Chromophoric dissolved organic matter (CDOM) was quantified by colorimetric light absorption for five blackwater intermittent streams draining into sinks (swallets) connected to the Floridan Aquifer underlying the Woodville Karst Plain, Wakulla County, Florida. Munson Slough receives drainage from the city of Tallahassee and the other streams; Fisher Creek, Black Creek, Jump Creek, and Lost Creek drain the Apalachicola National Forest. Previously conducted dye trace injections have shown the disappearing waters contribute to the discharge of Wakulla Springs, a first magnitude spring. Stage-discharge rating curves were developed for Black Creek and Jump Creek. Wakulla Springs CDOM was determined using UV-VIS spectrophotometry with a 10 cm path length and correlated to total organic carbon concentrations. The year-long study period included a two-month long baseflow period, followed by 12 inches of precipitation, an increase in discharge from 400 cfs to 1700 cfs, and a 41- day recession curve for Wakulla Springs. The Wakulla Springs 2009 water clarity extremes contained 28 percent (poorest water clarity) to 0.5 percent (best water clarity) stream water. The total CDOM mass associated with the streams exceeds the Wakulla Springs mass following storm events, indicating that some mass bypasses Wakulla Springs or is stored in the matrix/conduit aquifer system to be later released. Total stream mass equals Wakulla Springs mass for low baseflow conditions, but for higher baseflow, Wakulla Springs mass exceeds the total stream mass, indicating Wakulla Springs is still discharging mass from the preceding storm. This delayed mass is either from aquifer matrix/conduit storage or from the slower Lost Creek pathway. The storm mass associated with any one stream exceeds the Wakulla Springs lower baseflow mass by 4 to 9 times (for the two lowest mass streams) and has the ability to affect Wakulla Springs water clarity without contribution from any other stream. All of the water filled caves connected to Wakulla Springs contribute CDOM, with wet conditions contributing 25-67 percent more CDOM. A Wakulla Springs transmittance of 99 percent would have a NAC254nm of 0.1 and a TOC concentration of 0.69 mg/l. With the Wakulla Springs baseflow CDOM mass range of 600-1000 kg/day, this concentration indicates that the Floridan Aquifer clear water baseflow discharge will need to be 350-600cfs (10-17cms) to provide the necessary dilution for the bottom of the Wakulla Springs basin to be viewed with the water clarity of historic times. Investigation of upgradient Floridan aquifer water use indicated no change for the potentiometric surface entering Florida, but declines up to 16 feet were noted for northern Leon County, based on the 2008 potentiometric surface. Groundwater withdrawals by municipalities, Consumptive Use Permits, and private wells totaled 14,500 MGY for Leon and Wakulla counties or 9 percent of the 164,000 MGY discharged by Wakulla Spring in 2009. A decline in precipitation for the most recent decade, 1999-2009, was noted that may contribute, but groundwater use is the most likely cause of the decreased water clarity water. Wakulla Springs has an increasing trend for total dissolved solids and specific conductivity indicating a greater contribution of deep Floridan Aquifer water. More research is needed to understand vertical and lateral upgradient flow within the Floridan Aquifer and the fluctuating controls that either direct creek water to Wakulla Springs or result in it bypassing Wakulla Springs. / A Thesis submitted to the Department of Earth, Ocean and Atmospheric Science in partial fulfillment of the requirements for the degree of Master of Science. / Fall Semester, 2010. / October 18, 2010. / water clarity, absorption coefficient, transmittance, spectrophotometer, colorimeter / Includes bibliographical references. / Stephen A. Kish, Professor Directing Thesis; William C. Parker, Committee Member; Ming Ye, Committee Member.

The wind-driven oceanic circulation in the presence of bottom topography that isopycnals intersect is examined in an idealized setting. A modified quasi-geostrophic (QG) model has been designed and implemented. The model allows staircase bottom topography: topographic breaks decompose the lateral domain into subdomains consisting of fixed numbers of layers. Topographic shelves are placed within small (order Rossby number) vertical distances from the undisturbed layer interfaces. Each shelf can have topographic variations of the same scale. An elliptic solver inverting potential vorticity into geostrophic stream functions was designed based on the Capacitance matrix method. Solutions are matched at the topographic breaks by adding fictitious potential vorticity sources. The model has been tested against the problem of trapped topographic waves over a cliff. The results obtained for small-steepness disturbances agree with a weakly non-linear theory developed by Dewar and Leonov. Steeper disturbances break in a way that favors on shelf eddy detachment and transport of undiluted properties onto the shelf. The model has been further applied to the basin-scale wind-driven circulation problem in a 3-layer configuration with a continental shelf in the western part of the domain. Double-gyre wind forcing has been considered. The topographic shelves are responsible for dynamics absent in classical idealized eddy resolving QG models which have been the preferred numerical tool for the study of low frequency intrinsic ocean variability. The top-layer flow interacts with the shelf topography by means of vortex tube stretching and vorticity dissipation due to bottom drag. This mechanism reduces the role of horizontal friction as a controlling factor in the dynamics.The results obtained for different parameter regimes (free-slip, no-slip boundary condition, different values of the viscosity) show reduced sensitivity to the type of dynamic boundary condition, compared to classical results. The intrinsic variability of the flow is affected by the new mechanism of on- and off shelf transport of potential vorticity. The role of horizontal friction is again reduced, as shown by the modeling results. Spatiotemporal patterns of the variability have been analyzed. Most of the patterns are insensitive to the type of boundary condition (free-slip vs. no-slip), and qualitatively resemble classical no-slip results. / A Dissertation submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester, 2005. / May 31, 2005. / Wind-Driven Circulation, Decadal Climate Variability, Ocean Intrinsic Variability, Finite Topography, Trapped Topographic Waves / Includes bibliographical references. / William K. Dewar, Professor Directing Thesis; Ionel Michael Navon, Outside Committee Member; Allan J. Clarke, Committee Member; William M. Landing, Committee Member; James C. McWilliams, Committee Member; Doron Nof, Committee Member; Melvin E. Stern, Committee Member.

Gridded QuikSCAT data has been used to show that a strong confluence zone of the Southeast Pacific Intertropical Convergence Zone (SITCZ) existed in 2000 – 2002 during boreal spring, and the Panama wind jet contributes to its variability. Time series analysis of winds off the Gulf of Panama and convergence advection into the Southern Hemisphere (from 80W to 95W) show these winds kept the SE Trades out of the Northern Hemisphere and created a confluent zone in the Southern Hemisphere. A monthly averaged SITCZ is maintained by the deceleration of the SE Trades that flow from warm water toward the equatorial cold tongue, creating a speed convergent zone south of the equator. Images of wind trajectories show zonally orientated SE Trade winds that were deflected from a divergent zone parallel to the coast of South America converge with more meridional Trades over warm waters. Panamanian winds crossed into the Southern Hemisphere to contribute to this convergence. It is hypothesized that this confluent zone can be intensified by the Panamanian winds. In 2002, the SITCZ confluent zone occurred with more intense Panamanian gap flow than the previous two years. Cross equatorial SE Trades wrapped anti-cyclonically around a divergent pocket in the Northern Hemisphere and became southward winds, which allowed the Panamanian winds to enter the Southern Hemisphere and intensify the SITCZ. Variability in the Panamanian winds makes a substantial contribution to the evolution of the SITCZ. / A Thesis submitted to the Department of Meteorology in partial fulfillment of the requirements for the degree of Master of Science. / Summer Semester, 2004. / July 8, 2004. / Central American Wind Jets / Includes bibliographical references. / James J. O’Brien, Professor Directing Thesis; Mark. A. Bourassa, Committee Member; Guosheng Liu, Committee Member.

Dinoflagellates are unicellular, eukaryotic organisms that consist of both photosynthetic and non-photosynthetic species. The approximately 91 known species of bioluminescent dinoflagellates are the pre-dominate contributors to ocean surface bioluminescence. These species are distributed throughout the world, but are generally located in channels, seas, straits, and along coastlines. The bioluminescent properties of dinoflagellates can pose a threat for naval applications. Bioluminescence generated by submarine and SDV operations in coastal areas can result in increased vessel visibility. The initial steps of my research involved testing various chemical agents and physical factors that might be used to mitigate dinoflagellate bioluminescence in situ. I identified formaldehyde as the only chemical compound among many common compounds tested that successfully mitigated dinoflagellate bioluminescence. Formaldehyde was used in the form of formalin, a solution consisting of 37% formaldehyde and methanol as a stabilizing agent. Next, I performed experiments applying shear stress through a stirrer, and used photon counting to determine the extent and time-course of bioluminescence mitigation by formaldehyde in 1.0, 2.5, and 4.6 percent concentrations. Those concentrations were chosen to bracket the formaldehyde concentration commonly used to preserve phytoplankton samples. There was an initial, short-term burst in bioluminescence upon addition of formaldehyde, as formalin, to cultures of the two species before formaldehyde limited bioluminescence, presumably caused by denaturation of compounds in the bioluminescence apparatus. The initial burst lasted 34.6 seconds at 1.0 percent formaldehyde, 9.8 seconds at 2.5 percent formaldehyde, and 8.4 seconds at 4.6 percent formaldehyde for Lingulodinium polyedrum. After the initial burst, bioluminescence output of both Pyrocystis lunula and L. polyedrum was reduced by formaldehyde. For L. polyedrum, the effect was rapid for all concentrations tested, with a 100 percent bioluminescence reduction upon stirring one minute after formalin was added. Bioluminescence continued after administration of formalin, resulting in an afterglow effect for P. lunula. However, L. polyedrum, a species more typical of bioluminescent dinoflagellates found in marine waters compared to P. lunula, did not exhibit the afterglow effect after formalin administration. / A Thesis submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Master of Science. / Fall Semester, 2006. / August 4, 2006. / Calcium Channel, AI Hypothesis, Tensegrity Network, Scintillons, Phytoplankton, Luciferin, Luciferase, Shear Stress, Formalin, Action Potential / Includes bibliographical references. / Richard Iverson, Professor Directing Thesis; Markus Huettel, Committee Member; Behzad Mortazavi, Committee Member.

Though a large fraction of primary production and organic matter cycling in the oceans occurs on continental shelves dominated by sandy deposits, the microbial communities associated with permeable shelf sediments remain poorly characterized. Therefore, the primary objective of this study was to provide the first detailed characterization of microbial diversity in representative marine sands of the South Atlantic Bight (SAB) and the northeastern Gulf of Mexico (NEGOM) through analyses of SSU rRNA gene (Bacteria), nosZ (denitrifying bacteria), and amoA (ammonia-oxidizing bacteria) sequences. Communities were analyzed by DNA extraction, clone library construction, and terminal restriction fragment length polymorphism (T-RFLP) community fingerprinting. Sediment characteristics, geochemical parameters, and rate measurements were obtained in parallel with microbial community analysis. Microbiological and biogeochemical approaches were coupled, allowing the structure-function relationships of key microbial groups involved in carbon and nitrogen cycling in continental shelf sediments to be examined. In the SAB study (Ch. 1), clone libraries were constructed from both sediment core material and manipulated sediment within column experiments. Rapid organic matter degradation and coupled nitrification-denitrification were observed in column experiments at flow rates and oxygen concentrations resembling in situ conditions. Numerous SSU rRNA gene phylotypes were affiliated with the phyla Proteobacteria (classes Alpha-, Delta-, and Gammaproteobacteria), Planctomycetes, Cyanobacteria, Chloroflexi and Bacteroidetes. Detectable sequence diversity of nosZ and SSU rRNA genes increased in stratified redox-stabilized columns compared to in situ sediments, with the Alphaproteobacteria comprising the most frequently detected group. Alternatively, nitrifier communities showed a relatively low and stable diversity that did not co-vary with the other gene targets. In the NEGOM study (Ch. 2), high throughput techniques were developed and applied to extensively profile overall and denitrifying microbial communities in a large number of sediment samples over various sediment depth intervals, contrasting sites, and sampling periods. Cloning/sequencing and community fingerprinting (T-RFLP) approaches were applied in parallel to characterize microbial diversity and phylogenetic composition. Statistical estimators including species richness, Shannon-Weiner and 1/D indices, nucleotide diversity, gene diversity, evenness, and theta (pi) indicated little difference between four clone libraries constructed from selected depth intervals (0-2 cm, 18-20 cm) at each site in March. In contrast, T-RFLP profiles and robust phylogenetic analysis showed distinct trends in diversity according to site, depth, and time period sampled. The results elucidate predominant phylotypes that are likely to catalyze carbon and nitrogen cycling in marine sands. Several microbial groups (Deltaproteobacteria, Gammaproteobacteria, Planctomycetes) were confirmed as significant contributors to the microbial communities of permeable marine sediments in agreement with previous work. However, the robust sequence database of this study expanded current knowledge to reveal a large overall community diversity including additional groups (Alphaproteobacteria, Bacteriodetes/Chlorobi, and Cyanobacteria) that had not been previously recognized using cultivation-independent methods with inherently lower resolution. The Alphaproteobacteria, in particular, were shown to be relatively abundant in the overall and denitrifying communities at both SAB and NEGOM sites. Although overall diversity increased in response to redox stabilization and stratification in column experiments, the major phylotypes remained the same, indicating that the columns sufficiently mimic in situ conditions. While SSU rRNA gene phylotypes detected by clonal analysis were similar at the phylum level at all sites, the NEGOM site showed much higher species richness in comparison to SAB. At NEGOM, T-RFLP showed distinct differences in community diversity according to site, depth, and time. The sequence database from this thesis will facilitate the development of improved probes and primer sets to be used in quantifying the metabolically active members of permeable sand communities. Rapid community fingerprinting methods developed here should allow for more extensive comparisons across environmental gradients in order to better understand the factors controlling microbial diversity in permeable sediments. / A Thesis submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Master of Science. / Spring Semester, 2006. / March 20, 2006. / SSU rRNA, Microbial Community Analysis, Nitrogen Cycle, nosZ, amoA, Sandy Sediments / Includes bibliographical references. / Joel Kostka, Professor Directing Thesis; Heath Mills, Committee Member; Markus Huettel, Committee Member; Lee Kerkhof, Committee Member.

The community abundance and diversity of mRNA transcripts for sulfate-reducing prokaryotes were investigated in parallel with rate measurements of sulfate reduction activity in marine subsurface sediments of Aarhus Bay, Denmark. Solid phase and porewater chemistry and sulfate reduction rates were determined on subsamples from sediment cores to 5 m below the sediment surface. Molecular analysis of the dissimilatory (bi) sulfite reductase (dsrAB) mRNA transcripts and 16S rRNA were performed by quantitative reverse transcription real-time PCR and traditional clonal analysis. The distribution of dsrA transcripts was directly linked to both sulfate reduction rates and rRNA content. Quantitative analysis of dsrA gene transcripts indicated the presence of active sulfate reduction at 465 cm below the sediment-water interface, where high methane concentrations persist in regions of near sulfate depletion. These results suggest an abundance of active bacteria in zones of high sulfate reduction and a marked decrease in zones of low sulfate reduction rates. Archaeal communities showed a constant distribution in the sediment profile in zones of intermediate and low sulfate reduction rates, indicating their predominance in sediments where low sulfate and high methane concentrations were observed. Substantiated by biogeochemical and rRNA analysis, the analysis of mRNA gene transcripts serves as a versatile molecular proxy for the study of sulfate reducing communities in marine subsurface sediments. / A Thesis submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Master of Science. / Spring Semester, 2009. / September 5, 2008. / PCR, Microbial Ecology, Sufate Reduction / Includes bibliographical references. / Joel E. Kostka, Professor Directing Thesis; Markus Huettel, Committee Member; Kuki Chin, Committee Member.

This study addresses the decomposition of dissolved organic carbon (DOC) in highly permeable coastal sand sediments. DOC fluxes from shelf sediments (~180 Tg C yr-1) are significant, roughly equal to the DOC flux from rivers (~200 Tg C yr-1) and to the rate of carbon burial in marine sediments (~160 Tg C yr-1) (Burdige et al., 1999). DOC thus plays an important role in the global cycles of carbon and nitrogen (Hedges, 1992) and understanding the processes that control DOC dynamics is critical to clarify this role. The small concentrations of lignin in the ocean and the 13C-enriched composition of marine DOC suggest relatively rapid degradation of terrestrial DOC, however, the mechanisms by which the large volumes of DOC released to coastal waters are rapidly degraded following discharge are poorly understood (Hedges, 1992). Photooxidation can decompose DOC to low molecular weight substances (Kieber et al., 1989; Mopper et al., 1992), and this process may account for the removal of 20 to 30% of DOC in coastal waters (Mopper and Kieber, 2002). Microbial activity in the water column and shelf sediments degrades DOC, but the importance of these processes are not well constrained. Approximately 70% of the shelf sediments are relict sands (Riggs et al., 1996), and in the shallow coastal zone a large fraction of these sands are highly permeable and permit circulation of water through the interstitial space (Marinelli et al., 1998; Huettel et al., 1996; Huettel and Gust, 1992). In this shallow environment, strong boundary currents caused by wind, waves, and tides force bottom water loaded with DOC through the sediment ripples and upper surface layers of the sand. Abundance and diversity of microbes in permeable sediments exceed that of the overlying water column (Hunter et al., 2006), and the question arises whether the filtration through the sediment affects the decomposition of DOC and water column DOC dynamics. I tested the working hypotheses that rapid DOC transport along relatively short pathways through the sand significantly enhances the degradation of the DOC and that the sedimentary flushing tightly links sedimentary and water column DOC concentrations. The main objectives of the research were: 1) To measure degradation rates of DOC in percolated permeable sediment and to compare the rates to those in the water column; 2) To assess the magnitude and variability of DOC concentrations in water and pore water at two nearshore environments of the northeastern Gulf of Mexico with permeable sediments, and to determine the links between the sedimentary and water column DOC dynamics; 3) To investigate the processes that control the DOC distribution in the surface layer of the permeable bed. I combined time series and chamber experiments conducted in-situ with laboratory column reactor and flume experiments. While the laboratory experiments were designed to assess DOC degradation rates and processes controlling DOC distribution under well-defined conditions, the field experiments were conducted to gain insight on DOC fluxes and seasonal trends at two coastal sites differing in their DOC input and hydrodynamic characteristics. The flume experiment examined the distributions of DOC resulting from degradation of phytoplankton deposited on permeable sediments exposed to unidirectional flow. The results show that DOC from algal cell degradation in the sediment surface layer is rapidly transported deeper into the sediment by advective pore water flows and concentrated in specific zones dictated by the pore water flow field. The DOC profiles showed highest concentrations in the upper 2 cm of the sediment, lower concentrations below that layer and in some cases increasing DOC concentrations in the layers below the flushing zone, resulting in a concave profile shape. The laboratory column reactor experiments demonstrate that fresh DOC originating from phytoplankton, as well as older DOC from terrestrial sources, is rapidly degraded (2.15 to 124.04 µmol l-1 h-1) while passing short distances through permeable sands by the microbial community and that degradation rates in the sediment exceeded those in the water column, approximately 7-fold for my experimental settings. The measurements of water column and pore water DOC concentrations at St. George Island produced the first DOC time series for two shallow Gulf of Mexico coastal environments showing DOC ranges and temporal dynamics. These time series indicate that during the winter season, when hydrodynamic forcing is strongest, water column and sedimentary DOC concentrations are coupled, while no such link could be recorded during the calmer periods of the year. The similarity between the in-situ DOC profiles and those measured in the laboratory flume suggest that plankton deposition, combined with advective pore water transport processes and slow upward diffusion of refractory DOC from deeper layers, shape the concave DOC concentration profiles. The field measurements with advection chambers reveal seasonal variation of the magnitude and direction of DOC fluxes and showed that the permeable coastal sands can act as a sink (winter) or a source (summer) for DOC. / A Thesis submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Master of Science. / Summer Semester, 2008. / April 22, 2008. / Sediments, Biogeochemistry, Doc, Dissolved Organic Carbon, Dom, Degradation, Permeable / Includes bibliographical references. / Markus Huettel, Professor Directing Thesis; David Thistle, Committee Member; Thorsten Dittmar, Committee Member.

Sea Surface Temperatures (SSTs) are an important measure of our current weather and climate, as well as an essential variable in both short and long term weather forecasting. Infrared SST retrievals are reliant on passive sensors, and retrieval techniques are influenced by changes in atmospheric composition, including aerosols. Many empirically derived retrieval algorithms are based on matching Top of Atmosphere (TOA) Brightness Temperatures (BTs) from the Advanced Very High Resolution Radiometer (AVHRR) to buoy measurements during clear-sky conditions. Data is cloud-cleared to remove cloud-contaminated data. However, small, but influential, Aerosol Optical Depths (AODs) data may not be flagged as contaminated and the algorithms incorrectly calculate a cold SST due to the radiometer sensing the cooler, elevated aerosol layer temperature. Many studies on aerosol effects on SSTs focus on aerosols due to volcanic eruptions. However, truly operational tropospheric aerosol corrections for daytime and nighttime retrievals have yet to be implemented. This work constitutes a first step to creating an accurate aerosol correction by exploring the sensitivity of aerosols on SSTs. The Santa Barbra DISORT Radiative Transfer model is used to quantify the effects of aerosol contamination on retrieved TOA BTs. The calculated radiances are spectrally averaged over each channel, converted to BTs, and used to calculate an SST using the Naval Oceanographic Office AVHRR algorithms. A radiative transfer model is used to evaluate the SST retrieval error due to varying AOD, height of an aerosol layer, and the satellite zenith angle (or viewing angle). This analysis shows that errors greater than the stated retrieval uncertainty of 0.5 K are observed for AODs greater than 0.25. Two sites with state-of-the-art aerosol measurements are analyzed for AOD variability. The first site, at Anmyon in east Asia, is found to have 14% of the days during the springtime with an AOD greater than 0.25. Based on the AERONET data from a second site in Cape Verde, 65% of the days during the boreal summer are found to have AOD greater than 0.25. Unfortunately, this seasonal peak in dust activity coincides with the active tropical cylogensis season for the region, making accurate SSTs even more vital for prediction purposes. / A Thesis submitted to the Department of Earth, Ocean and Atmospheric Science in partial fulfillment of the requirements for the degree of Master of Science. / Fall Semester, 2010. / October 19, 2010. / Dust, Retrieval Error, Aerosols, Sea Surface Temperature / Includes bibliographical references. / Carol Anne Clayson, Professor Directing Thesis; Mark A. Bourassa, Committee Member; Guosheng Liu, Committee Member; Douglas L. Westphal, Committee Member.

By sampling individual rain events over a 1-year period at three sites situated around a known point source of atmospheric mercury, we have attempted to quantify its influence on local mercury deposition. A suite of trace elements was also analyzed on these rain event samples. A multi-element analytical program was set up using a Thermo-Finnigan "Element" ICP-MS. We identified 46 elements that are significantly enriched in rain samples relative to the method blank, including the alkali metals and alkaline earth elements, all three rows of the transition metals, and the rare earth elements. The total mercury concentrations in the rainwater samples ranged from 2-40 ng/L. The volume weighted mean rainfall mercury concentrations ranged from 9.2-9.8 ng/L, and there were no significant differences in the rainfall Hg deposition between the three sites. Principal component factor analysis (PCFA) was used to evaluate co-variance between mercury and trace element deposition. PCFA showed a strong crustal factor, a strong sea-salt factor, a mysterious "P" factor and a strong mercury factor. The mercury factor linked mercury with Bi, Ga, Pb, Sb and V. Plume dispersion modeling and air-mass back trajectory analysis have been conducted for each rain event. The goal of this research was to use mercury and trace element relationships in an effort to identify, and quantify, the impacts from various emission sources in the region on rainfall chemistry. We calculated the annual integrated percent of mercury associated with coal burning ranging between 15-47%. Using models to estimate the impact of local deposition we found that less than 1% of the mercury we measured is from the known point source. / A Thesis submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Master of Science. / Fall Semester, 2006. / July 14, 2006. / Pensacola, Trace Metal, Florida, Hg, Coal Fired Power Plant / Includes bibliographical references. / William M. Landing, Professor Directing Thesis; Philip Froelich, Committee Member; Markus Huettel, Committee Member.

This dissertation is a collection of five calcareous nannofossil and one stable isotope studies on materials from Ocean Drilling Program (ODP) Legs 183 (Site 1135), 206 (Site 1256), and 207 (Site 1259) that target two important paleoceanographic events: 1) the middle/late Miocene carbonate crash, and 2) the Paleocene/Eocene Thermal Maximum (PETM). Site 1256 nannofossil biostratigraphy in Chapter 1 refined the author's shore-based shipboard Quaternary-middle-Miocene nannofossil biostratigraphy with 16 zones/combined zones recognized based on 28 nannofossil datums. This chapter provides a chronologic framework for the age calibration of the first occurrence (7.18 Ma) and last occurrence (6.32 Ma) of Reticulofenestra rotaria, calculation of linear sedimentation rates, age determination of basalt basement (~14.5 Ma), and the recognition of the "carbonate crash" paleoceanographic event at the middle/late Miocene boundary. Reworked nannofossils and lithologic changes also allow a reading of a three-episode redepositional history (4.7, 8.3, and 10.7 Ma, respectively) in the eastern Pacific. The detailed examination of the Site 1256 material also yielded well-preserved Discoaster stellulus, for which only the distal view had been depicted in the original description. In Chapter 2, a redescription and re-illustration of both sides of this asterolith is provided. This should prevent misidentification of specimens in proximal view, thereby raising its potential application for middle-late Miocene biostratigraphy. Based on the above age model, in Chapter 3 stable oxygen and carbon isotopes were used for the first time to explore the late/middle Miocene "carbonate crash". This carbonate transition is a widespread (eastern and central equatorial Pacific, Indian, South Atlantic, and the Caribbean), sharp decrease in carbonate mass-accumulation rates, which has previously been considered only a dissolution event. The positive correlation (R2 = 0.75) between d13C and CaCO3 mass accumulation rates during 5-14 Ma at ODP Site 1256 clearly demonstrates that carbonate accumulation is mainly biologically controlled. The coincidence of the carbonate crash with negative excursions in d13C and d18O values suggests a causative mechanism related to surface-water productivity, as a result of surface-water warming and reduced upwelling. Based on these observations, one could speculate that the major middle/late Miocene sea-level drop may have caused the complete closure of the Indonesian Seaway, resulting in a piling-up of surface warm water in the west Pacific. The eastward spread of this nutrient-poor water then would have warmed sea-surface temperatures and reduced upwelling in the central and eastern Pacific, thereby creating a prolonged "El Nino" scenario and reducing biological productivity of phytoplankton. The reduction in carbonate supply to the deep waters consequently caused a rapid shoaling of the carbonate compensation depth, thereby triggering the carbonate crash. The PETM was a catastrophic, rapid greenhouse-forced global warming event ~55 m.y. ago that triggered an abrupt turnover in ocean chemistry and circulation as well as biota. Chapter 4 represents a quantitative study of the response of nannoplankton to the PETM at Demerara Rise, equatorial Atlantic (Site 1259). Toweius, Fasciculithus, and Chiasmolithus sharply decrease at the onset of the PETM, whereas Chiasmolithus, Markalius cf. M. apertus, and Neochiasmolithus thrive immediately after the event, which also signals the successive first appearances of Discoaster araneus, Rhomboaster, and Tribrachiatus. Two main environmental factors were extracted by correspondence analysis of relative abundance data. The time series of the two factors shows that during the PETM, 1) environmental stress (most likely from changes in seawater pH) increased and may well have also induced the evolution of ephemeral nannofossil "excursion taxa"; and 2) surface-water productivity increased at this site presumably due to higher runoff from continental areas. The local phytoplankton opportunist, Markalius cf. M. apertus, is described as a new species in Chapter 5, which will be published under the name Coccolithus bownii. Results presented in Chapter 6 from Site 1135 on the Kerguelen Plateau, Southern Ocean suggest that nannoplankton responded differently to the PETM at southern high latitudes. The onset of the carbon isotope excursion occurs within an 18-cm interval (instead of 1-2 cm as observed in most deep-sea sections) before the peak is reached, displaying a linear mixing curve. This indicates that the release of light carbon was a gradual, single injection, instead of multiple pulses as suggested in previous work, and that this sequence is highly expanded as a result of high sedimentation rates at this relatively shallow oceanic site. This is evidenced by the high numbers of dissolution-susceptible holococcoliths (Zygrhablithus bijugatus) preserved throughout the sequence. Although r- and K-selected specialists exponentially increase in abundance at the onset, Chiasmolithus abruptly drops but then rapidly recovers, whereas Discoaster and Fasciculithus show opposite trends, indicating that in high latitudes, surface-water oligotrophy prevailed at the carbon isotope excursion (CIE) onset but mesotrophic conditions dominated the CIE recovery. These observations confirm previous results from ODP Site 690 on Maud Rise. The intensive dissolution of susceptible holococcoliths and the poor preservation of the assemblages are believed to have been caused by the effects of corrosion caused by the methane release. The different responses of nannoplankton to the PETM and the contrasts evident in previous work from the open ocean vs the continental margins further demonstrate that the response to the PETM can be influenced by local differences in geologic setting and oceanographic conditions. / A Dissertation submitted to the Department of Geological Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Fall Semester, 2007. / July 13, 2007. / Paleoceanography, Paleocene/Eocene Thermal Maximum, Middle/Late Miocene Carbonate Crash, Productivity, Stable Isotopes, Calcareous Nannofossils / Includes bibliographical references. / Sherwood W. Wise, Jr., Professor Directing Dissertation; Richard L. Iverson, Outside Committee Member; Anthony J. Arnold, Committee Member; Joseph F. Donoghue, Committee Member; Yang Wang, Committee Member.