Life Sciences Commons^™

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 …

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 …

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 …

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 …

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 …

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 …

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 …

Patterns Of Ocean Current Variability On The West Florida Shelf Using The Self-Organizing Map, Yonggang Liu, Robert H. Weisberg

Marine Science Faculty Publications

Patterns of ocean current variability are examined on the West Florida Shelf by a neural network analysis based on the self‐organizing map (SOM), using time series of moored velocity data that span the interval October 1998–September 2001. Three characteristic spatial patterns are extracted in a 3 × 4 SOM array: spatially coherent southeastward and northwestward flow patterns with strong currents and a transition pattern of weak currents. On the synoptic weather timescale the variations of these patterns are coherent with the local winds. On the seasonal timescale the variations of the patterns are coherent with both the local winds and …

Hydrographic And Biological Changes In The Taiwan Strait During The 1997–1998 El Niño Winter, S. Shang, C. Zhang, H. Hong, Q. Liu, G. T. F. Wong, C. Hu, B. Huang

Marine Science Faculty Publications

During the 1997–1998 El Niño event, the average sea surface temperature (SST) in the Taiwan Strait (TWS) in the winter was ∼1.4°C higher than that of the winter climatological mean. The areal ratio of the warm water (≥2°C above the regional mean) to the cold water (≥2°C below the regional mean) in the TWS increased by 25% while the area of the eutrophic water (chlorophyll a >1 mg m⁻³) was halved. Field observations also indicate that the mixed layer in the TWS became more nutrient-poor during this winter. These observations are consistent with a diminished advection of the …

Interannual And Decadal Variability Of The Western Pacific Sea Surface Condition For The Years 1787-2000: Reconstruction Based On Stable Isotope Record From A Guam Coral, Ryuji Asami, Tsutomu Yamada, Yasufumi Iryu, Terrence M. Quinn, Christopher P. Meyer, Gustav Paulay

Marine Science Faculty Publications

We present a monthly resolved, 213‐year stable isotope time series from a coral from Guam (13°N, 145°E), which is located on the northern edge of the western Pacific warm pool. Oxygen isotopic composition of the coral skeleton (δ¹⁸O_coral) shows seasonal, interannual, and decadal variability, which documents significant oceanographic changes related to thermal and hydrologic variations in this region. The δ¹⁸O_coral anomaly reflects sea surface temperature (SST) anomaly and sea surface salinity (SSS) anomaly with significant r values of −0.69 and 0.49, respectively, which are strongly linked to oceanographic changes that occur during El …

Interannual Temperature Variability In The Tropical Pacific And Lagrangian Heat Transport Pathways, C. L. Holland, Gary T. Mitchum

Marine Science Faculty Publications

In a previous study we found that volume variability during an El Ni (n) over tildeo-Southern Oscillation (ENSO) event is well described by variations in, and redistribution of, the heat content for any given region within the tropical Pacific. In this study we use numerical model temperature and velocity fields in a Lagrangian analysis of heat content variability. These three-dimensional fields are used to examine specific warm and cool anomaly regions by computing trajectories back through time to the origins of the anomalously warm or cool water. In particular, we find that three distinct pathways are important in creating and …

Diffuse Attenuation Coefficient Of Downwelling Irradiance: An Evaluation Of Remote Sensing Methods, Zhongping Lee, Miroslaw Darecki, Kendall L. Carder, Curtiss O. Davis, Dariusz Stramski, W. Joseph Rhea

Marine Science Faculty Publications

The propagation of downwelling irradiance at wavelength λ from surface to a depth (z) in the ocean is governed by the diffuse attenuation coefficient, (λ). There are two standard methods for the derivation of (λ) in remote sensing, which both are based on empirical relationships involving the blue‐to‐green ratio of ocean color. Recently, a semianalytical method to derive (λ) from reflectance has also been developed. In this study, using (490) and (443) as examples, we compare the (λ) values derived from the three methods using data collected in three different regions that cover oceanic and coastal waters, with …

Assessment Of Biogeochemical Deposits In Landfill Drainage Systems, Audrey D. Levine, Valerie J. Harwood, Antonio J. Cardoso, Lisa R. Rhea, Bina S. Nayak, Barbara M. Dodge, Mindy L. Decker, George Dzama, Lawrence Jones, Edward Haller

Integrative Biology Faculty and Staff Publications

Design, operation, and closure practices for Class I municipal solid waste (MSW) landfills are based on RCRA Subtitle D requirements for control of leachates and gases generated during the life of the landfill. Because leachate is generated as a result of water percolating through the landfill and waste consolidation, it contains dissolved and suspended materials that reflect the characteristics of the material it contacts. Over the past two decades significant changes have occurred in the characteristics of the waste streams that are disposed in landfills. In addition, many Florida municipalities have implemented Waste-to-Energy (WTE) systems. The WTE ash is either …

Where Rivers And Oceans Collide, J. S. Crockett, C. A. Nittrouer, A. S. Ogston, R. W. Sternberg, N. W. Driscoll, J. Babcock, J. D. Milliman, R. Slingerland, D. F. Naar, B. Donahue, J. P. Walsh, W. Dietrich, G. Parker, M. Bera, H. Davies, P. Harris, M. Goni, R. Aller, J. Aller

Marine Science Faculty Publications

Fluvial sediment fills the coastal ocean, and sea level rise floods river valleys. This epic battle of terrestrial and marine processes occurs along all shorelines, and the complexities are especially well revealed in the Gulf of Papua, a foreland basin on the southern coast of New Guinea. Two hundred to four hundred million tons of sediment are supplied each year by the Fly and other rivers to a continental shelf that has been dissected by ancestors of these same rivers. The new sediment builds a large depositional feature known as a clinoform, which grows seaward and buries the record of …

Salinity Change In The Subtropical Atlantic: Secular Increase And Teleconnections To The North Atlantic Oscillation, Brad E. Rosenheim, Peter K. Swart, Simon R. Thorrold, Anton Eisenhauer, Philippe Willenz

Marine Science Faculty Publications

Recent studies comparing shipboard data between the 1950's and the 1990's have shown significant, heterogeneous adjustments of the temperature-salinity structure of the N. Atlantic Ocean. Here, we present proxy records of temperature and salinity from aragonite sclerosponge skeletons, extending existing records of the Salinity Maximum Waters (SMW) of the N. Atlantic back to 1890. These proxy records show secular temperature increases of 1.6–2.0°C, higher than published global averages, and salinity increases of 0.35–0.5 psu, smaller than short-term secular trends recently measured. Salinity reconstructions vary more significantly on the decadal scale, showing changes that are related to low-frequency variations of the …

Phaccs, An Online Tool For Estimating The Structure And Diversity Of Uncultured Viral Communities Using Metagenomic Information, Florent Angly, Beltran Rodriguez-Brito, David Bangor, Patrick Mcnairnie, Mya Breitbart, Peter Salamon, Ben Felts, James Nulton, Joseph Mahaffy, Forest Rohwer

Marine Science Faculty Publications

Background: Phages, viruses that infect prokaryotes, are the most abundant microbes in the world. A major limitation to studying these viruses is the difficulty of cultivating the appropriate prokaryotic hosts. One way around this limitation is to directly clone and sequence shotgun libraries of uncultured viral communities (i.e., metagenomic analyses). PHACCS http://phage.sdsu.edu/phaccs, Phage Communities from Contig Spectrum, is an online bioinformatic tool to assess the biodiversity of uncultured viral communities. PHACCS uses the contig spectrum from shotgun DNA sequence assemblies to mathematically model the structure of viral communities and make predictions about diversity.

Results: PHACCS builds models of possible …

Method For Discovering Novel Dna Viruses In Blood Using Viral Particle Selection And Shotgun Sequencing, Mya Breitbart, Forest Rohwer

Marine Science Faculty Publications

Rapid identification of viruses is needed to monitor the blood supply for emerging threats. Here we present a method that meets these criteria and allows for the shotgun sequencing of novel, uncultured DNA viruses directly from human blood. This method employs selection based on the physical properties of viruses combined with sequence-independent amplification and cloning. We show that both single- and double-stranded DNA viruses can be recovered from blood samples using this approach. In addition, we report the discovery of novel anellovirus sequences in the blood of healthy donors. PCR primers designed to amplify these novel anellovirus sequences were then …

A Regional Index Of Northeast Pacific Variability Based On Satellite Altimeter Data, Patrick F. Cummins, Gary S. Lagerloef, Gary Mitchum

Marine Science Faculty Publications

An index of climate variability to monitor the state of the upper ocean is proposed for the northeast (NE) Pacific Ocean based on sea surface height (SSH) data from satellite altimetry. While sea surface temperature (SST) is often used characterize ocean variability, SSH reflects the integrated influence of temperature and salinity anomalies through the water column. A canonical correlation analysis shows that SSH and SST anomalies vary coherently at large spatial scales and low frequencies over the region. SSH anomalies are less subject to short period variability and the temporal components for SSH resemble smoothed, low-pass-filtered versions of the SST …

Decadal-Scale Analysis Of Coastal Landslides Along The Big Sur Coast: Rates And Processes, Cheryl J. Hapke, Krystal R. Green

Marine Science Faculty Publications

Landslides in the coastal mountains of Big Sur in Monterey and San Luis Obispo Counties are common, especially during the winter months. These frequent landslides regularly disrupt Coast Highway 1, by blocking the highway with boulders and/or debris, or undercutting the roadway. Historical documentation of landslide activity in this area indicates slide activity closed portions of the road prior to its completion in 1937. The California Department of Transportation (Caltrans) maintains the Coast Highway 1 corridor and recently established the Big Sur Coast Highway Management Plan (CHMP) to develop management practices that will best maintain the highway while minimizing impact …

Coastal Change Rates And Patterns: Kaloko-Honokohau National Historical Park, Hawai’I, Cheryl J. Hapke, Rick Gmirkin, Bruce M. Richmond

Marine Science Faculty Publications

A collaborative project between the U.S. Geological Survey's Coastal and Marine Geology Program and the National Park Service (NPS) has been developed to create an inventory of geologic resources for National Park Service lands on the Big Island of Hawai’i. The NPS Geologic Resources Inventories are recognized as essential for the effective management, interpretation, and understanding of vital park resources. In general, there are three principal components of the inventories: geologic bibliographies, digital geologic maps, and geologic reports. The geologic reports are specific to each individual park and include information on the geologic features and processes that are important to …

The Antares Observation Network, Frank E. Muller-Karger, Chuamin Hu, Brock Murch, Charles Taylor

Marine Science Faculty Publications

The ANTARES network seeks to understand the variability of the coastal environment on a continental scale and the local, regional, and global factors and processes that modulate this variability. The target are coastal zones of South America and the Caribbean Sea. The initial approach includes developing time series of in situ and satellite-based environmental observations in coastal and oceanic regions. The network is constituted by experts that seek to exchange ideas, develop an infrastructure for mutual logistical and knowledge support, and link in situ time series of observations located around the Americas with real-time and historical satellite-derived time series of …

El Nino Southern Oscillation-Related Salinity Variations Recorded In The Skeletal Geochemistry Of A Porites Coral From Espiritu Santo, Vanuatu, K. H. Kilbourne, Terrence M. Quinn, Frederick W. Taylor, Thierry Delcroix, Yves Gouriou

Marine Science Faculty Publications

Coral skeletal geochemistry offers the potential to reconstruct the sea surface salinity (SSS) history of the tropical oceans on seasonal to interannual and perhaps centennial timescales because of the strong link between variation in SSS and seawater δ¹⁸O in tropical regions. We explore this potential using a monthly resolved, 65‐year record of skeletal δ¹⁸O and Sr/Ca variations in a Porites coral from Espiritu Santo, Vanuatu. We demonstrate that El Niño–Southern Oscillation–related climate variability strongly influences coral δ¹⁸O at Santo through local salinity changes associated with the position of the South Pacific Convergence Zone and …

Nitrogen Isotope Dynamics Of The Cariaco Basin, Venezuela, Robert C. Thunell, Daniel M. Sigman, Frank E. Muller-Karger, Yrene Astor, Ramon Varela

Marine Science Faculty Publications

We report ¹⁵N/¹⁴N measurements of water column nitrate and ammonium, sinking particles, and sediments from the Cariaco Basin, an anoxic marine basin off the coast of Venezuela. Water column denitrification occurring in the basin has only a very small isotopic imprint on nitrate in the basin because nitrate consumption is nearly complete in the actively denitrifying water near the oxic/anoxic interface (∼275 m). Being free of a large denitrification signal, the δ¹⁵N of shallow thermocline nitrate is ∼3.5‰, significantly lower than the mean deep ocean nitrate δ¹⁵N of 5‰. This may be due …

Preliminary Observations Of Global Ocean Mass Variations With Grace, D. Chambers, J. Wahr, R Steven Nerem

Marine Science Faculty Publications

Monthly estimates of the Earth's gravitational field from the GRACE mission are used to construct a time‐series of global mean ocean mass variations between August 2002 and December 2003. This time‐series is compared to a mean climatology determined from satellite altimeter measurements of global mean sea level corrected for the steric variation. The GRACE observations show a seasonal exchange of water mass with the continents of the same magnitude (∼8.5 mm) and phase (maximum in early‐ to mid‐October) as the steric‐corrected altimetry. This is one of the first direct validations over the ocean of the primary GRACE science mission to …

Tide, Buoyancy, And Wind-Driven Circulation Of The Charlotte Harbor Estuary: A Model Study, Lianyuan Zheng, Robert H. Weisberg

Marine Science Faculty Publications

The circulation of the Charlotte Harbor (CH) estuary is explored with a primitive equation model that encompasses the estuary and the adjacent West Florida Shelf. Tidal forcing is from the shelf through the inlets. We use the M₂, S₂, K₁, and O₁ constituents that account for 95% of the shelf tidal variance. River inflows are by the Peace, Myakka, and Caloosahatchee Rivers at their spring 1998 mean values. Wind effects are considered for upwelling or downwelling favorable winds that are either held constant or allowed to oscillate with varying periodicities. These factors are …

Generation, Transport, And Preservation Of The Alkenone-Based U37K' Sea Surface Temperature Index In The Water Column And Sediments Of The Cariaco Basin (Venezuela), Miguel A. Goni, Mark P. Woodworth, Heather L. Aceves, Robert C. Thunell, Eric Tappa, David Black, Frank E. Muller-Karger, Yrene Astor, Ramon Varela

Marine Science Faculty Publications

Alkenone fluxes in the water column of the Cariaco Basin ranged from 12 to 20 μg m⁻² d⁻¹ and were inversely related to upwelling strength. The U₃₇^K′ ratios of sinking particles varied from 0.78 to 0.96 and exhibited seasonal changes that were coherent with a 7°C variation in sea surface temperature (SST). The correlation between SST and U₃₇^K′ ratios closely overlapped with the calibration of Prahl et al. [1988]. Alkenone burial fluxes in Cariaco Basin sediments varied markedly over the past ∼6000 years, ranging from 0.2 to 5 μg m⁻² d^{−1 …}

Decadal Shifts In Biophysical Forcing Of Arctic Marine Food Webs: Numerical Consequences, John J. Walsh, Dwight A. Dieterle, Wieslaw Maslowski, Terry E. Whitledge

Marine Science Faculty Publications

Fall case studies of three‐dimensional circulation, plankton, and benthos models explored the consequences of interannual changes in ice cover and water motion on carbon/nitrogen cycling by the end of September within the Chukchi/Beaufort Seas. The coupled model scenarios were those of reduced (greater) northward flow, colder (warmer) temperatures, and more (less) extensive ice cover over the preceding ∼60 days of August and September during the negative (positive), anticyclonic (cyclonic) phase of the Arctic Oscillation in 1980 (1989). On the inner Chukchi shelf, stronger flows in 1989 advected nitrate and silicate stocks of Pacific origin ∼130 km farther northwest toward Wrangel …

A Fossil Coral Perspective On Western Tropical Pacific Climate Similar To 350 Ka, K. H. Kilbourne, Terrence M. Quinn, F. W. Taylor

Marine Science Faculty Publications

The nature of tropical climate variability ∼350 ka is addressed using δ¹⁸O and Sr/Ca records from a modern and a fossil coral from Vanuatu (southwestern tropical Pacific Ocean). Modern El Niño events at Vanuatu produce positive coral δ¹⁸O and Sr/Ca anomalies; similar anomalies observed in the fossil coral records suggest that El Niño was operative 350 kyr ago. Seasonal variations in coral Sr/Ca, a sea surface temperature (SST) proxy, have the same amplitude in both corals, whereas seasonal δ¹⁸O variations are smaller in the fossil coral than in the modern coral. This is consistent …

Glass Cplume‐Ridge Interaction, And Hydrous Melting Along The Galápagos Spreading Center, 90.5°W To 98°W, Buffy Cushman, John Sinton, Garrett Ito, Jacqueline Eaby Dixon

Marine Science Faculty Publications

The Galápagos Spreading Center (GSC) between 90.5°W and 98°W manifests its interaction with the nearby Galápagos plume by way of variations in lava geochemistry, crustal thickness, and morphology along the ridge axis. Natural glasses from stations with ∼9 km average spacing were analyzed for major and minor elements, H₂O, and CO₂. Samples can be classified as enriched mid‐ocean ridge basalts (E‐MORB), transitional MORB (T‐MORB), or normal MORB (N‐MORB) on the basis of K/Ti ratios. E‐MORB dominate the GSC east of 92.6°W. T‐MORB are mainly found between 92.6°W and 95.5°W. West of the propagating rift tip at …