Life Sciences Commons^™

The Nopp O-Scope And Mosean Projects: Advanced Sensing For Ocean Observing Systems, Tommy Dickey, Nick Bates, Robert H. Byrne, Grace Chang, Francisco P. Chavez, Richard A. Feely, Alfred K. Hanson, David M. Karl, Derek Manov, Casey Moore, Christopher L. Sabine, Rik Wanninkhof

Marine Science Faculty Publications

The National Oceanographic Partnership Program (NOPP) consecutively sponsored the Ocean-Systems for Chemical, Optical, and Physical Experiments (O-SCOPE) and Multi-disciplinary Ocean Sensors for Environmental Analyses and Networks (MOSEAN) projects from 1998 through 2008. The O-SCOPE and MOSEAN projects focused on developing and testing new sensors and systems for autonomous, concurrent measurements of biological, chemical, optical, and physical variables from a diverse suite of stationary and mobile ocean platforms. Design considerations encompassed extended open-ocean and coastal deployments, instrument durability, biofouling mitigation, data accuracy and precision, near-real-time data telemetry, and economy—the latter being critical for widespread sensor and system utilization. The complementary O-SCOPE …

National Assessment Of Historical Shoreline Change: A Pilot Study Of Historical Coastal Bluff Retreat In The Great Lakes, Erie, Pennsylvania, Cheryl J. Hapke, Shamus Malone, Meredith Kratzmann

Marine Science Faculty Publications

Coastal bluff retreat is a chronic problem along many high-relief coastlines in the United States. As coastal populations continue to grow and community infrastructures are threatened by erosion, there is increased demand for accurate information regard­ing trends and rates of bluff retreat. There is also a need for a comprehensive analysis that is consistent from one coastal region to another. To address these national needs, the U.S. Geological Survey (USGS), as part of the National Assessment of Coastal Change Hazards Project, conducted a pilot study of bluff retreat along the Lake Erie, Pa., coastline to assess the feasibility of undertaking …

The Framework Of A Coastal Hazards Model—A Tool For Predicting The Impact Of Severe Storms, Patrick L. Barnard, Bill O'Reilly, Maarten Van Ormondt, Edwin Elias, Peter Ruggiero, Li H. Erikson, Cheryl Hapke, Brian D. Collins, Robert T. Guza, Peter N. Adams, Julie Thomas

Marine Science Faculty Publications

The U.S. Geological Survey (USGS) Multi-Hazards Demonstration Project in Southern California (Jones and others, 2007) is a five-year project (FY2007-FY2011) integrating multiple USGS research activities with the needs of external partners, such as emergency managers and land-use planners, to produce products and information that can be used to create more disaster-resilient communities. The hazards being evaluated include earthquakes, landslides, floods, tsunamis, wildfires, and coastal hazards.

For the Coastal Hazards Task of the Multi-Hazards Demonstration Project in Southern California, the USGS is leading the development of a modeling system for forecasting the impact of winter storms threatening the entire Southern California …

Fishery-Independent Data Reveal Negative Effect Of Human Population Density On Caribbean Predatory Fish Communities, Christopher D. Stallings

Marine Science Faculty Publications

Background: Understanding the current status of predatory fish communities, and the effects fishing has on them, is vitally important information for management. However, data are often insufficient at region-wide scales to assess the effects of extraction in coral reef ecosystems of developing nations.

Methodology/Principal Findings: Here, I overcome this difficulty by using a publicly accessible, fisheries-independent database to provide a broad scale, comprehensive analysis of human impacts on predatory reef fish communities across the greater Caribbean region. Specifically, this study analyzed presence and diversity of predatory reef fishes over a gradient of human population density. Across the region, as human …

Evaluating Highly Resolved Paleoclimate Records In The Frequency Domain For Multidecadal-Scale Climate Variability, Kristine L. Delong, Terrence M. Quinn, Gary T. Mitchum, Richard Z. Poore

Marine Science Faculty Publications

[1] Do the chronological methods used in the construction of paleoclimate records influence the results of the frequency analysis applied to them? We explore this phenomenon using the Dongge Cave speleothem record (U-series chronology with variable time steps, Δt) and the El Malpais tree-ring index (cross-dating of ring-width series). Interpolation of the Dongge Cave record to a constant Δt resulted in the suppression of periodicities (<20 years) altering the red noise model used for significance testing. Frequency analysis of temporal subsets of the El Malpais tree-ring index revealed that concentrations of variance varied with the number of ring-width series. Frequency analyses of these records identified significant periodicities, some common to both (∼25 and ∼69 years). Cross-wavelet analysis, which examines periodicities in the time domain, revealed that coherency between these records occurs intermittently. We found the chronology methods can influence the ability of frequency analysis to detect periodicities and tests for coherency.

Transport Of Momentum And Scalar In Turbulent Flows With Anisotropic Dispersive Waves, Semion Sukoriansky, Nadejda Dikovskaya, Boris Galperin

Marine Science Faculty Publications

Most geophysical flows encompass turbulence and internal and/or Rossby waves. We demonstrate that these two different classes of waves cause remarkably similar anomalies in the turbulent transport. While all scales in both types of flows contribute to the momentum diffusion, the vertical (diapycnal) scalar diffusion in stratified flows and lateral diffusion in β-plane turbulence can be carried out only by turbulent eddies whose size is smaller than the thresholds of turbulence anisotropization. Beyond these thresholds, both flows become dominated by waves that provide no contribution to the scalar diffusion. Stably stratified flows exhibit enhanced isopycnal diffusion of both momentum and …

Integrated Ecosystem Assessments: Developing The Scientific Basis For Ecosystem-Based Management Of The Ocean, Phillip S. Levin, Michael J. Fogarty, Steven A. Murawski, David Fluharty

Marine Science Faculty Publications

No abstract provided.

Dynamically Constrained Ensemble Perturbations: Application To Tides On The West Florida Shelf, Alexander Barth, Aida Alvera-Azcarate, J. M. Beckers, Robert H. Weisberg, L. Vandenbulcke, F. Lenartz, M. Rixen

Marine Science Faculty Publications

A method is presented to create an ensemble of perturbations that satisfies linear dynamical constraints. A cost function is formulated defining the probability of each perturbation. It is shown that the perturbations created with this approach take the land-sea mask into account in a similar way as variational analysis techniques. The impact of the land-sea mask is illustrated with an idealized configuration of a barrier island. Perturbations with a spatially variable correlation length can be also created by this approach. The method is applied to a realistic configuration of the West Florida Shelf to create perturbations of the M2 tidal …

Hurricane Storm Surge Simulations Comparing Three-Dimensional With Two-Dimensional Formulations Based On An Ivan-Like Storm Over The Tampa Bay, Florida Region, Robert H. Weisberg, Lianyuan Zheng

Marine Science Faculty Publications

We provide a dynamics‐based comparison on the results from three‐dimensional and two‐dimensional simulations of hurricane storm surge. We begin with the question, What may have occurred in the Tampa Bay, Florida vicinity had Hurricane Ivan made landfall there instead of at the border between Alabama and Florida? This question is explored using a three‐dimensional, primitive equation, finite volume coastal ocean model. The results show that storm surges are potentially disastrous for the Tampa Bay area, especially for landfalls located to the north of the bay mouth. The worst case among the simulations considered is for landfall at Tarpon Springs, such …

Si Cycle In The Cariaco Basin, Venezuela: Seasonal Variability In Silicate Availability And The Si:C:N Composition Of Sinking Particles, Robert C. Thunell, Claudia Benitez-Nelson, Frank E. Muller-Karger, Laura Lorenzoni, Mary Scranton, Ramon Varela, Yrene Astor, Kent A. Fanning

Marine Science Faculty Publications

A 9‐year time series of water column and sediment trap measurements was used to examine silicon cycling within the anoxic Cariaco Basin. The dynamic hydrographic regime within Cariaco Basin results in strong seasonal changes in nutrient availability and the Si:C:N of sinking particles. Upwelling in early winter injects silicic acid (Si(OH)₄⁼ ) and nitrate (NO₃⁻) rich waters into the photic zone which stimulates primary production and results in opal fluxes in excess of 4 mmol Si m⁻² d⁻¹. However, even during upwelling, surface waters tend to be depleted (<1 μM) in …

Analysis Of Large-Scale Ocean Bottom Pressure Variability In The North Pacific, Don P. Chambers, Josh K. Willis

Marine Science Faculty Publications

[1] We use the leading empirical orthogonal functions (EOFs) of ocean bottom pressure (OBP) derived from an ocean model and the technique of EOF reconstruction to reduce noise in the large-scale OBP variations derived from the Gravity Recovery and Climate Experiment (GRACE). The subsequent OBP variations from the model and GRACE are then examined in the North Pacific between January 2003 and May 2007. Although annual and semiannual variations are similar, GRACE observes large interannual fluctuations poleward of 30°, where OBP increases from a low of nearly 3 cm below normal in early 2003 to normal throughout 2004 and 2005, …

Grace Observes Small-Scale Mass Loss In Greenland, B. Wouters, D. Chambers, E.J. O. Schrama

Marine Science Faculty Publications

Using satellite gravity data between February 2003 and January 2008, we examine changes in Greenland's mass distribution on a regional scale. During this period, Greenland lost mass at a mean rate of 179 ± 25 Gt/yr, equivalent to a global mean sea level change of 0.5 ± 0.1 mm/yr. Rates increase over time, suggesting an acceleration of the mass loss, driven by mass loss during summer. The largest mass losses occurred along the southeastern and northwestern coast in the summers of 2005 and 2007, when the ice sheet lost 279 Gt and 328 Gt of ice respectively within 2 months. …

Carbonatite And Silicate Melt Metasomatism Of The Mantle Surrounding The Hawaiian Plume: Evidence From Volatiles, Trace Elements, And Radiogenic Isotopes In Rejuvenated‐Stage Lavas From Niihau, Hawaii, Jacqueline Dixon, David A. Clague, Brian Cousens, Maria Luisa Monsalve, Jessika Uhl

Marine Science Faculty Publications

We present new volatile, trace element, and radiogenic isotopic compositions for rejuvenated‐stage lavas erupted on Niihau and its submarine northwest flank. Niihau rejuvenated‐stage Kiekie Basalt lavas are mildly alkalic and are isotopically similar to, though shifted to higher ⁸⁷Sr/⁸⁶Sr and lower ²⁰⁶Pb/²⁰⁴Pb than, rejuvenated‐stage lavas erupted on other islands and marginal seafloor settings. Kiekie lavas display trace element heterogeneity greater than that of other rejuvenated‐stage lavas, with enrichments in Ba, Sr, and light‐rare earth elements resulting in high and highly variable Ba/Th and Sr/Ce. The high Ba/Th lavas are among the least silica‐undersaturated of …

Estimating Geocenter Variations From A Combination Of Grace And Ocean Model Output, Sean Swenson, D. Chambers, John Wahr

Marine Science Faculty Publications

In this study, we estimate a time series of geocenter anomalies from a combination of data from the Gravity Recovery and Climate Experiment (GRACE) satellite mission and the output from ocean models. A matrix equation is derived relating total geocenter variations to the GRACE coefficients of degrees two and higher and to the oceanic component of the degree one coefficients. We estimate the oceanic component from t wo state-of-the-art ocean models. Results are compared to independent estimates of geocenter derived from other satellite data, such as satellite laser ranging and GPS. Finally, we compute degree one coefficients that are consistent …

Assimilation Of High-Frequency Radar Currents In A Nested Model Of The West Florida Shelf, Alexander Barth, Aida Alvera-Azcarate, Robert H. Weisberg

Marine Science Faculty Publications

High‐frequency radar currents are assimilated in a West Florida Shelf (WFS) model based on the Regional Ocean Model System (ROMS), which is nested in the Atlantic Hybrid Coordinate Ocean Model (HYCOM) for the purpose of including both local and deep‐ocean forcing, particularly the Gulf of Mexico Loop Current. Tides are not included in this model. An ensemble simulation of the WFS model is carried out under different wind‐forcings in order to estimate the error covariance of the model state vector and the covariance between ocean currents and winds. Radial currents measured by high‐frequency radar antennas near Saint Petersburg and Venice, …

Assessing The Globally Averaged Sea Level Budget On Seasonal To Interannual Timescales, Josh K. Willis, D. Chambers, R Steven Nerem

Marine Science Faculty Publications

Analysis of ocean temperature and salinity data from profiling floats along with satellite measurements of sea surface height and the time variable gravity field are used to investigate the causes of global mean sea level rise between mid-2003 and mid-2007. The observed interannual and seasonal fluctuations in sea level can be explained as the sum of a mass component and a steric (or density related) component to within the error bounds of each observing system. During most of 2005, seasonally adjusted sea level was approximately 5 mm higher than in 2004 owing primarily to a sudden increase in ocean mass …

A Nested Model Study Of The Loop Current Generated Variability And Its Impact On The West Florida Shelf, Alexander Barth, Aida Alvera-Azcarate, Robert H. Weisberg

Marine Science Faculty Publications

A West Florida Shelf model based on the Regional Ocean Modeling System (ROMS) is nested in the North Atlantic Hybrid Coordinate Ocean Model (NAT HYCOM). The focus of this work is the study of the impact of the Loop Current on the West Florida Shelf. In order to assess the model's accuracy, it is compared quantitatively to in situ temperature and velocity measurements on the shelf. A series of sensitivity experiments are conducted to determine the appropriate wind forcing, sea surface temperature relaxation, and mixing scheme. by the inclusion of the Loop Current, we are able to study the propagation …

Changes Of Temperature And Bio-Optical Properties In The South China Sea In Response To Typhoon Lingling, 2001, Shaoling Shang, Li Li, Fengqin Sun, Jingyu Wu, Chuanmin Hu, Dewen Chen, Xiuren Ning, Yun Qiu, Caiyun Zhang, Shaoping Shang

Marine Science Faculty Publications

A large patch of enhanced chlorophyll a concentration (Chla), lower sea surface temperature (SST), and lower sea surface height (SSH) was revealed in the central South China Sea (SCS) in November 2001 after the passage of typhoon Lingling. Maximum SST reduction of 11°C occurred one day after Lingling's passage on 11/11. Subsequently, against a background level of 0.08 mg/m³, average Chla within the area of 12.60–16.49°N, 112.17–117.05°E increased to 0.14 mg/m³ on 11/12 and then to 0.37 mg/m³ on 11/14. Dissolved organic matter and detritus were differentiated from Chla using a recent bio-optical algorithm. They contributed …

Middle Miocene Ice Sheet Dynamics, Deep‐Sea Temperatures, And Carbon Cycling: A Southern Ocean Perspective, Amelia E. Shevenell, James P. Kennett, David W. Lea

Marine Science Faculty Publications

Relative contributions of ice volume and temperature change to the global ∼1‰ δ¹⁸O increase at ∼14 Ma are required for understanding feedbacks involved in this major Cenozoic climate transition. A 3‐ma benthic foraminifer Mg/Ca record of Southern Ocean temperatures across the middle Miocene climate transition reveals ∼2 ± 2°C cooling (14.2–13.8 Ma), indicating that ∼70% of the increase relates to ice growth. Seawater δ¹⁸O, calculated from Mg/Ca and δ¹⁸O, suggests that at ∼15 Ma Antarctica's cryosphere entered an interval of apparent eccentricity‐paced expansion. Glaciations increased in intensity, revealing a central role for internal climate …

Antarctic Sediment Chronology By Programmed-Temperature Pyrolysis: Methodology And Data Treatment, Brad E. Rosenheim, Mary Beth Day, Eugene Domack, Heather Schrum, Albert Benthien, John M. Hayes

Marine Science Faculty Publications

We report a detailed programmed-temperature pyrolysis/combustion methodology for radiocarbon (14C) dating of Antarctic sub-ice shelf sediments. The method targets the autochthonous organic component in sediments that contain a distribution of acid-insoluble organic components from several sources of different ages. The approach has improved sediment chronology in organic-rich sediments proximal to Antarctic ice shelves by yielding maximum age constraints significantly younger than bulk radiocarbon dates from the same sediment horizons. The method proves adequate in determining isotope ratios of the pre-aged carbon end-member; however, the isotopic compositions of the low-temperature measurements indicate that no samples completely avoided mixing with some proportion …

A Bacterial Metapopulation Adapts Locally To Phage Predation Despite Global Dispersal, Victor Kunin, Shaomei He, Falk Warnecke, S. Brook Peterson, Hector Garcia Martin, Matthew Haynes, Natalia Ivanova, Linda Blackall, Mya Breitbart, Forest Rohwer, Katherine Mcmahon, Philip Hugenholtz

Marine Science Faculty Publications

Using a combination of bacterial and phage-targeted metagenomics, we analyzed two geographically remote sludge bioreactors enriched in a single bacterial species Candidatus Accumulibacter phosphatis (CAP). We inferred unrestricted global movement of this species and identified aquatic ecosystems as the primary environmental reservoirs facilitating dispersal. Highly related and geographically remote CAP strains differed principally in genomic regions encoding phage defense mechanisms. We found that CAP populations were high density, clonal, and nonrecombining, providing natural targets for “kill-the-winner” phage predation. Community expression analysis demonstrated that phages were consistently active in the bioreactor community. Genomic signatures linking CAP to past phage exposures were …

Metagenomic Analysis Of Lysogeny In Tampa Bay: Implications For Prophage Gene Expression, Lauren D. Mcdaniel, Mya Breitbart, Jennifer M. Mobberley, Amy Long, Matthew Haynes, Forest Rohwer, John Paul

Marine Science Faculty Publications

Phage integrase genes often play a role in the establishment of lysogeny in temperate phage by catalyzing the integration of the phage into one of the host's replicons. To investigate temperate phage gene expression, an induced viral metagenome from Tampa Bay was sequenced by 454/Pyrosequencing. The sequencing yielded 294,068 reads with 6.6% identifiable. One hundred-three sequences had significant similarity to integrases by BLASTX analysis (e≤0.001). Four sequences with strongest amino-acid level similarity to integrases were selected and real-time PCR primers and probes were designed. Initial testing with microbial fraction DNA from Tampa Bay revealed 1.9×10⁷, and 1300 gene …

Morphology And Filling Of Incised Submarine Valleys On The Continental Shelf Near The Mouth Of The Fly River, Gulf Of Papua, J. S. Crockett, C. A. Nittrouer, A. S. Ogston, D. F. Naar, B. T. Donahue

Marine Science Faculty Publications

Much historical perspective about terrestrial and marine processes can be obtained from examination of fluvial valleys formed during lower sea level on surfaces that are now continental shelves. The continental shelf near the mouth of the Fly River (Gulf of Papua) has three incised valleys, which were not extensively modified or filled during the Holocene Transgression. Multibeam mapping of the valleys documents their morphology; seismic profiling reveals stratigraphy of sediment fill; and coring within and near the valleys suggests mechanisms of filling. Kiwai Valley is deep (20–50 m relief), narrow (∼1 km wide), steep-sided and meandering, due to river flows …

A New Bathymetric Compilation Highlighting Extensive Paleo–Ice Sheet Drainage On The Continental Shelf, South Georgia, Sub-Antarctica, Alastair G. C. Graham, Peter T. Fretwell, Robert D. Larter, Dominic A. Hodgson, Christian K. Wilson, Alex J. Tate, Peter Morris

Marine Science Faculty Publications

A grid derived from a new compilation of marine echo-sounding data sets has allowed us to visualize and map the geomorphology of the entire continental shelf around South Georgia at an unprecedented level of detail. The grid is the first continuous bathymetric data set covering South Georgia to include multibeam swath bathymetry and represent them at a subkilometer resolution. Large and previously undescribed glacially eroded troughs, linked to South Georgia's modern-day fjords, radiate from the island, marking the former pathways of large outlet glaciers and ice streams. A tectonic or geological influence is apparent for the major troughs, where glaciers …

An Optical Model For Heat And Salt Budget Estimation For Shallow Seas, Hari Warrior, Kendall L. Carder

Marine Science Faculty Publications

The effects of the underwater light field on heat-budget calculations for shallow waters are developed and applied for the region of Bahamas. Most of the general circulation models use a simplified heat budget scheme based on Jerlov water types, and do not account for optical bottom effects. by optical bottom effect, we mean the bottom absorption and reflection of the short-wave radiation, which in turn affects the thermal stratification and heat exchange with the atmosphere. In this paper, this optical bottom effect is added to a 3D turbulence model (a 1D model called GOTM is coupled to a 3D model …

A High Resolution Satellite-Only Grace-Based Mean Dynamic Topography Of The South Atlantic Ocean, Marcio L. Vianna, Viviane V. Menezes, D. Chambers

Marine Science Faculty Publications

A new filtering method based on Singular Spectrum Analysis has been devised to extract high resolution (0.25° × 0.25° grid) satellite-only Mean Dynamic Ocean Topography(MDT) constructed by differencing of the GGM02 GRACE Gravity Model from the GSFCMSS00 Mean Sea Surface. This data-adaptive interpolation-type filter is adequate for the finite domain MDT processing since it minimizes smoothing and does not lose boundary points. It is applied to the computation of two new MDTs and MDT-derived mean geostrophic circulation maps of the South Atlantic region from 15°N to 50°S. Advantages of these new maps are clarified when contrasted with the Rio-2005, Chambers-Zlotnicki-2004 …

Reconstructing Twentieth-Century Sea Surface Temperature Variability In The Southwest Pacific: A Replication Study Using Multiple Coral Sr/Ca Records From New Caledonia, Kristine L. Delong, Terrence M. Quinn, Frederick W. Taylor

Marine Science Faculty Publications

Coral‐based climate reconstructions typically have not used multiple cores from a region to capture and replicate a climate signal largely because of concerns of coral conservation, analytical expense, and time constraints. Coral Sr/Ca reproducibility through the twentieth century was investigated using three intracolony and three intercolony coral records from the reefs offshore of Amédée Island, New Caledonia. Different sampling resolutions were examined in coral Sr/Ca (fortnightly and monthly) and δ¹⁸O (fortnightly, monthly, and seasonally) as well as similar scale subsampling of the daily in situ sea surface temperature (SST) record. The mean coral Sr/Ca, δ¹⁸O, and …

Evidence Of Compromised Blood-Spinal Cord Barrier In Early And Late Symptomatic Sod1 Mice Modeling Als, Svitlana N. Garbuzova-Davis, Samuel Saporta, Edward M. Haller, Irina Kolomey, Steven P. Bennett, Huntington Potter, Paul R. Sanberg

Integrative Biology Faculty and Staff Publications

Background: The blood-brain barrier (BBB), blood-spinal cord barrier (BSCB), and blood-cerebrospinal fluid barrier (BCSFB) control cerebral/spinal cord homeostasis by selective transport of molecules and cells from the systemic compartment. In the spinal cord and brain of both ALS patients and animal models, infiltration of T-cell lymphocytes, monocyte-derived macrophages and dendritic cells, and IgG deposits have been observed that may have a critical role in motor neuron damage. Additionally, increased levels of albumin and IgG have been found in the cerebrospinal fluid in ALS patients. These findings suggest altered barrier permeability in ALS. Recently, we showed disruption of the BBB and …

An Evaluation Of Movement Patterns And Effects Of Habitat Patch Size On The Demography Of The Florida Mouse (Podomys Floridanus), Irmgard Lukanik

USF Tampa Graduate Theses and Dissertations

Habitat degradation by humans has been the main reason for the decline in numbers of P. floridanus, the only mammal indigenous to the state of Florida, in the past century. The mouse inhabits what remains of scrub and sandhill associations, which are characterized by patches of sandy soils within a more mesic landscape. It has long been accepted that small populations are more prone to decline and extinction than are larger ones as a result of environmental fluctuations. I hypothesized that the demography of a population of P. floridanus would be affected by a restriction in numbers through habitat …

Upper Ocean Response Of The Mesoamerican Barrier Reef System To Hurricane Mitch And Coastal Freshwater Inputs: A Study Using Sea-Viewing Wide Field-Of-View Sensor (Seawifs) Ocean Color Data And A Nested-Grid Ocean Circulation Model, Jinyu Sheng, Liang Wang, Serge Andrefouet, Chuanmin Hu, Bruce G. Hatcher, Frank E. Muller-Karger, Bjoern Kjerfve, William D. Heyman, Bo Yang

Marine Science Faculty Publications

The passage of category‐5 Hurricane Mitch through the Mesoamerican Barrier Reef System (MBRS) in October 1998 was an extreme event with the potential to create unusual patterns of reef connectivity. The impact of this hurricane on the upper ocean of the MBRS is investigated using a triply nested grid ocean circulation modeling system. The model results are validated with contemporaneous ocean color data from the Sea‐viewing Wide Field‐of‐view Sensor (SeaWiFS) satellite and oceanographic measurements in the MBRS. The nested grid system is forced by 6‐hourly National Centers for Environmental Prediction/National Center for Atmospheric Research (NCEP/NCAR) winds for the first 294 …