Digital Commons Network^™

Coral-Based Climate Variability In The Western Pacific Warm Pool Since 1867, Terrence M. Quinn, Frederick W. Taylor, Thomas J. Crowley

Marine Science Faculty Publications

We have generated monthly resolved, stable isotope (δ¹⁸O and δ¹³C) and Sr/Ca time series from a massive Porites coral from Rabaul (4°S, 152°E): a site located in the warmest sector of the Western Pacific Warm Pool (WPWP). The coral δ¹⁸O and Sr/Ca time series are well correlated to each other and positive excursions in both records coincide with times of ENSO warm phase events. These time series contain abundant interannual variability that exhibits the well‐recognized pattern of low amplitude ENSO variation between ∼1920–1960 and high amplitude ENSO variation between 1880–1920 and 1960–1997. The …

Red Tides In The Gulf Of Mexico: Where, When, And Why?, John J. Walsh, J. K. Jolliff, B. P. Darrow, J. M. Lenes, S. P. Milroy, A. Remsen, D. A. Dieterle, Kendall L. Carder, F. R. Chen, Gabriel A. Vargo, Robert H. Weisberg, Kent A. Fanning, Eugene Shinn, K. A. Steidinger, Cynthia A. Heil, C. R. Tomas, J. S. Prospero, T. N. Lee, G. J. Kirkpatrick, T. E. Whitledge, D. A. Stockwell, T. A. Villareal, A. E. Jochens, P. S. Bontempi, Frank E. Muller-Karger

Marine Science Faculty Publications

Independent data from the Gulf of Mexico are used to develop and test the hypothesis that the same sequence of physical and ecological events each year allows the toxic dinoflagellate Karenia brevis to become dominant. A phosphorus‐rich nutrient supply initiates phytoplankton succession, once deposition events of Saharan iron‐rich dust allow Trichodesmium blooms to utilize ubiquitous dissolved nitrogen gas within otherwise nitrogen‐poor sea water. They and the co‐occurring K. brevis are positioned within the bottom Ekman layers, as a consequence of their similar diel vertical migration patterns on the middle shelf. Upon onshore upwelling of these near‐bottom seed populations to CDOM‐rich …

Subcentennial-Scale Climatic And Hydrologic Variability In The Gulf Of Mexico During The Early Holocene, Jenna M. Lodico, Benjamin P. Flower, Terrence M. Quinn

Marine Science Faculty Publications

An early Holocene record from the Gulf of Mexico (GOM) reveals climatic and hydrologic changes during the interval from 10.5 to 7 thousand calendar years before present from paired analyses of Mg/Ca and δ¹⁸O on foraminiferal calcite. The sea surface temperature record based on foraminiferal Mg/Ca contains six oscillations and an overall ∼1.5°C warming that appears to be similar to the September–March insolation difference. The δ¹⁸O of seawater in the GOM (δ¹⁸O_GOM) record contains six oscillations, including a −0.8‰ excursion that may be associated with the “8.2 ka climate event” or a …

Evaluation Of New Grace Time-Variable Gravity Data Over The Ocean, Don P. Chambers

Marine Science Faculty Publications

Monthly GRACE gravity field models from the three science processing centers (CSR, GFZ, and JPL) are analyzed for the period from February 2003 to April 2005 over the ocean. The data are used to estimate maps of the mass component of sea level at smoothing radii of 500 km and 750 km. In addition to using new gravity field models, a filter has been applied to estimate and remove systematic errors in the coefficients that cause erroneous patterns in the maps of equivalent water level. The filter is described and its effects are discussed. The GRACE maps have been evaluated …

Cold Event In The South Atlantic Bight During Summer Of 2003: Anomalous Hydrographic And Atmospheric Conditions, Alfredo Aretxabaleta, James R. Nelson, Jack O. Blanton, Harvey E. Seim, Francisco E. Werner, John M. Bane, Robert H. Weisberg

Marine Science Faculty Publications

Unusually cold seawater temperatures were observed along much of the U.S. eastern seaboard during the summer of 2003. In this study, hydrographic and atmospheric observations from spring through summer were analyzed to track the evolution of the cold water event in the South Atlantic Bight (SAB) and investigate links to various forcing mechanisms. The hydrographic observations included 13 cross‐shelf transects over the central region of the SAB, surface temperature time series from several NDBC stations, and bottom temperatures from a mid shelf mooring. Atmospheric data were obtained from NDBC stations. Additional data included water level from NOS stations and river …

Performance Evaluation Of The Self-Organizing Map For Feature Extraction, Yonggang Liu, Robert H. Weisberg, Christopher N. K. Mooers

Marine Science Faculty Publications

Despite its wide applications as a tool for feature extraction, the Self‐Organizing Map (SOM) remains a black box to most meteorologists and oceanographers. This paper evaluates the feature extraction performance of the SOM by using artificial data representative of known patterns. The SOM is shown to extract the patterns of a linear progressive sine wave. Sensitivity studies are performed to ascertain the effects of the SOM tunable parameters. By adding random noise to the linear progressive wave data, it is demonstrated that the SOM extracts essential patterns from noisy data. Moreover, the SOM technique successfully chooses among multiple sets of …

A Determination Of Phylogeny And Hybridization History Within Clematis L. (Ranunculaceae) Using Actin And Nitrate Reductase Intron Sequences, Kimberly Fearn Do

USF Tampa Graduate Theses and Dissertations

The phylogeny of Clematis, section Viorna, was characterized in this study using molecular data. Two nuclear introns were sequenced for a variety of taxa: actin and nitrate reductase. Actin intron sequence data yielded very little phylogenetic information. Some basal clades were resolved, but there were very few well supported relationships between species of the Viorna section in both the neighbor joining and maximum parsimony analyses. Nitrate reductase intron sequence data was slightly more variable. The number of well supported relationships in both the neighbor joining and maximum parsimony analyses for nitrate reductase was greater, but still not sufficient …

An Evaluation Of The Along Track Reef Imaging System (Atris) For Efficient Reef Monitoring And Rapid Groundtruthing Of Eaarl Lidar, Nicole O. Caesar

USF Tampa Graduate Theses and Dissertations

The Along-Track Reef-Imaging System (ATRIS) is a vessel-mounted, digital camera, depth sounder and Global Positioning System (GPS) package that facilitates the rapid capture of underwater images in shallow-water benthic environments. This technology has the potential to collect ecologically significant data, particularly in benthic habitats less than 10 m in depth, with better location referencing and in less time than is required for surveys carried out by Scuba divers. In October 2004, ATRIS was tested coincidently with SCUBA-assisted video along transects on five patch reefs in Biscayne National Park. Images from both data sets were subsampled, viewed, and benthic cover under …

Assessment Of Image Analysis As A Measure Of Scleractinian Coral Growth, Steven K. Gustafson

USF Tampa Graduate Theses and Dissertations

Image analysis was used to measure basal areas of selected colonies of Montastraea annularis and Porites astreoides, following the colonies over a three-year period from 2002 to 2004. Existing digital images of permanently-marked quadrats in the Caye Caulker Marine Reserve, Belize, were selected based on image quality and availability of images of selected quadrats for all three years. Annual growth rates were calculated from the basal-area measurements. Mean growth rates (radial skeletal extension) for M. annularis and P. astreoides were 0.02 cm yr-1 and -0.20 cm yr-1, respectively. Basal area measurements demonstrated a large degree of variability. Increases were approximately …

Reproducibility Of Geochemical And Climatic Signals In The Atlantic Coral Montastraea Faveolata, Jennifer M. Smith, Terrence M. Quinn, Kevin P. Helmle, Robert B. Halley

Marine Science Faculty Publications

Monthly resolved, 41‐year‐long stable isotopic and elemental ratio time series were generated from two separate heads of Montastraea faveolata from Looe Key, Florida, to assess the fidelity of using geochemical variations in Montastraea, the dominant reef‐building coral of the Atlantic, to reconstruct sea surface environmental conditions at this site. The stable isotope time series of the two corals replicate well; mean values of δ¹⁸O and δ¹³C are indistinguishable between cores (compare 0.70‰ versus 0.68‰ for δ¹³C and −3.90‰ versus −3.94‰ for δ¹⁸O). Mean values from the Sr/Ca time series differ by …

Observing Seasonal Steric Sea Level Variations With Grace And Satellite Altimetry, Don P. Chambers

Marine Science Faculty Publications

Sea level rises and falls as the temperature and salinity of the water column varies, which is known as steric sea level. Sea level also changes as water mass is redistributed within the ocean or is added or removed. Satellite radar altimeters measure the combination of both effects, while the Gravity Recovery and Climate Experiment (GRACE) was designed to measure time variable gravity caused by movement of water mass. Theoretically, altimetry and GRACE data can be combined in order to compute the steric sea level variations. We test this by combining current GRACE and Jason 1 altimeter data and comparing …

Circulation Of Tampa Bay Driven By Buoyancy, Tides, And Winds, As Simulated Using A Finite Volume Coastal Ocean Model, Robert H. Weisberg, Lianyuan Zheng

Marine Science Faculty Publications

The circulation of Tampa Bay is investigated using a high-resolution, three-dimensional, density-dependent, finite volume coastal ocean model (FVCOM) that includes Tampa Bay, the intracoastal waterway, and the inner portion of the west Florida continental shelf. Model performance over the three-month interval, September to November 2001, is assessed against available tide gauge and velocity profiler data before using the model to describe the circulation as driven by rivers, tides, and winds. Because of a mean wind velocity vector directed down the estuary axis, we ran a parallel model experiment without winds to distinguish the estuarine circulation by gravitational convection from the …

Fastgroupii: A Web-Based Bioinformatics Platform For Analyses Of Large 16s Rdna Libraries, Yanan Yu, Mya Breitbart, Pat Mcnairnie, Forest Rohwer

Marine Science Faculty Publications

Background: High-throughput sequencing makes it possible to rapidly obtain thousands of 16S rDNA sequences from environmental samples. Bioinformatic tools for the analyses of large 16S rDNA sequence databases are needed to comprehensively describe and compare these datasets.

Results: FastGroupII is a web-based bioinformatics platform to dereplicate large 16S rDNA libraries. FastGroupII provides users with the option of four different dereplication methods, performs rarefaction analysis, and automatically calculates the Shannon-Wiener Index and Chao1. FastGroupII was tested on a set of 16S rDNA sequences from coral-associated Bacteria. The different grouping algorithms produced similar, but not identical, results. This suggests that 16S …

Using Pyrosequencing To Shed Light On Deep Mine Microbial Ecology, Robert Edwards, Beltran Rodriguez-Brito, Linda Wegley, Matthew Haynes, Mya Breitbart, Dean Peterson, Martin Saar, Scott Alexander, E. Calvin Alexander Jr., Forest Rohwer

Marine Science Faculty Publications

Background: Contrasting biological, chemical and hydrogeological analyses highlights the fundamental processes that shape different environments. Generating and interpreting the biological sequence data was a costly and time-consuming process in defining an environment. Here we have used pyrosequencing, a rapid and relatively inexpensive sequencing technology, to generate environmental genome sequences from two sites in the Soudan Mine, Minnesota, USA. These sites were adjacent to each other, but differed significantly in chemistry and hydrogeology.

Results: Comparisons of the microbes and the subsystems identified in the two samples highlighted important differences in metabolic potential in each environment. The microbes were performing distinct biochemistry …

Hurricanes, Submarine Groundwater Discharge, And Florida's Red Tides, Chuanmin Hu, Frank E. Muller-Karger, Peter W. Swarzenski

Marine Science Faculty Publications

A Karenia brevis Harmful Algal Bloom affected coastal waters shallower than 50 m off west-central Florida from January 2005 through January 2006, showing a sustained anomaly of ∼1 mg chlorophyll m⁻³ over an area of up to 67,500 km². Red tides occur in the same area (approximately 26–29°N, 82–83°W) almost every year, but the intense 2005 bloom led to a widespread hypoxic zone (dissolved oxygen <2 mg L⁻¹) that caused mortalities of benthic communities, fish, turtles, birds, and marine mammals. Runoff alone provided insufficient nitrogen to support this bloom. We pose the hypothesis that submarine groundwater discharge (SGD) …

The Marine Viromes Of Four Oceanic Regions, Florent Angly, Ben Felts, Mya Breitbart, Peter Salamon, Robert Edwards, Craig Carlson, Amy Chan, Matthew Haynes, Scott Kelley, Hong Liu, Joseph Mahaffy, Jennifer Mueller, James Nulton, Robert Olson, Rachel Parsons, Steve Rayhawk, Curtis Suttle, Forest Rohwer

Marine Science Faculty Publications

Viruses are the most common biological entities in the marine environment. There has not been a global survey of these viruses, and consequently, it is not known what types of viruses are in Earth's oceans or how they are distributed. Metagenomic analyses of 184 viral assemblages collected over a decade and representing 68 sites in four major oceanic regions showed that most of the viral sequences were not similar to those in the current databases. There was a distinct “marine-ness” quality to the viral assemblages. Global diversity was very high, presumably several hundred thousand of species, and regional richness varied …

Rna Viral Community In Human Feces: Prevalence Of Plant Pathogenic Viruses, Tao Zhang, Mya Breitbart, Wah Heng Lee, Jin-Quan Run, Chia Lin Wei, Shirlena Wee Ling Soh, Martin Hibberd, Edison Liu, Forest Rohwer, Yijun Ruan

Marine Science Faculty Publications

The human gut is known to be a reservoir of a wide variety of microbes, including viruses. Many RNA viruses are known to be associated with gastroenteritis; however, the enteric RNA viral community present in healthy humans has not been described. Here, we present a comparative metagenomic analysis of the RNA viruses found in three fecal samples from two healthy human individuals. For this study, uncultured viruses were concentrated by tangential flow filtration, and viral RNA was extracted and cloned into shotgun viral cDNA libraries for sequencing analysis. The vast majority of the 36,769 viral sequences obtained were similar to …

Bleaching In Foraminifera With Algal Sybionts: Implications For Reed Monitoring And Risk Assessment, Pamela Hallock, D. E. Williams, E. M. Fisher, S. K. Toler

Marine Science Faculty Publications

Reef-dwelling larger foraminifers share key characteristics with reefbuilding corals: they are prolific producers of calcium carbonate, they are physiologically dependent upon algal endosymbionts, and representatives of both groups have suffered bleaching episodes in recent decades. Since 1991, bleaching has been observed in populations of Amphistegina in all subtropical oceans, with peak bleaching in 1992 and secondary peaks in 1998 and 2005. Amphistegina populations exhibiting chronic, intermediate-intensity bleaching characteristically show anomalously high incidences of shell breakage, shell deformities, evidence of predation, and microbial infestation. Asexual reproduction is profoundly affected; broods from partly bleached parents typically have fewer individuals, many of which …

Implications Of Subduction Rehydration For Earth's Deep Water Cycle, Lars Rüpke, Jason Phipps Morgan, Jacqueline Eaby Dixon

Marine Science Faculty Publications

The “standard model” for the genesis of the oceans is that they are exhalations from Earth’s deep interior continually rinsed through surface rocks by the global hydrologic cycle. No general consensus exists, however, on the water distribution within the deeper mantle of the Earth. Recently Dixon et al. [2002] estimated water concentrations for some of the major mantle components and concluded that the most primitive (FOZO) are significantly wetter than the recycling associated EM or HIMU mantle components and the even drier depleted mantle source that melts to form MORB. These findings are in striking agreement with the results of …

A Quasi-Normal Scale Elimination Model Of Turbulence And Its Application To Stably Stratified Flows, S. Sukoriansky, B. Galperin, V. Perov

Marine Science Faculty Publications

Models of planetary, atmospheric and oceanic circulation involve eddy viscosity and eddy diffusivity, KM and KH, that account for unresolved turbulent mixing and diffusion. The most sophisticated turbulent closure models used today for geophysical applications belong in the family of the Reynolds stress models. These models are formulated for the physical space variables; they consider a hierarchy of turbulent correlations and employ a rational way of its truncation. In the process, unknown correlations are related to the known ones via "closure assumptions'' that are based upon physical plausibility, preservation of tensorial properties, and the principle of the invariant modeling …

Anisotropic Turbulence And Zonal Jets In Rotating Flows With A Β-Effect, B. Galperin, S. Sukoriansky, N. Dikovskaya, P. L. Read, Y. H. Yamazaki, R. Wordsworth

Marine Science Faculty Publications

Numerical studies of small-scale forced, two-dimensional turbulent flows on the surface of a rotating sphere have revealed strong large-scale anisotropization that culminates in the emergence of quasi-steady sets of alternating zonal jets, or zonation. The kinetic energy spectrum of such flows also becomes strongly anisotropic. For the zonal modes, a steep spectral distribution, E(n)=CZ (Ω/R)2 n-5, is established, where CZ=O(1) is a non-dimensional coefficient, Ω is the angular velocity, and R is the radius of the sphere, respectively. For other, non-zonal modes, the classical, Kolmogorov-Batchelor-Kraichnan, spectral law is preserved. This flow regime, referred to as a zonostrophic regime, appears to …

Evidence Of Multidecadal Salinity Variability In The Eastern Tropical North Atlantic, Christopher S. Moses, Peter K. Swart, Brad E. Rosenheim

Marine Science Faculty Publications

Ocean circulation and global climate are strongly influenced by seawater density, which is itself controlled by salinity and temperature. Although adequate instrumental sea surface temperature (SST) records exist for most of the surface oceans over the past 100–150 years, records of salinity really only exist for the last 40–50 years. Here we show that longer proxy records from corals (Siderastrea radians) in the eastern tropical North Atlantic are dominated by multidecadal variations in salinity which are correlated with the relationship between SST and the North Atlantic Oscillation (NAO) over the course of the 20th century. The data reveal …

National Assessment Of Shoreline Change Part 3: Historical Shoreline Change And Associated Coastal Land Loss Along Sandy Shorelines Of The California Coast, Cheryl Hapke, David Reid, Bruce M. Richmond, Peter Ruggiero, Jeff List

Marine Science Faculty Publications

Beach erosion is a chronic problem along many openocean shores of the United States. As coastal populations continue to grow and community infrastructures are threatened by erosion, there is increased demand for accurate information regarding past and present trends and rates of shoreline movement. There is also a need for a comprehensive analysis of shoreline movement that is consistent from one coastal region to another. To meet these national needs, the U.S. Geological Survey is conducting an analysis of historical shoreline changes along open-ocean sandy shores of the conterminous United States and parts of Hawaii and Alaska. One purpose of …