Life Sciences Commons^™

Automated High-Resolution Time Series Mapping Of Mangrove Forests Damaged By Hurricane Irma In Southwest Florida, Matthew J. Mccarthy, Brita Jessen, Michael J. Barry, Marissa Figueroa, Jessica Mcintosh, Tylar Murray, Jill Schmid, Frank E. Muller-Karger

Marine Science Faculty Publications

In September of 2017, Hurricane Irma made landfall within the Rookery Bay National Estuarine Research Reserve of southwest Florida (USA) as a category 3 storm with winds in excess of 200 km h−1. We mapped the extent of the hurricane’s impact on coastal land cover with a seasonal time series of satellite imagery. Very high-resolution (i.e., <5 m pixel) satellite imagery has proven effective to map wetland ecosystems, but challenges in data acquisition and storage, algorithm training, and image processing have prevented large-scale and time-series mapping of these data. We describe our approach to address these issues to evaluate Rookery Bay ecosystem damage and recovery using 91 WorldView-2 satellite images collected between 2010 and 2018 mapped using automated techniques and validated with a field campaign. Land cover was classified seasonally at 2 m resolution (i.e., healthy mangrove, degraded mangrove, upland, soil, and water) with an overall accuracy of 82%. Digital change detection methods show that hurricane-related degradation was 17% of mangrove forest (~5 km2). Approximately 35% (1.7 km2) of this loss recovered one year after Hurricane Irma. The approach completed the mapping approximately 200 times faster than existing methods, illustrating the ease with which regional high-resolution mapping may be accomplished efficiently.

Supporting The Essential - Recommendations For The Development Of Accessible And Interoperable Marine Biological Data Products, D. Lear, P. Herman, G. Van Hoey, L. Schepers, N. Tonné, M. Lipizer, F. E. Muller-Karger, W. Appeltans, W. D. Kissling, N. Holdsworth, M. Edwards, E. Pecceu, H. Nygård, G. Canonico, S. Birchenough, G. Graham, K. Deneudt, S. Claus, P. Oset

Marine Science Faculty Publications

In this paper we outline the stakeholder-led approaches in the development of biological data products to support effective conservation, management and policy development. The requirements of a broad range of stakeholders and iterative, structured processes framed the development of tools, models and maps that support the FAIR (Findable, Accessible, Interoperable, Reusable) data principles. By structuring the resultant data products around the emerging biological Essential Ocean Variables, and through the engagement with a broad range of end-users, the EMODnet (European Marine Observation and Data Network) Biology project has delivered a suite of demonstration data products. These products are presented in the …

Mapping Hurricane Damage: A Comparative Analysis Of Satellite Monitoring Methods, Matthew J. Mccarthy, Brita Jessen, Michael J. Barry, Marissa Figueroa, Jessica Mcintosh, Tylar Murray, Jill Schmid, Frank E. Muller-Karger

Marine Science Faculty Publications

Wetlands are the second-most valuable natural resource on Earth but have declined by approximately 70 % since 1900. Restoration and conservation efforts have succeeded in some areas through establishment of refuges where anthropogenic impacts are minimized. However, these areas are still prone to wetland damage caused by natural disasters. Severe storms such as Hurricane Irma, which made landfall as a Category 3 hurricane in southwest Florida (USA) on September 11, 2017, can cause the destruction of mangroves and other wetland habitat. Multispectral images from commercial satellites provide a means to assess the extent of the damage to different wetland habitat …

Altered Tropical Seascapes Influence Patterns Of Fish Assemblage And Ecological Functions In The Western Indian Ocean, D. H. Chacin, C. D. Stallings, M. Eggertsen, C. Åkerlund, C. Halling, C. Berkström

Marine Science Faculty Publications

The arrangement and composition of habitats within landscapes and fine-scale habitat characteristics influence community structure and ecological processes. These aspects can be altered by anthropogenic activities, thus influencing associated assemblages. Farming of macroalgae is a common practice in tropical settings and alters the natural composition of seascapes by introducing monoculture patches. The farmed macroalgae may also differ in palatability compared to naturally-occurring macroalgae, influencing herbivory. This study assessed how these farms may differ from natural macroalgal beds in terms of habitat heterogeneity, fish assemblages, and herbivory. We surveyed fish assemblages and deployed macroalgal assays within macroalgal beds, farms and at …

Climate-Driven Aerobic Habitat Loss In The California Current System, Evan M. Howard, Justin L. Penn, Hartmut Frenzel, Brad A. Seibel, Daniele Bianchi, Lionel Renault, Fayçal Kessouri, Martha A. Sutula, James C. Mcwilliams, Curtis Deutsch

Marine Science Faculty Publications

Climate warming is expected to intensify hypoxia in the California Current System (CCS), threatening its diverse and productive marine ecosystem. We analyzed past regional variability and future changes in the Metabolic Index (Φ), a species-specific measure of the environment’s capacity to meet temperature-dependent organismal oxygen demand. Across the traits of diverse animals, Φ exhibits strong seasonal to interdecadal variations throughout the CCS, implying that resident species already experience large fluctuations in available aerobic habitat. For a key CCS species, northern anchovy, the long-term biogeographic distribution and decadal fluctuations in abundance are both highly coherent with aerobic habitat volume. Ocean warming …

Increasing Rates Of Carbon Burial In Southwest Florida Coastal Wetlands, Joshua L. Breithaupt, Joseph M. Smoak, Thomas S. Bianchi, Derrick R. Vaughn, Christian J. Sanders, Kara R. Radabaugh, Michael J. Osland, Laura C. Feher, James C. Lynch, Donald R. Cahoon, Gordon H. Anderson, Kevin R.T. Whelan, Brad E. Rosenheim, Ryan P. Moyer, Lisa G. Chambers

Marine Science Faculty Publications

Rates of organic carbon (OC) burial in some coastal wetlands appear to be greater in recent years than they were in the past. Possible explanations include ongoing mineralization of older OC or the influence of an unaccounted-for artifact of the methods used to measure burial rates. Alternatively, the trend may represent real acceleration in OC burial. We quantified OC burial rates of mangrove and coastal freshwater marshes in southwest Florida through a comparison of rates derived from ²¹⁰Pb, ¹³⁷Cs, and surface marker horizons. Age/depth profiles of lignin: OC were used to assess whether down-core remineralization had depleted the …

Paleoceanography: Lessons For A Changing World, Amelia Shevenell, Peggy Delaney, Katrin Meissner, Laurie Menviel, Alan C. Mix

Marine Science Faculty Publications

No abstract provided.

Trace Metal And Nutrient Dynamics Across Broad Biogeochemical Gradients In The Indian And Pacific Sectors Of The Southern Ocean, David J. Janssen, Matthias Sieber, Michael J. Ellwood, Tim M. Conway, Pamela M. Barrett, Xiaoyu Chen, Gregory F. De Souza, Christel S. Hassler, Samuel L. Jaccard

Marine Science Faculty Publications

The Southern Ocean is the largest high-nutrient low-chlorophyll environment in the global ocean, and represents an important source of intermediate and deep waters to lower latitudes. Constraining Southern Ocean trace metal biogeochemical cycling is therefore important not just for understanding biological productivity and carbon cycling regionally, but also for understanding trace metal distributions throughout the lower latitude oceans. We present dissolved Fe, Ni, Cu, Zn, Cd, Pb and macronutrient concentrations in the Indian and Pacific sectors of the Southern Ocean from the Antarctic Circumnavigation Expedition (austral summer 2016-17), which included the first opportunities to study trace metal cycling at the …

Cliff Feature Delineation Tool And Baseline Builder Tool, Version 1.0 User Guide, Alexander C. Seymour, Cheryl J. Hapke, Jonathan Warrick

Marine Science Faculty Publications

Coastal cliffs constitute 80 percent of the world’s coastline, with seacliffs fronting a large proportion of the U.S. West Coast shoreline, particularly in California. Erosion of coastal cliffs can threaten infrastructure and human life, yet the spatial and temporal scope of cliff studies have been limited by cumbersome traditional methods that rely on the manual interpretation of seacliff features—especially seacliff toes and top edges. The Cliff Feature Delineation Tool (CFDT) and the Baseline Builder Tool are designed to increase the efficiency of deriving seacliff features from remote sensing datasets by utilizing an automated, quantitative approach that eliminates traditional interpretive methods …

Disturbances Drive Changes In Coral Community Assemblages And Coral Calcification Capacity, Travis A. Courtney, Brian B. Barnes, Iliana Chollett, Robin Elahi, Kevin Gross, James R. Guest, Ilsa B. Kuffner, Elizabeth A. Lenz, Hannah R. Nelson, Caroline S. Rogers, Lauren T. Toth, Andreas J. Andersson

Marine Science Faculty Publications

Anthropogenic environmental change has increased coral reef disturbance regimes in recent decades, altering the structure and function of many coral reefs globally. In this study, we used coral community survey data collected from 1996 to 2015 to evaluate reef-scale coral calcification capacity (CCC) dynamics with respect to recorded pulse disturbances for 121 reef sites in the Main Hawaiian Islands and Mo'orea (French Polynesia) in the Pacific and the Florida Keys Reef Tract and St. John (U.S. Virgin Islands) in the western Atlantic. CCC remained relatively high in the Main Hawaiian Islands in the absence of recorded widespread disturbances; declined and …

Mapping Benthic Habitat On The West Florida Shelf Using Multibeam Acoustics And Towed Underwater Video To Improve Fisheries Science And Management, Alexander Ilich, Jennifer Brizzolara, Sarah Grasty, John Gray, Matthew Hommeyer, Chad Lembke, Stanley Locker, Alex Silverman, Theodore Switzer, Abigail Vivlamore, Steven Murawski

Marine Science Faculty Publications

The West Florida Shelf (WFS) is an extremely important area for both commercial and recreational fisheries. However, the lack of habitat maps in this area makes planning fisheries independent monitoring surveys difficult, and hinders the ability to manage and monitor fish stocks and ecosystems over time. As of 2015, only 5% of the WFS had been mapped in high resolution using a multibeam echosounder with little effort expended to infer and verify habitat type. In 2015, The Continental Shelf Characterization, Assessment, and Mapping Project (C-SCAMP) began using a multibeam echosounder and towed underwater video to map benthic habitats and improve …

Phylogeny Of Terrestrial Isopods Based On The Complete Mitochondrial Genomes, Subvert The Monophyly Of Oniscidea, Rui Zhang, Ruru Chen, Jianmei An, Carlos A. Santamaria

Integrative Biology Faculty and Staff Publications

Background: Oniscidea is the only truly terrestrial taxon within the Crustacea, and vital to soil formation. However, the monophyly of suborder Oniscidea has been in dispute since 1995, with different studies disagreeing on whether the coastal Ligiidae are included within the suborder. To clarify the phylogenetic hypothesis of suborder Oniscidea, we sequenced the complete mitochondrial genomes of Ligia exotica (Roux, 1828) and Mongoloniscus sinensis (Dollfus, 1901).

Results: Like most metazoan, the complete mitogenomes of two species with circular double strands. The structure and characters of mitogenomes of these two species are analyzed. The constructed phylogenetic analyses show that Oniscidea is …

First Genome Sequence Of The Gunnison’S Prairie Dog (Cynomys Gunnisoni), A Keystone Species And Player In The Transmission Of Sylvatic Plague, Mirian T. N. Tsuchiya, Rebecca B. Dikow, Loren Cassin-Sackett

Integrative Biology Faculty and Staff Publications

Prairie dogs (genus Cynomys) are a charismatic symbol of the American West. Their large social aggregations and complex vocalizations have been the subject of scientific and popular interest for decades. A large body of literature has documented their role as keystone species of western North America’s grasslands: They generate habitat for other vertebrates, increase nutrient availability for plants, and act as a food source for mammalian, squamate, and avian predators. An additional keystone role lies in their extreme susceptibility to sylvatic plague (caused by Yersinia pestis), which results in periodic population extinctions, thereby generating spatiotemporal heterogeneity in both …

Molecular Tools For Coral Reef Restoration: Beyond Biomarker Discovery, John Everett Parkinson, Andrew C. Baker, Iliana B. Baums, Sarah W. Davies, Andréa G. Grottoli, Sheila A. Kitchen, Mikhail V. Matz, Margaret W. Miller, Andrew A. Shantz, Carly D. Kenkel

Integrative Biology Faculty and Staff Publications

As coral reefs continue to decline due to climate change and other stressors, scientists have proposed adopting genomic tools, such as biomarkers, to aid in the conservation and restoration of these threatened ecosystems. Biomarkers are easily measured indicators of biological processes that can be used to predict or diagnose health, resilience, and other key performance metrics. The ultimate goal of developing biomarkers is to determine the conservation value and utility of a given coral colony, including the host animal, its algal symbionts, and their microbial partners. However, this goal remains distant because most efforts have not yet moved beyond the …

Diversity And Abundance Of Dragonflies And Damselflies In Tampa Bay, Florida, Meredith A. Krause, Thomas Koster, Bryan N. Macneill, Daniel J. Zydek, Nicholas T. Ogburn, Jonathan Sharpin, Robert Shell, Marc J. Lajeunesse

Integrative Biology Faculty and Staff Publications

Little is known about the community of dragonflies and damselflies in Tampa Bay, Florida, USA. To address this gap, we conducted 2 longitudinal surveys of adult odonates in a natural floodplain of the Hillsborough River in 2013 and 2017. Along with abundance and species diversity, we also measured intraspecific variation in body size, sexual dimorphism, wing-cell asymmetry, and water mite ectoparasitism. Our first weekly survey from Oct 2013 to Oct 2014 sampled 327 adults (230 female, 97 male) from 8 dragonfly species, with the eastern pondhawk (Erythemis simplicicollis Say; Odonata: Libellulidae) representing 79% of captures, followed by the second …

Genome Sequence Of Vibrio Natriegens Phage Vb_Vnas-Aqkl99, Noah Yonas, Paige Boleman, Y Nguyen, Makenzie Kerr, Kema Malki, Anthony M. Greco, Mya Breitbart

Marine Science Faculty Publications

Vibrio natriegens is a naturally occurring marine bacterium that is emerging as a microbiological model system. Here, we describe Aquatic Killer 99 (AQKL99), a novel phage that infects Vibrio natriegens 14048. The genome of the phage is 58,464 bp long, has a GC content of 45.9%, and contains 51 protein-coding genes.

Life History Of Northern Gulf Of Mexico Warsaw Grouper Hyporthodus Nigritus Inferred From Otolith Radiocarbon Analysis, Beverly K. Barnett, Jeffrey P. Chanton, Robert Ahrens, Laura Thornton, William F. Patterson Iii

C-IMAGE Publications

Warsaw grouper, Hyporthodus nigritus, is a western Atlantic Ocean species typically found at depths between 55 and 525 m. It is listed as a species of concern by the U.S. National Marine Fisheries Service and as near threatened by the International Union for the Conservation of Nature. However, little information exists on the species’ life history in the northern Gulf of Mexico (nGOM) and its stock status in that region is currently unknown. Age of nGOM Warsaw grouper was investigated via opaque zone counts in otolith thin sections (max age = 61 y), and then the bomb 14C chronometer …

Transmission Of West Nile And Five Other Temperate Mosquito-Borne Viruses Peaks At Temperatures Between 23°C And 26°C, Marta S. Shocket, Anna B. Verwillow, Mailo G. Numazu, Hani Slamani, Jeremy M. Cohen, Fadoua El Moustaid, Jason Rohr, Leah R. Johnson, Erin A. Mordecai

Integrative Biology Faculty and Staff Publications

The temperature-dependence of many important mosquito-borne diseases has never been quantified. These relationships are critical for understanding current distributions and predicting future shifts from climate change. We used trait-based models to characterize temperature-dependent transmission of 10 vector–pathogen pairs of mosquitoes (Culex pipiens, Cx. quinquefascsiatus, Cx. tarsalis, and others) and viruses (West Nile, Eastern and Western Equine Encephalitis, St. Louis Encephalitis, Sindbis, and Rift Valley Fever viruses), most with substantial transmission in temperate regions. Transmission is optimized at intermediate temperatures (23–26°C) and often has wider thermal breadths (due to cooler lower thermal limits) compared to pathogens with …

Draft Genome Sequence Of Verrucosispora Sp. Strain Cwr15, Isolated From A Gulf Of Mexico Sponge, Sarah J. Kennedy, Eleonora Cella, Mohammad Jubair, Taj Azarian, Bill J. Baker, Lindsey N. Shaw

Molecular Biosciences Faculty Publications

Here, we present the draft genome sequence of Verrucosispora sp. strain CWR15, a bacterial symbiont of a Gulf of Mexico sponge. The genome consists of 35 contigs encoding 5,840 genes. The genome is the basis for future study and presents an underexplored taxonomy and biosynthetic potential.

Heat, Health And Hatchlings: Associations Of In Situ Nest Temperatures With Morphological And Physiological Characteristics Of Loggerhead Sea Turtle Hatchlings From Florida, Kelsey Alexandra Fleming, Justin R. Perrault, Nicole I. Stacy, Christina M. Coppenrath, Alison M. Gainsbury

USF St. Petersburg campus Faculty Publications

Incubation temperatures, in addition to an embryo’s genetic makeup, are critical in many aspects of adequate sea turtle embryonic development. The effects of high and low incubation temperatures on hatchling quality have been previously examined; however, many of these studies were conducted on relocated or laboratory-reared nests, which do not accurately reflect natural nest temperature fluctuations. To observe the impacts of varying in situ incubation temperatures on loggerhead sea turtle (Caretta caretta) hatchling morphology, various health variables and locomotor performance, temperature data loggers were deployed in 15 loggerhead nests on Juno Beach, Florida, between May and July 2018. Over the …

The First Global Deep-Sea Stable Isotope Assessment Reveals The Unique Trophic Ecology Of Vampire Squid Vampyroteuthis Infernalis (Cephalopoda), A. V. Golikov, F. R. Ceia, R. M. Sabirov, J. D. Ablett, Ian G. Gleadall, Gudmundur Gudmundsson, Henk-Jan T. Hoving, Heather L. Judkins

USF St. Petersburg campus Faculty Publications

Vampyroteuthis infernalis Chun, 1903, is a widely distributed deepwater cephalopod with unique morphology and phylogenetic position. We assessed its habitat and trophic ecology on a global scale via stable isotope analyses of a unique collection of beaks from 104 specimens from the Atlantic, Pacific and Indian Oceans. Cephalopods typically are active predators occupying a high trophic level (TL) and exhibit an ontogenetic increase in δ15N and TL. Our results, presenting the first global comparison for a deep-sea invertebrate, demonstrate that V. infernalis has an ontogenetic decrease in δ15N and TL, coupled with niche broadening. Juveniles are mobile zooplanktivores, while larger …

Temporal Variability Of Polycyclic Aromatic Hydrocarbons In Deep-Sea Cephalopods Of The Northern Gulf Of Mexico, Isabel C. Romero, Heather L. Judkins, Michael Vecchione

USF St. Petersburg campus Faculty Publications

As part of the effort to understand the effects of the Deepwater Horizon Oil Spill (DWHOS), we analyzed tissue from five species of midwater oceanic cephalopods in the northern Gulf of Mexico (GoM) during three time periods, including one period sampled fortuitously just before the spill (2010), and two periods sampled after the spill (2011 and 2015–2016). The species, Japetella diaphana, Abralia redfieldi, Histioteuthis corona, Leachia atlantica, and Onychoteuthis banksii were collected in three geographic areas in the GoM (east, south and southeast of the Macondo wellhead). Results indicate a shift in the composition of polycyclic aromatic hydrocarbons (PAHs) in …

Mir146a-Mediated Targeting Of Fancm During Inflammation Compromises Genome Integrity, Devakumar Sundaravinayagam, Hye Rim Kim, Tingting Wu, Hyun Hee Kim, Semo Jun, Jeong-Heon Cha, Younghoon Kee, Ho Jin You, Jung-Hee Lee

Molecular Biosciences Faculty Publications

Inflammation is a potent inducer of tumorigenesis. Increased DNA damage or loss of genome integrity is thought to be one of the mechanisms linking inflammation and cancer development. It has been suggested that NF-κB-induced microRNA-146 (miR146a) may be a mediator of the inflammatory response. Based on our initial observation that miR146a overexpression strongly increases DNA damage, we investigated its potential role as a modulator of DNA repair. Here, we demonstrate that FANCM, a component in the Fanconi Anemia pathway, is a novel target of miR146a. miR146a suppressed FANCM expression by directly binding to the 3’ untranslated region of the gene. …

Cornus Officinalis Promotes Igfbp2 And Autophagy In Human 1.1b4 Pancreatic Cell Line As Revealed By Employing A Global Proteomic Approach Via Mass Spectrometry, Arielle Elizabeth Tawfik, Jennifer Guergues, Stanley M. Stevens Jr, Brant Roger Burkhardt

Molecular Biosciences Faculty Publications

Type 1 diabetes (T1D) results in the loss of pancreatic beta cells and subsequent loss of insulin production. Exogenous insulin is the only effective treatment, but there is still no cure or interventional therapy available to inhibit progression of T1D. Successful T1D interventional therapy must protect pancreatic beta cells from autoimmunity while enhancing beta cell survival and function. Our data suggests Cornus officinalis (CO) may be a candidate for interventional therapy to protect pancreatic beta cells from autoimmune attack and increase their function. CO has been used in traditional Chinese medicine (TCM) for over 2,000 years and has shown characteristics …