Prior studies of the long-term temperature record in the Southeastern United States (SE US) mostly discuss the long-term cooling trend, and the inter-annual variability produced by the region's strong ties to El Niño Southern Oscillation (ENSO). An examination of long-term temperature records in the SE US show clear multi-decadal variations in temperature, with relative warm periods in the 1920's through the mid 1950's and a cool period in the late 1950's through the late 1990's. This substantial shift in multi-decadal variability is not well understood and has not been fully investigated. It appears to account for the long-term downward trend in temperatures. An accurate characterization of this variability could lead to improved interannual and long-term forecasts, which would be useful for agricultural planning, drought mitigation, water management, and preparation for extreme temperature events. Statistical methods are employed to determine the spatial coherence of the observed variability on seasonal time scales. The goal of this study is to characterize the nature of this variability through the analysis of National Weather Service Cooperative Observer Program (COOP) station data in Florida, Georgia, Alabama, North Carolina, and South Carolina. One finding is a shift in the temperature Probability Distribution Function (PDF) between warm regimes and cool regimes. / 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. / Summer Semester, 2010. / July 2, 2010. / Meteorology, Climate Variability, Climate, Warm Regime, Cold Regime / Includes bibliographical references. / Mark. A. Bourassa, Professor Directing Thesis; Eric P. Chassignet, Professor Directing Thesis; Philip Sura, Committee Member; David F. Zierden, Committee Member.

Statistics of extreme events in weather and climate (e.g. rare floods or strong wind storms) are commonly based on the assumption of Gaussian statistics. Sixty-two years of National Centers for Environmental Prediction / National Center for Atmospheric Research (NCEP / NCAR) Reanalysis I data and thirty-one years of National Centers for Environmental Prediction / Department of Energy (NCEP / DOE) Reanalysis II data are analyzed to determine if this assumption is true. The mean and variance of several atmospheric variables are calculated. Furthermore, the higher statistical moments — skewness and kurtosis — are calculated for geopotential height, relative vorticity, and the meridional and zonal wind components. Zonal averages of these higher statistical moments are also analyzed. It is found that statistically significant deviations from Gaussianity are found for every variable in the atmosphere on the synoptic to global scales. This empirical analysis is linked to particular atmospheric phenomena such as tropical cyclones, sudden stratospheric warming events, and the concept of rectifica- tion. In essence, there are fundamental forcing asymmetries in the atmospheric equa- tions of motion that lead to the existence of non-Gaussian distributions. Additionally, the relationship between skewness and kurtosis and the existence of power-law tails in non-Gaussian systems is examined. / 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. / August 24, 2010. / Extreme Events, Non-Gaussianity / Includes bibliographical references. / Philip Sura, Professor Directing Thesis; Jon Ahlquist, Committee Member; Robert Hart, Committee Member.

The oceanic mixed layer is a region of intense mixing, where turbulence homogenizes vertical temperature and salinity distributions down to depths of O(100) m. Below the mixed layer, in the upper layers of the stratified thermocline, turbulent energy levels are greatly reduced. The transition between these two regions is the focus of this investigation. Traditionally, this transition is assumed to take place abruptly at the mixed-layer base. However, observations suggest that enhanced turbulence penetrates significantly into the stratified water below the mixed layer. Here, I present an examination of existing turbulence data documenting open ocean conditions with steady wind forcing in both the sub-tropical Atlantic and Pacific. These data will allow for direct estimates of diffusivity and diapycnal flux occurring in the mixed layer/thermocline transition layer. This analysis establishes statistics for turbulence dissipation levels occurring just below the well-mixed layer, which have not been previously documented. My investigation suggests that while the transition layer thickness can vary considerably (from O(10) to O(100) m for my data), the diabatic fluxes in this region, as measured by the turbulent dissipation rate, are 4-8 times greater than in the thermocline under typical surface forcing conditions. / A Thesis submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Master of Science. / Summer Semester, 2010. / April 29, 2010. / Dissipation, One-dimensional Models, Turbulence, Transition Layer, Surface Ocean / Includes bibliographical references. / Carol Anne Clayson, Professor Directing Thesis; Louis St. Laurent, Committee Member; William K. Dewar, Committee Member; Philip N. Froelich, Committee Member.

Southern Alaska crustal exposures provide an excellent opportunity to study the growth of collisional continental margins through the processes of terrane accretion, magmatism, accretionary prism development, and subduction of oceanic spreading ridges. Kodiak Island is one of the world's best exposed accretionary complexes, and is characterized by transport along dominant large-magnitude strike-slip faults of west North America and South Alaska. In this study we focus on detrital zircon dating of the Kodiak accretionary complex on Kodiak Island Alaska. Accretionary complexes are an important fundamental element of convergent plate margins and are also important structures in continental crust formation. Their presence in the geologic record is an indicator of past subduction zones. Six graywacke detrital zircon samples from the Kodiak and the Ghost Rocks Formations were analyzed using U/Pb dating of single crystals via laser-ablation inductively coupled plasma mass spectroscopy. The maximum depositional age of the three major formations are as follow: Kodiak Formation 56.2-69.2 Ma, and Ghost Rock 58.5 Ma. The age for the small outcrop of Narrow Cape Formation is 54.1. Kodiak and Ghost Rock Formation detrital zircon age are consistent with fossil ages of these two formations, but the fossil content of Narrow Cape is younger than the detrital zircon age we measured for this formation. Some evidence in our data like resurrection of certain age zircon grains between the accreted sequences, age gaps between the accreted sequences, different rate of sedimentation and etc. are evidenc for episodical accretion in the complex and also displacement of the accreted units along the west North America and Alaska right lateral large magnitude strike slip faults. / A Thesis submitted to the Department of Earth, Ocean and Atmospheric Sciences in partial fulfillment of the requirements for the degree of Master of Science. / Summer Semester, 2011. / June 17, 2011. / detrital zircon dating, accretionary prism, Kodiak Island / Includes bibliographical references. / David Farris, Professor Directing Thesis; James F. Tull, Committee Member; A. Leroy Odom, Committee Member.

This study presents the first high-resolution long-term history of seawater lithium isotope ratio (δ7LiSW) reconstructed from analyses of chemically cleaned planktonic foraminifera. The lithium isotope ratio of seawater (δ7LiSW ~31.0‰) is at secular equilibrium with its input sources via chemical weathering of the silicate continents (δ7LiRiv ~23‰), hydrothermal weathering of seafloor silicate basalts (δ7LiHT ~5.6‰) and removal by reverse weathering of authigenic sediments and seafloor basalts (δ7LiSED ~15‰). The δ7LiSW preserved in marine calcitic planktonic foraminifera provides a unique time tracer of changes in the global silica cycle. The Cenozoic 7Li/6Li record of seawater was constructed by analyzing over 300 age and species overlapping foraminifera samples, including both individual species and 'reverse picked' bulk foraminifera samples, from eight DSP/ODP Sites (588, 757, 758, 926, 1262, 1263, 1265, and 1267) with existing high resolution strontium isotope record. To meet the analytical requirements of foraminiferal δ7Li analyses an improved quadrupole-ICP-MS method for 7Li/6Li determination with low total lithium consumption (<0.2 ng/quintuplicate analyses) and high isotope ratio precision (≤ ±0.8‰, 2σ) was developed. A refined single step ion-exchange chromatographic method for quantitative lithium seperation, characterized by low blanks (1.0 ± 0.5 pg-Li) and high column yields (>99.98%), was also developed. The effects of foraminifera cleaning on calcite bound lithium concentrations and isotopic compositions were evaluated. A new analytical ICP-MS method for simultaneous determination of lithium, magnesium, manganese, vanadium, strontium, and barium ratios to calcium in chemically cleaned planktonic foraminifera was also developed. The newly developed analytical method and the improved foraminiferal cleaning technique was applied to late Cretaceous and Cenozoic samples to investigate the correlation between lithium isotopic composition and their lithium, magnesium, and strontium concentrations of the calcite shell as a guide to the to better explain the δ7Li record of seawater. The 68 Ma history of δ7LiSW spanning Late Cretaceous to Holocene demonstrates that the δ7LiSW decreased sharply by ~5‰ at the Cretaceous-Tertiary boundary and during the rest of the Cenozoic δ7LiSW increased by 8-9‰ over the last 60 Ma. Unlike the 87Sr/86Sr and 187Os/186Os isotope history of seawater, the rise in δ7LiSW during Cenozoic is not monotonous in nature. Plateaus and quasi-linear increases in δ7LiSW punctuate the 8-9‰ rise in seawater δ7Li during the Cenozoic. The sharp drop in δ7LiSW across K-Pg boundary was probably due to rapid supply large masses of isotopically light lithium to seawater from the congruent weathering of freshly erupted continental flood basalts (CFB's of Deccan Traps). The 8-9‰ rise in δ7LiSW during the rest of the Cenozoic suggests that hydrothermal contribution of isotopically light lithium to seawater has decreased over the Cenozoic, whereas, both lithium flux (FRiv) and isotopic composition (δ7LiRiv) of rivers have increased over the same period. Our findings suggest that neither δ7LiSW nor [Li]SW are buffered to oceanic basalts. / A Dissertation submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester, 2010. / April 22, 2010. / Geochemical Proxy, Paleoclimate, Cretaceous - Tertiary Boundary, Lithium Isotopes, Silicate Weathering, Paleoceanography, Cenozoic / Includes bibliographical references. / Philip N. Froelich, Professor Directing Dissertation; Munir Humayun, University Representative; Willium C. Burnett, Committee Member; Jeffery P. Chanton, Committee Member; Marcus Huettel, Committee Member.

Traditionally, research on bulk electrical conductivity is focused on the subject of soil salinity effects. Herein, bulk electrical conductivity was used to investigate the transport processes of soil. Electrical conductivity indicates the ability of the material to carry the electrons. In soils, water content is the dominant factor controlling conductivity. In addition to water content, salinity, clay content and temperature are also important factors in determining bulk electrical conductivity. Bulk electrical conductivity ECa is composed of the electrical conductivity of the liquid phase and surface electrical conductivity. The concept of critical water content has been proposed by different scientists in different ways. Here the critical water content is defined as the water content when the system transits from disconnected water films to a network of connected water filled pores, the critical water content occurs, mass transport becomes significant and tortuosity decreases. This work investigates the potential of using bulk electrical conductivity ECa to determine the critical water content. We used a relatively uniform sand and clay-sand mixtures as the porous medium instead of a complex soil. A test cell was designed to collect the electrical conductivity data of soil at different water content and the Wenner-array method was used. The electrolyte concentrations used in the experiment were 0.01 M KCl, 0.05 M KCl and 0.10 M KCl. Both error calculation and duplicated experiment has been done to determine the precision of our measurements. A plot of ECa vs. volumetric water content (è) failed to prove the evidence of the critical water content. The data analysis then used a Formation factor, or F factor which is closely related to ECa as a basis. The Fc factor proposed by Low and the F factor proposed by Rhoades were compared and it was determined that Rhoads model was consistent with observed trends. The F factor showed a significant change as water content increased, and samples with more clay had the sudden decrement in F at the higher water contents. Tuller's pore-scale model failed to provide a conceptual model of the observed trends. The critical path analysis (CPA) model provided an explanation of the F factor change with è, The CPA model represents porous medium as a system of large pores and thin pores with larger pores connected by thin pores. At certain water content, there is a critical condition wherein a network of thin pores is filled, and at this critical condition, the larger pores are connected and then mass transport becomes significant and the F factor decreases. The CPA model not only described a progression that fits our F factor data well, suggesting that samples with more clay have more thin pores, so it reaches the critical condition at higher water content. / 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, 2011. / March 30, 2011. / Formation Factor, Transportation, Transmission Coefficient / Includes bibliographical references. / Lynn Dudley, Professor Directing Thesis; Vincent Salters, Committee Member; Ming Ye, Committee Member; Gang Chen, Committee Member.

Riverine inputs, groundwater efflux, and terrestrial runoff enrich coastal waters with silica. Diatoms, which require silicic acid (Si(OH)4) for frustule formation and cell growth, are therefore predominantly found in these waters. Less than half of the pelagic primary production is consumed in the shallow water column; the remaining fraction settles on the seafloor. However, large fractions of these shelf sediments are composed of permeable relict sands, which do not accumulate organic matter. As a result, the fate of the deposited diatoms and the biogenic silica (bSiO2) is poorly understood, and little is known about the processes that control transport and decomposition of sedimented diatoms in permeable shelf beds. To determine the fate of these deposited diatoms, four study objectives were addressed. These objectives were: I. To determine how diatoms are deposited on permeable sediments and how Si(OH)4 is distributed in upper-sediment layers; II. To determine how flushing of permeable sediments affects degradation and dissolution of diatoms embedded in the sands; III. To determine fluxes of Si(OH)4 from permeable sediments under different filtration conditions; and IV. To assess Si(OH)4 concentration ranges in the water and the pore water in the northern Gulf of Mexico in a time series to determine the coupling between water-column and pore-water concentrations. In the laboratory, two flume experiments were conducted to address the first objective. The first experiment revealed that deposition of algal cells occurred at the bottom of sediment-ripple troughs and the upper slopes of the ripples, while the ripple crest was associated with a deposition minimum. The second experiment demonstrated that the highest Si(OH)4 concentrations were found in the upwelling zone at the downstream slope of the ripple and the ripple crest (~100 µmol Si(OH)4). The upwelling pore-water flows that carry Si(OH)4 upwards focus near the ripple crest and dissolution of diatoms deposited in the ripple slopes add to the Si(OH)4 concentration in this zone. Meanwhile, the lowest concentrations were seen in the downwelling zone (e.g., ripple troughs and lower flanks). Here flume water with relatively low Si(OH)4 concentrations penetrated into the sediment. To address the second objective, the dissolution of the frustules in the permeable sand was quantified in five column-reactor experiments that permitted sediment flushing at well-defined pore-water flow velocities. The column experiments showed that the Si(OH)4 remobilization was higher in the pore space than in reaction columns that were filled with water only, suggesting that the dissolution of diatoms is more rapid in flushed sediments. The measured dissolution-rate constants (k) were 0.0144-0.0150 in columns with sediment versus 0.0070-0.0082 in columns with water only. This finding can be explained by the depression of the diffusive-boundary layer at the surface of the frustule when the diatoms are embedded in the sand. Sediment-water flux measurements with in-situ chamber incubations addressed the third objective and revealed that advective pore-water exchange enhanced Si(OH)4 flux up to a factor of six. Day and night fluxes differed due to the changes in Si(OH)4 uptake during daytime. Fluxes of Si(OH)4 were an order of magnitude higher in the sediments than in the water column at both the Gulf and the Bay sites. To address the fourth objective, monthly field samples were taken on St. George Island at the two field sites. These samplings revealed peaks in benthic primary production in the summer months and maxima in water and sediment silica concentrations in the fall and winter months. However, when nutrients became depleted during summer, an increase in Si(OH)4 concentrations was observed, suggesting that diatom growth was limited by other nutrients than Si(OH)4. The results of this study show that in permeable coastal sediments the dissolution of deposited diatom frustules and the release of the mobilized Si(OH)4 from the sediment are enhanced by the advective-pore water flows caused by bottom flow-topography interaction and emphasize the importance of coastal permeable sediments in the cycling of marine silica. / A Thesis submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Master of Science. / Fall Semester, 2008. / October 20, 2008. / Florida Panhandle, Biogenic Silica Dissolution, Permeable Sediments, Biogeochemistry / Includes bibliographical references. / Markus Huettel, Professor Directing Thesis; Thorsten Dittmar, Outside Committee Member; Richard Iverson, Committee Member.

Numerical ocean models have become powerful tools for providing a realistic view of the ocean state and for describing ocean processes that are difficult to observe. Recent improvements in model performance focus on simulating realistic ocean interior mixing rates, as ocean mixing is the main physical process that creates water masses and maintains their properties. Below the mixed layer, diapycnal mixing primarily arises from the breaking of internal waves, whose energy is largely supplied by winds and tides. This is particularly true in abyssal regions, where the barotropic tide interacts with rough topography and where high levels of diapycnal mixing have been recorded (e.g., the Hawaiian Archipelago). Many studies have discussed the representation of internal wave generation, propagation, and evolution in ocean numerical models. Expanding on these studies, this work seeks to better understand the representation of internal wave dynamics, energetics, and their associated mixing in several different classes of widely used ocean models (e.g., the HYbrid Coordinate Ocean Model, HYCOM; the Regional Ocean Modeling System, ROMS; and the MIT general circulation model, MITgcm). First, a multi-model study investigates the representation of internal waves for a wide spectrum of numerical choices, such as the horizontal and vertical resolution, the vertical coordinate, and the choice of the numerical advection scheme. Idealized configurations are compared to their corresponding analytical solutions. Some preliminary results of realistic baroclinic tidal simulations are shown for the Gulf of Mexico. Second, the spurious diapycnal mixing that exists in models with fixed vertical coordinates (i.e., geopotential and terrain following) is documented and quantified. This purely numerical error arises because, in fixed-coordinate models, the numerical framework cannot properly maintain the adiabatic properties of an advected water parcel. This unrealistic mixing of water masses can be a source of major error in both regional and global ocean models. We use the tracer flux method to compute the spurious diapycnal diffusivities for both a lockexchange scenario and a propagating internal wave field using all three models. Results for the lock exchange experiments are compared to the results of a recent study. Our results, obtained by using three different model classes, provide a comprehensive analysis of the impact of model resolution choice and numerical framework on the magnitude of the spurious diapycnal mixing and the representation of internal waves. / A Dissertation submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Fall Semester, 2010. / September 29, 2010. / spurious mixing, numerical modeling, internal wave, tide / Includes bibliographical references. / Eric Chassignet, Professor Directing Dissertation; Carol Anne Clayson, University Representative; Louis St Laurent, Committee Member; Steven Morey, Committee Member; Markus Huettel, Committee Member; James O’Brien, Committee Member.

With the aid of a 3-part modeling system forced by various satellite-remote sensed atmospheric inputs controlled by cloudiness, this study: (1) describes the space-time variations of surface net CO2 flux exchange over the large scale Amazon basin, (2) determines the key factors controlling these variations, and ultimately (3) determines the optimal spatial configuration of a network of tower observing posts, which if deployed, could capture in area-wide averages the main variant properties of the Amazon basin's surface net carbon flux on an absolute basis. The philosophy guiding this research is that whereas a sufficiently detailed model can do very well in capturing the space-time gradients of carbon flux exchange and thus the relative source-sink properties of the Amazonian landscape, current modeling knowledge does not allow an adequate model determination of absolute source-sink properties. Direct observations are needed to obtain meaningful absolute accuracies of the source-sink properties, properties that are highly sensitive to environmental and bio-physiological factors that effectively produce a heterogeneous fabric of source and sink magnitudes across the basin at any given instant of time. However, for the Amazon basin, and as a general rule of thumb in carbon budget monitoring over a large expanse, there seems to be never enough observation posts to eliminate the systematic bias problem -- nor are those that do exist sited according to a network strategy that optimizes their collective ability to eliminate such a bias problem. A hydrometeorological model coupled to a mixed layer (ML) model of the planetary boundary layer (PBL) then equipped with a set of three CO2 assimilation models, and finally forced by high resolution satellite-retrieved incoming surface radiation fluxes and rainfall, forms a detailed carbon flux exchange modeling system linked to satellite inputs, that achieves the desired research objectives. The forcing of the model by remotely sensed solar/infrared radiative flux and rainrate variables, which exert dominant influences on the surface carbon budget and whose variant properties are determined by the position and diurnal timing of cloudiness, is an essential element of the modeling system. This is because one of the greatest shortcomings in prognostic modeling is the ability to reproduce real clouds, particularly convective clouds, in the right place at the right time. In understanding how environmental and bio-physiological factors exert their respective controls on carbon flux exchange variability, the underlying variables are classified into four categories: (1) meteorological factors; (2) radiation factors; (3) water cycle factors; and (4) bio-physiological factors. The three different CO2 assimilation models are investigated to achieve optimal performance insofar as obtaining validated surface carbon, heat, and moisture fluxes in the framework of the Florida State University (FSU) hydrometeorological model -- developed over the last decade by E.A. Smith & H.J. Cooper. Of the three carbon models examined, the one selected for the final net CO2 flux calculations was developed by G. Bonan, beginning with his Ph.D. dissertation research and now included in a land surface model (LSM) facility at NCAR. This carbon scheme contains a respiration component consistent with its photosynthetic component and physically couples the CO2, sensible, and latent heat fluxes through stomatal resistance. Test calculations of net ecosystem productivity (NEP) show that it is essential to model canopy-boundary layer interactions in order to reproduce observed morning CO2 effluxes measured at various forest sites located within Brazil and operated as part of the Large Scale Biosphere-Atmosphere Research Programme for Amazônia (LBA) -- specifically the LBA tower sites at Manaus and Jaru. This is because under typical conditions of a stable nocturnal PBL, the forest canopy remains stagnant, allowing carbon concentrations to become elevated until after sunrise when PBL stability flips and CO2 is rapidly vented into the atmosphere. In the PBL model developed for the study, CO2 concentrations and the concomitant fluxes are determined for five layers in and above the forest canopy following the progression of the ML during the daytime and the nocturnal boundary layer at night, which are treated as separate components of the diurnal PBL. It is important to point out that canopy heat capacity must be accounted for in the hydrometeorological modeling (an oft-overlooked factor in LSM modeling), to prevent sensible heat fluxes from being systematically overestimated. Values of observed canopy heat storage (needed in the development of the heat capacity scheme) are found using observed differences between net incoming radiation and sensible-latent heat fluxes, or observed total residual energy. Calibration and validation of CO2, sensible, and latent fluxes at the three LBA tower sites are accomplished using modeled total residual energy at the forest sites and modified photosynthesis parameters at the pasture site. Application of the modeling system over the large-scale Amazon basin shows that while vegetation type is the most important factor controlling area-wide CO2 fluxes, incoming surface solar radiation and ambient temperature (both directly responsive to the cloud field) are the primary factors producing spatial and temporal variability of CO2 fluxes at a given location. Modeled CO2 fluxes show mean monthly uptake values in the range of 1-3 mmol m-2 s-1. Due to the superimposed annual and daily march of the solar elevation angle, diurnal progressions of large coherent expanses of CO2 efflux over forest areas, progressing from SE to NW in December and from NE to SW in June, are an essential variational mode in the surface carbon budget. Inspection of area-wide modeled fluxes near the tower sites reveals that the systematic use of ECMWF-analyzed winds and temperatures in forcing the modeling system creates instances of spurious nocturnal stability that produce larger morning efflux magnitudes than observations suggest. Finally, CO2 fluxes at some 20,000 forest grid points within the Amazônia region and for eight months of model output, are analyzed to determine the optimal sampling configuration vis-à-vis capturing in area-wide averages, the space-time variability of net CO2 flux. These results lead to the conclusion that flux observations from five strategically placed towers, measuring in conjunction with the existing three LBA towers at Manaus and Jaru, would be sufficient in baselining area-wide net CO2 fluxes needed for an understanding of carbon sequestration within the Amazon basin on an absolute scale. / A Dissertation submitted to the Department of Meteorology In partial fulfillment of the Requirements for the degree of Doctor of Philosophy. / Spring Semester, 2004. / March 4, 2004. / Amazon, Carbon Cycle, Variability, Carbon / Includes bibliographical references. / Eric A. Smith, Professor Co-Directing Dissertation; Paul H. Ruscher, Professor Co-Directing Dissertation; James B. Elsner, Outside Committee Member; Henry E. Fuelberg, Committee Member; Carol A. Clayson, Committee Member.

This dissertation examines the role of microorganisms in marine biogeochemical cycles with a particular emphasis on sedimentary nitrogen transformations. Nitrogen is required by all living organisms and is a key nutrient controlling the productivity of Earth's oceans. Pervasive endeavors of modern human society, such as fossil fuel combustion and Haber-Bosch N2 fixation for agricultural fertilizers, have caused large-scale perturbations in the natural, global nitrogen cycle such that the rate of anthropogenic reactive nitrogen creation now exceeds that of all natural processes combined. A substantial fraction of this man-made reactive nitrogen is being lost to the environment where, as a macro-nutrient, excessive nitrogen loading is causing extensive disruptions to natural primary production cycles and food webs. Basic scientific research on nitrogen cycling in coastal oceans is imperative as human activities are increasingly adding to the reactive nitrogen influx to near-shore environments. Shallow coastal areas (< 200 m water depth) cover only ~ 7% of the ocean although up to 30% of marine primary production occurs in these zones. Biogenic debris settling in coastal zones largely escapes degradation in the water column, and thus, as much as 60% of locally-produced organic matter undergoes benthic deposition and diagenesis. Nutrients regenerated during organic matter mineralization in shallow sediments are essential in fueling high rates of marine primary production in continental margins. Coastal sediments are also important sites of reactive nitrogen removal with the majority of marine microbial N2 production occurring in these areas. Production of N2 in continental shelf sediments via microbial denitrification and anammox (anaerobic ammonium oxidation) is an essential process for nitrogen removal and maintaining a balance of reactive nitrogen in the oceans. Denitrification and anammox are two of the least understood pathways in the nitrogen cycle; explorations of rates and mechanisms for N2 production have been hindered mainly by methodological difficulties, spatial and temporal variability in benthic processes, and previously-overlooked nitrogen cycling pathways. Due largely to a paucity of direct N2 flux rate measurements, most global marine nitrogen budget estimates are tenuous (Capone 2008). Thus, the foci of this dissertation were to better constrain known rates of denitrification and anammox, elucidate the principal controls on these processes in situ, and explore the ecology of microorganisms mediating these reactions in coastal sediments. Rates and controls of nitrogen removal by microbial N2 production were studied at three field areas in two different estuaries. Field research sites within the Apalachicola National Estuarine Research Reserve included stations adjacent to St. George Island in the Gulf of Mexico (for the investigation of nitrogen cycling in permeable sediments) in addition to stations within an oligohaline marsh near the mouth of the Apalachicola River (for a study of nitrogen removal by coastal wetlands). Benthic microbial nitrogen cycling was also studied in fjords of the Svalbard islands in the Arctic Ocean. The first of four chapters of this dissertation describes a study identifying the microbial taxa which catalyze phytodetritus degradation and denitrification in permeable coastal sediments of the northeast Gulf of Mexico. Coastal benthic environments typically receive intermittent pulses of organic matter following phytoplankton bloom events and permeable sediments have been demonstrated to rapidly degrade this material. Microorganisms act as the primary agents of benthic organic matter decomposition through the production of extracellular hydrolytic enzymes, fermentation, and terminal carbon mineralization coupled with respiratory processes. Although the role of bacteria in the decomposition of organic matter in marine sediments has long been recognized, the mechanisms regulating organic matter decomposition, and relationships between the phylogeny of benthic microorganisms and changes in biogeochemical and ecological function, are under-explored. In this study of detritus-degrading microorganisms, stable isotope probing experiments were used to track the assimilation of isotopically-labeled substrate into bacterial DNA and to directly link the taxonomic identification of benthic microorganisms with particulate organic matter degradation and denitrification activity. Phytodetritus deposition events were simulated in the laboratory by the addition of 13C-enriched, heat-killed Spirulina cells to intact sediment core incubations. Immediate increases in O2 consumption, N2 efflux, and dissolved inorganic nitrogen efflux were observed following phytodetritus addition relative to unamended treatments, suggesting that the benthic microbial community was poised to immediately begin oxidizing deposited organic matter. Analyses of 16S rRNA gene sequences amplified from 13C-enriched DNA fractions demonstrated that members of the Gammaproteobacteria (Vibrionales and Alteromonadales), Deltaproteobacteria, Actinobacteria, Verrucomicrobia, and Planctomycetes metabolized the phytodetritus amendment. Terminal restriction length polymorphism analyses showed increases in the relative abundance of Gammaproteobacteria, Planctomycetes, and Bacteroidetes with phytodetritus addition. Alphaproteobacteria were identified as metabolically active denitrifiers by phylogenetic analysis of nitrous oxide reductase gene sequences from 13C-enriched DNA fractions. This study provides the first identification of microorganisms responsible for organic matter degradation in marine sediments by DNA sequence analysis. Microbial assemblages recognized for high molecular weight organic matter oxidation in the marine water column were important in catalyzing these processes in permeable sediments. Permeable sediments are also the focus of Chapter 2 which describes nitrogen cycling over a one-year period in sublittoral sands from two contrasting sites near St. George Island. Nitrogen stable isotope tracer techniques were used to measure N2 production rates and pathways in sediment cores and slurries. To simulate pore-water advection, which occurs in permeable sands due to interactions between water currents and surface topography, intact sediment cores were perfused with aerated seawater. Pore-water perfusion increased denitrification rates up to 2.5-fold and 15-fold for the Apalachicola Bay and Gulf of Mexico sites, respectively, relative to static cores. Seasonal N2 production rates were highest in spring and fall. Denitrified nitrate was derived almost entirely from benthic nitrification at the Gulf site whereas water column nitrate was more important at the Bay site. Stirred chambers with intact sediment cores were used to determine net fluxes O2, N2, nitrate, and ammonium across the sediment-water interface during varied degrees of continuous pore-water exchange. Rates of N2 efflux were directly correlated with the extent of pore-water flow increasing from 0.13 mmol N m-2 d-1 under diffusion-limited solute transport conditions up to 0.87 mmol N m-2 d-1 with pore water advection. Mineralized nitrogen was completely converted to N2 gas in Gulf of Mexico sediments. These data provide clear evidence that permeable sediments are important in nitrogen removal and N2 production occurs over a continuum of rates dependent on bottom current conditions. Results from a study of benthic nitrogen cycling in two Arctic fjords are presented in Chapter 3. Intact sediment core incubations were used to quantify net fluxes of dissolved inorganic nitrogen, organic nitrogen, organic carbon, and oxygen at the sediment-water interface. Rates of gross denitrification, anammox, nitrification, dissimilatory nitrate reduction to ammonium, and N2 fixation were quantified using core incubations and slurry experiments. Profiles of dissolved inorganic nitrogen in pore-water, and organic carbon and nitrogen in the solid phase, were also obtained. Net nitrogen losses as N2 ranged from 0.152 to 0.453 mmol N m-2 d-1 and denitrification comprised 2% to 11% of total carbon oxidation. Rates of anammox ranged from 20 to 51 μmol N m-2 d-1 and contributed 5% to 23% of gross N2 generation. Nitrification rates were as high as 0.833 mmol N m-2 d-1 and sediments were a substantial source of nitrate to the water column (0.169 to 0.393 mmol N m-2 d-1 efflux). Uptake of ammonium (0.052 to 0.087 mmol N m-2 d-1), dissolved organic nitrogen (0.291 to 0.486 mmol N m-2 d-1), and dissolved organic carbon (1.31 to 2.50 mmol N m-2 d-1) was observed. Benthic nitrogen fixation was estimated at 0.020 mmol N m-2 d-1 in one of the fjords. Dissimilatory nitrate reduction to ammonium and net N2O production were not detected. This study provides direct evidence that nitrogen loss rates, mainly via denitrification, in Arctic sediments rival those measured in temperate or subtropical environments. Chapter 4 describes a study sponsored by the NOAA National Estuarine Research Reserve System Graduate Research Fellowship program to investigate nitrogen cycling in the Apalachicola River distributary marsh. Coastal, fringing marshes have been thought to remove dissolved inorganic and particulate nitrogen from external sources via benthic denitrification and burial, respectively, and to export considerable loads of dissolved organic nitrogen (DON) to the greater estuary. There is, however, little data available from tidal freshwater and oligohaline marshes to confirm these hypotheses and benthic nitrogen cycling in the Apalachicola National Estuarine Research Reserve (ANERR) marsh has not been previously studied. This work addressed the hypotheses that the ANERR marshes comprise a significant sink of river-derived dissolved inorganic nitrogen through nitrification-denitrification and burial, and provide a substantial source of nitrogen to the Bay as DON. Denitrification rates were measured between July 2006 and August 2008 using intact sediment core incubations. Rates of net N2 flux ranged from 0.23 to 1.72 mmol N m-2 d-1 with a mean of 0.72 mmol N m-2 d-1 for all sites over the course of the study. Preliminary results indicate that burial of particulate nitrogen (1.46 mmol N m-2 d-1) is a larger annualized loss term than denitrification. A study of tide-driven exchange of nitrogen between marsh creeks and river distributaries showed net uptake of nitrate by marsh sediments and export of DON. / A Dissertation submitted to the Department of Oceanography in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester, 2009. / April 27, 2009. / Nitrogen, Anammox, Marine, Biogeochemistry, Denitrification, Estuary / Includes bibliographical references. / Joel Kostka, Professor Directing Dissertation; Munir Humayun, Outside Committee Member; Jeff Chanton, Committee Member; Stefan Green, Committee Member; Markus Huettel, Committee Member.