Mesoscale convective complexes (MCCs) over subtropical South America contribute an average annual volume of precipitation equal to approximately seven km3 and occur with an average regularity in the region, with more than 30 per warm season. Isotopic characteristics of precipitation, such as δ2H and δ18O values, provide information that can be used to identify unique processes and sources related to precipitation events. The largest database of isotope characteristics of precipitation within the region is the Global Network of Isotopes in Precipitation (GNIP), which provides varying temporal resolution data from stations around the world, including subtropical South America. Using this database, isotope characteristics of precipitation samples within the study area of Brazil were examined to identify patterns in storm characteristics, the isotope characteristics in MCC events, and to assess the use of event (daily) resolution data for storm events that lasted 14 hours, on average. This research resulted in Local Meteoric Water Lines (LMWL) that describe the isotopic composition of precipitation and rivers at various points throughout the year and found precipitation within the study region much closer to the Global Meteoric Water Line (GMWL) than river water. While event (daily) resolution is useful, a greater number of samples at higher-resolution would provide better descriptions for specific storm events, such as MCCs, as well as to differentiate between MCC and non-MCC events more effectively. Differences in source waters and processes were evident in the data, meaning future research at higher resolutions could benefit from identifying the contribution of each source and process to any distinct MCC event in the region.

<p> Passive longwave infrared radiometric satellite-based retrievals of sea surface temperature (SST) at instrument nadir are investigated for cold bias caused by unscreened optically-thin cirrus (OTC) clouds (cloud optical depth &le; 0.3; COD). Level 2 split-window SST retrievals over tropical oceans (30&deg; S - 30&deg; N) from Moderate Resolution Imaging Spectroradiometer (MODIS) radiances collected aboard the NASA Aqua satellite (Aqua-MODIS) are collocated with cloud profiles from the Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) instrument, mounted on the independent NASA CALIPSO satellite. OTC are present in approximately 25% of tropical quality-assured (QA) Aqua-MODIS Level-2 data, representing over 99% of all contaminating cirrus found. This results in cold-biased SST retrievals using either split- (MODIS, AVHRR and VIIRS) or triple-window (AVHRR and VIIRS only) retrieval methods. SST retrievals are modeled based on operational algorithms using radiative transfer model simulations conducted with a hypothetical 1.5 km thick OTC cloud placed incrementally from 10.0 - 18.0 km above mean sea level for cloud optical depths (COD) between 0.0 - 0.3. Corresponding cold bias estimates for each sensor are estimated using relative Aqua-MODIS cloud contamination frequencies as a function of cloud top height and COD (assuming them consistent across each platform) integrated within each corresponding modeled cold bias matrix. Split-window relative OTC cold biases, for any single observation, range from 0.40&deg; - 0.49&deg; C for the three sensors, with an absolute (bulk mean) bias between 0.10&deg; - 0.13&deg; C. Triple-window retrievals are more resilient, ranging from 0.03&deg; - 0.04&deg; C relative and 0.11&deg; - 0.16&deg; C absolute. Cold biases are constant across the Pacific and Indian Ocean domains. Absolute bias is smaller over the Atlantic, but relative bias is larger due to different cloud properties indicating that this issue persists globally.</p>

Paleoclimatic data including orbital eccentricity, mollusk species counts and carbonate isotope data are combined in an event based, time synchronized, parameter mapped sonification that plays backwards through geologic time from ~3.2 million years ago to ~7.4 million years ago. Interpretations of the sonified data are compared to the interpretations of previously published studies and insight has been gained regarding the usefulness of auditory display methods in this scientific context. The field of auditory display has grown exponentially in recent years but there is a lack of papers that use sonification to explore science-based data within a legitimate scientific framework. The end result allow users to monitor a substantial portion of the Late Neogene period (around 4.2 million years in length) in less than 2 minutes. Users perceive shifts in mollusk counts (a temperature proxy) as the pink noise changes structure and travels L and R in the sound field. Low frequency discrete tones mimic the changing eccentricity of Earth's orbit as bell tones (representing isotope trends) move chaotically in the center channel. It is shown that sonification can preserve both simple and advanced structures in scientific data as shown in numerous sound examples and verified with unique figures that compare sonification waveforms or spectrograms to original publication figures. / 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. / Spring Semester, 2014. / April 15, 2014. / Auditory display, Csound, Eccentricity, Ecological abundance, Isotope, Sonification / Includes bibliographical references. / William Parker, Professor Directing Thesis; Leroy Odom, Committee Member; Yang Wang, Committee Member.

Continuous event-based rainfall samples were collected at three sites throughout the Pensacola airshed from 2005 - 2011. Samples were analyzed for total mercury (Hg), a suite of trace metals (TMs), and major ions in order to understand how thunderstorms affected their wet deposition and concentrations in rainfall, estimate the contributions from regional coal combustion and other anthropogenic sources to Hg and TMs in rainfall along the Gulf Coast, and investigate the possible influence that a local 950 megawatt coal-fired power plant had on rainfall chemistry in the Pensacola airshed. Mercury was measured with a Tekran 2600 using a method that was a variation of the standard method used by the US Environmental Protection Agency (EPA) to measure total Hg in water which allowed for the analysis of TMs from the same bottle without having to worry about contamination from reagents during sample preparation. Trace metals were measured used an Agilent 7500cs quadrupole inductively coupled plasma mass spectrometer (ICP-MS) while utilizing an octopole reaction cell (ORC) which allowed for the detection of key coal-combustion tracers like arsenic (As) and selenium (Se). Our findings show that summertime rainfall Hg concentrations are higher compared to other months despite higher rainfall amounts. In contrast, other measured pollutant TMs and ions did not show a consistent seasonal pattern. By incorporating Automated Surface Observing System data from nearby Pensacola International Airport and WSR-88D radar data from Eglin Air Force Base, we were able to classify the storm type (thunderstorms or non-thunderstorms) and analyze altitudes of hydrometeor formation for individual rain events. This showed that mid-altitude and high-altitude composite reflectivity radar values were higher for both thunderstorm and non-thunderstorm ”warm season” (May - Sept) rain events compared to ”cool season” (Oct - Apr) events including cool season thunderstorms. Thus, warm season events can scavenge more soluble reactive gaseous Hg from the free troposphere. Two separate multiple linear regression analyses were conducted on log-transformed data using interaction and non-interaction terms to understand the relationship between precipitation depth, season, and storm-type on sample concentrations. The regressions without interaction terms showed that the washout coefficients for more volatile TMs like Hg and Se were less pronounced compared to other pollution-type elements and that their concentrations were therefore less diluted for a given increase in precipitation depth, but otherwise displayed similar coefficients for season and storm-type. The regression model with interaction terms revealed a more interesting dynamic where thunderstorms caused enhanced Hg concentrations in rainfall regardless of season or precipitation depth while showing a more volume-dependent relationship with TM concentrations as concentrations increased with increasing rainfall amounts relative to non-thunderstorm events. This suggests a vacuum cleaner effect such that for increasing storm strength, non-Hg aerosol TMs in the boundary layer are further entrained into a storm cell. With this understanding, a positive matrix factorization (PMF) analysis was conducted using the EPA PMF 5.0 software to estimate the contribution of different sources to Hg deposition. Our results suggest that approximately 84% (72 - 89%; 95% CI) of Hg in rainfall along the northern Gulf of Mexico is due to long-range transport from distant sources while a negligible amount (0 - 21%; 95% CI) comes from regional coal combustion. However, we found that anthropogenic sources like regional coal combustion and ore smelting were significant contributors to rainfall concentrations of other pollution-type TMs like copper, zinc, As, Se, and non-sea salt SO42-. Using modeled wind profiles via the HYSPLIT trajectory model, we assessed whether plumes from a local coal-fired power plant (”Plant Crist”) could be detected in the rainfall chemistry of rain events occurring downwind of the plant. We limit this analysis to cool season rain events between June 2007 (when the model began) and December 2011 (when the study ended) because modeled wind profiles showed better agreement with observations during this time period compared to the warm season. We also limit this analysis to cool season events since the spatial distribution of rainfall throughout the area is more even during this time which makes sample comparisons between sites easier since Hg/TM concentrations are affected by precipitation depth. Furthermore, we focus on Hg and other pollution-type TMs and major ions such as As, Se, and non-sea salt SO42- in this analysis as they serve as tracers of coal combustion. For our ”unpaired-site” analysis, we analyzed, for each individual site, the rainfall chemistry in a given sample as a function of the proportion of rain events associated with that sample that occurred downwind of Plant Crist. Using this method, we were not able to find evidence that the plant had a significant influence on Hg/TM concentrations or Hg/TM:Al enrichment ratios in rainfall. Similarly, for our ”paired-site” analysis, we consider the differences in rainfall chemistry between two sites - an upwind and downwind site pair - that were impacted by the same rain event where the downwind site was exposed to plumes from Plant Crist while the upwind site was not. As with the unpaired-site analysis, we did not find significant differences in the rainfall chemistry between upwind-downwind site pairs with regards to sample concentrations or enrichment ratios. A multiple linear regression analysis was then conducted using interaction terms to understand the relationship between the operation of a wet flue-gas desulfurization system (which began operation at the plant during the middle of the study), the relative exposure a rainfall sample had to the plumes coming from the plant, and the log-transformed precipitation depth on log-transformed sample concentrations. Besides for As, the first regression analysis did not find coefficient values of any statistical significance for any of the variables that would indicate that the scrubber affected the rainfall chemistry at the two urban sites nearest to the plant. The calculations for As gave mixed results as the coefficients for the non-interaction terms suggested that the scrubber and the plumes emanating from Plant Crist affected the concentration of As in rainfall while the interaction terms suggested that they did not. We perform another multiple linear regression analysis, but remove the complicating effects of precipitation depth on Hg/TM concentrations and instead analyze the effects that the scrubber and the plumes coming from the plant might have had on Hg/TM:Al ratios. Again, these results were inconclusive as the regression coefficients suggested that the scrubber helped reduce Hg and TM emissions from the plant while also suggesting that samples with more exposure to the plant’s plumes had lower enrichment ratios. We propose that we were unable to detect a chemical signal from Plant Crist in our rain samples due to a few possible reasons including quick scavenging of TMs from the plume at the onset of a rain event before reaching our sites, the reliance on radar data to determine start and stop times for rain events at the sites as opposed to on-site measurements, and relatively low spatiotemporal resolution for the wind trajectory model. / A Dissertation submitted to the Department of Earth, Ocean and Atmospheric Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester 2018. / July 16, 2018. / Coal combustion, Mercury, Source-apportionment, Thunderstorms, Trace metals, Trajectory analyis / Includes bibliographical references. / William M. Landing, Professor Directing Dissertation; Thomas E. Miller, University Representative; Christopher D. Holmes, Committee Member; Henry E. Fuelberg, Committee Member; Vincent J. M. Salters, Committee Member.

Tornadoes cause numerous deaths and significant property damage each year, yet how tornado activity varies across climate states, particularly under global warming, remains poorly understood. Importantly, severe weather events arise during transient periods of extreme thermodynamic environments whose variability may differ from that of the environmental mean state. This study analyzes the climatological relationships between commonly-used severe weather environmental proxies (the product of convective available potential energy and bulk vertical wind shear, energy-helicity index, and the significant tornado parameter) and tornado density on three dominant timescales of climate forcing: diurnal, seasonal, and interannual. We utilize reanalysis data to calculate the spatial distributions of the mean, median, and a range of extreme percentiles of these proxies across each timescale as well as for the full climatology. We then test the extent to which each measure captures the spatiotemporal variability of tornado density over the continental United States. Results indicate that the mean is a suitable statistic when used with the full climatology of the energy-helicity index and the significant tornado parameter without using convective inhibition in calculations, the diurnal cycle for convective available potential energy and the product of convective available potential energy and bulk vertical wind shear, and the interannual variations for all proxies except convective available potential energy. The mean is outperformed by extreme percentiles otherwise. This understanding of climatological relationships between tornadoes and the large scale environments can improve prediction of tornado frequency and provides a foundation for understanding how changes in the statistics of large-scale environments may affect tornado activity in a future warmer climate state.

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This document is a summary of research conducted to develop and apply climate analysis tools toward a better understanding of the past and future of hydroclimate variability in the state of Utah. Two pilot studies developed data management and climate analysis tools subsequently applied to our region of interest. The first investigated the role of natural atmospheric forcing in the inter-annual variability of precipitation of the Sahel region in Africa, and found a previously undocumented link with the East Atlantic mode, which explains 29% of variance in regional precipitation. An analysis of output from an operational seasonal climate forecast model revealed a failure in the model to reproduce this linkage, thus highlighting a shortcoming in model performance. The second pilot study studied long-term trends in the strength of the Great Plains low-level jet, an driver of storm development in the region’s wet spring season. Our analysis showed that since 1979 the low-level jet has strengthened as shifted the timing of peak activity, resulting in shifts both in time and location for peak precipitation, possibly the result of anthropogenic forcing. Our third study used a unique tree-ring dataset to create a reconstruction of April 1 snow water equivalent, an important measure of water supply in the Intermountain West, for the state of Utah to 1850. Analysis of the reconstruction shows the majority of snowpack variability occurs monotonically over the whole state at decadal to multidecadal frequencies. The final study evaluated decadal prediction performance of climate models participating in the Coupled Model Intercomparison Project 5. We found that the analyzed models exhibit modest skill in prediction of the Pacific Decadal Oscillation and better skill in prediction of global temperature trends post 1960.

Marine viruses are the most numerous biological entities in the ocean, with an estimated abundance of 4 x 1030. They merit study not only because of their sheer abundance, but also because of the role they play in the Earth's biogeochemical cycles. Viral lysis of bacteria redirects the flow of nutrients among marine microbes, which ultimately affects the efficiency of the biological pump. Viral diversity is important because most viruses are host-specific. In preying on a certain type of bacteria, viruses affect the diversity and structure of the bacterial community, leading to changes in carbon and nutrient flows. In turn, such variations can alter the amount of carbon dioxide in the Earth's atmosphere. However, studying viral diversity presents challenges. Morphological similarities among many types of viruses make it preferable to use genetic methods of investigation, but the absence of a single gene common to all families of viruses hampers the identification of viruses in environmental samples. Nonetheless, some genes are shared within phage families, and those shared ("signature") genes can be used as markers to identify members of a family. In addition, community profiling methods can fingerprint the diversity of a viral community. Most previous studies of marine viral communities consist of a single glimpse—a representation of the community at a single time and place, or at a few depths sampled at one time. While the resources required to collect marine samples often make broader or repeated sampling impracticable, without studies conducted over greater time and spatial ranges, our knowledge of marine viral dynamics will remain limited. To gain strides in understanding spatial and temporal variability in marine viral diversity, this dissertation focused on a detailed examination of viral diversity at a single site in the Sargasso Sea. Time and depth intervals for sampling were kept as uniform as possible in order to strengthen the conclusions to be drawn from the research. The Sargasso Sea is a seasonally oligotrophic portion of the North Atlantic Ocean, characterized by deep convective winter mixing and summer stratification of the water column. A tremendous amount of oceanographic research has been conducted in the Sargasso Sea because it is home to the Bermuda Atlantic Time-series Study (BATS), one of the world's longest-running ocean time series studies. Because of the core monthly measurements made at the BATS site and the vast amount of ancillary research that uses BATS as a platform, the site is an excellent place to study viral diversity. Using a variety of techniques, this research aimed to expand our knowledge of viral dynamics by analyzing the viral community of the Sargasso Sea over a several-year period, through different seasons, and at different depths. The first chapter developed phoH as a new signature gene for assessing marine viral diversity. The phoH gene is disproportionately present in fully-sequenced marine phage, as opposed to phage isolated from non-marine environments, and is widespread in the marine environment. Diversity of the phoH gene was high, and most of the sequences recovered belonged to phylogenetic groups that did not contain any cultured representatives, indicating that cultured phage isolates do not adequately represent the diversity found in marine environments. Composition of the phoH communities at each sampled location and depth was distinguishable according to phylogenetic clustering, although most phoH clusters were recovered from multiple sites. These factors demonstrate that phoH will be useful for studying marine phage diversity worldwide. Chapter 2 analyzed the viral diversity of a depth profile at BATS by amplifying and deep sequencing the phoH gene. This comprehensive study of the gene's diversity over three different years, several seasons, and a range of depths from the surface to 1000 m revealed that the viruses at BATS contain a large pool of phoH sequences, but that most of those sequences are rare. The phoH sequences were dominated by just a few operational taxonomic units (OTUs). Rarefaction analysis showed that the sequencing was sufficient to capture the diversity of the gene at BATS, and in fact no new phylogenetic clusters were identified that were not seen in the small amount of Sanger sequencing performed for the initial phoH study in Chapter 1. Some of the more abundant phoH OTUs recurred every season and every year, in varying degrees, although similar depths and seasons clustered together. Overall, the phoH gene revealed depth-based, seasonal, and interannual differences in the diversity of the viral community at BATS. Chapter 3 continued the extensive examination of viral diversity at BATS by using several signature genes and a fingerprinting technique to assess changes between winter and summer viral communities over two depths in three different years. This chapter investigated whether the annually recurring subsurface peak in viral abundance corresponded to recurring changes in composition of the viral community in the vicinity of the peak. Clustering analysis was used to determine which samples were most similar. The results demonstrated that the viral communities at the surface and at 100 m depth were more similar to each other in winter (March), regardless of the year, than they were in summer (September), when the water column is stratified as opposed to well-mixed. These findings may stem from physical factors such as UV irradiation of viral particles during stratification, as well as seasonal and depth-related differences in host communities associated with the depth of the mixed layer. This dissertation provides substantial advances to the field of microbial ecology. First, the development of phoH as a signature gene is an important addition to the limited set of tools available for studying marine viral diversity. This research also constitutes the first deep sequencing of a signature gene for marine viruses, providing a guide for the depth of sequencing needed to capture the diversity of a marine viral community and a benchmark for the level of viral diversity to expect in an oligotrophic marine system. Finally, the dissertation expands our knowledge of the viral community at BATS by examining the community based on four different measures of composition, rather than abundance. The research presented here also suggests several avenues of future investigation, including redesigning the phoH primers to expand their scope, sampling the viral community at BATS at the precise depth of the peak in abundance, working to identify the hosts of aquatic gokushoviruses, and culturing and sequencing additional marine viruses in order to improve the reflection of natural environmental communities in genomic databases.

<p>Global Navigation Satellite System (GNSS) radio occultation (RO) is a remote sensing technique that exploits existing navigation signals to make global, real-time observations of the Earth's atmosphere. A specialized RO receiver makes measurements of signals originating from a transmitter onboard a GNSS spacecraft near the Earth's horizon. The radio wave is altered during passage through the Earth's atmosphere. The changes in the received signals are translated to the refractivity characteristics of the intervening medium, which enable the calculation of atmospheric pressure, temperature, and humidity. Current satellite missions employing GNSS RO have provided invaluable and timely information for weather and climate applications. Existing constellations of occultation satellites, however, are aging and producing fewer quality measurements. Replacement fleets of RO satellites are imperative to sustain and improve the global coverage and operational impact achieved by the current generation of RO satellites. This dissertation describes studies that facilitate the development of next generation RO receivers and satellite constellations. Multiple research efforts were conducted that aim to improve the quantity and quality of measurements made by a future satellite-based RO collection system. These studies range in magnitude and impact, and begin with a receiver development study using ground-based occultation data. Future RO constellations and collection opportunities were simulated and autonomous occultation prediction and scheduling capabilities were implemented. Finally, a comprehensive study was conducted to characterize the stability of the GNSS atomic frequency standards. Oscillator stability for a subset of satellites in the GNSS was found to be of insufficient quality at timescales relevant to RO collections and would degrade the atmospheric profiling capabilities of an RO system utilizing these signals. Recommendations for a high-rate clock correction network are proposed, which provides significant improvement to the fractional errors in the derived refractivity, pressure, and temperature values caused by the oscillator instabilities.

Our limited knowledge of convection and its poor representation in climate models is one of the factors that most hamper our ability to understand and predict the climate system. In this thesis, the dynamics of shallow cumulus convection are probed using Large-eddy simulations (LES) and simple models. / Earth and Planetary Sciences