Marine Biology Commons^™

Flight Of The Freshwater Fish, Michael H. Wilson

Capstones

Michael H. Wilson

Capstone Abstract

December 27, 2016

Flight of the Freshwater Fish

The Hudson River provides for millions of people as a path for commercial and private transportation, a source of food and energy, and perhaps most importantly for many living in the tri-state area as a destination for recreation and relaxation. The most overlooked feature of the river is how the wildlife shows clear signs of a changing climate and rapid environmental response to the impacts of global warming on the river.

Entire populations of fish species in the lower Hudson have been forced to leave the river …

The Forgotten Cousin In Freshwater Community Ecology: Tidal Freshwater Wetlands, Jack R. Mclachlan

Electronic Theses and Dissertations

Tidal freshwaters are unique in their placement in the landscape, forming where freshwater riverine flows are sufficient to overwhelm the saline water of the incoming tide, but not strong enough to suppress tidal water-height fluctuations. Tidal freshwaters and their wetlands have been overlooked by freshwater and marine researchers alike; neither discipline considers tidal freshwaters to fall under their purview. Invertebrate communities in tidal freshwaters are thought to be species depauperate; the consensus is that they support fewer taxa than nearby non-tidal freshwaters, but little is known about how these communities are structured. This study investigated how tidal hydrology, an atypical …

Towards Quantitative Viromics For Both Double-Stranded And Single-Stranded Dna Viruses., Simon Roux, Natalie E Solonenko, Vinh T Dang, Bonnie T Poulos, Sarah M Schwenck, Dawn B Goldsmith, Maureen L Coleman, Mya Breitbart, Matthew B Sullivan

Marine Science Faculty Publications

BACKGROUND: Viruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative viral metagenomes (viromes). This leaves the ecology of non-dsDNA viruses nearly unknown, including single-stranded DNA (ssDNA) viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation).

METHODS: Here we designed mock viral communities including both ssDNA and dsDNA viruses to evaluate the capability of a sequencing library preparation …

The Vertical And Horizontal Distribution Of Deep-Sea Crustaceans Of The Order Euphausiacea (Malacostraca: Eucarida) From The Northern Gulf Of Mexico With Notes On Reproductive Seasonality., Charles Douglas Fine

HCNSO Student Theses and Dissertations

The vertical and horizontal distributions of Euphausiacea in the northern Gulf of Mexico, including the location of the Deepwater Horizon oil spill, were analyzed from 340 trawl samples collected between April-June, 2011. This study is the first comprehensive survey of euphausiid distributions from depths deeper than 1000 m in the Gulf of Mexico and included stratified sampling from five discrete depth ranges (0-200 m, 200-600 m, 600-1000 m, 1000-1200 m, and 1200-1500 m). In addition, this study encompasses the region heavily impacted by the Deepwater Horizon oil spill. Data presented here could potentially be used in ecosystem models investigating trophic …

Trophic Ecology Of Green Turtles (Chelonia Mydas) From Dry Tortugas National Park, Florida, David C. Roche

HCNSO Student Theses and Dissertations

Located 100 km west of Key West, Florida, Dry Tortugas National Park (DRTO) is a largely untouched subtropical marine ecosystem that serves as an important developmental habitat, nesting ground, and foraging area for several species of sea turtles, including green turtles. The Park supports a recovering population of green turtles comprised of resident juveniles, subadults, and adults of both sexes; nesting females include residents and migrating females that only return to nest. Stable isotope analysis has been applied widely to describe the trophic ecology of green turtles, from urbanized bays with significant anthropogenic input, to relatively pristine ecosystems with healthy …

Gulf Sturgeon (Acipenser Oxyrinchus Desotoi) Pre-Restoration Occupancy Patterns On Ship Island, Mississippi Sound With An Evaluation Of Designated Critical Habitat Use By Eastern And Western Population Segments, Page Elizabeth Vick

Master's Theses

Critical spawning and feeding habitat was designated for federally threatened, anadromous Gulf Sturgeon (GS) to aid in population recovery. This study examined GS occupancy, habitat use, and movement through critical habitat monitored by the Ship Island (SI) acoustic array during overwintering periods from 2011 to 2015 prior to MsCIP SI restoration. An occupancy index analyzed patterns of spatial and temporal habitat use of both western and eastern population segments (WPS and EPS, respectively) of GS on the SI array. The ends of SI along with the passes and cuts of the island, especially Dog Keys Pass (DKP), were occupied by …

Bloom Or Bust: Retrospective Analysis Of The Giant Jellyfish, Nemopilema Nomurai (Scyphozoa: Rhizostomeae), Ecology In The East Asian Marginal Seas, Naomi Yoder

Master's Theses

The Giant Jellyfish, Nemopilema nomurai, is a large-bodied bloom-forming jellyfish that occurs in the semi-enclosed basins of the East Asian Marginal Seas. N. nomurai has bloomed more frequently in the past 20 years than in any period previously recorded. In Japan, recent N. nomurai blooms were responsible for millions of dollars in lost revenue and equipment damage to commercial fisheries alone. This study statistically analyzed 21 environmental factors in connection with N. nomurai occurrence (using occurrence as a proxy for blooms). Eight factors resulted in a statistically significant or marginally significant (p ≤ 0.10), linear or non-linear relationship with …

Examining The Combined Effects Of Dissolved Oxygen, Temperature, And Body Size On The Physiological Responses Of A Model Macrobenthic Polychaete Species, Capitella Teleta, Kelsey Burns Gillam

Dissertations

While the scientific community is in consensus that coastal systems are threatened by climate change, few climate change studies test the effects of more than one variable directly related to climate change. The dissolved oxygen (DO) levels of the ocean are currently subject to both global warming and eutrophication; 94% of all hypoxia zones are expected to experience >2°C increase by 2035. This dissertation aims to examine how a model organism responds to simultaneous thermal and DO stress involving four levels of DO (100%, 70%, 50%, and 20%) saturation and three temperatures (15°C, 20°C, and 25°C).

The polychaete, Capitella teleta …

Effect Of Oxygen-Limiting Tidal Conditions On Muscle Metabolism And Structure In The Giant Acorn Barnacle, Balanus Nubilus, Katie O. Grady

Master's Theses

Crustacean muscle fibers are some of the largest cells in the animal kingdom, with fiber diameters in the giant acorn barnacle (Balanus nubilus) exceeding 3 mm. Sessile animals with extreme muscle sizes and that live in the hypoxia-inducing intertidal zone – like B. nubilus – represent ideal models for probing the effects of oxygen limitation on muscle cells. We investigated changes in metabolism and structure of B. nubilus muscle in response to: normoxic immersion, anoxic immersion, or air emersion, for acute (6h) or chronic (6h exposures twice daily for 2wks) time periods. Following exposure, we immediately measured hemolymph …

First Occurrence Of The Invasive Hydrozoan Gonionemus Vertens A. Agassiz, 1862 (Cnidaria: Hydrozoa) In New Jersey, Usa, John J. Gaynor, Paul A.X. Bologna, Dena J. Restaino, Christie Barry

Department of Biology Faculty Scholarship and Creative Works

Gonionemus vertens A. Agassiz, 1862 is a small hydrozoan native to the Pacific Ocean. It has become established in the northern and southern Atlantic Ocean as well as the Mediterranean Sea. We report on the first occurrence of this species in estuaries in New Jersey, USA,and confirm species identification through molecular sequence analysis. Given the large number of individuals collected, we contend that this is a successful invasion into this region with established polyps. The remaining question is the vector and source of these newly established populations.

Effects Of Catastrophic Seagrass Loss And Predation Risk On The Ecological Structure And Resilience Of A Model Seagrass Ecosystem, Robert J. Nowicki

FIU Electronic Theses and Dissertations

As climate change continues, climactic extremes are predicted to become more frequent and intense, in some cases resulting in dramatic changes to ecosystems. The effects of climate change on ecosystems will be mediated, in part, by biotic interactions in those ecosystems. However, there is still considerable uncertainty about where and how such biotic interactions will be important in the context of ecosystem disturbance and climactic extremes.

Here, I review the role of consumers in seagrass ecosystems and investigate the ecological impacts of an extreme climactic event (marine heat wave) and subsequent widespread seagrass die-off in Shark Bay, Western Australia. Specifically, …

Penobscot River Restoration, Catherine Schmitt

Maine Sea Grant Publications

BETWEEN THE HEAD of tide above Bangor to where it widens into the bay at Searsport, the Penobscot River shifts from a flowing freshwater waterway banked by cedar and pine to a brackish, wave-lapped marsh with a rocky shoreline. In this estuary, salt concentrations fluctuate as the winds and tides push sea water and sediments back and forth. The estuary and the river that feeds it have taken on a new character recently, and have become an international example of watershed restoration. Despite two centuries of intensive timber harvesting and pulp and paper manufacturing, and the construction of hundreds of …

Population Size And Survival Rates Of Blue Catfish In Chesapeake Bay Tributaries, Mary C. Fabrizio, Troy D. Tuckey, Robert J. Latour, Gary C. White, Alicia J. Norris, Mary Groves

Reports

This report comprises two studies conducted from 2012 to 2015 to estimate population size, survival rates, and movements of invasive blue catfish in Chesapeake Bay tributaries. The first study of population-size and survival was conducted in the James River, VA (Population Size and Survival Rates of Invasive Blue Catfish in Tidal Waters of the James River Subestuary). The second study on movement and survival of blue catfish was conducted in the Potomac River, the natural boundary between Maryland and Virginia (Movement Patterns and Survival Rate of Blue Catfish in a Non-Native Habitat Estimated with a Tagging Study). The Executive Summary …

Diet Assessment Of The Atlantic Sea Nettle Chrysaora Quinquecirrha In Barnegat Bay, New Jersey, Using Next-Generation Sequencing, Robert W. Meredith, John J. Gaynor, Paul Ax Bologna

Department of Biology Faculty Scholarship and Creative Works

Next-generation sequencing (NGS) methodologies have proven useful in deciphering the food items of generalist predators, but have yet to be applied to gelatinous animal gut and tentacle content. NGS can potentially supplement traditional methods of visual identification. Chrysaora quinquecirrha (Atlantic sea nettle) has progressively become more abundant in Mid-Atlantic United States’ estuaries including Barnegat Bay (New Jersey), potentially having detrimental effects on both marine organisms and human enterprises. Full characterization of this predator’s diet is essential for a comprehensive understanding of its impact on the food web and its management. Here, we tested the efficacy of NGS for prey item …

Eelgrass/Macroalgae Discussion Primer For Tac Activities 2016-2017, Piscataqua Region Estuaries Partnership

PREP Reports & Publications

See also: "Eelgrass Distribution and Biomass in the Great Bay Estuary for 2015" http://scholars.unh.edu/prep/354

"Eelgrass Distribution in the Great Bay Estuary for 2014" http://scholars.unh.edu/prep/352/

The issue of eelgrass and macroalgae in the Great Bay Estuary (GBE) is extremely important and complex. The purpose of this document is to clarify issues and questions to make for a more productive and informed discussion.

To Fish Or Not To Fish? What Effect Do California’S Marine Protected Areas Have On Up-And-Coming Kellet’S Whelk Fishery?, Jennifer Greene

STAR Program Research Presentations

Kellet’s whelk, Kelletia kelletii, were observed at sample sites throughout their range from Baja California, Mexico, to Monterey, CA to determine patterns of population density. Sample sites in each region were either located within California marine protected areas where take of the Kellet’s whelk in prohibited, or in non-protected areas where the whelks can be fished both commercially and recreationally. Kellet’s whelk population density was compared between all MPA and non-MPA sample sites. These mean densities were also found for sites in Santa Barbara and San Diego near active fishing ports and compared to data from the same sites collected …

The Effects Of Sub-Lethal Predation On The Reproductive Output Of Acanthaster Planci (Crown-Of-Thorns Starfish), Emily Mucha

Independent Study Project (ISP) Collection

Wide-scale declines in live coral cover have been observed throughout history. Modern day coral populations face a multitude of environmental disturbances, however one of the most devastating to the reefs in the Indo-Pacific is the crown-of-thorns starfish (Acanthaster planci), which feeds on the tissues of live corals. The rate at which these individuals feed combined with the explosion of populations in times of outbreak have been seen to exert some of the biggest pressures on coral reefs to date. Following recent episodes of crown-of-thorns starfish (COTS) outbreaks, research on the organism has become increasingly prevalent on the scientific …

Fish Diversity And Coral Health Of Tanzania's Reefs: A Comparative Study Between The Ushongo Village Reef And The Fungu Zinga Reef Over Time, Della Turque, Corinne Casper

Independent Study Project (ISP) Collection

The world’s oceans are becoming increasing acidic due to global climate change, posing a threat to marine ecosystems, including coral carbonate systems. Environmental threats are exacerbated by human development stressors as well: growing populations, dependency on marine resources, and unsustainable practices invaluable marine ecosystems at risk. Tanzania’s coral reef system extends for 3580 km2 (Muhando et al. 2008) near the Tanga region, serving over half a million people who are highly dependent on fishing and other marine resources as their livelihoods (Samoilys et. al. 2008). With Tanzania’s population rapidly growing, the unsustainable pressure on coral reefs for sustenance and livelihood …

A Study Of Defensive Mechanisms Employed By Two Species Of Nudibranchs Using Toxicity And Unpalatability Analyses, Sean Youn

Independent Study Project (ISP) Collection

Nudibranchs are marine invertebrates that have developed an intriguing defense mechanism, including warning coloration and the use of chemicals accumulated through their sponge diet. The goal of this study was to determine whether the strength of chemical defenses differs between dietary and accumulated secondary metabolites for two species: Glossodoris vespa and Ceratosoma brevicaudatum. First, NMR spectroscopy was used to not only identify specific compounds in the mantle (outer covering) and the viscera (gut) but also to analyze the possibility of nudibranch species transporting more toxic compounds for defensive purposes. Next, toxicity (brine shrimp) and palatability (Palaemon shrimp) assays …

Investigating The Spatial Distribution And Effects Of Nearshore Topography On Acropora Cervicornis Abundance In Southeast Florida, Nicole D'Antonio, David S. Gilliam, Brian K. Walker

Marine & Environmental Sciences Faculty Articles

Dense Acropora cervicornis aggregations, or patches, have been documented within nearshore habitats in Southeast Florida (SE FL) despite close proximity to numerous anthropogenic stressors and subjection to frequent natural disturbance events. Limited information has been published concerning the distribution and abundance of A. cervicornis outside of these known dense patches. The first goal of this study was to conduct a spatially extensive and inclusive survey (9.78 km²) to determine whether A. cervicornis distribution in the nearshore habitat of SE FL was spatially uniform or clustered. The second goal was to investigate potential relationships between broad-scale seafloor topography and …

Eelgrass Distribution And Biomass In The Great Bay Estuary For 2015, Frederick T. Short

PREP Reports & Publications

See also: "Eelgrass/Macroalgae Discussion Primer for TAC Activities 2016-2017" http://scholars.unh.edu/prep/355

Eelgrass (Zostera marina L.) is an essential habitat for the Great Bay Estuary (GBE) because it is the basis of an estuarine food web that supports many of the recreationally, commercially and ecologically important species in the estuary and beyond. Eelgrass provides food for ducks, geese and swans, as well as food, nursery habitat, and shelter for juvenile fish and shellfish. Eelgrass filters estuarine waters and improves water clarity, removing both nutrients and suspended sediments from the water column; its roots and rhizomes bind and hold sediments in place, thereby …

Eelgrass Distribution In The Great Bay Estuary For 2014, Frederick T. Short

PREP Reports & Publications

See also: "Eelgrass/Macroalgae Discussion Primer for TAC Activities 2016-2017" http://scholars.unh.edu/prep/355

Eelgrass (Zostera marina L.) is an essential habitat for the Great Bay Estuary (GBE) because it is the basis of an estuarine food web that supports many of the recreationally, commercially and ecologically important species in the estuary and beyond. Eelgrass provides food for ducks, geese and swans, as well as food, nursery habitat, and shelter for juvenile fish and shellfish. Eelgrass filters estuarine waters and improves water clarity, removing both nutrients and suspended sediments from the water column; its roots and rhizomes bind and hold sediments in place, thereby …

The Demographic Consequences Of Growing Older And Bigger In Oyster Populations, Jl Moore, Rom Lipcius, B Puckettt, Sj Schrieber

VIMS Articles

Structured population models, particularly size-or age-structured, have a long history of informing conservation and natural resource management. While size is often easier to measure than age and is the focus of many management strategies, age-structure can have important effects on population dynamics that are not captured in size-only models. However, relatively few studies have included the simultaneous effects of both age-and size-structure. To better understand how population structure, particularly that of age and size, impacts restoration and management decisions, we developed and compared a size-structured integral projection model (IPM) and an age-and size-structured IPM, using a population of Crassostrea gigas …

Guideline For Stakeholder Engagement On Aquatic Resource Management-Related Processes, Department Of Fisheries

Fisheries occasional publications

No abstract provided.

Community Structure And Production Of The Macrobenthos On Four Artificial Reefs In The Mississippi Sound In Relation To Substrate And Profile Type, Patrick Daniel Gillam

Master's Theses

In recent years, the Mississippi Department of Marine Resources (DMR) has made a concerted effort to enhance its coastal fishery resources by creating artificial reefs. Through this effort, 73 nearshore reefs have been created across the MS coast. Different substrate types used to construct MS artificial reefs include oyster shell and cement rubble. Two types of reef architecture used include high profile breakwater and low profile submerged structures. This study compared the benthic biota associated with oyster shell and cement rubble substrates among four artificial reefs representing high and low profile structures in summer 2011. Colonized benthic biota were quantified …

Spatial Ecology Of Great Barracuda (Sphyraena Barracuda) Around Buck Island Reef National Monument, St. Croix, U.S.V.I., Sarah L. Becker

Masters Theses

Marine protected areas (MPAs) are increasing in popularity as a tool to manage fish stocks through conservation of entire habitats and fish assemblages. Quantifying the habitat use, site fidelity, and movement patterns of marine species is vital to this method of marine spatial planning. The success of these protected areas requires that sufficient habitat is guarded against fishing pressure. For large animals, which often have correspondingly large home range areas, protecting an entire home range can be logistically challenging. For MPAs to successfully protect large top predator species, it is important to understand what areas of a home range are …

Host-Parasite Relationships Between The Copepod Naobranchia Lizae And Its Host (Striped Mullet, Mugil Cephalus): A Description Of Morphological Development, Sara R. Teemer

DePaul Discoveries

The parasitic copepod, Naobranchia lizae, is often found within the gill arches of the striped mullet, Mugil cephalus, in the Charleston Harbor Estuarine System of South Carolina. The parasite is relatively common, but little is known about its early stages of development. In order to describe the developmental stages and pattern of morphological development, 221 female N. lizae that were collected between February 2002 and May 2003 were used. Using variation in morphological characters (maxilla, trunk), these parasites were assigned to developmental stages (juvenile, subadult, adult). A small number of the males (three ‘dwarf’ males) were also found …

Biofouling Management In The Pacific Northwest And Predation On Native Versus Non-Native Ascidians, Erin Suzanne Kincaid

Dissertations and Theses

Marine non-native species threaten economic and environmental health, making it crucial to understand factors that make them successful. Research on these species, therefore, allows for greater preparedness and informed management of biological invasions and increases understanding of elements structuring biological communities. Among the marine non-native species, and particularly the fouling community, non-native ascidians are a taxon of particular concern because they can crowd out native benthic species and smother mariculture products. This thesis addresses management for ascidians and other fouling organisms and includes research on the invasiveness of this taxon in addition to the invasibility of recipient fouling communities. On …

Automated Detection Of Deep-Sea Animals, Dallas J. Hollis, Duane Edgington, Danelle Cline

STAR Program Research Presentations

The Monterey Bay Aquarium Research Institute routinely deploys remotely operated underwater vehicles equipped with high definition cameras for use in scientific studies. Utilizing a video collection of over 22,000 hours and the Video Annotation and Reference System, we have set out to automate the detection and classification of deep-sea animals. This paper serves to explore the pitfalls of automation and suggest possible solutions to automated detection in diverse ecosystems with varying field conditions. Detection was tested using a saliency-based neuromorphic selective attention algorithm. The animals that were not detected were then used to tune saliency parameters. Once objects are detected, …

Population Dynamics And Community Composition Of Ammonia Oxidizers In Salt Marshes After The Deepwater Horizon Oil Spill, Anne E. Bernhard, Roberta Sheffer, Anne E. Giblin, John M. Marton, Brian J. Roberts

Biology Faculty Publications

The recent oil spill in the Gulf of Mexico had significant effects on microbial communities in the Gulf, but impacts on nitrifying communities in adjacent salt marshes have not been investigated. We studied persistent effects of oil on ammonia-oxidizing archaeal (AOA) and bacterial (AOB) communities and their relationship to nitrification rates and soil properties in Louisiana marshes impacted by the Deepwater Horizon oil spill. Soils were collected at oiled and unoiled sites from Louisiana coastal marshes in July 2012, 2 years after the spill, and analyzed for community differences based on ammonia monooxygenase genes (amoA). Terminal Restriction Fragment …