Life Sciences Commons^™

Spatiotemporal Chlorophyll-A Dynamics On The Louisiana Continental Shelf Derived From A Dual Satellite Imagery Algorithm, Chengfeng Le, John C. Lehrter, Chuanmin Hu, Michael C. Murrell, Lin Qi

Marine Science Faculty Publications

A monthly time series of remotely sensed chlorophyll-a (Chla_rs) over the Louisiana continental shelf (LCS) was developed and examined for its relationship to river discharge, nitrate concentration, total phosphorus concentration, photosynthetically available radiation (PAR), wind speed, and interannual variation in hypoxic area size. A new algorithm for Chla_rs, tuned separately for clear and turbid waters, was developed using field-observed chlorophyll-a (Chla_obs) collected during 12 cruises from 2002 to 2007. The new algorithm reproduced Chla_obs, with ∼40% and ∼60% uncertainties at satellite pixel level for clear offshore waters and turbid nearshore …

Time To Competitive Exclusion, Andrew M. Kramer, John M. Drake

Integrative Biology Faculty and Staff Publications

A predictive theory of population extinction for natural populations requires integrating the effects of stochasticity with the interactions engaged in with populations of other species. The theory of competitive exclusion predicts that inferior competitors for a limiting resource will be driven to extinction, but the effects of resource competition on time to extinction have not been examined. We studied a stochastic version of Tilman's resource competition model to examine two species competition-driven extinction. Simulations showed that competitive imbalance, population size and demographic rates of the “inferior” competitor were the most important determinants of mean extinction time, while factors including resource …

Linking Rainforest Ecophysiology And Microclimate Through Fusion Of Airborne Lidar And Hyperspectral Imagery, Eben N. Broadbent, Angélica M. Zambrano, Gregory P. Asner, Christopher B. Field, Brad E. Rosenheim, Ty Kennedy-Bowdoin, David E. Knapp, David Burke, Christian Giardina, Susan Cordell

Marine Science Faculty Publications

We develop and validate a high-resolution three-dimensional model of light and air temperature for a tropical forest interior in Hawaii along an elevation gradient varying greatly in structure but maintaining a consistent species composition. Our microclimate models integrate high-resolution airborne waveform light detection and ranging data (LiDAR) and hyperspectral imagery with detailed microclimate measurements. We then use modeled microclimate and forest structural and compositional variables to explain variation in spatially explicit measurements of leaf traits, including gas exchange and structure. Our results highlight the importance of: (1) species differences in leaf traits, with species explaining up to 65% of the …

Habitat-Specific Density And Diet Of Rapidly Expanding Invasive Red Lionfish, Pterois Volitans,, Populations In The Northern Gulf Of Mexico, Kristen A. Dahl, William F. Patterson Iii

C-IMAGE Publications

Invasive Indo-Pacific red lionfish, Pterois volitans, were first reported in the northern Gulf of Mexico (nGOM) in summer 2010. To examine potential impacts on native reef fish communities, lionfish density and size distributions were estimated from fall 2010 to fall 2013 with a remotely operated vehicle at natural (n = 16) and artificial (n = 22) reef sites. Lionfish (n = 934) also were sampled via spearfishing to examine effects of habitat type, season, and fish size on their diet and trophic ecology. There was an exponential increase in lionfish density at both natural and artificial reefs over the study …

Prevalence Of External Skin Lesions And Polycyclic Aromatic Hydrocarbon Concentrations In Gulf Of Mexico Fishes, Post-Deepwater Horizon, Steven Murawski, William T. Hogarth, Ernst B. Peebles, Luiz Barbeiri

C-IMAGE Publications

We surveyed offshore fish populations in the Gulf of Mexico in 2011 and 2012, following persistent reports of abnormal skin lesions and other pathologies in the aftermath of the Deepwater Horizon oil spill. The incidence of skin lesions in 2011 sampling was most frequent in some bottom-dwelling species along the continental shelf edge north of the Deepwater Horizon site. Longline surveys revealed that by 2012 the overall frequency of lesions in northern Gulf of Mexico (NGM) fishes in the vicinity of the Deepwater Horizon had declined 53%, with severity also declining. Relatively high concentrations of polycyclic aromatic hydrocarbon (PAH) metabolites …

A Time-Series View Of Changing Surface Ocean Chemistry Due To Ocean Uptake Of Anthropogenic Co2 And Ocean Acidification, Nicholas R. Bates, Yrene M. Astor, Matthew J. Church, Kim Currie, John E. Dore, Melchor González-Dávila, Laura Lorenzoni, Frank E. Muller-Karger, Jon Olafsson, J. Magdalena Santana-Casiano

Marine Science Faculty Publications

Sustained observations provide critically needed data and understanding not only about ocean warming and water cycle reorganization (e.g., salinity changes), ocean eutrophication, and ocean deoxygenation, but also about changes in ocean chemistry. As an example of changes in the global ocean carbon cycle, consistent changes in surface seawater CO2-carbonate chemistry are documented by seven independent CO2 time series that provide sustained ocean observations collected for periods from 15 to 30 years: (1) Iceland Sea, (2) Irminger Sea, (3) Bermuda Atlantic Time-series Study (BATS), (4) European Station for Time series in the Ocean at the Canary Islands (ESTOC), (5) CArbon Retention …

On The Ability Of Global Sea Level Reconstructions To Determine Trends And Variability, F. M. Calafat, D. P. Chambers, M. N. Tsimplis

Marine Science Faculty Publications

We investigate how well methods based on empirical orthogonal functions (EOFs) can reconstruct global mean sea level (GMSL). We first explore the analytical solution of the method and then perform a series of numerical experiments using modeled data. In addition, we present a new GMSL reconstruction for the period 1900–2011 computed both with and without a spatially uniform EOF (EOF0). The method without the EOF0 uses global information, which leads to a better reconstruction of the variability, though with some underestimation. The trend, however, is not captured, which motivates the use of the EOF0. When the EOF0 is used the …

Southern Ocean Velocity And Geostrophic Transport Fields Estimated By Combining Jason Altimetry And Argo Data, Michael Kosempa, Don P. Chambers

Marine Science Faculty Publications

Zonal geostrophic velocity fields above 1975 dbar have been estimated for the Southern Ocean from 2004 into 2011 based on sea surface topography observed by Jason altimetry and temperature/salinity measured by Argo autonomous floats. The velocity at 1000 dbar estimated with the method has been compared to Argo drift trajectory at the same pressure level available from the Asia Pacific Data Research Center (APDRC). The inferred velocities agree with those from the Argo drift within the estimated sampling error of the latter, but have fewer gaps in space and time. The velocity has also been integrated from depth to surface …

Evidence For Permafrost Thaw And Transport From An Alaskan North Slope Watershed, Kathryn M. Schreiner, Thomas S. Bianchi, Brad E. Rosenheim

Marine Science Faculty Publications

Burial of organic carbon (OC) in marine sediments is one of the most important linkages between the short-term biologic carbon cycle and the long-term geologic carbon cycle. Yet much is still unknown about the fate of terrigenous OC in marine coastal margins. Here the delivery of particulate OC (POC) to the Colville River deltaic region in the Alaskan Beaufort Sea by particulates of varying densities is studied through the use of ramped temperature pyrolysis and radiocarbon analyses. The Colville River is the largest river in North America whose watershed is underlain completely by high Arctic permafrost tundra. A variety of …

Relative Contributions Of Ocean Mass And Deep Steric Changes To Sea Level Rise Between 1993 And 2013, Sarah G. Purkey, Gregory C. Johnson, Don P. Chambers

Marine Science Faculty Publications

Regional and global trends of Sea Level Rise (SLR) owing to mass addition centered between 1996 and 2006 are assessed through a full-depth SLR budget using full-depth in situ ocean data and satellite altimetry. These rates are compared to regional and global trends in ocean mass addition estimated directly using data from the Gravity Recovery and Climate Experiment (GRACE) from 2003 to 2013. Despite the two independent methods covering different time periods with differing spatial and temporal resolution, they both capture the same large-scale mass addition trend patterns including higher rates of mass addition in the North Pacific, South Atlantic, …

Identification And Ss-Lactam Resistance In Aquatic Isolates Of Enterobacter Cloacae And Their Status In Microbiota Of Domica Cave In Slovak Karst (Slovakia), Barbora Gaalova, Alena Donauerova, Milan Seman, Helena Bujdakova

International Journal of Speleology

Domica Cave is located in the Slovak Karst National Park in southern Slovakia. Heterotrophic cultivable psychrophilic and mesophilic microbiota were confirmed to be prevalent in this cave. Escherichia coli was the most abundant bacterium, followed by Enterobacter species and Serrratia species. Enterobacter cloacae isolates belong to the group of faecal contaminants (coliforms) of concern in water. Their status in cave ecosystem is questionable, but we observed E. cloacae in water samples all years round suggesting an autochthonous origin. We were concerned with possible contamination of the cave water with resistant E. cloacae from animal farms located 2-3 km from the …

A Framework For A Marine Biodiversity Observing Network Within Changing Continental Shelf Seascapes, Frank Muller-Karger, Maria Kavanaugh, Enrique Montes, William Balch, Mya Breitbart

Marine Science Faculty Publications

Continental shelves and the waters overlying them support numerous industries as diverse as tourism and recreation, energy extraction, fisheries, transportation, and applications of marine bio-molecules (e.g., agribusiness, food processing, pharmaceuticals). Although these shelf ecosystems exhibit impacts of climate change and increased human use of resources (Halpern et al., 2012; IPCC, 2013, 2014; Melillo et al., 2014), there are currently no standardized metrics for assessing changes in ecological function in the coastal ocean. Here, we argue that it is possible to monitor vital signs of ecosystem function by focusing on the lowest levels of the ocean food web. Establishment of biodiversity, …

Detection Of Dominant Algal Blooms By Remote Sensing, Chuanmin Hu, Shubha Sathyendranath, Jamie D. Shutler, Christopher W. Brown, Tim S. Moore, Susanne E. Craig, Inia Soto, Ajit Subramaniam

Marine Science Faculty Publications

No abstract provided.

An Eof-Based Algorithm To Estimate Chlorophyll A Concentrations In Taihu Lake From Modis Land-Band Measurements: Implications For Near Real-Time Applications And Forecasting Models, Lin Qi, Chuanmin Hu, Hongtao Duan, Brian B. Barnes, Ronghua Ma

Marine Science Faculty Publications

For near real-time water applications, the Moderate Resolution Imaging Spectroradiometers (MODIS) on Terra and Aqua are currently the only satellite instruments that can provide well-calibrated top-of-atmosphere (TOA) radiance data over the global aquatic environments. However, TOA radiance data in the MODIS ocean bands over turbid atmosphere in east China often saturate, leaving only four land bands to use. In this study, an approach based on Empirical Orthogonal Function (EOF) analysis has been developed and validated to estimate chlorophyll a concentrations (Chla, μg/L) in surface waters of Taihu Lake, the third largest freshwater lake in China. The EOF approach analyzed the …

The Conservation Value Of Karst Dolines For Vascular Plants In Woodland Habitats Of Hungary: Refugia And Climate Change, Zoltán Bátori, János Csiky, Tünde Farkas, E. Anna Vojtkó, László Erdős, Dániel Kovács, Tamás Wirth, László Körmöczi, András Vojtkó

International Journal of Speleology

Limestone (karst) surfaces in Hungary are rich in dolines, in which many endangered vascular plant species occur. To date, the majority of studies dealing with doline vegetation have focused on the local rather than the landscape level, without using comparative data from other areas. However, in this study we aimed to compare the vegetation pattern and species composition of dolines under different climate regimes of Hungary with regard to regional species pools. The fieldwork was carried out between 2005 and 2012. Twenty dolines were selected in the Mecsek Mountains (southern Hungary) and nine dolines in the Aggtelek Karst area (northern …

Diversity Of Cultivable Bacteria Involved In The Formation Of Macroscopic Microbial Colonies (Cave Silver) On The Walls Of A Cave In Slovenia, Blagajana Herzog Velikonja, Rok Tkavc, Lejla Pašić

International Journal of Speleology

Karstic caves often support white, yellow, grey or pink microbial colonies that are termed ‘cave silver’ by speleologists. Using various sample pre-treatments and culture media, a wide variety of bacteria associated with these colonies were recovered from a cave in Slovenia, Pajsarjeva jama. Decreasing the inoculum size resulted in significant increases in viable counts, while pre-treatments had the opposite effect with the exception of microwave irradiation. While all growth media yielded viable counts, the maximal counts were observed on a low-nutrient TWA medium.

Based on the 16S rRNA gene sequence of OTU representatives, the majority of the 80 isolates examined …

Evolution And Functional Morphology Of The Cephalic Lobes In Batoids, Samantha Lynn Mulvany

USF Tampa Graduate Theses and Dissertations

Cephalic lobes are unique structures derived from the anterior pectoral fins, found in select myliobatid stingrays. Many benthic batoids utilize undulatory locomotion and use their pectoral fins for both locomotion and prey capture. Pelagic myliobatids that possess cephalic lobes utilize oscillatory locomotion, using their pectoral fins to locomote and their cephalic lobes for prey capture. Despite differences in habitat usage and locomotor modes, these batoids feed on very similar benthic organisms. The purpose of this study was to 1.) compare the morphology of the cephalic lobes and anterior pectoral fins in lobed and lobeless species, looking at skeletal elements, musculature …

Climate Impacts On Zooplankton Population Dynamics In Coastal Marine Ecosystems, Harold P. Batchelder, Kendra L. Daly, Cabell S. Davis, Rubao Ji, Mark D. Ohman, William T. Peterson, Jeffrey A. Runge

Marine Science Faculty Publications

The 20-year US GLOBEC (Global Ocean Ecosystem Dynamics) program examined zooplankton populations and their predators in four coastal marine ecosystems. Program scientists learned that environmental controls on zooplankton vital rates, especially the timing and magnitude of reproduction, growth, life-cycle progression, and mortality, determine species population dynamics, seasonal and spatial distributions, and abundances. Improved knowledge of spatial-temporal abundance and distribution of individual zooplankton taxa coupled with new information linking higher trophic level predators (salmon, cod, haddock, penguins, seals) to their prey yielded mechanistic descriptions of how climate variation impacts regionally important marine resources. Coupled ecological models driven by improved regional-scale climate …

Skeletal Muscle Contraction Simulation: A Comparison In Modeling, Jonathan M. Ford

USF Tampa Graduate Theses and Dissertations

Computer generated three-dimensional (3-D) models are being used at increasing rates in the fields of entertainment, education, research, and engineering. One of the aspects of interest includes the behavior and function of the musculoskeletal system. One such tool used by engineers is the finite element method (FEM) to simulate the physics behind muscle mechanics. There are several ways to represent 3-D muscle geometry, namely a bulk, a central line of action and a spline model. The purpose of this study is to exmine how these three representations affect the overall outcome of muscle movement. This is examined in a series …

National Park Service Cave Ecology Inventory And Monitoring Framework, Gretchen M. Baker, Steven J. Taylor, Shawn Thomas, Rick Olson, Kathy Lavoie, Marie Denn, Steven Thomas, Hazel Barton, Kurt Helf, Rene Ohms, Joel Despain, Jim Kennedy, David Larson

National Cave and Karst Management Symposium 2013

A team developed the Cave Ecology Inventory and Monitoring Framework for National Park Service (NPS) units. It contains information for NPS cave managers across the United States to determine how to inventory and monitor cave ecology. Due to the wide geographical scope of NPS caves and their many different types, the document does not prescribe exact protocols. Instead, it provides guidance for what types of inventory and monitoring are possible, a framework for deciding how to prioritize inventory and monitoring activities, and references to specific protocols that are already in place at NPS cave parks.

Keywords: cave ecology, cave microbiology, …

Incorporating Cave And Karst Management Into The Forest Plan Revision Process Of Arizona Forests, Ray Keeler, Richard Bohman

National Cave and Karst Management Symposium 2013

Arizona National Forest land managers have a multitude of tasks and priorities; historically, caves and karst management has not been amongst the priorities receiving any significant allocation of resources. When caves and karst management is not included in the Forest Plan, even when large and significant cave and karst areas exist, active cave and karst management often falls below the waterline of available manpower and resources. Additionally, there is entropy associated with normal changes in personnel assignments and new staff coming onboard. When combined with a general lack of written policies and guidelines, these personnel transitions lead to unnecessary degradation …

Mycological Study For A Management Plan Of A Neotropical Show Cave (Brazil), Erika Linzi Silva Taylor, Maria Aparecida De Resende Stoianoff, Rodrigo Lopes Ferreira

International Journal of Speleology

Caves are stable environments with characteristics favoring the development of microorganisms. The allocthonous input of organic matter and microbes into the warm Neotropical caves may favor the development of filamentous fungi, including pathogenic species. Histoplasma capsulatum is a pathogenic species commonly found in caves and associated with bat and bird guano. Many Brazilian caves have been historically visited due to scenic and religious tourism. The objective of this study was to perform a microbiology study for a management plan of a show cave in Brazil, focusing on the presence and distribution of pathogenic and opportunistic fungi in the cave. Statistics …

Draft Genome Sequence Of Xylella Fastidiosa Subsp. Multiplex Strain Griffin-1 From Quercus Rubra In Georgia, Jianchi Chen, Hong Huang, Chung-Jan Chang, Drake C. Stenger

School of Information Faculty Publications

The draft genome sequence of Xylella fastidiosa subsp. multiplex strain Griffin-1, isolated from a red oak tree (Quercus rubra) in Georgia, is reported here. The bacterium has a genome size of 2,387,314 bp, with a G+C content of 51.7%. The Griffin-1 strain genome contains 2,903 predicted open reading frames and 50 RNA genes.

Differences In Aquatic Microcrustacean Assemblages Between Temporary And Perennial Springs Of An Alpine Karstic Aquifer, Nataša Mori, Anton Brancelj

International Journal of Speleology

Microcrustacean (Copepoda, Ostracoda) assemblages were investigated at the interface of the vadose and phreatic zones in the alpine karstic aquifer from the Julian Alps in Slovenia (SE Europe). Two temporary and one perennial karstic outlets were sampled by filtering the water several times over 2 years. Concurrently, benthos from the mouth of a perennial spring and from an adjacent spring brook were collected. Altogether 24 microcrustacean species were recorded. The spatial and temporal variation in drift densities and species composition was high indicating complex groundwater hydrological pathways being dependent on precipitation regime. Non-metric Multidimensional Scaling (NMDS) clearly separated drift samples …

Epilithic And Aerophilic Diatoms In The Artificial Environment Of Kungsträdgården Metro Station, Stockholm, Sweden, Lena Norbäck Ivarsson, Magnus Ivarsson, Johannes Lundberg, Therese Sallstedt, Catarina Rydin

International Journal of Speleology

The Kungsträdgården metro station is an artificial and urban subsurface environment illuminated with artificial light. Its ecosystem is almost completely unknown and as a first step to better understand the biology and rock wall habitats the diatom flora was investigated. A total of 12 species were found growing on the rock walls of Kungsträdgården metro station. The results show the diatom flora in Kungsträdgården to be dominated by e.g. Diadesmis contenta, Diadesmis perpusilla, Pinnularia appendiculata, Nitzschia amphibia, Nitzschia sinuata and Diploneis ovalis. One species, Caloneis cf. aerophila, has never been reported from Sweden before. …

Spatial And Temporal Changes In Invertebrate Assemblage Structure From The Entrance To Deep-Cave Zone Of A Temperate Marble Cave, Benjamin W. Tobin, Benjamin T. Hutchins, Benjamin F. Schwartz

International Journal of Speleology

Seasonality in surface weather results in seasonal temperature and humidity changes in caves. Ecological and physiological differences among trogloxenes, troglophiles, and troglobionts result in species-dependent responses to this variability. To investigate these responses, we conducted five biological inventories in a marble cave in the Sierra Nevada Range, California, USA between May and December, 2010. The cave was divided into six quadrats and temperature was continuously logged in each (humidity was logged at the entrance and in the deep cave). With increasing distance from the entrance, temperature changes were increasingly attenuated and lagged relative to surface temperature. Linear regressions were created …

Comparative Microbial Community Composition From Secondary Carbonate (Moonmilk) Deposits: Implications For The Cansiliella Servadeii Cave Hygropetric Food Web, Annette Summers Engel, Maurizio G. Paoletti, Mattia Beggio, Luca Dorigo, Alberto Pamio, Tiziano Gomiero, Claudio Furlan, Mauro Brilli, Angelo Leandro Dreon, Roberto Bertoni, Andrea Squartini

International Journal of Speleology

The microbial diversity of moonmilk, a hydrated calcium carbonate speleothem, was evaluated from two Italian caves to provide context for the food web of highly-specialized troglobitic beetles, Cansiliella spp. (Leptodirinae), with distinctive carbon and nitrogen isotope values indicative of a novel food source. The moonmilk and associated percolating waters had low to no extractable chlorophyll, with an average organic C:N ratio of 9, indicating limited allochthonous input and a significant contribution from microbial biomass. The biomass from moonmilk was estimated to be ~10⁴ micro- and meiofaunal individuals per m² and ~10⁷ microbial cells/ml. Betaproteobacteria dominated the …

Generalized Additive Models Used To Predict Species Abundance In The Gulf Of Mexico: An Ecosystem Modeling Tool, Michael Drexler, Cameron H. Ainsworth

C-IMAGE Publications

Spatially explicit ecosystem models of all types require an initial allocation of biomass, often in areas where fisheries independent abundance estimates do not exist. A generalized additive modelling (GAM) approach is used to describe the abundance of 40 species groups (i.e. functional groups) across the Gulf of Mexico (GoM) using a large fisheries independent data set (SEAMAP) and climate scale oceanographic conditions. Predictor variables included in the model are chlorophyll a, sediment type, dissolved oxygen, temperature, and depth. Despite the presence of a large number of zeros in the data, a single GAM using a negative binomial distribution was suitable …

Blood-Brain Barrier Alterations Provide Evidence Of Subacute Diaschisis In An Ischemic Stroke Rat Model, Svitlana Garbuzova-Davis, Maria C. O. Rodrigues, Diana G. Hernandez-Ontiveros, Naoki Tajiri, Aric Frisna-Deyo, Sean M. Boffeli, Jerry V. Abraham, Mibel Pabon, Andrew Wagner, Hiroto Ishikawa, Kazutaka Shinozuka, Edward M. Haller, Paul Sanberg, Yuji Kaneko, Cesario Borlongan

Integrative Biology Faculty and Staff Publications

Background: Comprehensive stroke studies reveal diaschisis, a loss of function due to pathological deficits in brain areas remote from initial ischemic lesion. However, blood-brain barrier (BBB) competence in subacute diaschisis is uncertain. The present study investigated subacute diaschisis in a focal ischemic stroke rat model. Specific focuses were BBB integrity and related pathogenic processes in contralateral brain areas.

Methodology/Principal Findings: In ipsilateral hemisphere 7 days after transient middle cerebral artery occlusion (tMCAO), significant BBB alterations characterized by large Evans Blue (EB) parenchymal extravasation, autophagosome accumulation, increased reactive astrocytes and activated microglia, demyelinization, and neuronal damage were detected in the striatum, …

The Economic Impact Of Commensal Rodents On Small Businesses In Manhattan’S Chinatown: Trends And Possible Causes, Anthony Almeida, Robert Corrigan, Ronald Sarno

Suburban Sustainability

Given the history of well-documented rodent infestations in New York City we were interested in assessing the economic impact of rats and mice on small businesses in The Lower East Side of Manhattan. Via mailed surveys and on-site interviews , we quantified damage to structures, loss of saleable goods and merchandise, the cost of pest-control professionals, and/or self-applied poison/traps. Overall, 16% of business (n = 76) responded to our queries. To those businesses reporting some level of rodent damage, average losses included $513 in merchandise, $726 in pest-control fees, $371 in repair costs to structure, and $125 in do-it-yourself deployment …