FRC) in Oak Ridge, TN, was established by the U.S. Department of Energy's Natural and Accelerated Bioremediation Research (NABIR) Program to develop strategies for bioremediation of contaminant metals and radionuclides. The FRC is centered on groundwater plumes that originate from former S-3 Waste Disposal Ponds located at the Y-12 Plant where acidic nitrate- and uranium-contaminated waste was disposed. The groundwater and sediment surrounding this area are in need of remediation. To test the bioremediation potential of microorganisms in the contaminated FRC sediment, Fe(III)-reducing bacteria (FeRB) were enriched for, as they represent indigenous microorganisms capable of immobilizing uranium in situ. DNA was extracted from more than 20 Fe(III)-reducing enrichment cultures at both neutral and low pH. Through cloning and sequencing of 16S rRNA genes, considerable differences in phylotypes found in Fe(III)-reducing enrichments from background and contaminated FRC sediment were discovered. In the background Fe(III)- reducing enrichments (pH 7), over two-thirds of the 16S rRNA gene sequences obtained were closely related to members of the Geobacteraceae family. The cultivated isolates from this family are capable of Fe(III)-reduction, and are commonly found in sedimentary environments. However, sediment from the contaminated neutrophilic Fe(III)-reducing enrichments revealed that almost half of the 16S rRNA gene sequences were 96% similar to the newly described Fe(III)-reducing species Anaeromyxobacter dehalogenans, but no Geobacteraceae sequences were detected. In Fe(III)-reducing enrichments cultured at low pH (4 to 5), only 16S rRNA gene sequences closely related to Gram positive organisms were detected. From the contaminated sediment enrichment cultures at low pH, the most predominant 16S rRNA gene sequences retrieved were closely related to Gram positive organisms Brevibacillus and Paenibacillus. T-RFLP analysis of enrichment cultures strongly supported the sequencing results. Following the experiments with Fe(III)-reducing enrichment cultures, cultivation-independent studies were conducted using a quantitative method. Quantitative molecular techniques provided a direct determination of the abundance of selected groups of FeRB before and after sediment biostimulation. Using DNA extracted directly from the sediment, MPN-PCR was conducted to quantify the differences in abundance of Geobacter-, Anaeromyxobacter-, Paenibacillus-, and Brevibacillus- type sequences using primer sets specifically designed for these groups. The only sequences that increased in abundance after biostimulation were Geobacter-type 16S rRNA gene sequences. To account for other groups of stimulated organisms, cloning and sequencing was conducted in parallel with the quantitative PCR experiments. A large diversity of microorganisms from FRC sediment were revealed, including species from alpha, beta, delta, and gamma subdivisions of the Proteobacteria, as well as low and high G+C Gram positive species. Phylogenies suggesting certain physiologies, such as nitrate reduction, metal reduction, dechlorination, and degradation of metal-chelator complexes and fuel hydrocarbons were identified. Obvious trends in 16S rRNA gene sequences following the biostimulation of FRC sediments included an increase in sequences within the delta Proteobacteria, as well as the maintenance of a large abundance of sequences within the genus Methylobacterium, in the alpha Proteobacteria. Due to the diversity of organisms detected after biostimulation of contaminated sediments, we suggest that new model organisms should be pursued to aid in the ongoing development of bioremediation strategies for uranium contamination. / A Thesis submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Master of Science. / Summer Semester, 2003. / July 8, 2003. / Strategies For Bioremediation Contaminant Metals A / Includes bibliographical references. / David Balkwill, Professor Directing Thesis; Joel Kostka, Committee Member; Nancy Marcus, Committee Member; Sherry Dollhopf, Committee Member.

The input of potential vorticity (PV) over the Oceans is estimated from observations to produce a climatological map of PV flux and to study the interannual forcing variability. Particular attention is paid to the North Atlantic subtropical mode water potential temperature range from 17 to 19 ºC. The sea surface PV flux is estimated through buoyancy and wind stress contributions and using a climatological mixed layer depth product. Wind forcing of PV is found to be weak. A major observational subtropical mode water program named CLIMODE was conducted during the winters of 2004 to 2006. These years appear to be slightly stronger in their forcing than climatology, although the difference is comparable to the uncertainty. Attempts are made to relate the fluctuations to the NAO, a major mode of North Atlantic atmospheric variability, showing that there is a strong correlation between March values of the NAO and the PV fluctuation / A Thesis Submitted to the Department of Oceanography in Partial Fulfillment of the Requirements for the Degree of Master of Science. / Summer Semester, 2009. / April 15, 2008. / Includes bibliographical references. / William Dewar, Professor Directing Thesis; Kevin Speer, Committee Member; Jeff Chanton, Committee Member.

Many productive coastal areas, such as estuaries, are important fisheries. However, increased respiration associated with the high productivity often occurring in coastal zones may result in low dissolved oxygen conditions (dysoxia). The areal magnitude of coastal waters with low dissolved oxygen is expected to increase in the future. Therefore, understanding how organisms are affected by dysoxia is important for predicting changes to fisheries. This research extends the current knowledge of how pelagic organisms are affected by sublethal and lethal dissolved oxygen concentrations under different diet conditions. The warm-water copepod, Acartia tonsa, was chosen as the model organism due to its abundance in many temperate and tropical coastal areas. Results suggest that A. tonsa egg production may not be significantly decreased by dysoxia under some conditions of food limitation. Temperature and the timing of food availability when oxygen is present affected egg production in A. tonsa exposed to fluctuating food and dissolved oxygen. Food quality also significantly affected egg production of A. tonsa under low oxygen, but no significant differences in egg production efficiencies were found between a high- or low-carbohydrate diet. Egg production was higher and development time shorter under dysoxia for A. tonsa populations from environments with seasonal severe dysoxia compared to A. tonsa from an environment with less severe dysoxia. Therefore, the consequences of low oxygen stress on Acartia tonsa population dynamics may be affected by migration behavior, food quantity, food quality, temperature, the intensity and frequency of low dissolved oxygen waters, and the history of dysoxia. / A Dissertation Submitted to the Department of Oceanography in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy. / Fall Semester, 2006. / June 19, 2006. / Food Quality, Hypoxia, Copepod, Acartia Tonsa, Population Dynamics / Includes bibliographical references. / Nancy H. Marcus, Professor Directing Dissertation; Joseph Travis, Outside Committee Member; Richard L. Iverson, Committee Member; William M. Landing, Committee Member; David Thistle, Committee Member.

The ocean is coupled to the atmosphere via heat and freshwater fluxes. Ocean processes that play a role in the flux of heat in the ocean and atmosphere are of primary concern in this age of global climate change. These fluxes can act to convert one water mass into another. For example if the rate of conversion varies, water masses then tend to either accumulate or deplete. Walin used this theory to study the relationship between water mass volume and its heat supply. Speer and Tziperman, utilizing Walin's principle, calculated the water mass formation rates in Eighteen Degree Mode Water using climatological data. They report a formation rate of 15-20 Sverdrups. Here, Walin's theory and equations are also used, but mixing is neglected and only the air-sea heat flux is accounted for. The formation rate is calculated between two isotherms using the MITgcm data, averaged over various time scales. It is hoped that the values will be able to help explain the unusually large values obtained by Tziperman and Speer. / A Thesis submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Master of Science. / Spring Semester, 2008. / April 1, 2008. / Water Mass, Mode Water, Water Formation, MITgcm / Includes bibliographical references. / William Dewar, Professor Co-Directing Thesis; Kevin Speer, Professor Co-Directing Thesis; Jeff Chanton, Committee Member.

The Southern Ocean is one of the stormiest places on earth; here strong mid-latitude storms frequently traverse large distances of this ocean. Underlying these passing storms, the Southern Ocean is characterized by having some of the highest eddy kinetic energy ever measured (eddies occupying the meso to sub-mesoscale). The presence of the passage of intense storms and meso to sub-mesoscale eddy variability has the potential to strongly impact the intraseasonal variability of the upper ocean environment where phytoplankton live. Yet, exactly how phytoplankton growth rates and its variability are impacted by the dominance of such features is not clear. Herein, lies the problem addressed by the core of this thesis, which seeks to advance the understanding of intra-seasonal variability of Southern Ocean primary production. The drivers of this intra-seasonal variability have been explored from two points of view: the local-scale and the remote-scale perspectives, with a suite of physicalbiogeochemical (NEMO-PISCES) numerical models of varying complexity. At the local-scale, these model experiments have suggested that intra-seasonal stormlinked physical supplies of dissolved iron (DFe) during the summer played a considerably more active and influential role in explaining the sustained summer productivity in the surface waters of the Southern Ocean than what was thought previously. This was through two important insights: 1. Storm-eddy interactions may strongly enhance the magnitude and extent of upperocean vertical mixing in both the surface mixed layer as traditionally understood as well as in the subsurface ocean. These two mixing regimes have different dynamics but act in concert to amplify the DFe fluxes to the surface ocean. 2. Storm initiated inertial motions may, through interaction with eddies, greatly reinforce w and thus, enhance the vertical advection of DFe to the surface ocean, an effect that may last several days after the storm. At the local-scale, such storm-eddy dynamics may greatly increase the intra-seasonal variability of primary production, a step towards helping to explain why this variability is so strong in large regions of the Southern Ocean. At the remote-scale, the cumulative impact of these short-term storm-eddy interactions have unexpected implications in respect of the larger-scale mean flow and its influence on the effectiveness of intra-seasonal forcing of DFe fluxes. This counter intuitive feedback is a reduced strength of the intra-seasonal variability in primary production despite what was shown at the local-scale. Moreover, the addition of storms intensified the main clockwise cell of the meridional overturning circulation particularly the downward branch thus, reducing DFe inventory from the upper-ocean. Such an impact could potentially be enhanced with increasing storm intensities as suggested by climate projections. Understanding these remote-scale and local-scale responses of primary productivity to storms and their interaction with the underlying ocean mesoscale turbulence may be key to better understanding the sensitivities of the carbon cycle to short-term variability and long-term trends in atmospheric forcing.

The ocean circulation dynamics in the greater Agulhas Current system are dominated by mesoscale variability, which is highly non-linear, and therefore difficult to measure and simulate accurately. Moreover, the shedding of Agulhas rings from the retroflection south of Africa, which is the dominant mechanism by which warm and saline water flows from the Indian into the Atlantic Ocean, is thought to be a crucial component of the thermohaline circulation. With the goal of providing an accurate simulation of the greater Agulhas Current system, and in particular its mesoscale variability, a high resolution Hybrid Coordinate Ocean Model is set up in a nested configuration. In two 11 year simulation experiments, the effect of a higher order momentum advection scheme on the simulated ocean dynamics is tested and evaluated against available satellite observations and in-situ measurements. Quantitative analyses and model validation methods are developed to objectively evaluate the simulation experiments. The resultant skewness analyses and spatial variograms are objective measures for assessing the model simulation and additionally provide new insights on the mesoscale dynamics of the greater Agulhas Current system. A 4th order momentum advection scheme is shown to significantly improve the simulation of the region, in particular the dynamics of the southern Agulhas Current and the retroflection are greatly improved. From the analyses of the two model simulations in conjunction with satellite observations and in-situ measurements, it is found that the Indo-Atlantic inter-ocean exchange, and the shedding of Agulhas rings from the retroflection, is sensitive to the strength of the Agulhas Current, which in turn is influenced by the flow dynamics in the Mozambique Channel and south of Madagascar. Mesoscale eddies drifting from these source regions to the Agulhas Current play an important role, and the connection between the Agulhas Current and the respective source regions provides a link to large-scale variability in the Indian Ocean, which in turn is related to interannual modes of variability such as the Indian Ocean Dipole and El NiÑo Southern Oscillation.