Marine Biology Commons^™

Generation Of Germ-Free /Ciona Intestinalis For Studies Of Gut-Microbe Interactions, Brittany A Leigh, Assunta Liberti, Larry J Dishaw

Marine Science Faculty Publications

Microbes associate with animal hosts, often providing shelter in a nutrient-rich environment. The gut, however, can be a harsh environment with members of the microbiome settling in distinct niches resulting in more stable, adherent biofilms. These diverse communities can provide orders of magnitude more gene products than the host genome; selection and maintenance of a functionally relevant and useful microbiome is now recognized to be an essential component of homeostasis. Germ-free (GF) model systems allow dissection of host-microbe interactions in a simple and direct way where each member of the symbiosis can be studied in isolation. In addition, because immune …

Review Of The Cultivation Program Within The National Alliance For Advanced Biofuels And Bioproducts, Peter J. Lammers, Michael Huesemann, Wiebke Boeing, Daniel B. Anderson, Robert G. Arnold, Xuemei Bai, Manish Bhole, Yalini Brhanavan, Louis Brown, Jola Brown, Judith K. Brown, Stephen Chisholm, C. Meghan Downes, Scott Fulbright, Yufeng Ge, Jonathan E. Holladay, Balachandran Ketheesan, Avinash Khopkar, Ambica Koushik, Paul Laur, Babetta L. Marrone, John B. Mott, Nagamany Nirmalakhandan, Kimberly L. Ogden, Ronald L. Parsons, Juergen Polle, Randy D. Ryan, Tzachi Samocha, Richard T. Sayre, Mark Seger, Thinesh Selvaratnam, Ruixiu Sui, Alex Thomasson, Adrian Unc, Wayne Van Vorrhies, Peter Waller, Yao Yao, José A. Olivares

Publications and Research

The cultivation efforts within the National Alliance for Advanced Biofuels and Bioproducts (NAABB)were developed to provide four major goals for the consortium, which included biomass production for downstream experimentation, development of new assessment tools for cultivation, development of new cultivation reactor technologies, and development of methods for robust cultivation. The NAABB consortium test beds produced over 1500 kg of biomass for downstream processing. The biomass production included a number of model production strains, but also took into production some of the more promising strains found through the prospecting efforts of the consortium. Cultivation efforts at large scale are intensive and …

Influence Of A Suite Of Environmentally Relevant Conditions On Pbt Leaching From, And Sorption To, Marine Microplastic Debris, Robert C. Hale, Da Chen

Reports

Synthetic polymers (plastics) enter marine environments from terrestrial and marine-based sources. The manner of release, the plastic’s composition/properties and ambient marine conditions determine debris fate and its impacts on living resources. It was long assumed that all plastics were persistent and inert, possessing negligible potential for chemical impacts. However, in reality, commercial polymers exhibit a range of potentials for interactions. Persistent, bioaccumulative and toxic (PBT) chemicals are lipophilic and may concentrate from ambient waters by orders of magnitude on polymer surfaces (Teuten et al., 2007). The type of polymer affects the degree of PBT sorption. Indeed, plastics have been found …

Watershed Modeling And Sediment Yield Prediction Of The Los Olmos Creek Watershed In South Texas, Rockford Miller, Jungseok Ho, Chu-Lin Cheng

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

Studying the sediment that accumulates in a stream is an important aspect in the study of water quality and resources. With respect to water quality, the main issue is the turbidity of the water. Increased losses of natural landscape increase the erosion process in turn raising the turbidity of the water and reducing the light that can penetrate to the water reducing the growth of aquatic life. With respect to water resources, sediment accumulates in the river ways, harbors, and in dams reducing the effectiveness of these resources. This study focused on determining the amount of sediment that is outputted …

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 …

Temporal Variability Of Diapycnal Mixing In The Northern South China Sea, Hui Sun, Qingxuan Yang, Wei Zhao, Xinfeng Liang, Jiwei Tian

Marine Science Faculty Publications

Temporal variability of diapycnal mixing over 7 months in the northern South China Sea was examined based on McLane Moored Profiler observations from 850 to 2200 m by employing a finescale parameterization. Intensified diffusivity exceeding the order of 10⁻³ m²/s in magnitude was found over the first half of October 2014, and from 2 December 2014 to 21 January 2015 (a typical wintertime). Strong internal tides and winds in winter were the likely candidates for the high‐level diapycnal mixing in winter. As for the enhanced mixing during October 2014, we suspect the generation of near‐bottom near‐inertial waves …

Molecular Measurement Of Toxicity In Fish; Case Examples And Policy Implications, Jessica A. Freedman

Senior Honors Projects

Stormwater and oil are common urban contaminants that can be harmful to fish species. One way of recognizing exposed and impaired fish is by monitoring gene expression and gene induction. This study focused on the identification and validation of reference genes for measuring contaminant-induced changes in gene expression due to urban influence. In this study, reference genes (which are genes used to normalize data and remain consistent in varying exposures regardless of organism and tissue type) were established. Six genes were identified as reference genes (ef1a, wdtc1, mtm1, spop, rxrba and tuba1) from a longer list of potential …

A Tale Of Two Antennules: The Performance Of Crab Odor-Capture Organs In Air And Water, Lindsay D. Waldrop, Laura A. Miller, Shilpa Khatri

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Odour capture is an important part of olfaction, where dissolved chemical cues (odours) are brought into contact with chemosensory structures. Antennule flicking by marine crabs is an example of discrete odour capture (sniffing) where an array of chemosensory hairs is waved through the water to create a flow–no flow pattern based on a narrow range of speeds, diameters of and spacings between hairs. Changing the speed of movement and spacing of hairs at this scale to manipulate flow represents a complicated fluid dynamics problem. In this study, we use numerical simulation of the advection and diffusion of a chemical gradient …

Lipid Composition Of Oil Extracted From Wasted Norway Lobster (Nephrops Norvegicus) Heads And Comparison With Oil Extracted From Antarctic Krill (Euphasia Superba), Amaya Albalat, Lauren E. Nadler, Nicholas Foo, James R. Dick, Andrew J. R. Watts, Heather Philp, Douglas M. Neil, Oscar Monroig

Marine & Environmental Sciences Faculty Articles

In the UK, the Norway lobster (Nephrops norvegicus) supports its most important shellfish fishery. Nephrops are sold either whole, or as “tails-only” for the scampi trade. In the “tailing” process, the “head” (cephalothorax) is discarded as waste. A smaller crustacean species, the Antarctic krill Euphasia superba, represents an economically valuable industry, as its extractable oil is sold as a human dietary supplement. The aim of this study was to determine the amount and composition of the oil contained in discarded Nephrops heads and to compare its composition to the oil extracted from krill. Differences due to Geographical …

Global Ocean Data Science Ocg 250, Joanna Burkhardt

Library Impact Statements

No abstract provided.

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.

Variability Of Particle Size Distributions In The Bohai Sea And The Yellow Sea, Zhongfeng Qui, Deyong Sun, Chuanmin Hu, Sengquiang Wang, Lufei Zheng, Yu Huang, Tian Peng

Marine Science Faculty Publications

Particle size distribution (PSD) is an important parameter that is relevant to many aspects of marine ecosystems, such as phytoplankton functional types, optical absorption and scattering from particulates, sediment fluxes, and carbon export. However, only a handful of studies have documented the PSD variability in different regions. Here, we investigate the PSD properties and variability in two shallow and semi-enclosed seas (the Bohai Sea (BS) and Yellow Sea (YS)), using in situ laser diffraction measurements (LISST-100X Type C) and other measurements at 79 stations in November 2013. The results show large variability in particle concentrations (in both volume and number …

Effect Of Elevated Carbon Dioxide On Shoal Familiarity And Metabolism In A Coral Reef Fish, Lauren E. Nadler, Shaun S. Killen, Mark I. Mccormick, Sue-Ann Watson, Philip L. Munday

Marine & Environmental Sciences Faculty Articles

Atmospheric CO₂ is expected to more than double by the end of the century. The resulting changes in ocean chemistry will affect the behaviour, sensory systems and physiology of a range of fish species. Although a number of past studies have examined effects of CO₂ in gregarious fishes, most have assessed individuals in social isolation, which can alter individual behaviour and metabolism in social species. Within social groups, a learned familiarity can develop following a prolonged period of interaction between individuals, with fishes preferentially associating with familiar conspecifics because of benefits such as improved social learning and greater …

Development Of A Risk Assessment Framework To Predict Invasive Species Establishment For Multiple Taxonomic Groups And Vectors Of Introduction, Alisha D. Davidson, Abigail J. Fusaro, Rochelle A. Sturtevant, Edward S. Rutherford, Donna R. Kashian

Biological Sciences Faculty Research Publications

A thorough assessment of aquatic nonindigenous species’ risk facilitates successful monitoring and prevention activities. However, species- and vector-specific information is often limited and difficult to synthesize across a single risk framework. To address this need, we developed an assessment framework capable of estimating the potential for introduction, establishment, and impact by aquatic nonindigenous species from diverse spatial origins and taxonomic classification, in novel environments. Our model builds on previous approaches, while taking on a new perspective for evaluation across species, vectors and stages to overcome the limitations imposed by single species and single vector assessments. We applied this globally-relevant framework …

27 Years Of Benthic And Coral Community Dynamics On Turbid, Highly Urbanised Reefs Off Singapore, James R. Guest, K. Tun, Jeffrey A. Low, A. Vergés, Ezequiel M. Marzinelli, A. H. Campbell, Andrew G. Bauman, David A. Feary, Loke Ming Chou, Peter D. Steinberg

Marine & Environmental Sciences Faculty Articles

Coral cover on reefs is declining globally due to coastal development, overfishing and climate change. Reefs isolated from direct human influence can recover from natural acute disturbances, but little is known about long term recovery of reefs experiencing chronic human disturbances. Here we investigate responses to acute bleaching disturbances on turbid reefs off Singapore, at two depths over a period of 27 years. Coral cover declined and there were marked changes in coral and benthic community structure during the first decade of monitoring at both depths. At shallower reef crest sites (3–4 m), benthic community structure recovered towards pre-disturbance states …

Characterization Of Interaction Between Brevetoxin And Its Native Receptor And Identification Of The Role Of Brevetoxin In Karenia Brevis, Wei Chen

FIU Electronic Theses and Dissertations

Algae are important to marine and fresh-water ecosystems. However, some species of algae are harmful or even toxic. They can consume oxygen or block sunlight that is essential for other organisms to live. Indeed, some algae blooms can produce toxins that damage the health of the environment, plants, animals, and humans. Harmful algal blooms (HABs) which are often more green, brown, or dark-colored than red have spread along the coastlines and in the surface waters of the United States. Therefore, scientists are making great efforts to study HABs in order to maintain human and ecosystem health.

Karenia brevis, the …

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, …

Adsorptive And Kinetic Characterization Of Aqueous Zinc Removal By Biochars, Sergio Mireles, Yongsik Ok, Chu-Lin Cheng, Jihoon Kang

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

Biochars have shown a great potential to treat stormwater runoff contaminated with heavy metals due to their favorable physical and chemical characteristics. Biochar materials were produced from pyrolysis of oak tree and wood at 400C and 450C respectively, and their Zn adsorption behavior from aqueous solutions were evaluated to assess their applicability as a filter media for stormwater treatment. Two adsorption isotherm models, Freundlich and Langmuir, were used to fit the batch-scale experimental data. The kinetics of Zn adsorption was investigated under two contrasting physical condition (stagnant vs. agitated). The adsorption isotherm was better fitted with the Langmuir model (R2 …

Antagonistic Effects Of Ocean Acidification And Rising Sea Surface Temperature On The Dissolution Of Coral Reef Carbonate Sediments, Daniel Trnovsky, Laura Stoltenberg, Tyler Cyronak, Bradley D. Eyre

Marine & Environmental Sciences Faculty Articles

Increasing atmospheric CO₂ is raising sea surface temperature (SST) and increasing seawater CO₂ concentrations, resulting in a lower oceanic pH (ocean acidification; OA), which is expected to reduce the accretion of coral reef ecosystems. Although sediments comprise most of the calcium carbonate (CaCO₃) within coral reefs, no in situ studies have looked at the combined effects of increased SST and OA on the dissolution of coral reef CaCO₃ sediments. In situ benthic chamber incubations were used to measure dissolution rates in permeable CaCO₃ sands under future OA and SST scenarios in a coral reef …

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 …

Fluctuating Asymmetry In Two Common Freshwater Fishes As A Biological Indicator Of Urbanization And Environmental Stress Within The Middle Chattahoochee Watershed, William I. Lutterschmidt, Samantha L. Martin, Jacob F. Schaefer

Faculty Publications

Deviations in bilateral symmetry or fluctuating asymmetry of an organism may result under environmental stressors that reduce developmental homeostasis and stability. Anthropogenic stressors such as increased urbanization can negatively impact environmental quality of aquatic ecosystems. Researchers have stressed the value in finding easy, accurate and inexpensive methods for assessing potential stress within ecosystems. Here we use fluctuating asymmetry (FA) as a useful quantitative tool in assessing the environmental quality and potential urban-based stressors within eight creeks of the Bull and Upatoi Creeks Watershed within the larger watershed of the Middle Chattahoochee. Using Geographic Information System (GIS), we characterize land-use patterns …

Accelerating Tropicalization And The Transformation Of Temperate Seagrass Meadows, Glenn A. Hyndes, Kenneth L. Heck Jr., Et Al, R J. Orth

VIMS Articles

Climate-driven changes are altering production and functioning of biotic assemblages in terrestrial and aquatic environments. In temperate coastal waters, rising sea temperatures, warm water anomalies and poleward shifts in the distribution of tropical herbivores have had a detrimental effect on algal forests. We develop generalized scenarios of this form of tropicalization and its potential effects on the structure and functioning of globally significant and threatened seagrass ecosystems, through poleward shifts in tropical seagrasses and herbivores. Initially, we expect tropical herbivorous fishes to establish in temperate seagrass meadows, followed later by megafauna. Tropical seagrasses are likely to establish later, delayed by …

Calibration Of Vims Research Vessel Catch Data To Ensure Continuity Of Recruitment Indices For The Chesapeake Bay Region, Mary C. Fabrizio, Troy D. Tuckey

Reports

The VIMS Juvenile Fish Trawl Survey, which has been in operation since 1955, has undergone considerable changes to the sampling gear, location of sampling sites, and the methodology used to select sampling sites. Recently, a new vessel, the R/V Tidewater, replaced the R/V Fish Hawk, which had been in service for 25 years. In addition to the change in vessel, a new net was used; this net design is more robust to deployment methods and performs more consistently under varying environmental conditions. Therefore, a calibration study was conducted whereby the two research vessels with different nets fished in the same …

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 …

Testing Raised Foot Lines In Virginia's Striped Bass Fishery: A Gear Based Method Of Reducing Sturgeon Interactions In Anchored Gillnets, Thomas J. Murray

Reports

Working with commercial fishermen and scientists, the project evaluated the efficacy of altering net designs to achieve reductions in incidental contacts with protected species while maintaining harvest efficiency. In addition project participants assisted in the transfer of the new gear technology to industry as a gear-based method to reduce sturgeon interactions in gillnets targeting striped bass. The intent was to raise the effective fishing depth (webbing) of anchored gillnets interactions with protected Atlantic sturgeon while not impacting direct harvest of striped bass, the target species. The gear was shown to not impact Catch Per Unit Effort (CPUE) of the directed …

Coastal Wetland Response To Sea-Level Rise In A Fluvial Estuarine System, Karim Alizad, Scott C. Hagen, James T. Morris, Stephen C. Medeiros, Matthew V. Bilskie, John F. Weishampel

Faculty Publications

Coastal wetlands are likely to lose productivity under increasing rates of sea-level rise (SLR). This study assessed a fluvial estuarine salt marsh system using the Hydro-MEM model under four SLR scenarios. The Hydro-MEM model was developed to apply the dynamics of SLR as well as capture the effects associated with the rate of SLR in the simulation. Additionally, the model uses constants derived from a 2-year bioassay in the Apalachicola marsh system. In order to increase accuracy, the lidar-based marsh platform topography was adjusted using Real Time Kinematic survey data. A river inflow boundary condition was also imposed to simulate …

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 …

Condition Of Larval Spanish Mackerel Scomberomorus Maculatus In Relation To The Deepwater Horizon Oil Spill, John Timothy Ransom, J.E. Filbrun, Frank J. Hernandez Jr.

Faculty Publications

The Deepwater Horizon oil spill (DWHOS) coincided with the pelagic larval stages of many valued commercial and recreational fishes in the northern Gulf of Mexico. Larval fish survival and eventual recruitment into adult populations may have been impacted directly through toxicity or indirectly through changes in the planktonic food web caused by the release of oil and chemical dispersants during the DWHOS event. Using samples from a long-term ichthyoplankton survey off the coast of Alabama, USA, in a region impacted by the DWHOS, the abundance and condition of larval Spanish mackerel Scomberomorus maculatus were compared during summer months in years …

The Skp1 Homologs Skr-1/2 Are Required For The Caenorhabditis Elegans Skn-1 Antioxidant/Detoxification Response Independently Of P38 Mapk., Cheng-Wei Wu, Andrew Deonarine, Aaron Przybysz, Kevin Strange, Keith P. Chloe

Molecular Biosciences Faculty Publications

SKN-1/Nrf are the primary antioxidant/detoxification response transcription factors in animals and they promote health and longevity in many contexts. SKN-1/Nrf are activated by a remarkably broad-range of natural and synthetic compounds and physiological conditions. Defining the signaling mechanisms that regulate SKN-1/Nrf activation provides insights into how cells coordinate responses to stress. Nrf2 in mammals is regulated in part by the redox sensor repressor protein named Keap1. In C. elegans, the p38 MAPK cascade in the intestine activates SKN-1 during oxidative stress by promoting its nuclear accumulation. Interestingly, we find variation in the kinetics of p38 MAPK activation and tissues with …

Newsroom: The Legal Impact Of Marine Debris 10-21-2016, Roger Williams University School Of Law

Life of the Law School (1993- )

No abstract provided.