Marine Biology Commons^™

Complete Bacterial Symbiont Genome Sequences From Anglerfish Cryptopsaras Couesii And Melanocetus Johnsonii, Lindsay L. Freed, Dana Fadera, Dante Fenolio, Tracey Sutton, Jose V. Lopez

DEEPEND Datasets

These are the complete bacterial symbiont genome sequences from anglerfish Cryptopsaras couesii (individual CC26) and one individual Melanocetus johnsonii. These data were generated and analyzed by the laboratory of Dr Tory Hendry (Cornell University). The full sequences of two symbiotic bacterial genomes have been submitted to public DDBJ/ENA/GenBank repositories under the accessions CP020660- CP020663 (CC26 Cryptopsaras couesii) and NBYY01000001-NBYY01000039 (Melanocetus johnsonii). The total genome size for each of the symbiont species is about 2-2.6 Mb.

Microbial And Genomic Analysis Of Environmental Samples In Search Of Pathogenic Salmonella, Jorie L. Skutas

HCNSO Student Theses and Dissertations

Salmonellosis or “food poisoning” is a foodborne infection brought on by the pathogen Salmonella from the ingestion of the bacterium on contaminated foods such as vegetables. Infection from Salmonella leads to the highest incidence of hospitalizations and deaths each year, compared to any other bacterial foodborne illness. South Florida is the second largest agricultural winter vegetable producer in the United States, and contamination of vegetables is often observed in preharvest practices. A hardy bacterium, Salmonella, has been shown to live up to 6 weeks in soil and water up to 42°C without a host.

The Florida Everglades is a tropical …

Seasonal Shifts In Bacterial Community Responses To Phytoplankton-Derived Dissolved Organic Matter In The Western Antarctic Peninsula, Catherine M. Luria, Linda A. Amaral-Zettler, Hugh W. Ducklow, Daniel J. Repeta, Andrew L. Rhyne, Jeremy J. Rich

Arts & Sciences Faculty Publications

Bacterial consumption of dissolved organic matter (DOM) drives much of the movement of carbon through the oceanic food web and the global carbon cycle. Understanding complex interactions between bacteria and marine DOM remains an important challenge. We tested the hypothesis that bacterial growth and community succession would respond differently to DOM additions due to seasonal changes in phytoplankton abundance in the environment. Four mesocosm experiments were conducted that spanned the spring transitional period (August-December 2013) in surface waters of the Western Antarctic Peninsula (WAP). Each mesocosm consisted of nearshore surface seawater (50 L) incubated in the laboratory for 10 days. …

Timing Anthropogenic Stressors To Mitigate Their Impact On Marine Ecosystem Resilience, Paul Pao-Yen Wu, Kerrie Mengersen, Kathryn Mcmahon, Gary A. Kendrick, Kathryn Chartrand, Paul H. York, Michael A. Rasheed, M. Julian Caley

Research outputs 2014 to 2021

Better mitigation of anthropogenic stressors on marine ecosystems is urgently needed to address increasing biodiversity losses worldwide. We explore opportunities for stressor mitigation using whole-of-systems modelling of ecological resilience, accounting for complex interactions between stressors, their timing and duration, background environmental conditions and biological processes. We then search for ecological windows, times when stressors minimally impact ecological resilience, defined here as risk, recovery and resistance. We show for 28 globally distributed seagrass meadows that stressor scheduling that exploits ecological windows for dredging campaigns can achieve up to a fourfold reduction in recovery time and 35% reduction in extinction risk. Although …

Dataset For: Toxicity And Mutagenicity Of The Gulf Of Mexico Waters During And After The Deepwater Horizon Oil Spill, July 2010-August 2013, Lauren Mcdaniel

C-IMAGE data

The dataset is representative of 20 research cruises spanning from July 2010 to August 2013 in the North and West Florida Shelf regions of the Gulf of Mexico. This dataset reports microtoxicity data from each site and is an extension and revision of C-IMAGE I dataset R1.x135.119:0005. The North Florida Self data also contains PAH measurements for three cruises (12/6/2010, 12/15/2011, 8/6/2013).

Species-Specific Metabolism Of Naphthalene And Phenanthrene In 3 Species Of Marine Teleosts Exposed To Deepwater Horizon Crude Oil, Erin Pulster, Kevan Main, Dana Wetzel, Steven Murawski

C-IMAGE Publications

The 2 most abundant polycyclic aromatic hydrocarbons (PAHs) measured in Deepwater Horizon crude oil, naphthalene and phenanthrene, and their associated homologs have both been shown to be acutely toxic in fish. Although fish have a relatively high metabolic capacity for PAHs, hydroxylated PAH (OH-PAH) derivatives formed during the initial metabolic response can negatively impact the health of fish. Species-specific metabolism of naphthalene and phenanthrene was evaluated in 3 marine teleosts, red drum (Scianops ocellatus), Florida pompano (Trachinotus carolinus), and southern flounder (Paralichthys lethostigma). Fish were exposed to Deepwater Horizon crude oil by intraperitoneal injections at time 0 and 48 h, …

Validating Sidescan Sonar As A Fish Survey Tool Over Artificial Reefs, Michael A. Bollinger, Richard Kline

School of Earth, Environmental, & Marine Sciences Faculty Publications

Visual observation methods via SCUBA are commonly used to survey artificial reef fish, although conditions in the Gulf of Mexico often make surveys difficult or even dangerous for divers. In this study, sidescan sonar was used to quantify water-column fish abundance and was compared to the established visual observation methods on SCUBA over four reef sites. Calibrated intensity values measured from sidescan sonar echo returns were used to estimate fish body length and to calculate scaled biomass (g/m2 reef) from a pooled fish length–weight relationship of commonly observed reef fish in the area. Sidescan sonar methods were equivalent to SCUBA …

Composition And Quantification Of Polycyclic Aromatic Hydrocarbons In Deep-Pelagic Fauna. Cruises Dp02, Dp03, And Dp04 From August 2015 - August 2016, Isabel C. Romero

DEEPEND Datasets

Samples were collected in the northern Gulf of Mexico on cruises DP02, DP03 and DP04 from August 2015 - August 2016. Polycyclic Aromatic Hydrocarbons (PAH) data were integrated with those from population dynamics and stable isotope analysis to provide evidence for effects of oil exposure to deep pelagic communities. The target fish species include Argyropelecus spp., Ceratoscopelus warmingii, Chauliodus sloani, Diaphus spp., Lampanyctus alatus, Lepidophanes guentheri, and Sigmops elongatus. Analysis of PAHs was conducted on different fish tissues (muscle, guts, gills, and eggs) following modified EPA method 8270D and QA/QC strict protocols. Detection and quantification of PAH homologues was performed …

Sun Glint Critical Angle Oil Detection, Shaojie Sun

C-IMAGE data

This dataset includes two MODIS L1B images and the generated sun glint reflectance (LGN) data after atmospheric correction. LGN was also modeled for the two images according to the sun/view geometry, oil and water fresnel reflection. This dataset introduced atmospheric correction and different oil fresnel reflection with water in the calculation of sun glint reflectance from MODIS imagery. By doing this, the calculated sun glint reflectance results are more accurate and the original concept of sun glint critical angle is refined.

Emerging Hotspot Analysis Of Florida Manatee (Trichechus Manatus Latirostris) Mortality (1974-2012), Crystal Ann Bass

HCNSO Student Theses and Dissertations

The Florida manatee (Trichechus manatus latirostris) is a protected species that is vulnerable to both anthropogenic and natural causes of mortality. The ability of wildlife managers to oversee regulation of this species is based on available abundance estimates and mortality data. Using existing manatee mortality data collected by Florida Fish and Wildlife Conservation Commission (FWC) from 1974-2012, this study focuses on identifying significant spatial clusters of high values or “hotspots” of manatee mortality and the temporal patterns of these hotspots using the novel “emerging hotspot analysis” ArcGIS tool. The categories of manatee mortality included in this analysis were …

Anaerobic Oxidation Of Ethane, Propane, And Butane By Marine Microbes: A Mini Review, Rajesh Singh, Michael S. Guzman, Arpita Bose

Biology Faculty Research

The deep ocean and its sediments are a continuous source of non-methane short-chain alkanes (SCAs) including ethane, propane, and butane. Their high global warming potential, and contribution to local carbon and sulfur budgets has drawn significant scientific attention. Importantly, microbes can use gaseous alkanes and oxidize them to CO₂, thus acting as effective biofilters. A relative decrease of these gases with a concomitant ¹³C enrichment of propane and n-butane in interstitial waters vs. the source suggests microbial anaerobic oxidation. The reported uncoupling of sulfate-reduction (SR) from anaerobic methane oxidation supports their microbial consumption. To date, strain …

Fish Exposure Studies: Associated Water, Sediment And Food Microbiology And Mutagenic Potential, Lauren Mcdaniel

C-IMAGE data

As part of an ongoing assessment of the long-term impacts of oil and dispersants on ecosystem health experiments were performed to examine the effects of exposure on different species of fish and varying routes of exposure. As a part of this study we directly assessed the mutagenic potential of the contaminated treatments as well as the surrounding environment in which the fish were contained. For these assessments we used the biologically based assay of DNA damage termed the Microscreen Assay. General microbiological parameters including total viral and bacterial counts and culturable bacterial counts were also measured. Fish experiment data are …

Development Of A Marine Compatible Biological Assay For Mutagenic Compounds, Lauren Mcdaniel

C-IMAGE data

One of the primary negative effects of environmental oil exposure is the potential for mutagenic, or DNA damaging effects. This can lead to heritable genetic damage in higher organisms with long-term environmental impact. The biological effect of contamination is difficult to estimate on the basis of chemical profiles due to the complexity of environmental samples. Thus, biologically based assays give a closer approximation of the actual ecological impacts of contamination. To measure the mutagenic or DNA damaging potential of samples we currently utilize the Microscreen Assay, which is based upon a strain of Escherichia coli that is sensitive to mutagenic …

Capturing Species-Level Drought Responses In A Temperate Deciduous Forest Using Ratios Of Photochemical Reflectance Indices Between Sunlit And Shaded Canopies, Taehee Hwang, Hamed Gholizadeh, Daniel A. Sims, Kimberly A. Novick, Edward R. Brzostek, Richard P. Phillips, Daniel T. Roman, Scott M. Robeson, Abdullah F. Rahman

School of Earth, Environmental, & Marine Sciences Faculty Publications

Highlights

• We examine capability of spectral indices to capture isohydric/anisohydric behavior.

• We used both in-situ spectral measurements and multi-angle MODIS images.

• Only PRI could capture species-level drought responses.

• This study presents a step forward to directly mapping emergent isohydricity.

Abstract

To classify trees along a spectrum of isohydric to anisohydric behavior is a promising new framework for identifying tree species' sensitivities to drought stress, directly related to the vulnerability of carbon uptake of terrestrial ecosystems with increased hydroclimate variability. Trees with isohydric strategies regulate stomatal conductance to maintain stationary leaf water potential, while trees with anisohydric strategies allow leaf …

Effects Of A Beach Nourishment Project In Jamaica Bay, New York, On Horseshoe Crab (Limulus Polyphemus) Spawning Activity And Egg Deposition, Christina P. Colon

Publications and Research

Restoration of horseshoe crab spawning habitats through beach nourishment may be considered as a potential strategy to enhance reproductive success in areas where estuarine beaches have been lost to coastal erosion and development. The US Army Corps of Engineers performed a beach nourishment project at Plumb Beach (Jamaica Bay, Brooklyn, NY) in 2012 to stabilize the shoreline. While the addition of sand was done to protect infrastructure, it created an opportunity to examine the responses of American horseshoe crabs (Limulus polyphemus) to beach nourishment using a BACI (before-after control impact) design. During Spring 2012, be fore beach nourishment, horseshoe crabs …

The Utility Of Bioenergetics Modelling In Quantifying Predation Rates Of Marine Apex Predators: Ecological And Fisheries Implications, A. Barnett, M. Braccini, C. L. Dudgeon, N. L. Payne, K. G. Abrantes, M. Sheaves, E. P. Snelling

Fisheries Research Articles

Predators play a crucial role in the structure and function of ecosystems. However, the magnitude of this role is often unclear, particularly for large marine predators, as predation rates are difficult to measure directly. If relevant biotic and abiotic parameters can be obtained, then bioenergetics modelling offers an alternative approach to estimating predation rates, and can provide new insights into ecological processes. We integrate demographic and ecological data for a marine apex predator, the broadnose sevengill shark Notorynchus cepedianus, with energetics data from the literature, to construct a bioenergetics model to quantify predation rates on key fisheries species in …

Nitrate Leaching From Sand And Pumice Geomedia Amended With Pyrogenic Carbon Materials, James Jihoon Kang, Marissa Davila, Sergio Mireles, Jungseok Ho

School of Earth, Environmental, & Marine Sciences Faculty Publications

There is increasing interest in using pyrogenic carbon as an adsorbent for aqueous contaminants in stormwater. The objective of this study was to investigate pyrogenic carbon materials as an amendment to geomedia to reduce nitrate leaching. Batch adsorption and column experiments were conducted to evaluate the performance of a commercial activated carbon and two biochars incorporated (5% by weight) into sand and pumice columns. The batch adsorption with 50 mg L−1 of nitrate solution showed that only activated carbon resulted in a substantial adsorption for nitrate up to 41%. Tested biochars were not effective in removing aqueous nitrate and even …

Dietary Transfer Of Heavy Metals In Manatees, E. M. Smith, Dimitri Giarikos, A. Daniels, Amy Hirons

Chemistry and Physics Faculty Proceedings, Presentations, Speeches, Lectures

In recent decades, manatees and dugongs globally have exhibited potentially detrimental levels of a variety of heavy metals in their body tissues. The threatened Florida manatee (Trichechus manatus latirostris), which is a subspecies of the West Indian manatee (Trichechus manatus), has shown corresponding high levels of heavy metals in their blood, skin, liver, and kidneys. As obligate herbivores, these animals rely heavily upon seagrasses as a major component of their diet. Globally, seagrasses at low latitudes have high levels of heavy metals in their tissues. Detrimental levels of heavy metals in Sirenians have not been established …

North Pacific Marine Mammals Populations Rocked By Heavy Metal Concentrations, Pilar Ferdinando, Chitra Gotluru, Tanya Juneja, Kevin Cash, Karanja Sekou, Emily Pope, L. K. Duffy, Dimitri Giarikos, Amy Hirons

Chemistry and Physics Faculty Proceedings, Presentations, Speeches, Lectures

No abstract provided.

A Comparison Of The Rate Of Oxygen Store Development In Phocid Sealsq, Rachael Stevenson, Tamara Frank, Amy Hirons

Marine & Environmental Sciences Faculty Proceedings, Presentations, Speeches, Lectures

No abstract provided.

Peruvian Pinnipeds As Archivist Of Enso Effects Off The Coast Of Peru, Mickie Edwards, Michael Adkesson, Susana Cardenas-Alayza, Amy Hirons

Marine & Environmental Sciences Faculty Proceedings, Presentations, Speeches, Lectures

No abstract provided.

Coral Species Distribution And Percent Cover Of Sessile Organisms On Protected And Non-Protected Coral Reefs In Digir, Buga, Dubbir, And Kanir Kinnidup, Guna Yala, Panama, Sarah Paulson

Independent Study Project (ISP) Collection

Coral reefs are the most productive, biodiverse ecosystems in the ocean despite covering only <.5% of the ocean floor. In today’s changing climate, coral reefs face a multitude of threats including ocean warming, coral bleaching, ocean acidification, overfishing, increasing human population, and coral mining, among others. One way to protect coral reefs is to establish a marine protected area to limit damage and contamination. This study aimed to examine coral species distribution as well as percent cover of sessile organisms and substrates including coral, fire coral, algae, and sponges on protected and non-protected reefs in order to attempt to analyze the effect of protection on coral reefs in Guna Yala, Panama. Based on the data collected, protected areas had higher algae cover (P<.01, df=107), lower coral cover (P<.0001, df=138), and a higher relative abundance of corals with a “weedy” life history such as Porites astreoides (P<.05, df=80). The data also showed that uninhabited islands tended to have significantly higher average coral cover (P<.0001, df=146) and lower average algae cover (P<.0001, df=161), as well as lower relative abundance of P. astreoides (P<.01, df=134). When the protected site sampled was compared to an unprotected site that was around the same island, the protected area was found to have higher coral cover (P<.01, df=71) and lower algae cover (P<.05, df=72) than the unprotected area. Ultimately, lack of human population and protected status were found to be positive factors for coral reef health, and future study should be done to further examine the relationship between these two factors.

Counting Crabs: Assessment Of Mangrove Crab Diversity And Density Among Three Sites In Ushongo, Tanzania, Clarasophia Gust

Independent Study Project (ISP) Collection

This study assessed the density and diversity of crabs across three mangrove forest zones in Ushongo, Tanzania. The aim was to understand variance in the composition and distribution of mangrove crabs in relation to mangrove tree composition gradients in the area. Sites were measured using a 200m line transect and 40-plot method. Data was also collected from a sand beach habitat to compare to the diversity and distribution of mangrove habitats. Diversity was analyzed using Simpson’s Index of Diversity and an ANOVA test on the average number of species found per plot in each site. Density was analyzed using an …

The Sponge Microbiome Project, Lucas Moitinho-Silva, Shaun Nielsen, Amnon Amir, Antonio Gonzalez, Gail Ackermann, Carlo Cerrano, Carmen Astudillo-Garcia, Cole Easson, Detmer Sipkema, Fang Liu, Georg Steinert, Giorgos Kotoulas, Grace Mccormack, Guofang Feng, James J. Bell, Jan Vicente, Johannes R. Bjork, Jose M. Montoya, Julie B. Olson, Julie Reveillaud, Laura Steindler, Mari-Carmen Pineda, Maria V. Marra, Micha Ilan, Michael W. Taylor, Paraskevi Polymenakou, Patrick M. Erwin, Peter J. Schupp, Rachel L. Simister, Rob Knight, Robert W. Thacker, Rodrigo Costa, Russell T. Hill, Susanna Lopez-Legentil, Thanos Dailianis, Timothy Ravasi, Ute Hentschel, Zhiyong Li, Nicole S. Webster, Torsten Thomas

Marine & Environmental Sciences Faculty Articles

Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other …

Life History And Management Methods For Blueline Tilefish (Caulolatilus Microps) From The United States Mid-Atlantic Region, Michael A. Schmidtke

OES Theses and Dissertations

Blueline tilefish (Caulolatilus microps) have recently undergone an increase in landings from waters off the US Mid-Atlantic region (Virginia-Massachusetts). Currently, life history characteristics of blueline tilefish in this area are undescribed. Additionally, appropriate indices of population abundance are not available for this region, necessitating the use of data-limited management methods to set restrictions for harvest of blueline tilefish in this area. This dissertation describes growth and reproductive characteristics of blueline tilefish caught off the coast of Virginia and explores improvements of data-limited management methods that have been applied to blueline tilefish in the US Mid-Atlantic. Blueline tilefish from …

Bottom-Up Control Of Parasites, David S. Johnson, Richard W. Heard

Faculty Publications

Parasitism is a fundamental ecological interaction. Yet we understand relatively little about the ecological role of parasites compared to the role of free-living organisms. Bottom-up theory predicts that resource enhancement will increase the abundance and biomass of free-living organisms. Similarly, parasite abundance and biomass should increase in an ecosystem with resource enhancement. We tested this hypothesis in a landscape-level experiment in which salt marshes (60,000 m2 each) received elevated nutrient concentrations via flooding tidal waters for 11 yr to mimic eutrophication. Nutrient enrichment elevated the densities of the talitrid amphipod, Orchestia grillus, and the density and biomass of its trematode …

Prey Naïveté And Predator-Prey Interactions Between Pterois Volitans, Pomacentridae, And Tetraodontidae In Two Reefs In The Guna Yala Archipelago, Panama, Jesse Garrett-Larsen

Independent Study Project (ISP) Collection

The invasion of Pterois volitans along the Atlantic coast of the Americas is one of the top marine conservation issues of the century. Prey naïveté has been suggested as a mechanism for the success of P. volitans, but conclusive field observations have not been completed. This study tested for prey naïveté in situ by comparing time spent by Pomacentridae and Tetraodontidae in close proximity to P. volitans and a native predator, Cephalopholis cruentata. Difference in time spent by Pomacentridae and Tetraodontidae in the presence of the two predators was observed. The predators P. volitans and C. cruentata were sequentially observed …

A Novel Diffuse Fraction-Based Two-Leaf Light Use Efficiency Model: An Application Quantifying Photosynthetic Seasonality Across 20 Ameriflux Flux Tower Sites, Hao Yan, Shao-Qiang Wang, Kai-Liang Yu, Bin Wang, Qin Yu, Gil Bohrer, Dave Billesbach, Rosvel Bracho, Abdullah F. Rahman, Herman H. Shugart

School of Earth, Environmental, & Marine Sciences Faculty Publications

Diffuse radiation can increase canopy light use efficiency (LUE). This creates the need to differentiate the effects of direct and diffuse radiation when simulating terrestrial gross primary production (GPP). Here, we present a novel GPP model, the diffuse-fraction-based two-leaf model (DTEC), which includes the leaf response to direct and diffuse radiation, and treats maximum LUE for shaded leaves (ɛmsh defined as a power function of the diffuse fraction (Df)) and sunlit leaves (ɛmsu defined as a constant) separately. An Amazonian rainforest site (KM67) was used to calibrate the model by simulating the linear relationship …

Linear And Nonlinear Effects Of Temperature And Precipitation On Ecosystem Properties In Tidal Saline Wetlands, Laura C. Feher, Michael J. Osland, Kereen T. Griffith, James B. Grace, Rebecca J. Howard, Camille L. Stagg, Nicholas M. Enwright, Ken W. Krauss, Christopher A. Gabler, Richard H. Day, Kerrylee Rogers

School of Earth, Environmental, & Marine Sciences Faculty Publications

Climate greatly influences the structure and functioning of tidal saline wetland ecosystems. However, there is a need to better quantify the effects of climatic drivers on ecosystem properties, particularly near climate-sensitive ecological transition zones. Here, we used climate- and literature-derived ecological data from tidal saline wetlands to test hypotheses regarding the influence of climatic drivers (i.e., temperature and precipitation regimes) on the following six ecosystem properties: canopy height, biomass, productivity, decomposition, soil carbon density, and soil carbon accumulation. Our analyses quantify and elucidate linear and nonlinear effects of climatic drivers. We quantified positive linear relationships between temperature and above-ground productivity …

You, Me And Life In The Sea Ocg 106g, Joanna Burkhardt

Library Impact Statements

No abstract provided.