Influence Of Structural Complexity And Location On The Habitat Value Of Restored Oyster Reefs, 2016 College of William and Mary
Influence Of Structural Complexity And Location On The Habitat Value Of Restored Oyster Reefs, Melissa Ann Karp
Dissertations, Theses, and Masters Projects
In the Chesapeake Bay, < 1% of the historic oyster population remains, and efforts have been increasing to restore oysters and the services they provide. Building reefs that successfully provide ecosystem services–especially habitat and foraging grounds–may require different restoration techniques than those previously used, and success may depend on reef morphology (complexity), location, and environmental conditions. Salinity and habitat complexity are two important factors that may interact to effect benthic communities and predator-prey interactions on restored reefs. The goals of this project were: (1) Characterize the benthic communities on restored oyster reefs in lower Chesapeake Bay, and (2) examine the effects of structural complexity and salinity on benthic communities and predator-prey interactions. A two-year field survey of restored reefs was carried out in four rivers in lower Chesapeake Bay to characterize faunal communities on restored reefs and to quantify the effect of reef complexity on faunal communities. A laboratory mesocosm experiment was conducted to examine the effect of reef complexity on predator foraging. In total, 61 macrofaunal species were identified among all samples, and restored reefs supported on average, 6,169 org/m2 and 67.88 g-AFDW/m2. There were significant differences in the community composition and diversity among the rivers, and salinity was the environmental factor that best explained the observed differences in species composition across the rivers. Salinity and rugosity (i.e., structural complexity) both positively affected diversity, while salinity negatively affected macrofaunal abundance and biomass. Oyster density and rugosity positively affected macrofaunal biomass, and oyster density positively affected mud crab, polychaete, and mussel densities. In the mesocosm experiment, predator foraging, measured by proportion and number of prey consumed, was significantly reduced in the presence of oyster shell structure. However, predators were able to consume more prey when prey density was increased, even in the presence of oyster shell structure. These results combine to enhance our understanding of the benefits of increased habitat complexity for both prey and predators on restored oyster reefs. Increasing complexity worked to increase the abundance, biomass, and diversity of organisms inhabiting restored reefs, and even though predator consumption was reduced in the presence of structure compared to non-structured habitat, predators were able to consume more prey individuals when prey density was increased. Therefore, increasing the structure of oyster reef habitat may benefit prey species by providing refuge habitat, and benefit predators by providing an increased abundance of available prey items.
How The Bending Kinematics Of Swimming Lampreys Build Negative Pressure Fields For Suction Thrust, 2016 University of South Florida
How The Bending Kinematics Of Swimming Lampreys Build Negative Pressure Fields For Suction Thrust, Brad J. Gemmell, Stephanie M. Fogerson, John H. Costello, Jennifer R. Morgan, John O. Dabiri, Sean P. Colin
Integrative Biology Faculty and Staff Publications
Swimming animals commonly bend their bodies to generate thrust. For undulating animals such as eels and lampreys, their bodies bend in the form of waves that travel from head to tail. These kinematics accelerate the flow of adjacent fluids, which alters the pressure field in a manner that generates thrust. We used a comparative approach to evaluate the cause-and-effect relationships in this process by quantifying the hydrodynamic effects of body kinematics at the body-fluid interface of the lamprey, Petromyzon marinus, during steady-state swimming. We compared the kinematics and hydrodynamics of healthy control lampreys to lampreys whose spinal cord had been …
Patterns Of Transcript Abundance Of Eukaryotic Biogeochemically-Relevant Genes In The Amazon River Plume, 2016 University of South Florida
Patterns Of Transcript Abundance Of Eukaryotic Biogeochemically-Relevant Genes In The Amazon River Plume, Brian L. Zielinski, Andrew E. Allen, Edward J. Carpenter, Victoria J. Coles, Byron C. Crump, Mary Doherty, Rachel A. Foster, Joaquim I. Goes, Helga R. Gomes, Raleigh R. Hood, John P. Mccrow, Joseph P. Montoya, Ahmed Moustafa, Brandon M. Satinsky, Shalabh Sharma, Christa B. Smith, Patricia L. Yager, John H Paul
Marine Science Faculty Publications
The Amazon River has the largest discharge of all rivers on Earth, and its complex plume system fuels a wide array of biogeochemical processes, across a large area of the western tropical North Atlantic. The plume thus stimulates microbial processes affecting carbon sequestration and nutrient cycles at a global scale. Chromosomal gene expression patterns of the 2.0 to 156 μm size-fraction eukaryotic microbial community were investigated in the Amazon River Plume, generating a robust dataset (more than 100 million mRNA sequences) that depicts the metabolic capabilities and interactions among the eukaryotic microbes. Combining classical oceanographic field measurements with metatranscriptomics yielded …
A Highly Sensitive Underwater Video System For Use In Turbid Aquaculture Ponds, 2016 Old Dominion University
A Highly Sensitive Underwater Video System For Use In Turbid Aquaculture Ponds, Chin-Chang Hung, Shih-Chieh Tsao, Kuo-Hao Huang, Hsu-Kunag Chang, Fred C. Dobbs
OES Faculty Publications
The turbid, low-light waters characteristic of aquaculture ponds have made it difficult or impossible for previous video cameras to provide clear imagery of the ponds' benthic habitat. We developed a highly sensitive, underwater video system (UVS) for this particular application and tested it in shrimp ponds having turbidities typical of those in southern Taiwan. The system's high-quality video stream and images, together with its camera capacity (up to nine cameras), permit in situ observations of shrimp feeding behavior, shrimp size and internal anatomy, and organic matter residues on pond sediments. The UVS can operate continuously and be focused remotely, a …
The Contribution Of Marine Aggregate-Associated Bacteria To The Accumulation Of Pathogenic Bacteria In Oysters: An Agent-Based Model, 2016 Old Dominion University
The Contribution Of Marine Aggregate-Associated Bacteria To The Accumulation Of Pathogenic Bacteria In Oysters: An Agent-Based Model, Andrew M. Kramer, J. Evan Ward, Fred C. Dobbs, Melissa L. Pierce
OES Faculty Publications
Bivalves process large volumes of water, leading to their accumulation of bacteria, including potential human pathogens (e.g., vibrios). These bacteria are captured at low efficiencies when freely suspended in the water column, but they also attach to marine aggregates, which are captured with near 100% efficiency. For this reason, and because they are often enriched with heterotrophic bacteria, marine aggregates have been hypothesized to function as important transporters of bacteria into bivalves. The relative contribution of aggregates and unattached bacteria to the accumulation of these cells, however, is unknown. We developed an agent-based model to simulate accumulation of vibrio-type bacteria …
You Can't Catch A Fish With A Robot, 2016 ECOS
You Can't Catch A Fish With A Robot, R. Grant Gilmore Jr.
Gulf and Caribbean Research
Abstract
In this essay I will relate the challenges associated with deep sea ocean exploration as well as the advantages and disadvantages of today’s ocean technologies based on experience with most of these systems. After nearly five decades using robotic vehicles (Remotely Operated Vehicles = ROVs and Autonomous Underwater Vehicles = AUVs) and manned submarines for fish research, I thought it would be appropriate to briefly describe a career spent using these technologies as they were developed. Deep sea ichthyologists cannot effectively catch a swimming fish with a robot even 40 years after the development of the first ROV for …
Isolation And Identification Of Bacterial Endosymbionts In The Brooding Brittle Star Amphipholis Squamata, 2016 University of New Hampshire - Main Campus
Isolation And Identification Of Bacterial Endosymbionts In The Brooding Brittle Star Amphipholis Squamata, Abbey Rose Tedford
Honors Theses and Capstones
Symbiotic associations with subcuticular bacteria (SCB) have been identified and studied in numerous echinoderms, including the SCB of the brooding brittle star, Amphipholis squamata. These SCB, however, have not been studied using current next generation sequencing technologies. Previous studies on the SCB of A. squamata placed these bacteria in the genus Vibrio (γ-Proteobacteria), but subsequent studies suggested that the SCB are primarily composed of α-Proteobacteria. The present study examines the taxonomic composition of SCB associated with A. squamata from the Northwest Atlantic. DNA was extracted using a CTAB protocol and 16S rRNA sequences were amplified …
Attached Algae As An Indicator Of Water Quality: A Study Of The Viability Of Genomic Taxonomic Methods, 2016 University of New Hampshire, Durham
Attached Algae As An Indicator Of Water Quality: A Study Of The Viability Of Genomic Taxonomic Methods, Allison R. Wood
Honors Theses and Capstones
This research involved evaluating algae as an indicator of water quality in New Hampshire's rivers, with a focus on the Great Bay Estuary. The project had three main goals. First, determining whether or not algae would work as an indicator of water quality in the great bay ecosystem, an environment where tidal currents are strong and water composition is mixed. The second goal was to compare traditional microscopic methods of taxonomy with emerging genomic methods, increasing the economic viability of attached algae monitoring. The third project goal, still underway, is to evaluate massive amounts of genomic data from the Great …
Responses Of Antarctic Marine And Freshwater Ecosystems To Changing Ice Conditions, 2016 Virginia Institute of Marine Science
Responses Of Antarctic Marine And Freshwater Ecosystems To Changing Ice Conditions, Mk Obryk, Pt Doran, Et Al, Deborah K. Steinberg, Hw Ducklow
VIMS Articles
Polar regions are warming more rapidly than lower latitudes, and climate models predict that this trend will continue into the coming decades. Despite these observations and predictions, relatively little is known about how polar ecosystems have responded and will continue to respond to this change. Two Long-Term Ecological Research (LTER) sites, located in contrasting environments in Antarctica, have been studying marine and aquatic terrestrial ecosystems for more than two decades. We use data from these research areas to show that the extent and thickness of ice covers are highly sensitive to short- and long-term climate variation and that this variation …
Themed Issue Article: Conservation Physiology Of Marine Fishes Fisheries Conservation On The High Seas: Linking Conservation Physiology And Fisheries Ecology For The Management Of Large Pelagic Fishes, 2016 Virginia Institute of Marine Science
Themed Issue Article: Conservation Physiology Of Marine Fishes Fisheries Conservation On The High Seas: Linking Conservation Physiology And Fisheries Ecology For The Management Of Large Pelagic Fishes, Andrij Z. Horodysky, Steven J. Cooke, John Graves, Richard Brill
VIMS Articles
Populations of tunas, billfishes and pelagic sharks are fished at or over capacity in many regions of the world. They are captured by directed commercial and recreational fisheries (the latter of which often promote catch and release) or as incidental catch or bycatch in commercial fisheries. Population assessments of pelagic fishes typically incorporate catch-per-unit-effort time-series data from commercial and recreational fisheries; however, there have been notable changes in target species, areas fished and depth-specific gear deployments over the years that may have affected catchability. Some regional fisheries management organizations take into account the effects of time-and area-specific changes in the …
Short-Term Habitat Use Of Juvenile Atlantic Bluefin Tuna, 2016 Virginia Institute of Marine Science
Short-Term Habitat Use Of Juvenile Atlantic Bluefin Tuna, Benjamin J. Marcek, Mary C. Fabrizio, John Graves
VIMS Articles
Bluefin Tuna Thunnus thynnus are highly sought after in commercial and recreational fisheries along the East Coast of North America. To appropriately assess and manage Atlantic Bluefin Tuna (ABT), it is necessary to understand their habitat use during multiple ontogenetic stages. We tagged 17 juvenile ABT in the northwest Atlantic Ocean with pop-up satellite archival tags (PSATs) to determine environmental factors that may affect habitat use. The PSATs were deployed off the coast of Massachusetts in August and September 2012. A generalized linear mixed model was applied to determine factors affecting the mean depth occupied by fish, and beta regression …
The Kinome Of Pacific Oyster Crassostrea Gigas, Its Expression During Development And In Response To Environmental Factors, 2016 Virginia Institute of Marine Science
The Kinome Of Pacific Oyster Crassostrea Gigas, Its Expression During Development And In Response To Environmental Factors, Yanouk Epelboin, Laure Quintric, Eric Guevelou, Pierre Boudry, Vianney Pichereau, Charlotte Corporeau
VIMS Articles
Oysters play an important role in estuarine and coastal marine habitats, where the majority of humans live. In these ecosystems, environmental degradation is substantial, and oysters must cope with highly dynamic and stressful environmental constraints during their lives in the intertidal zone. The availability of the genome sequence of the Pacific oyster Crassostrea gigas represents a unique opportunity for a comprehensive assessment of the signal transduction pathways that the species has developed to deal with this unique habitat. We performed an in silico analysis to identify, annotate and classify protein kinases in C. gigas, according to their kinase domain taxonomy …
Potential Drivers Of Virulence Evolution In Aquaculture, 2016 Virginia Institute of Marine Science
Potential Drivers Of Virulence Evolution In Aquaculture, David A. Kennedy, Gael Kurath, Ilana L. Brito, Maureen K. Purcell, Andrew F. Read, James R. Winton, Ar Wargo
VIMS Articles
Infectious diseases are economically detrimental to aquaculture, and with continued expansion and intensification of aquaculture, the importance of managing infectious diseases will likely increase in the future. Here, we use evolution of virulence theory, along with examples, to identify aquaculture practices that might lead to the evolution of increased pathogen virulence. We identify eight practices common in aquaculture that theory predicts may favor evolution toward higher pathogen virulence. Four are related to intensive aquaculture operations, and four others are related specifically to infectious disease control. Our intention is to make aquaculture managers aware of these risks, such that with increased …
Why Biodiversity Is Important To The Functioning Of Real-World Ecosystems, 2016 Virginia Institute of Marine Science
Why Biodiversity Is Important To The Functioning Of Real-World Ecosystems, Da Siegel, Ko Buessler, Et Al, Deborah K. Steinberg
VIMS Articles
Ocean ecosystems play a critical role in the Earth's carbon cycle and the quantification of their impacts for both present conditions and for predictions into the future remains one of the greatest challenges in oceanography. The goal of the EXport Processes in the Ocean from Remote Sensing (EXPORTS) Science Plan is to develop a predictive understanding of the export and fate of global ocean net primary production (NPP) and its implications for present and future climates. The achievement of this goal requires a quantification of the mechanisms that control the export of carbon from the euphotic zone as well as …
Influence Of Increased Sediment Exposure On Suspension-Feeder Assemblages In A Temperate Seagrass Meadow, 2016 Edith Cowan University
Influence Of Increased Sediment Exposure On Suspension-Feeder Assemblages In A Temperate Seagrass Meadow, Pierre Bouvais
Theses: Doctorates and Masters
The impact of increased sediment exposure on coastal marine ecosystems is one of the most important contemporary environmental issues. Sediment exposure is defined as the concentrations of sediment particles suspended in the water column and the amount of sediment depositing on the seabed. In addition to natural events, such as land erosion, rainfall, and tidal currents, anthropogenic activities such as land use, road building, logging, mining, port maintenance and dredging, contribute to the discharge of a great amount of sediment in the water column. As sessile suspension-feeder assemblages play a critical role in marine ecosystems through their active transfers of …
Gene Flow And Genetic Structure Of The Seagrass Thalassia Hemprichii In The Indo-Australian Archipelago, 2016 Edith Cowan University
Gene Flow And Genetic Structure Of The Seagrass Thalassia Hemprichii In The Indo-Australian Archipelago, Udhi Eko Hernawan
Theses: Doctorates and Masters
How genetic variation is distributed across space (genetic structure) and what factors influence the spatial genetic structuring is one of the primary questions in population genetics. The interaction between species biology (e.g. life-history traits) and physical processes operating in the seascape over time, including palaeo-historical events (e.g. sea level fluctuations) and contemporary processes (e.g. ocean currents), have been predicted to influence the extent of gene flow and the spatial genetic structuring in marine organisms. However, the relative contribution of each factor in governing the genetic pattern remains unclear. This study examined the pattern of genetic structure and the factors influencing …
Foundation Species Identity And Trophic Complexity Affect Experimental Seagrass Communities, 2016 Virginia Institute of Marine Science
Foundation Species Identity And Trophic Complexity Affect Experimental Seagrass Communities, Althea F. P. Moore, J. Emmett Duffy
VIMS Articles
The abundance and species composition of marine foundation species is changing due to range expansion or contraction, with potentially important ecosystem-level consequences. In Chesapeake Bay, USA, warming is likely to favor the more heat and stress-tolerant Ruppia maritima (widgeongrass) over Zostera marina (eelgrass). Because of the key role of seagrasses in providing habitat and trophic support, it is important to determine whether the more stress-tolerant seagrass provides similar ecological functions to the species it may replace. We addressed how trophic control differs between communities associated with the 2 seagrass species in a mesocosm experiment. Grazing of epiphytic algae can benefit …
Seasonal Shifts In The Movement And Distribution Of Green Sea Turtles Chelonia Mydas In Response To Anthropogenically Altered Water Temperatures, 2016 Virginia Institute of Marine Science
Seasonal Shifts In The Movement And Distribution Of Green Sea Turtles Chelonia Mydas In Response To Anthropogenically Altered Water Temperatures, Daniel P. Crear, Daniel D. Lawson, Jeffrey A. Seminoff, Et Al
VIMS Articles
Anthropogenically altered water temperatures (AAWT) have the potential to affect the movement and distribution of marine ectothermic species. Green sea turtles (GSTs) Chelonia mydas are an ectothermic species observed inhabiting 2 sites with AAWT at the northern point of their geographical range in the eastern Pacific. An acoustic receiver array was deployed with temperature loggers at the San Gabriel River, Long Beach, CA, where 2 power plants discharge warm water into the river, and at the 7th St. Basin, Seal Beach, CA, a dredged shallow basin with warmer water compared to surrounding coastal habitats during the summer months. Juvenile GSTs …
Vertical Movements Of Shortfin Mako Sharks Isurus Oxyrinchus In The Western North Atlantic Ocean Are Strongly Influenced By Temperature, 2016 Virginia Institute of Marine Science
Vertical Movements Of Shortfin Mako Sharks Isurus Oxyrinchus In The Western North Atlantic Ocean Are Strongly Influenced By Temperature, Jeremy J. Vaudo, Bradley M. Wetherbee, Anthony D. Wood, Kevin C. Weng, Et Al
VIMS Articles
Although shortfin mako sharks Isurus oxyrinchus are regularly encountered in pelagic fisheries, limited information is available on their vertical distribution and is primarily restricted to cooler areas of their geographic range. We investigated the vertical movements of mako sharks across differing temperature regimes within the western North Atlantic by tagging 8 individuals with pop-up satellite archival tags off the northeastern United States and the Yucatan Peninsula, Mexico. Depth and temperature records across 587 d showed vertical movements strongly associated with ocean temperature. Temperatures150 m compared to only 1% in the coldest water columns. The sharks showed diel diving behavior, with …
Out Of The Tower And Into The Classroom Or How Classroom Partnerships Give Marine Science Grad Students An Edge, 2016 Virginia Institute of Marine Science
Out Of The Tower And Into The Classroom Or How Classroom Partnerships Give Marine Science Grad Students An Edge, Carol Hopper Brill
VIMS Articles
Ocean science graduate students face a challenge. They must prepare for two careers: research scientist and communication specialist. Successful researchers have to be creative, innovative, and competitive within their disciplines in order to promote their work and build collaborations among their peers. But, the higher stakes surrounding current environmental concerns, shifting public perceptions of science, and growing emphasis on broader impacts mean that scientists also have to be effective communicators, able to explain the value of their research to a wide audience. How do we effectively give graduate students an edge in preparing for this dual role?