SURF 2014 projects

December 1, 2014

Project Title: How can public understanding of marine ecosystems be enhanced through novel representations of environmental monitoring data?

Project Mentor(s): Neal Overstrom (Rhode Island School of Design) &  Jennifer Bissonnette (Rhode Island School of Design)

Project Description: In collaboration with colleagues at the University of Rhode Island and the Metcalf Institute for Marine and Environmental Reporting we will explore the visualization and representation of long-term data sets from Narragansett Bay as a case studies for developing interactive, highly engaging data narratives with the goal of expanding public interest in and understanding of the effects of climate change in Rhode Island. This pilot project will support the data compilation and development of a suite of data visualizations that will be critiqued and enhanced at a Data Narratives Workshop to be held at RISD in summer 2014. The outcomes of the Data Narratives Workshop will be discussed in the context of relevant best practices developed by science communication practitioners at a final workshop in spring 2015.

Project Significance: There is a growing need among researchers and science communicators to make scientific data available in new forms that can better engage public audiences. Rhode Island is well positioned to make nationally relevant advances in this arena because of its deep local expertise in natural and social sciences as well as the arts.

Does this project involve field work, lab work, or both? Lab work

Techniques Involved:

  • Principles of visual communication.
  • Software platforms for computer-aided representation of the objects, phenomena and data of science.
  • Understanding and analysis of data sets.
  • Awareness of approaches to informal learning and creative public engagement.

Project Title: What role do marine microbes, isolated from Mount Hope Bay, play in the biogeochemical cycling of sulfur and in particular dimethylsulfide metabolism?

Project Mentor(s): Erica Oduaran (Roger Williams University)

Project Description: Microorganisms from Mount Hope Bay will be isolated and grown in culture media in the laboratory. They will be studied for their ability to grow on and metabolize dimethylsulfide, dimethylsulfoxide, and/or dimethylsulfone. Each of the isolated bacteria will be characterized by microscopy, ability to grow on different culture media and by 16s DNA. Enzyme activity measurements will be used to verify their ability to reduce DMSO2, DMSO and DMS. Enzyme activity studies will also address whether or not the microbes can oxidize dimethylsulfide.

Project Significance: Dimethylsulfide (DMS) is a volatile sulfur species important for its role in the biogeochemical cycling of sulfur and regulation of the global climate. Marine DMS production comes primarily from the microbial catabolism of dimethylsulfoniopropionate (DMSP), a common metabolite in phytoplankton and seaweed, and accounts for the majority of the total global production of DMS. Only a small fraction of the DMS produced escapes into the atmosphere due to microbial remineralization of DMS. The processes in which DMS is consumed are diverse and poorly understood since the sulfur cycle is complex and sulfur can exist in oxidation states ranging from -2 to +6. Microbes have developed a variety of metabolic uses for DMS ranging from using DMS as a carbon source to oxidizing DMS to sulfate, thiosulfate or tetrathionate to gain energy from the reducing equivalents that it contains. This project addresses the role of microbes in Mount Hope Bay with regards to the biogeochemical cycling of sulfur.

Does this project involve field work, lab work, or both? Lab work

Techniques Involved:

  • Cell culturing
  • Genotyping/Phenotyping microorganisms
  • Metabolic analyses by differentiating growth media
  • Protein purification using HPLC/FPLC
  • Enzyme activity assays using UV/Vis
  • Maintaining a research notebook
  • Read and discuss current literature

Project Title: How will microbe-mineral interactions in Earth’s deep oceans respond to climate change?

Project Mentor(s): Dawn Cardace (University of Rhode Island)

Project Description: How marine microbes respond to environmental change is incompletely understood, particularly when their habitat is the relatively metal-rich and oxygen-poor rocks of the seabed. In this project, we will conduct simultaneous lab-based experiments and geochemical modeling work to understand if/how increases in atmospheric carbon dioxide will (1) change the chemistry of deeper ocean waters near the seafloor and (2) change the habitability of seabed rocks.

We will model as closed systems the impacts of changing gas concentrations on deep ocean habitats (natural ocean-type waters and rock packages, considered under biotic and abiotic conditions), constructing lab-based mesocosm experiments. We will also model the same systems to determine mineral saturation states and activities of aqueous species important to the ocean’s deep microbes.

Project Significance: This work examines the net impact of changing surface ocean biogeochemistry on deep ocean habitats in rocks. Not only will this work clarify shifting carbon mineralization in the seabed from a carbon flux perspective, but it will also be predictive in terms of favored microbial metabolic schema that can operate in the future seabed.

Does this project involve field work, lab work, or both? Both

Techniques Involved:

  • Mineralogy through x-ray diffraction
  • Mesocosm experiments
  • Microscopy/cell visualization
  • Biogeochemical modelling with Geochemist’s Workbench

Project Title: Heat shock proteins in Geukensia demissa as indicators of climate change and environmental stress on marine life in Narragansett Bay

Project Mentor(s): John Williams (Rhode Island College) & Breea Governar ((Rhode Island College))

 Project Description: The EPSCoR SURF student(s) will collect mussels from various sites along the RI coast and observe their expression of heat shock proteins, specifically Hsp 70, when collected and when subjected to water temperature increases in a laboratory aquarium. The project is in collaboration with Breea Governor (RIC Biology) who has provided the collection sites for gathering mussels and consulted on design of the experiments. This is a continuing research program began last summer under EPSCoR SURF and continuing through the current academic year as independent study projects by RIC undergraduates. The mussels will be dissected (gill and gut), homogenized and centrifuged. The supernatant subjected to electrophoresis and Western Blot analysis with Hsp70-specific antibodies. The proteins will also be isolated for analysis by MALDI-TOF MS. We will observe levels of expression of the protein at the temperatures when collected and in heat-treated mussels (up to 40 C) vs. the baseline animals kept at 18 C. Over expression of Hsp’s is considered to be a significant indicator of climate change as the ambient temperature of ectotherms’ habitat slowly increases, perhaps irreversibly. The work will be done in the RIC Biology and Physical Sciences and in the EPSCoR and INBRE Core Facility laboratories and in the field at the Bay collection sites.

Project Significance: We have begun a study of the impact of climate change on one marine organism whose habitat is in the periphery of Narragansett Bay. This body of water is representative of intertidal waters in the mid-latitudes. It is an optimal ecosystem for study of climate change and its effects on marine life in these types of waters and one that can provide insight into climate dynamics both in the Bay and in similar systems around the world.

Does this project involve field work, lab work, or both? Both

Techniques Involved:

Students will learn dissection, extraction and analysis of protein from animal tissue using electrophoresis and Western Blot analysis and mass spectroscopy. They will also get to visit the Bay collection sites several times to collect the mussels for analysis. They will examine the current literature on the relationship between Hsp expression levels and other possible indictors of climate change.

Project Title: Ocean acidification effects on fish larvae

Project Mentor(s): Andrew Rhyne (Roger Williams University)

Project Description: If a larval fish cannot avoid predators and cannot orient itself in three-dimensional space, the consequences to the individual and the population are dramatic. Otoliths are the primary system used by teleost fish to navigate and play a vital role in gravity and acceleration sensing. They are formed by precipitation of calcium carbonate (CaCO3(s)) in a protein-rich matrix within a bicarbonate-rich and alkaline pH fluid (endolymph). There are two sets of three otoliths occurring on either side of the head (sagittae, lapilli, asterisci). Four polymorphs of calcium carbonate are found in otoliths: aragonite (dominant in the sagittae and lapilli), vaterite (dominant in the asterisci), calcite (rare), and high-magnesium calcite (rare). In addition to polymorph composition, the crystal habit can vary with aragonite exhibiting both orthorhombic and prismatic habits and vaterite exhibiting a hexagonal crystal habit. Despite recent research regarding impacts of ocean acidification on larval marine fish, we know very little about the impact of ocean acidification on the systems that enable fish to move and orient themselves in three dimensions. This lack of understanding is the motivation for the proposed research.

Project Significance: We will test the effect(s) of ocean acidification (increased pCO2(aq)) on otolith morphology and mineralogy in larval tautog (Tautoga onitis) reared, in triplicate, at 380 ppmv CO2 (control), 480, 760, and 1000 ppmv CO2 (treatments) .

Does this project involve field work, lab work, or both? Lab work

Techniques Involved:

  • Larvae Rearing
  • Live Feeds Production
  • Clearing and Staining of larval fish
  • Dissection of otoliths
  • SEM

Project Title: How does increased turbulence impact predation by the ctenophore Mnemiopsis leidyi

Project Mentor(s): Sean Colin (Roger Williams University) & John Costello (Providence College)

Project Description: We will use a combination of laboratory and in situ methods to quantify the effects of turbulent flows on the feeding mechanics and predator-prey interactions of Mnemiopsis at the organismal level. Laboratory experiments will involve video analysis of individual interactions between Mnemiopsis and its prey under different mixing conditions. These experiments will be used to evaluate how mixing alters the encounter rates and capture efficiencies of Mnemiopsis with different prey types. We will then evaluate how these feeding effects translate to the community level by using in situ sampling techniques that will relate natural turbulence levels to ingestion rates, prey selection and predatory impact of Mnemiopsis in the field. By combining direct observations of small-scale effects in the laboratory and field with community level patterns of trophic exchange, to establish clear cause and effect relationships in a new approach to biological-physical interactions that extends beyond current laboratory and modeling limits.

Project Significance: How Mnemiopsis feed under different natural conditions observed in the environment carries significant implications. If we better understand how different environmental conditions affect the ecological impact of the comb jellyfish, we can predict with greater precision which types of ecosystems are more vulnerable to predation by Mnemiopsis and susceptible to potential invasion by the ctenophore. The level of environment mixing is expected to increase as a consequence of climate change. We need to understand how the trophic role of Mnemiopsis is related to turbulence conditions to be able to predict how these changes may alter the trophic role of Mnemiopsis.

Does this project involve field work, lab work, or both? Both

Techniques Involved: The student will learn multiple laboratory techniques that can be applied generally. These techniques include culturing of zooplankton species, video recording and analysis techniques and data analysis. The student will also learn important field sampling techniques such as plankton net sampling, gut content analysis and environmental condition sampling.

Project Title: Can we synthesize structurally diverse pyrazolines to better understand the requirements for inhibition of amebic growth and enzymatic activity?

Project Mentor(s): Lauren Rossi (Roger Williams University) & Avelina Espinosa (Roger Williams University)

Project Description: Amitochondriates, protists without mitochondria, are likely abundant in marine waters. Three known amitochondriate parasites, found in contaminated drinking water, are Giardia, Entamoeba, and Trichomonas and have been shown to sicken humans. Previous studies have indicated that substituted pyrazoline derivatives inhibit amebic growth by inhibiting Entamoeba histolytica alcohol dehydrogenase 2 (EhADH2), a crucial enzyme of the parasite. The goal of this project is to structurally modifiy the pyrazoline core and its substitution pattern to elucidate the structural and electronic characteristics essential for successful inhibition of amebic growth and enzymatic activity. These studies will increase our understanding of E. histolitica and potentially other amitochondriates that may be in our marine environment.

Project Significance: Amitochondriates, protists without mitochondria, are likely abundant in marine waters. Three known amitochondriate parasites are Giardia, Entamoeba, and Trichomonas. Entamoeba histolytica is an anaerobic parasite that infects millions of humans annually through contaminated food or water. The current treatment for amebiasis, metronidazole, is toxic and potentially carcinogenic. Small libraries of pyrazolines derivatives will be constructed in order to increase structural diversity, improve solubility, and to provide more potent inhibitors.

Does this project involve field work, lab work, or both? Lab

Techniques Involved:

  • Read and discuss primary scientific articles relevant to the reactions to be conducted.
  • Setup bench-top and microwave chemical reactions.
  • Safe handling of different chemicals.
  • Setup, operate, and assess the progress and success of a chemical reaction (TLC, GC, NMR)
  • Maintain a research notebook
  • Safely operate and interpret data from instruments (GC, IR, NMR)

Project Title: Can novel representations of living marine plankton foster public interest in and understanding of marine ecosystems?

Project Mentor(s): Neal Overstrom (Rhode Island School of Design) & Jennifer Bissonnette (Rhode Island School of Design)

Project Description: Phytoplankton and Zooplankton together form the base of ocean food webs and play crucial roles in planetary photosynthesis and carbon cycling. Public understanding of their influence on climate is a crucial part of marine science literacy yet it is often difficult to draw public attention to marine life at this scale. This project will involve collecting and imaging plankton from Narragansett Bay. In addition, we will review propagation maintenance techniques for gelatinous zooplankton (jellyfishes and ctenophores) and explore the topic of how novel representations of marine plankton might foster broader public interest in the ecosystem as a whole.

Project Significance: Phytoplankton and Zooplankton together form the base of ocean food webs and play crucial roles in planetary photosynthesis and carbon cycling. Public understanding of their influence on climate is a crucial part of marine science literacy yet it is often difficult to draw public attention to marine life at this scale.

Does this project involve field work, lab work, or both? Both

Techniques Involved:

  • Field and laboratory techniques for collecting, imaging, and maintaining cultures of marine plankton
  • Concepts around communication of science and public engagement
  • Marine aquarium keeping
  • Critical thinking
  • Specimen preparation and microscopy

Project Title: Identification and characterization of genes associated with the pathogenicity of trypanosomatiae

Project Mentor(s): Alison Shakarian (Salve Regina University)

Project Description: The research in my lab is designed to contribute to the understanding of mechanisms of parasite survival, growth and development. Proteins released or secreted by Leishmania are of interest because it is through these molecules that the parasites are able to sense, respond to and alter their environments. One such secreted enzyme is lipase. Lipases are ubiquitous enzymes being found in animals, plants, protozoa and prokaryotes. There is little published literature with regard to lipase activity in kinetoplastid protozoa. In other systems, lipase activity is involved in the reorganization of membrane structure and cell signaling and in some cases for nutrient acquisition. These data suggests that lipase activity is an essential enzyme for this group of parasites. Thus, a characterization of the protist lipase could lead to a better understanding of these processes/mechanisms and subsequently how they affect their human, plant and animal host organisms.

Project Significance: Kinetoplastid protozoa, commonly known as trypanososmes, are a family of unique and diverse organisms found worldwide. These parasitic protists are found in a diverse range of vertebrate and invertebrate host organisms, such as insects, marine fish, mollusks, plants, reptiles and mammals. Some kinetoplastids have a profound negative impact on the agricultural economies of endemic areas by infecting fish, animals or plant crops, making them unsuitable for human consumption and resulting in the loss of millions of dollars annually in endemic areas. The research in my lab is designed to contribute to the understanding of mechanisms of survival, growth and development of tyrpanosomatid parasites that infect this diverse group of animal hosts by identifying and characterizing differentially expressed genes among kinetoplastid species. We hypothesize that differences in the expression of genes among various kinetoplastid species should identify some of the genes that are critical to the survival and important to the virulence of these parasites. Thus, in the current study we will identify differentially expressed genes between pathogenic and nonpathogenic species of kinetoplastids by cDNA-AFLP and subsequently characterize these genes by sub cloning the amplified fragments and subjecting them to DNA sequence and analyses. The characterization of genes differentially expressed between pathogenic and non pathogenic species could lead to a better understanding of these processes/mechanisms and subsequently how they affect their host organisms.

Does this project involve field work, lab work, or both? Lab

Techniques Involved:

Students will purify the lipase enzyme using column chromatography and perform enzyme assays to determine optimal conditions for enzyme activity. Protocols for this project are well established. Students will identify genes that encode genes associated with pathogenicity in several kinetoplastid protozoa. This work will involve PCR and cloning techniques as well as sequencing which will be carried out at the URI genomics sequencing center.

Project Title: How does signaling in Entamoeba spp affected by environmental stresses (climate change)?

Project Mentor(s): Avelina Espinosa (Roger Williams University)

Project Description: Amoebozoans include Dictyostelium, Gymnamoeba, and Entamoeba. Most amoebozoans are free living, a few are parasitic. Little is known about the basic biology of marine and fresh water amoebozoans, their complex behaviors and interactions, or the effect of climate change on these unexplored groups. Chemical interactions that deter feeding on prokaryotic cells may be common, and may contribute to population- and community-scale processes, affecting trophic structure. Most of free-living protists are unculturable in the laboratory. The Entamoeba lineage is an ideal model to analyze comparative cell signaling between/among amoeba with morphological, multigene, and ecological studies in a laboratory setting. We hypothesize that chemical signaling between diverse Entamoeba will be limited because they live under different ecological conditions. Understanding chemical signaling at the unicellular level will help us understand the effect of environmental stresses, including climate change on fresh water, marine and parasitic marine protists

Project Significance: Understanding chemical signaling at the unicellular level will help us understand the effect of environmental stresses, including climate change on fresh water, marine and parasitic marine protists

Does this project involve field work, lab work, or both? Lab work

Techniques Involved:

  • Fluorescence microscopy, cell culture, protein electrophoresis, bioinformatics, gene cloning, protein expression

Project Title: What are the mechanical properties of the bones and ligaments in the avian shoulder girdle?

Project Mentor(s): David Baier (Providence College)

Project Description: Climate change has been associated with expanding some bird species’ ranges towards the poles which, in turn, is associated with increased migration distance. Flight is also among the most energetically expensive forms of locomotion. Hence any energetic savings may be selectively advantageous, particularly for long distance migratory birds. It has been hypothesized that birds may have elastic storage mechanisms in the shoulder girdle that could conserve energy. Most studies have concentrated on the wishbone (or furcula) an unusually flexible bone that has been shown to bend and recoil during flight. Mechanical testing of the wishbone in isolation suggests that most species could not store useful energy in the furcula, with the notable exception of one long distance migrant possibly gaining a very small energetic benefit. Even tiny energetic savings on short could have major impacts on long distance flights. However, the wishbone is tied to other bones the shoulder girdle by a complex membrane and other joint movements can cause the wishbone to spread. In our lab, we found that structures other than the wishbone may instead store elastic energy. We predict that the strength of these structures should be capable of withstanding expected forces during flight. Measuring their material properties will test this prediction and can be used to estimate potential energy storage.

Project Significance: A classic study suggested that the avian wishbone acted as a spring that could return useful energy during flight. Recent studies in my lab suggest that other structures may act in this capacity. As climate change affects bird migration distances, knowledge of the underlying mechanisms of energy savings are needed to predict the impacts on birds. We currently know very little about how the shoulder girdle transmits forces during flight. Shoulder girdle form varies greatly between species. Knowing the material properties of the ligaments, membranes and bones of the avian shoulder girdle will provide a foundation for exploring how different species may be affected by changes in migratory patterns.

Does this project involve field work, lab work, or both? Lab

Techniques Involved:

  • Dissection, anatomy, mechanical testing and material properties techniques, 3-D modeling combining biomechanics and computer modeling approaches

Project Title: Understanding the evolution of parasitism in red algae

Project Mentor(s): Chris Lane (University of Rhode Island)

Project Description: Red algal parasites are ideal model organisms for investigating the origins of a parasitic life-style for two important reasons. First, most red algal parasites share an immediate common ancestor with an extant free-living red algal species, which is almost always their host, earning them the title adelphoparasites (adelphose is the Greek term for “kin”).

Project Significance: Because of this sister-species relationship between parasite and host, a single pair of organisms can provide direct comparative data on the cellular and genomic changes occurring early in the evolution of a parasite, as well as information on host/parasite co-evolutionary dynamics. Second, hundreds of independently evolved red algal parasites have been described, all with varying degrees of divergence and relationship with their hosts, providing an enormous amount of comparative data with which to test mechanistic hypotheses.

Techniques Involved:

  • We seek students interested in field, laboratory and computer work necessary to use comparative genomics to gain evolutionary insights.

Project Title: The Bermuda Seaweed Project

Project Mentor(s): Chris Lane (University of Rhode Island)

Project Description: The islands of Bermuda are ideally located for marine biodiversity assessment studies, because the isolated archipelago is at the interface of tropical and warm temperate biogeographic zones. Despite its distant location from North America and its tropical summer temperatures, Bermuda’s small size at present supports only ca. 450 species of red, brown and green seaweeds, and endemism among these groups is reportedly less than 3%. The small size of the total flora make it possible to completely assess this archipelago’s algal diversity over a short time period; a project that would be near impossible for larger-sized, and more diversely populated, islands in the Caribbean.

Techniques Involved:

  • Help with the molecular characterization of seaweed samples and assist in the analysis of evolutionary relationships among Bermuda seaweeds
  • DNA extraction, PCR, DNA sequencing and sequence data manipulation

Project Title: Impact of historic industrial waste in Narragansett watershed on microbial life

Project Mentor(s): Christopher Reid (Bryant University)

Project Description: Climate change forecasts for the Northeastern U.S. predict increased precipitation and more severe storm events. This will result in a greater influx of fresh water into Narragansett Bay, in many areas carrying high contaminant loads from inland sites or flushing contaminants from near shore contaminated sites. This transport of historic industrial waste and its degradation products from the Narragansett watershed into the bay and shore communities could have dramatic consequences for marine and human life in and around the bay.     This study proposes to look at the systematics of historic river sediment contamination of the Blackstone river, its transport and effects on the freshwater and intertidal microbial communities. This work is tied to Dr. Parmentier’s work on the Providence River and metal contamination into the intertidal regions of Narragansett bay.   This year’s work will focus on refining our analytical tools to identify degradation products of textile dyes in river sediment and investigate the distribution of these compounds between the sediment and bulk water. This project will continue to develop methods for the analysis of carcinogenic amines from river sediment and the evaluation of the microbial community from these contaminated sites. The link between industrial waste and antimicrobial resistance will be investigated.

Project Significance: This project will investigate the impact of historical industrial waste contamination in the Blackstone River on the microbial community.

Does this project involve field work, lab work, or both? Both

Techniques Involved:

  • Solid-phase extraction
  • High performance liquid chromatography (HPLC)
  • Microbiology
  • PCR

Project Title: How is protein expression of marine invertebrates affected by projected ocean temperature and pH changes?

Project Mentor(s): Steven Irvine (University of Rhode Island) & Thomas Meedel (Rhode Island College)

Project Description: Ciona intestinalis adults will be reared at control conditions and at conditions simulating ocean warming and acidification. Gonads will be dissected and protein extracted and sent to the Brown Epscor Proteomics Center to be analyzed using liquid chromatography/mass spectroscopy. The data will be analyzed to determine which proteins are up or down-regulated in the different conditions. Relative fecundity of animals at different conditions will also be tested. Protein expression and fecundity changes, if detected, will be compared to infer possible physiological stresses on the reproductive system of the animals.

Project Significance: Protein expression profiles are readouts of the physiological state of an organism. New technology enables global assessment of protein expression in detail at low cost. The aim is a pilot project to determine if protein expression changes can be detected when the ascidian Ciona intestinalis is reared at temperature and pH levels consistent with projected ocean warming.

Does this project involve field work, lab work, or both? Both

Techniques Involved:

  • Aquarium setup and animal care at the EPSCoR Marine Life Sciences Center at URI Bay Campus
  • Dissection and protein extraction in the lab
  • Analysis of proteomic datasets

Project Title: Do chemicals in the environment affect embryonic development in the cartilaginous marine fish?

Project Mentor(s): Rebeka Merson (Rhode Island College)

Project Description: The little skate, Leucoraja erinacea, deposits eggs on marine substrates where they spend 8-12 months prior to hatching. We have cloned and partially characterized the aryl hydrocarbon receptor (AHR) from sharks and skates (cartilaginous fish in the class Chondrichthyes); this receptor mediates the toxicity of dioxins and similar chemicals known to be widespread and persistent in the environment, including Narragansett Bay. The research undertaken will address questions regarding the impacts of exposure to environmental AHR agonists on the health of the developing embryo. Certain functional characteristics of the AHR will be evaluated (ligand binding, transcriptional activation).

Project Significance: Numerous chemicals known to be toxic are widespread and persistent in the environment. Some have suggested that changes in global and local weather patterns could alter contaminant distribution; of concern is the possibility of higher level inputs into aquatic and marine environments. These pollutants cause adverse health effects in humans, domestic animals, and wildlife. Revealing the molecular mechanisms behind toxic responses can aid in assessing species sensitivities, predicting impacts, and planning interventions.

Does this project involve field work, lab work, or both? Lab

Techniques Involved:

  • Light microscopy
  • Several experimental methods including mammalian cell culture and reporter gene experiments
  • Excel and Prism software, Adobe Illustrator

Project Title: To determine the molecular mechanism of action of stichodactyla toxin

Project Mentor(s): Geoff Stilwell (Rhode Island College)

Project Description: We will use Drosophila melanogaster as a model system to express candidate peptide toxin genes. In this initial phase, we will use molecular biology techniques to clone stichodactyla toxin (STX) derived from the Caribbean sea anemone into a transformation vector and insert this peptide toxin gene into Drosophila under the control of an inducible promoter. We will then use genetic screening techniques to mutagenize Drosophila and isolate mutants that are resistant to the toxin.

Project Significance: Many marine organisms produce large number of toxins, which are used for predation or self-defense. To address this large and uncharacterized biodiversity, we are establishing a model to understand how peptide toxins exert toxicity at a molecular level. This research will lay a foundation for further studies that involve cataloging toxins and understanding biological action. This work will also provide background data for future studies to characterize the effect of climate change on toxin production for various species.

Does this project involve field work, lab work, or both? Lab

Techniques Involved:

  • General molecular biology techniques including cloning, PCR, gel electrophoresis, etc. Students will also learn advanced genetic techniques including creating and working with Drosophila transgenic lines.

Project Title: What is the potential for evolutionary adaptation of marine organisms to climate change?

Project Mentor(s): Jason Kolbe (University of Rhode Island) & Carol Thornber (University of Rhode Island)

Project Description: The broad objective of our research is to investigate the potential for evolutionary adaptation to climate change, using a rapidly reproducing species of marine shrimp (Neomysis americana) that is native to Narragansett Bay, Rhode Island as our model organism. We have identified two main goals, as follows:

  • Aim I — to estimate genetic basis of a suite of behavioral, life history, morphological, and physiological traits that may be sensitive to increased temperatures.
  • Aim II — to conduct a laboratory natural selection experiment to estimate the phenotypic response of traits in populations experiencing current and predicted future temperatures.

We will accomplish these goals through a series of controlled laboratory experiments, including breeding shrimp to estimate genetic variances and subjecting populations to different water temperatures to measure the response to selection.

Project Significance: The scientific merit of this research is to identify which traits are capable of responding to natural selection due to increased ocean temperatures. We will collect detailed genetic data from breeding and natural selection experiments that will evaluate the evolutionary potential of a suite of traits in a species of marine shrimp. Our research will contribute to a broader understanding of the evolutionary potential of marine species to climate change. By using a species that has been extensively studied in ecological contexts, we will be able to track potential changes in a broad suite of ecologically significant traits.

Does this project involve field work, lab work, or both? Both

Techniques Involved:

  • A mixture of labwork and fieldwork in Narragansett Bay, URI, and at the US EPA facility in Narragansett, RI
  • Perform marine evolutionary laboratory experiments at the EPA facility, working directly with a graduate student
  • Learn lab husbandry of mysid shrimp populations and use of video analysis equipment to collect data on swimming speed and thermal tolerances
  • Ability to identify marine invertebrates/knowledge of using dichotomous taxonomy keys is definitely a plus
  • May have to work some weekend/irregular hours to accommodate low tide schedules, but this research is primarily lab based

Project Title: Differential effects of temperature change on southern New England intertidal consumers

Project Mentor(s): Patrick Ewanchuk (Providence College)

Project Description: We plan to conducted laboratory experiments using two consumers in the southern New England shoreline, Nucella lapillus and Urosalpinx cinerea, both of which play an important role in maintaining the abundance and diversity of intertidal species. We will examined the response of N. lapillus and U. cinerea to potential changes in average summer water temperature as well as how these changes affect their competitive interactions.

Project Significance: Impacts of climate change has been shown to effect air and water temperature, weather patterns, species distributions and ecological interactions. Marine intertidal species may provide a unique model to address the effects of these changes as they are situated at the border of marine and terrestrial environments. In addition, species at the extremes of their thermal limit may be positively or negatively affected by temperature as shown through changes in an organism’s feeding rate, growth rate, and survivorship.

Does this project involve field work, lab work, or both? Both

Techniques Involved:

  • Care for marine intertidal organisms
  • Set up and design of competition experiments
  • Data collection and analysis
  • Field work to collect animals for study
  • Field work may also involve population density and size structure data collection

Project Title: The cellular structure of complex colonial animals

Project Mentor(s): Casey Dunn (Brown University)

Project Description: The siphonophores are a group of pelagic colonial cnidarians found throughout the oceans of the world. We recently described the distribution of stem cells in siphonophore colonies, and are currently testing ideas about how they give rise to all the different cell types that are present. A critical challenge, though, is the incomplete descriptions of which mature cell types are even present at the end of the developmental process. In this project, a student will describe the histology of siphonophore colonies using advanced gene expression and microscopical imaging technologies. Specimens will be collected in Rhode Island Sound.

Project Significance: Siphonophores are top predators and among the most abundant large organisms in the open ocean. Little is known about them, though, because they are fragile and difficult to collect. This project addresses an important gap in our understanding of these organisms – the distribution of cell types within and between the zooids that make up siphonophore colonies. The findings are relevant to understanding the functional biology, behavior, development, morphology, and life cycles of these organisms. The findings will help integrate a fine cycle understanding of cell proliferation and differentiation with larger scale topics such as life history and ecology.

Does this project involve field work, lab work, or both? Both

Techniques Involved:

  • Transmission electron microscopy
  • In situ mRNA hybridization
  • Two-photon microscopy
  • Confocal microscopy
  • Immunohistochemistry

Project Title: How is hydrocarbon contamination affecting the microbial population at the intertidal zone under changing conditions?

Project Mentor(s): Dan McNally (Bryant University)

Project Description: This work will focus on the PAH component of a historic diesel spill on Prudence Island in Narragansett Bay. The diesel oil floats on top of the groundwater that flows out into the bay. Preliminary work indicates there are no PAH degraders. Further investigation is needed to characterize the microbial community and determine why specifically, there are no bacteria utilizing the diesel oil as a carbon and energy source. Toxicity studies will be conducted to determine inhibiting factors and indicate what needs to be done to enhance bioremediation of the site.

Project Significance: Much of the shoreline around Narragansett Bay  is contaminated with toxic chemicals and these chemicals are seeping into the bay. An investigation into the contaminations effect on microbial communities, under changing growth conditions due to climate change, will provide knowledge on the potential bioremediation and cleanup of these sites.

Does this project involve field work, lab work, or both? Both

Techniques Involved:

  • Conduct field work (develop a sampling plan, implementing sampling protocols, utilizing sampling equipment, measuring site conditions, etc.)
  • Characterize and enumerate bacteria under aerobic and anaerobic conditions
  • Screen for PAH degrading bacteria
  • Characterize the sediment using multi-meters and ion chromatograph instrumentation
  • Identify and quantify contaminates using a GC/MS
  • Conduct a statistical analysis and interpretation of the data

Project Title: Do stress and diet affect the composition of intestinal mucus in Summer Flounder?

Project Mentor(s): Bruno Soffientino (Community College of Rhode Island) & Marta Gomez-Chiarri (University of Rhode Island)

Project Description: The study will focus on the role of intestinal mucus on defenses against infection by Vibrio harveyi. Because of the protective function of intestinal mucus, a more thorough characterization of the effect of stress and dietary challenges on the intestinal mucus layer is necessary to understand their physiological implications for health and disease.  The SURF student will carry out lectin histochemistry on intestinal samples of summer flounder exposed to different stressors (such as transport or temperature stress) and dietary challenges and characterize changes in cell membrane and mucus oligosaccharide composition.  The work will be carried out in the laboratory of Dr. Marta Gomez-Chiarri at the University of Rhode Island.  The student will be recruited from the Community College of Rhode Island, and will be mentored jointly by Drs. Soffientino and Gomez-Chiarri.

Project Significance: The projected climate change-induced temperature increase in our coastal waters is expected to increase stress and cause higher susceptibility to disease in wild and aquaculture species.  It is therefore necessary to study how potentially commercially and ecologically important fish like summer flounder fight off disease, and to develop rearing strategies that maximize growth while boosting immune function. As part of this effort, Dr. Marta Gomez-Chiarri and other researchers at URI have undertaken studies on the immune function of summer and their responses to pathogens, such as the bacterial pathogen Vibrio harveyi.   This opportunistic pathogen causes disease in many marine species, including crustacean, molluscs and fish, in temperate estuaries worldwide during warm summer months.  The goal of this work is to use summer flounder as a model to understand the pathogenesis of disease caused by Vibrio harveyi, as well as determine which stresses lead to disease outbreaks.

Does this project involve field work, lab work, or both? Lab

Techniques Involved:

  • Tissue preparation for histological examination
  • Tissue staining
  • Tissue histochemistry
  • Light microscopy

Project Title: Can we develop a robust and general esterification protocol to determine the FA content in marine samples?

Project Mentor(s): Lauren Rossi (Roger Williams University)

Project Description: Fatty acids are acquired through the human diet and play a role in cellular functions, including inflammation. A diet rich in unsaturated fatty acids, particularly omega-3 and omega-6 polyunsaturated fatty acids (PUFAs) from marine food sources, have been associated with a greater cardiovascular health and a decrease in the risk of some cancers. The common means of determining the content of the beneficial PUFAs within food samples is to derivatize the fatty acid (carboxylic acid functional group) to a fatty acid methyl ester (FAME), which subsequently is analyzed through gas chromatography. Preliminary results have resulted in an esterification protocol that involves microwaving a known FA sample in under two minutes. Optimization of the conditions is required to permit this method to be robust and general. Both optimization and application of the resulting protocol will be examined.

Project Significance: Fatty acids (FAs) are lipidic carboxylic acid compounds that can be found in various organisms including plants and animals. The AOCS (American Oil Chemistry Society) official method of determining the free fatty acid content (qualitative or quantitative) within food samples is to derivatize the carboxylic acid functional group to a fatty acid methyl ester (FAME) using a boron trifluoride- methanol complex.The AOCS official method has been shown to have limitations and variable effectiveness. Inconsistent FA content profiles of marine samples have been reported, likely due to the reactivity of the PUFA unsaturation unit under the reaction conditions. A better esterification method would subsequently allow a better understanding of the fatty acid content in the fish samples. In addition, variability in FA profile due to environmental stresses would provide a better understanding of the effects climate change may have upon the marine environment as well as our food web.

Does this project involve field work, lab work, or both? Lab

 Techniques Involved:

  • Read and discuss primary scientific articles relevant to the reactions to be conducted
  • Setup bench-top and microwave chemical reactions
  • Safe handling of different chemicals
  • Setup, operate, and assess the progress and success of a chemical reaction (TLC, GC, NMR)
  • Maintain a research notebook
  • Safely operate and interpret data from instruments (GC, IR, NMR)

Project Title: What is the adhesion strength of Ulva linza as a function of temperature?

Project Mentor(s): Lucie Maranda (University of Rhode Island) & Wayne Tucker (Naval Undersea Warfare Center)

Project Description: The benthic green alga Ulva linza is often used as a model organism in studies of the fouling process, as well as for testing the capacity of experimental materials to resist fouling. This alga releases flagellated spores (5 to 7 μm) to the surrounding water; the planktonic cells swim toward a solid surface where they attach by producing a permanent adhesive. This leads to the subsequent development of the attached mature plant. This species survives within a wide range of temperatures. However spore discharge is more abundant in summer than spring months, whereas the adhesive is of a greater strength when produced at low rather than high temperatures (e.g., 4 °C vs. 20 °C). These propensities imply a potential modification to the fouling burden imposed on underwater man-made structures with the rise in temperature associated with climate change.  This project seeks to characterize the adhesion strength of U. linza as a function of temperature. Glass slides will be exposed to a suspension of competent spores obtained from mature specimens collected in the field. The attached spores will be exposed at three temperatures to a range of water turbulence generated from calibrated water jets. The concentration of remaining attached spores after water-jet exposure will be compared to the concentration of unexposed spores. The water-jet system is a patent-pending apparatus that allows water flowing at a chosen pressure to strike an underwater surface for a chosen length of time; an algorithm can translate the pressure at the point of impact to the speed of a moving vessel.  This project offers hands-on approaches in biology (field and lab) and statistics, with a touch of engineering. This inquiry falls within one of the three specific EPSCoR research questions, namely:  How will global climate change affect the ecology of marine pathogens and parasites? Although Ulva linza is not considered a pathogen or a parasite, it is a nuisance alga given its fouling habit that leads to loss of performance in the maritime industries, and associated economic costs. The Graduate School of Oceanography and the College of Engineering at the University of Rhode Island are collaborating with the Naval Undersea Warfare Center, Newport, on this project.

 Project Significance: Ulva linza is a nuisance alga because it settles on any underwater structures, natural or man-made. The resulting fouling affects performance and increases maintenance costs. Because the strength of the initial spore adhesion is a function of temperature, it is important to determine to which extent this temperature effect might influence fouling load.

Does this project involve field work, lab work, or both? Both

Techniques Involved:

  • Collection of algal material in the intertidal zone
  • In-lab forced algal sporulation
  • Experimental design and hypothesis testing
  • Microscopy: light and epifluorescence, manual and/or software-based cell enumeration, photography
  • Detailed record keeping
  • Statistical analysis

Project Title: How can cutting edge genetic methods best be used in conservation biology?

Project Mentor(s): Jeffrey Markert (Providence College) & Thomas J. McGreevy, Jr. (University of Rhode Island)

Project Description: Genome sequencing technologies are now speedy and affordable.  In principle, NextGeneration sequencing can be used as a tool in conservation biology in two distinct ways.  The first is that it can be used to identify populations that are at risk due to lost genetic diversity.  The second is that it can be used to identify alleles that are important for population survival.

In order to explore the utility of these methods, we work with a small estuarine species – the opossum shrimp, Americamysis bahia.  By working with large numbers of isolated populations of these creatures in the lab, we can simulate various environmental challenges and then use genomic technologies to assess the impacts of these challenges.  Our ultimate goal is to use the results of these laboratory studies to develop NextGeneration genomic assessment techniques that can be used to both identify populations and species that are ‘at risk’ AND to design conservation strategies to protect them.

Background information and early steps in this process are described in this BMC Evolutionary Biology paper written by our team — http://www.biomedcentral.com/1471-2148/10/205

We encourage interested students from any RI EPSCoR institution to consider working with our group.

Project Significance: DNA sequencing technologies continue to become more powerful and more affordable.  For the first time, these technologies have the potential to be applied as a practical tools in conservation biology.  However the methods for applying these tools and interpreting the results have yet to be fully developed.

Does this project involve field work, lab work, or both? Both

Techniques Involved:

  • Mysid culture
  • Experimental design
  • Population genomic analyses
  • DNA isolation
  • Next generation DNA sequencing
  • Field ecology

Project Title: Systematics of trace metal transport, and bio-uptake in urban intertidal zones, Narragansett Bay, RI

Project Mentor(s): Julia Crowley Parmentier (Bryant University)

Project Description: This study proposes to look at the systematics of trace metal transport and deposition in the intertidal zone of the Providence River where existing and former industrial sites are located at the shoreline. Previous work identified the presence of elevated concentrations of metals at several sites in this area.  This year’s work will focus on collecting the data necessary to understand the mechanisms governing dissolution and precipitation of these metals in the estuarine/groundwater mixing zone, known as the subterranean estuary.

Project Significance: Climate change forecasts for the Northeastern U.S. predict increased precipitation and more severe storm events.  This will result in a greater influx of fresh water into Narragansett Bay, in many areas carrying high contaminant loads from inland sites or flushing contaminants from near shore contaminated sites.  Complex chemical interactions at the saltwater-groundwater interface result in some metal contaminants precipitating, others dissolving into seawater, or complexing with organic or inorganic compounds.  The ultimate fate of a metal species governs its potential uptake by marine organisms and incorporation into the food chain.

Does this project involve field work, lab work, or both? Both

Techniques Involved:

  • Students will learn the following techniques:
  • Developing a sampling plan
  • Collecting sediment and water samples for metals analysis
  • Measuring pH, Conductivity, Dissolved Oxygen at sampling sites
  • Acid digestion for metals analysis
  • Preparation of Standards
  • ICP MS analysis and data reduction
  • Report preparation

Project Title: Impacts of climate change on harmful macroalgal blooms

Project Mentor(s): Carol Thornber (University of Rhode Island) & JD Swanson (Salve Regina University)

Project Description: This project will be conducted under the guidance of Dr. Carol Thornber (URI) and Dr. JD Swanson (SRU). Drs. Thornber and Swanson are currently investigating the regulation of algal blooms by determining the responses of algae to different climate change scenarios. The fellow’s project will involve frequent fieldwork (Thornber lab) to conduct surveys of, and experiments on, bloom recruitment and growth, as well as more limited genomic work (Thornber and Swanson labs). The student will spend the majority of his/her time at the URI Marine Life Sciences Facility conducting macroalgal bloom experiments.

Required skills for this project include an ability to work carefully and independently, comfort in working outside in inclement weather, a valid driver’s license and vehicle, a flexible work schedule as some weekend work may be required, and a familiarity with Microsoft Excel. It is preferred that the student has experience in identifying marine macroalgae (seaweed). The student may expected to spend part of his/her time at URI and part of his/her time at SRU.

Project Significance: Blooms of macroalgae (seaweed) frequently occur in estuarine systems worldwide. Macroalgal blooms can cause serious ecological and economic impacts on nearshore marine communities and are thus of considerable interest to scientists, managers, and coastal human populations. As climate change occurs, the magnitude and duration of blooms is predicted to increase, which may also have strong impacts on the structure and functioning of coastal marine food webs. This project will investigate the responses of these blooms to different climate change scenarios, on both ecological and molecular levels.

Does this project involve field work, lab work, or both? Both

Techniques Involved:

  • Learn how to identify bloom-forming algae using morphological and likely molecular approaches, algal culturing techniques and ecological field protocols.
  • Gain extensive experience setting up, maintaining, and analyzing data from laboratory-based seawater experiments.
  • Work collaboratively with Thornber’s colleague Swanson at SRU to gain experience in DNA and RNA extraction protocols.

Project Title: Sea star wasting disease

Project Mentor(s): Marta Gomez-Chiarri (University of Rhode Island) & Gary Wessel (Brown University)

Project Description: The local sea star Asterias forbesi has been decimated this past year by an infectious disease. The goal of this research is to characterize Sea Star Wasting Disease (SSWD) and try to identify the causative agent of this disease. We will take a multipronged approach to identify the pathogen(s) and the infectivity — 1) re-test infectivity conditions of sea stars, using a cross species assay and define conditions for transfer of infectivity;  2) the infectious sea water and tissues from infected sea stars showing clinical signs of the disease will be tested for microbe growth on media plates, identification of species both by morphology and by DNA sequencing of PCR ampicons of the ribosomal intervening sequences; 3) the pathology of the infected organisms will be characterized using histology; 4) following its identification we will test its prevalence and distribution in sea stars and other marine organisms along the northeast coast to determine the extent of its habitat.

Project Significance: Six Rhode Island investigators and three students representing three different Rhode Island Institutions will identify the pathogenic cause of the sea star wasting disease that has devastated this prevalent organism in the ocean waters of Rhode Island and along the northeastern coast of the United States. It is important to understand the etiology of this disease because we believe it represents a larger issue of environmental instability and pathogen invasiveness that impacts a prevalent biomass of our region. The disease appears to spread even across species, making the economic base of the commercial marine biomass of Rhode Island susceptible to future attack.  It is possibly a pending disaster for our state’s fisheries industry that needs to be identified before the industry collapses.

Does this project involve field work, lab work, or both? Both

Techniques Involved: 

  • Microbiological techniques
  • Polymerase chain reaction
  • Microscopy
  • Exposure of sea stars to pathogens
  • Field collection of sea stars
  • Evaluation of clinical signs

Project Title: Phylogenetic relationships of the species of the mysid crustacean Americamysis

Project Mentor(s): Elisabeth Arevalo (Providence College) & Anne Kuhn (EPA-AED)

Project Description: A team of researchers from three institutions in RI are collaborating to study several biological aspects of two local species of the mysid shrimp of the genus Americamysis, which is distributed along the US east coast. We would like to assess the potential effects of climate change on the population genetics, natural history and demographic parameters. Specifically, my participation in this project involves the development of diagnostic nuclear and mitochondrial markers for the sequencing and assessment of the phylogenetic relationships between the different species within this genus. Currently, the distinction between its six species is solely done by morphological characters. The boundaries between these morphospecies need to be revised.

Project Significance: Species within the genus Americamysis are so far defined solely on morphological characters. Assessing the phylogenetic relationships of this group would be use to determine whether existing morphospecies are concordant with genetic species. The results from this project will be critical to ensure that subsequent experiments are conducted on “true” species. Ultimately, we will try to assess whether the impact of environmental change is differentially affecting the distribution and biological parameters of these RI estuarine species.

Does this project involve field work, lab work, or both? Both

Techniques Involved:

  • Different microscopy techniques will be learned: dissecting, confocal and scanning electron.
  • Molecular methods used include: DNA extraction, PCR, DNA sequencing; sequence alignment and analysis with different software programs, phylogenetic and statistical analysis.
  • Field sample collections

Project Title: Effect of climate on competition

Project Mentor(s): Maia Bailey (Providence College) & Diane Nacci (EPA)

Project Description: Opossum shrimp (Americamysis spp.) are important members of estuary food webs. Two Americamysis species live in Narragansett Bay and may shift distributions under climate change. We will be looking at competitive relationships between these two species, A. bahia and A. bigelowi, under a range of temperature and salinity conditions to try to predict the role of competition in future distributions and changes in local food webs.

Project Significance: Climate change is expected to shift species distributions toward the poles as the climatic regions which they can tolerate move. This will change the species we will find in Narragansett Bay as well as the relationships among species including predator-prey interactions. By looking at the effect of climate on important estuarine species, we can better predict how climate change will affect economically important fish stocks and other upper-level consumers.

Does this project involve field work, lab work, or both? Both

Techniques Involved:

Students will learn about experimental design, animal culture, as well as morphological and genetic markers for species identification.

Project Title: How does the gene expression change in Ulva blooms

Project Mentor(s): JD Swanson (Salve Regina University) & Carol Thornber (University of Rhode Island)

Project Description: Students will identify differentially expressed candidate genes from our next generation sequencing data bank and will create qPCR primers.  They will then finely track gene expression of these genes using a RNA bank that is from Ulva samples collected monthly over a one year period.  They will then correlate these data with ecological data collected by Thornber over the same time period to try to identify if any correlation exists between observed gene expression and environmental factors.

As well as looking at single genes, students will also be encouraged to survey the global data sets to identify if classes of genes or pathways are changing in response to the changes in the environment over the course of a year.

Project Significance: As ocean temperatures have risen and anthropogenic nutrient inputs into marine systems have increased, the number and severity of harmful algal blooms have risen steadily worldwide. When bloom-forming algae, including macroalgae, experience the appropriate suite of nutrient, temperature, and light conditions, the resulting increase in algal biomass can far exceed the ability of herbivores to control them, resulting in severe negative ecological and economic impacts.  Because most algae have complex, multiphasic life cycles, a bloom may be composed of one or more separate life stages, which may have specific, distinct triggers for rapid growth. However, little data exist on the population dynamics of macroalgal blooms (including ploidy level and degree of relatedness of individuals within blooms) and their underling functional genetics. Thus, assessing the impacts of climate change on bloom dynamics can be challenging. Knowledge of how these populations respond to changes in bloom-promoting factors is critical to understanding the potential for genomic and ecological controls to altered bloom dynamics in response to a changing climate.

Does this project involve field work, lab work, or both? Lab

Techniques Involved:

  • Work with computational tools in particular the analysis of Next-generation data.
  • Extract DNA and RNA samples,  conduct PCR, and qPCR.
  • Learn how to prepare and run agarose gels and will learn to quantify nucleic acids.

Project Title: Causes of long-term declines of coral reef communities

Project Mentor(s): Graham Forrester (University of Rhode Island)

Project Description: Students would participate in a 21-year long project that has been examining the interactive effects of multiple stressors on 8 coral reefs in the British Virgin Islands.  The goal of the SURF project is to examine the relative effects of local (boat anchoring and coastal development) and global (climate-induced bleaching) on coral communities

Project Significance: Coral reef communities are being progressively altered by a mix of human activities, the most important of which are overfishing and climate change.  Understanding the relative effects of different agents of change is important to design conservation strategies for reefs.

 Does this project involve field work, lab work, or both? Field

Techniques Involved: The project will include a mix of analyzing existing coral monitoring data that has been collected annually since 1992, and the collection of new data in the field during summer 2014. I will hold regular meetings with the SURF fellow(s) during which I will first assist with the location of primary research literature and help them write a short proposal outlining their project. I will provide training in data management and analysis.  Students will learn how to test hypotheses using linear models in SPSS. Fieldwork in the Virgin Islands will be for 4 weeks in late June/early July. I will be present at the field site working with the student full-time every day. They will learn quantitative methods for underwater coral monitoring on reefs. Before and during the trip I will provide training and supervision on methods for the safe performance of SCUBA-based research, following URI diving safety training procedures. Certification as an AAUS research diver is required before the trip. I will also help with graphical and visual presentation of the results, writing of the poster, and possible preparation of the results for publication.

Project Title: Mechanisms that contribute to nitrous oxide production from marine sediments and invertebrates

Project Mentor(s): Melanie Garate (University of Rhode Island)

Project Description: This summer, working in the Moseman-Valtierra lab, I plan to measure the contributions of subtidal tube and burrow-building taxa (M. mercenaria and A. abdita) to N2O fluxes by comparing emissions from modified sediments vs sediments with active invertebrates. Quantify the relative contributions of sediments, water and invertebrate organisms on N2O fluxes. Students who are research diving certified are strongly encouraged.

Project Significance: Efforts are needed to quantify the global budget of greenhouse gases, particularly to those of the pertinent greenhouse gas, nitrous oxide (N2O). This study could provide substantial evidence that anthropogenic nitrogen pollution and ocean warming are contributing to global climate change and that this occurs in part by increase direct and indirect N2O releases from invertebrates. Results from this study will provide information that can be used to evaluate responses of valuable coastal ecosystems to anthropogenic nutrient pollution.

 Does this project involve field work, lab work, or both? Both

Techniques Involved:

  • We will use two instruments: gas chromatograph and cavity ring down spectrometer. We will also be regularly measuring water chemical/physical parameters: pH, dissolved oxygen, temperature, and redox potential.  Students will also learn basic animal care in aquaria and how to measure their composition index.

Project Title: What are the implications of climate change on the population dynamics and biotic interactions among winter flounder, summer flounder, and blue crabs?

Project Mentor(s): David Taylor (Roger Williams University)

Project Description: The summer flounder and blue crab support lucrative fisheries throughout their geographic distribution. These temperate species mainly occupy estuarine and inner continental shelf waters, with maximal abundances occurring in the Middle-Atlantic Bight. Empirical data, however, note a recent northward shift in the distribution of juvenile summer flounder and adult blue crabs, such that their abundances have increased in southern New England estuaries, e.g., the Narragansett Bay (RI/MA, USA) and its associated tidal rivers and coastal ponds. Moreover, the apparent geographic range expansion of these species may be mediated by climate change, with potential implications to local food-web dynamics and benthic community structure.

The winter flounder have historically supported a premier fishery along the northeastern United States. There are continued concerns, however, because winter flounder populations have declined precipitously in southern New England since the early 1980’s and have yet to rebound during the last three decades. Although overexploitation was paramount in their initial population decline, several other factors could continue to adversely affect winter flounder recruitment, and thus keep adult populations at depressed levels. The decline in winter flounder abundance in Narragansett Bay, for example, coincides with a significant warming trend in northern-temperate estuaries. Elevated temperatures, in turn, may intensify the predator-induced mortality of juvenile winter flounder by increasing the metabolism and consumption rate of local predators. Further, subtle increases in temperature may cause a poleward shift in the distribution of more southerly-located species, including the summer flounder and blue crabs, resulting in a spatio-temporal overlap with juvenile winter flounder in the Bay and newly established competitive and/or predator-prey interactions. The decline in winter flounder abundance in Narragansett Bay, coupled with changes in climatic conditions, has raised the question of whether these previously overexploited stocks can recover in the face of altered trophic dynamics.

The objectives of the proposed research are to examine the population dynamics and biotic interactions among winter flounder, summer flounder, and blue crabs, and evaluate how these relationships are affected by climate change. Further, the proposed research will perform a broader examination of each focal species impact on local food webs and benthic community structure. The specific aims of the research are as follows:

  • Aim 1 — Assess the suitability of Narragansett Bay as habitat for juvenile winter flounder, juvenile summer flounder, and blue crabs, and thereby quantify the spatio-temporal overlap among species. Species-specific abundance patterns will be used to evaluate habitat use, which will be further analyzed in the context of local environmental conditions (e.g., water temperature, salinity, and dissolved oxygen).
  • Aim 2 — Examine the putative biotic interactions among winter flounder, summer flounder, and blue crabs with three approaches: (a) conventional stomach content analysis, (b) stable isotope measurements, and (c) biochemical techniques, i.e., polymerase chain reaction (PCR)-based molecular methods for detecting prey DNA. Diet indices and direct visual analysis of stomach contents will be used to assess competitive and predator-prey interactions among the focal species, as well as assessing their ecological roles in structuring the benthic community.

Project Significance: The waters of northern-temperate estuaries have been experiencing a significant warming trend over the last several decades.  Concurrent with the changes in water temperature has been a significant decline in local populations of winter flounder (Pseudopleuronectes americanus), perhaps due to the increased mortality of the juvenile life stage.  The potential negative effect of increased temperature on juvenile flounder is imposed, not directly as a physiological mortality factor, but rather by altering trophic dynamics.  For example, elevated temperatures intensify the predator-induced mortality of juvenile winter flounder by increasing the metabolism and thus consumption rate of local predators.  Moreover, in the northwest Atlantic, subtle increases in water temperature have caused a poleward shift in the distribution of several marine species, including the summer flounder (Paralichthys dentatus) and blue crab (Callinectes sapidus), which in turn could adversely affect winter flounder populations by altering local predator-prey and competitive interactions.

Does this project involve field work, lab work, or both? Both

Techniques Involved:

  • Field sampling techniques — beach seines, otter trawls, beam trawls, small-boat handing, measuring environmental parameters
  • Laboratory techniques — visual analysis of predator stomach contents via the use of stereomicroscopes; diet analysis via the use of molecular techniques, e.g., polymerase chain reaction (PCR) methods; sample preparation via the use of lyophilizer
  • Data analysis — statistical analysis via Excel “data analysis” and SAS statistical software; analysis of spatially explicit data via ArcMap GIS software

Project Title: Is the new nitrogen removal process at the Field’s Point wastewater treatment plant a significant source of nitrous oxide emissions?

Project Mentor(s): Elizabeth Brannon (University of Rhode Island) & Serena Moseman-Valtierra (University of Rhode Island)

Project Description: Nitrous oxide fluxes will be measured at the Field’s Point wastewater treatment plant in Providence, RI twice a month. Measurements will be made in each zone of the nutrient removal process (2 aerated and 2 anoxic) by connecting a floating gas-trapping chamber to a Picarro G2508, a cavity ring down (CRDS) spectrometer that measures nitrous oxide concentrations in real time. Water samples from each zone will also be collected, equilibrated, and analyzed for dissolved nitrous oxide on a gas chromatograph.

Project Significance: Nitrous oxide is a greenhouse gas with 300 times the radiative forcing potential of carbon dioxide and is the major source of ozone-depleting nitric oxide and nitrogen dioxide. The concentration of nitrous oxide in the atmosphere has increased 44 ppb from its pre-industrial level. The primary source of this increase is believed to be enhanced microbial production in expanding fertilized agricultural lands. However, recently nitrous oxide has also been found to be a significant by-product of the nitrogen removal process employed at some wastewater treatment plants. Quantifying the magnitude of the emissions is necessary before mitigation can begin.

Does this project involve field work, lab work, or both? Both

Techniques Involved:

  • The undergraduate involved with the project will assist with the measurements at the wastewater treatment plant. The student will learn to use the gas analyzer (Picarro G2508) and how to analyze the data output of the instrument, which involves work with MatLab.  The student will also learn how to run dissolved samples on the gas chromatograph.

Project Title: Does Phragmites australis invasion alter fluxes of the greenhouse gases carbon dioxide and methane?

Project Mentor(s): Rose Martin (University of Rhode Island)

Project Description: This project is a continuation of research that began last summer as a component of Rose Martin’s dissertation research in the lab of P.I. Serena Moseman-Valtierra, Ph.D.  As part of the investigation, SURF students will have the opportunity to assist with all aspects of the project: from field and lab experiments to data management using Excel and MatLab.

This research is being conducted at two study sites: one in Jamestown, RI and the other in Falmouth, MA.  Both these sites experiencing Phragmites invasion.  Bi-weekly, CO2 and CH4 measurements will be taken from within Phragmites-invaded zones of each marsh and from within the native species-dominated high marsh.  Supporting data on soil and plant parameters will be collected, and soil cores will be collected and brought back to the lab for subsequent analysis of microbial communities related to methane production.

Results of this research will provide insight into effects of invasive Phragmites on net greenhouse gas emissions from coastal marshes, which will help to inform management decisions as Phragmites invasion progresses.

Project Significance: Carbon dioxide (CO2) and methane (CH4) emissions are increasing as a result of anthropogenic activity, driving global climate change.  Although salt marshes do not typically produce significant CH4 emissions due to their high salinities, exotic species invasions, which may be exacerbated by climate change, has been shown to lead to increased CH4 fluxes from salt marshes.  Given the rapid rate at which the invasive Eurasian grass Phragmites australis is invading wetlands on the North American East Coast, understanding its potential impacts on climate-altering CO2 and CH4 emissions will help inform coastal management decisions.

 Does this project involve field work, lab work, or both? Both

 Techniques Involved/Field:

  • Use of cavity ringdown spectroscopy real-time greenhouse gas analyzer (Picarro Labs) to measure greenhouse gas fluxes from the marsh surface
  • Soil parameter measurements: pH, soil moisture, oxidation-reduction potential, porewater collection and sulfide analyses, salinity
  • Plant measurements: stem density, percent cover, salt marsh species identification
  • Collection of soil cores and proper storage for molecular analyses

 Techniques Involved/Lab: 

  • DNA extraction and purification from soil cores
  • PCR to amplify specific genes from archaea involved in methanogenesis
  • qPCR to quantify methanogens in soil samples
  • Data analysis:
  • Use of MatLab to organize gas flux data from the Picarro analyzer

Project Title: How will sea level rise affect abundance and distribution of near shore invertebrate and fish populations

Project Mentor(s): Jameson Chace (Salve Regina University)

Project Description: Ecological theory predicts that organisms are most abundant within the optimal range of limiting physical conditions.  In the intertidal zone, small fish and invertebrates are sensitive to temperature change.  Changes in water temperature with climate change will stress some populations causing an evolved response or migration.  The project measures those conditions today and builds a model to predict the abundance and distribution of these organisms with sea level rise based on abiotic tolerances, substrate availability, and projected marine productivity.  These organisms form the foundation of the food web for sea ducks, comorants, loons, grebes, gulls and terns of the near shore marine coastal environment.  Changes to the distribution, abundance and timing of prey availability will have a cascading effect through the marine trophic community resulting in changes in the abundance and distribution of these birds.  Based on current modeling of habitat use by invertebrates, small fish, and predatory birds, we will model community level changes predicted with a warming climate and sea levels rise.

Project Significance: Sea level rise will cause a change in the near shore substrate, of which we can measure and model. Habitat selection of small fish and invertebrates along the rocky shore of Newport Neck is not well known, yet changes to the prey base is predicted to affect higher trophic levels.

 Does this project involve field work, lab work, or both? Field

 Techniques Involved:

  • Small boat handling
  • Repeated measures of quadrat sampling for intertidal invertebrates
  • Near shore trapping of lobster, crabs and small fish
  • Quadrat sampling of sub tidal, intertidal and super tidal substrate
  • Quantifying foraging behavior of sea ducks, cormorants and gulls
  • Quantifying plankton type and abundance
  • Statistical Analysis