Metagenomics and Metatranscriptomics to Profile Microbial Activity as a Determinant of Methane Production in Narragansett Bay Sediment ($80,000)

In the near future, quantifying microbial emissions of methane will be essential to controlling the climate change impact of human agriculture and anthropogenic terrestrial runoff. CH4 is a potent greenhouse gas with 50-100 times the warming potential of carbon dioxide. It is estimated to contribute as much as 25% to the overall warming force of the atmosphere. In shallow coastal zones, like the estuaries of Narragansett Bay, the majority of CH4 is produced by anaerobic, methanogenic archaea that inhabit the sediment. In the same environment, methanotrophic microbes will consume a portion of the produced methane. Thus, the net CH4 released is a result of the balance in microbial consumption and production. The research team proposes that profiling the microbial composition and activity of sedimentary samples can estimate and predict the relative methane flux.
 
Peter Belenky, Brown University
Roxanne Beinart, University of Rhode Island

Streamlining marine sensors development by improving testing infrastructure ($79,296)

Testing materials for resistance to biofouling is essential to advance the collection of data in the marine environment, since biofouling can impact the functioning of sensors within a few days of their deployment. Zoospores of the marine alga Ulva are commonly used as model organisms for biofouling screening tests. Current protocols to screen for antibiofouling properties rely on the field collection of reproductive Ulva, which make the tests extremely vulnerable to perturbations in the environment such as unexpected weather events, marine heat waves, and shifts in Ulva species abundance and distribution. These unexpected events severely hinder our capability to perform assays consistently, causing delays in critical marine sensors research. This project will address these issues by developing novel and unique infrastructure that could provide year-round Ulva specimens for testing. The interdisciplinary team will support researchers developing new antifouling compounds as well as streamline the deployment of these materials in the future.
 
Vinka Craver, University of Rhode Island
Lindsay Green-Gavrielidis, Salve Regina University
Carol Thornber, University of Rhode Island
Matthew J. Bertin, University of Rhode Island
Lucie Maranda, University of Rhode Island

Multi-scale modeling of bacterial plankton-mediated nutrient cycling in the Narragansett Bay ($79,995)

Microbial planktons are key players in the global biogeochemical cycling. Nowadays, a great amount of genomics data has been accumulated from microbial communities across the ocean, yet a tool that connects these data to the ecosystems and biogeochemical cycles is missing. How do different genotypes influence the impact of an organism on the environment? Many questions regarding this topic remain, and a quantitative model can provide implications for them. In this project, the research team is combining two types of models with different molecular resolutions, to reflect genomics data on the cellular properties necessary to predict genome’s impacts on the environment, using bacterial species from the Narragansett Bay. Broader impacts of the modeling effort will be extended through the development of an education app that can be exhibited for public education in museums and science fairs.
 
Kei Inomura, University of Rhode Island
Ying Zhang, University of Rhode Island
Matthew J. Bertin, University of Rhode Island
Katia Zolotovsky, Rhode Island School of Design

Testing the ontogenetic migration hypothesis in the emerging Rhode Island Jonah crab fishery with novel molecular isotope geochemistry and acoustic tagging ($79,948)

Despite the rapid growth in size and value of the RI Jonah crab fishery in the past decade, management of this emerging fishery has lagged its increased exploitation due to the lack of knowledge of the species’ life history and an associated stock assessment. This project will apply cutting edge molecular isotope geochemistry tools to test a fundamental ecological question about whether the significant size differences in the terminal harvested size of Jonah crab between inshore and offshore harvest zones represents ontogenetic migration of the same population or potentially differential growth patterns of two isolated subpopulations. Simultaneously, the research team will examine the impact of novel acoustic geolocation tags on Jonah crab mortality rate and molt success to explore the viability of upscaling this new technology development to assess fine scale movement of Jonah crabs across regional fishing zones. This work will fill significant knowledge gaps in the life history of Jonah crabs with direct applications to the successful management of the burgeoning inshore and offshore RI Jonah crab fishery.
 
Kelton McMahon, University of Rhode Island
Melissa Omand, University of Rhode Island
Skylar Bayer, Roger Williams University
Corinne Truesdale, Division of Marine Fisheries, RIDEM

Parameterizing nutrient recycling from plankton interactions for ecosystem modeling ($80,000)

The research team's aim is to quantitatively measure release of nutrients by single celled herbivorous protists during the grazing process to better parameterize regeneration of nutrients essential for primary production. These data will be used to develop novel approaches for the integration of biological rates into ecosystem models. The research team’s work will lay the foundation for high resolution plankton population dynamics and nutrient cycling measurements in Narragansett Bay and deliver critically needed data for C-AIM Thrust 2 modeling goals and C-AIM Thrust 1 observation capabilities. The team will be able to inform the design specification of nutrient sensors to meet the needs of ecosystem wide biologically-relevant measurement tools in line with C-AIM Thrust 3.
 
Susanne Menden-Deuer, University of Rhode Island
Sarah Knowlton, Rhode Island College
Heather McNair, University of Rhode Island

Evaluating abundance and persistence of the neurotoxin domoic acid in shellfish following Pseudo-nitzschia bloom events in Narragansett Bay, Rhode Island ($79,415)

While effective seafood monitoring programs have greatly diminished the impact of acute domoic acid (DA) poisonings, there is a major lack of knowledge with respect to the potential impacts of chronic low-level domoic acid exposure with respect to human and environmental health. The proposed work under this collaborative research grant will begin to fill this knowledge gap by determining the concentrations of domoic acid that mussels and quahogs accumulate during and after toxic events and by histologically examining these animals for chronic pathological impairments to the tissues of the animals. The investigators will bring a multidisciplinary and integrative approach to the emerging problem of harmful algal toxins for Rhode Island’s coast.
 
Matthew J. Bertin, University of Rhode Island
Roxanna Smolowitz, Roger Williams University

Interaction of micro- and nano-plastics with marine and freshwater bacteria – what’s happening under the tip of the ‘plastic-berg’? ($80,000)

About 150 million tons of plastic are in the world’s oceans currently, and 8 million additional tons of plastics are dumped into the ocean each year. By 2050, the weight of plastics in the ocean will exceed the weight of all marine organisms. This is a highly concerning statistic since plastics can have a half-life of several hundred years. Through ocean action, light and wind exposure these plastic pieces eventually break up into millimeter- and lower-sized objects, known as microplastics. Since the density of many common plastics is greater than that of seawater, these materials sink – indeed, about 14 million tons of plastic are currently on the ocean floor. In the water they encounter an extensive microbial community that is responsible for maintaining local oxygen and nitrogen levels – these bacteria play a critical role in maintaining the marine ecosystem in balance. In this project, the collaborative research partners will use imaging as well as gene sequencing and enzyme analysis to monitor the binding of microplastics to bacteria, and explore the biological response of the bacteria to this anthropogenic stressor. The longstanding collaboration and combined expertise of the groups at URI and Brown University are critical for the success of the project.
 
Arijit Bose, University of Rhode Island
Anubhav Tripathi, Brown University

Towards the Smart Interconnected Bay – Artificially intelligent detection of harmful algal blooms in Narragansett Bay, Rhode Island ($79,943)

In order to better manage shellfish populations and protect the livelihoods of coastal communities this project aims to determine the underlying links between driving environmental factors and Pseudo-nitzschia bloom formation in Narragansett Bay. To do this the team will develop a novel in situ monitoring and remote sampling approach that integrates real-time chemical and physical oceanographic data with co-located high-frequency field sampling and biological/chemical analysis within an artificially intelligent model framework. We aim to better enable the detection and forecasting of harmful algal blooms. This proposed project is relevant to RI-CAIM as oceanographic measurements of Narragansett Bay, particularly those that are far higher in frequency than before, can be used to help develop an enhanced understanding of how environmental drivers influence ecosystems.
 
Andrew Davies, University of Rhode Island
Karianne Bergen, Brown University
Baylor Fox-Kemper, Brown University
Matthew J. Bertin, University of Rhode Island
Kristofer Gomes, University of Rhode Island

Pathway to Robot-Integrated Bay-scale Ecosystem Observatory (RI-BSCO) ($79,941)

This collaborative research project is organized around three actions: marine robot deployment, robot-model interaction, and data visualization. It will foster an interdisciplinary team of engineers, scientists and artists from two Rhode Island institutes. The synergic effort is not limited in bringing new technology and advancing the science in coastal ecosystem modeling and observation, but also intend to engage the public and stakeholders. The collaborative research team will also provide concrete evidence and valuable experience to support the future development of the Robot-Integrated Bay-scale Ecosystem Observatory (RI-BSCO) with other external funds.
 
Mingxi Zhou, University of Rhode Island
Christopher Kincaid, University of Rhode Island
Christopher Roman, University of Rhode Island
Georgia Rhodes, Rhode Island School of Design
Shona Kitchen, Rhode Island School of Design

Towards measuring the pulse of Narragansett Bay: Applying high resolution oxygen sensors to quantify ecosystem primary production and respiration ($80,000)

The oxygen concentration in marine waters is the result of the balance between primary production by algae and respiration by all living organisms, as well as the rate of diffusive exchange of atmospheric oxygen. As such, oxygen is a key component of quantifying ecosystem dynamics. Oxygen is also an essential indicator of ecosystem health in the context of climate change and anthropogenic pressures. Warming temperatures and eutrophication are well known to favor ecosystems disequilibria, such as hypoxia (absence of oxygen in bottom coastal waters), which can have tremendous impact on aquatic life resulting in fish kills. Because of logistical constraints, rate measurements of marine food web dynamics are sparse, resulting in low resolution in poor spatial and temporal coverage. As a consequence, most modelling efforts rely on inferring rates from concentrations of constituents, which limits the predictive capacity of our understanding and predictive capacity. The goal for this STAC effort is to test a promising, commercially available optical oxygen sensor (PreSens Oxygen Sensor Spot) to quantify rates of primary production and respiration of planktonic communities. This would be a first step in studying the feasibility of widespread application of this instrument for production/respiration measurements within the Narragansett Bay Observatory.
 
Susanne Menden-Deuer, University of Rhode Island
James Lemire, Roger Williams University
Jason S. Grear, US Environmental Protection Agency
Pierre Marrec, University of Rhode Island

Establishing the Spatial and Temporal Distribution of Microplastics in Narragansett Bay

This project seeks to design an integrated water sampling and chemical analysis device for profiling the commercially and environmentally important polysaccharide component of dissolved organic matter. Once designed, the new device will dramatically simplify sample processing and improve analysis reliability and performance by enabling real time monitoring.
 
Andrew Davies, University of Rhode Island
Scott Rutherford, Roger Williams University
Mike Jarbeau, Save the Bay
Coleen Suckling, University of Rhode Island
Christopher Kincaid, URI Graduate School of Oceanography
Kelton McMahon, URI Graduate School of Oceanography
Vinka Craver, University of Rhode Island

A Species-Specific Approach to Enhance Ecosystem Models for Planktivorous Fishes

This project will supply new information that enables predictive models to better describe how coastal fish communities will be influenced by climate change. Predicative models are a widely used tool to determine how marine communities will respond to changing temperatures which can influence decision making processes. However, these models are often parameterized using historical and literature data. The team will assess the responses of three key model fish species used within NSF EPSCoR’s RI C-AIM program to near future climate change by making stronger links with physiology to explain any alterations in responses commonly incorporated in modeling efforts (e.g. food consumption, growth, survival).
 
Coleen Suckling, University of Rhode Island
Terry Bradley, University of Rhode Island
Andrew Davies, University of Rhode Island
Austin Humphries, University of Rhode Island
Anabela Maia, Rhode Island College
Conor McManus, RI Department of Environmental Management

Novel Denitrification Sensor for Narragansett Bay Coastal Ecosystems: Testing Response to Shifting Nutrient Loans

This collaborative research will expand understanding human impacts on nutrient dynamics in Narragansett Bay by providing a new tool that can dramatically increase availability of data on denitrification, a key functional metric of nutrient remediation in costal ecosystems. The research offers promise for demonstrating a novel, simple, and inexpensive field-deployable tool to measure denitrification with which resource managers may better assess functional resilience of coastal ecosystems.
 
Serena Moseman-Valterra, Department of Biological Sciences, University of Rhode Island
Mark Stolt, Department of Natural Resources Sciences, University of Rhode Island
Jose Amador, Department of Natural Resources Sciences, University of Rhode Island
Brett Pollock, Department of Biology, Providence College

Large Scale Projection Mapping as a Collaborative Platform for Communication and Discourse Using Oceanographic Data and Physical Modeling of Narragansett Bay

This project provides for the first iteration of a three-dimensional mobile visualization platform for viewing animations of ocean model simulations using data obtained through C-AIM projects. This project provides for the first essential step in transforming model data into 3D meshes that can be visually explored in ways that facilitate refinement of models and scientific understanding of complex system dynamics for both professional and lay audiences. Support for this collaboration between RISD and Brown researchers will facilitate the type of innovation only possible when experts in diverse fields collaborate, strengthen Rhode Island’s position as a leader in data visualization for imaging.
 
Jennifer Bissonnette, Rhode Island School of Design
Baylor Fox-Kemper, Brown University
Georgia Rhodes, Rhode Island School of Design
Stewart Copeland, University of Illinois
Aakash Sane, Brown University

Pathways to the Modeling of Microbial Ecology in the Narragansett Bay Through Deep Omics Sequencing

Microbial populations play fundamental roles in the biogeochemical cycling of marine environments by mediating the transfer of carbon and nutrients to higher trophic levels. This project team aims at bridging the gap between our understanding of population dynamics and the underlying mechanisms in nutrient cycling, species interactions, and stress responses, with a focus on the microbial community in the Bay.
 
Ying Zhang, University of Rhode Island
Peter Belenky, Brown University

Engineering reliable and affordable tools for environmentally- and economically- driven aquatic monitoring

Plastic pollution is of growing concern for coastal communities around the world, as it threatens the structure, function, and health of marine ecosystems and humans alike. In this collaborative study, the team proposes to couple hydrodynamic models (computer simulations of water movement), the use of Lagrangian Drifters (trackable floats that move with the currents), and spatial and time-series sampling at strategic locations within Narragansett Bay to develop a baseline understanding of the distribution of plastic pollution.
 
Jason Dwyer, University of Rhode Island
Amit Basu, Brown University
Bernard Munge, Salve Regina University

Testing nanographene as passive samplers for emerging contaminants of concerns in Narragansett Bay

The overall goal of this project is to bring together expertise in environmental chemistry and nanomaterials to first formulate novel advanced graphene nanomaterials then and to field test a passive sampler for emerging contaminants in the water of Narragansett Bay. This project will lead to the development of novel tools for the detection and remediation of contaminated sites.
 
Rainer Lohmann, University of Rhode Island
Robert Hurt, Brown University

Coupling physical and ecological models to understand how climate drives disease outbreaks in Narragansett Bay

This collaborative project combines expertise in ocean modeling, aquatic pathology, ecological interactions in plankton, aquatic diagnostics and epidemiological modeling to quantify the processes that shape the longevity of the oyster parasite Perkinsus marinus outside its host environment. As part of the project, the team would test ocean circulation models that predict the spread of the parasite in coastal waters. The modeling framework would catalyze future research predicting how climate variability and human activities impact coastal ecological and economic sustainability.
 
Marta Gomez-Chiarri, University of Rhode Island
Tal Ben-Horin, University of Rhode Island
Susanne Menden-Deuer, University of Rhode Island
Baylor Fox-Kemper, Brown University
Roxanna Smolowitz, Roger Williams University
Eric Schneider, RI Dept. of Environmental Management

Building essential bridges between ecosystem data and hydrodynamic-ecosystem models of Rhode Island coastal waters through CHN analysis

This project seeks to extend knowledge of Narragansett Bay zooplankton populations and their relationships with other aspects of the marine ecosystem. Advances expected include development of a comprehensive table that will relate zooplankton biomass, nitrogen concentration and carbon concentration, overlapping temporal-spatial zooplankton records from the pump station, in-situ net tows and ADCP backscatter proxy and more accurate coupled ROMS-Fennel ecosystem models that incorporate new zooplankton observations and observational capacity in process-simulation of key processes.
 
Christopher Kincaid, University of Rhode Island
Barbara Sullivan-Watts, Providence College

Quantifying wet and dry deposition of ammonium to Narragansett Bay

This project will contribute new data and new methods to quantify AD of ammonia/um, likely an important anthropogenic stressor, which can be used to improve understanding on non-point source nutrient loading to the coastal ecosystem for more accurate modeling of biogeochemical and ecological processes. Data derived can also be used to inform non-point source management decisions, ultimately improving the health and resilience of the Bay. This work will contribute first-of-its-kind applications for quantification of air-sea fluxes of ammonia/um and the purchase of equipment that can be used for future studies in coastal and urban areas of Rhode Island.
 
Meredith Hastings, Brown University
Brian Heikes, University of Rhode Island

Exploring the capabilities of a new benthic lander system for investigating sediment biogeochemical exchange – a critical boundary condition for ecosystem modeling in Narragansett Bay

The proposed work is a proof-of-concept exploring the utility of the new instrument to measure seafloor processes being acquired as part of the C-AIM Bay Observatory. The project will provide basic data for determining the role of sediments in influencing nutrient and contaminant input to the waters of the bay and will be used to support future modeling efforts
 
Rebecca Robinson, University of Rhode Island
John King, University of Rhode Island
Brice Loose, University of Rhode Island
David Taylor, Roger Williams University

Assessing changes in coastal ecosystem engineers and associated communities in Narragansett Bay

This project will assess the current health of economically and ecologically important habitats in Narragansett Bay by surveying the fish, invertebrate, and seaweed communities through a combination of traditional methods (e.g. random quadrat sampling) and a novel video transect method at sites dominated by rockweed or kelp and for which there are historical records.
 
Carol Thornber, University of Rhode Island
Lindsay Green-Gavrielidis, University of Rhode Island
David Taylor, Roger Williams University
Niels Viggo-Hobbs, University of Rhode Island
Giancarlo Cicchetti, U.S. Environmental Protection Agency

Glider-Based Observations of Hydrography and Nutrients in Rhode Island Sound in Support of RI C-AIM Modeling

The main goal of the project is to equip a Slocum glider, an autonomous underwater survey vehicle, with a sensor to measure dissolved nitrate in the ocean. The objective is to obtain data on the temporal and spatial variability in nitrate concentration in the coastal ocean south of Narragansett Bay.

David Ullman, University of Rhode Island
Melissa Omand, University of Rhode Island
Benjamin Knorlein, Brown University

Developing novel molecular geochemistry tracers to understand phytoplankton community contribution of food web architecture of Narragansett Bay

This project centers on characterizing phylogenetically-diagnostic molecular “fingerprints” (stable carbon isotope values of essential amino acids) of major evolutionary branches of coastline-relevant phytoplankton.
 
Kelton McMahon, University of Rhode Island
Breea Govenar, Rhode Island College

The Response of Marine Bacteria in Narragansett Bay to Microplastics, a Key Anthropogenic Stressor

The goal of this project is an experimental approach that combines high resolution imaging, DNA sequencing and enzyme analytics that will uncover both the physicochemical and biological responses to stressors and is unique. It will lead to a reliable assessment of the health and resilience of the Bay, spawn new imaging infrastructure, and will be important for developing policies aimed at safeguarding marine life in the Bay.
 
Arijit Bose, University of Rhode Island
Anubhav Tripathi, Brown University