Research 2010-2012

Research Projects 2010-2012
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Alan Desbonnet
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Rhode Island and Block Island Sounds include important habitat, fishing grounds, and marine transportation routes, and are an area where offshore wind farm development is being proposed. However, research is needed to understand the physical and biological processes that govern the sounds’ circulation patterns and living ecosystems. Though more is known about Narragansett Bay, its response to climate change and other anthropogenic changes is just beginning to be understood, and it isn’t known how well that might translate to Rhode Island or Block Island Sound.

To help fill this void and provide new information for both science and management, Rhode Island Sea Grant issued a request for research proposals that focused on Rhode Island and Block Island Sounds, and on Narragansett Bay and its response to climate change. The response to this quest for knowledge was excellent, and for the 2010–2012 omnibus period Rhode Island Sea Grant has funded nine research projects that are described below.

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Improving understanding of nutrient cycling in marine ecosystems

Just like adding fertilizer (nutrients) to your lawn makes the grass grow more vigorously, adding nutrients—particularly nitrogen—to marine waters fuels the growth of marine plants from microscopic phytoplankton to larger “seaweeds” (macroalgae). The nutrients are then recycled between organisms living in the water column and the sediments, fueling the functions of the marine ecosystem. The state of Rhode Island is pursuing an aggressive program of nitrogen reduction from sewage treatment plants, and it is important to understand how this reduction will change phytoplankton growth in the bay and adjacent coastal waters.

[toggle title=”Providence River v. Rhode Island Sound”]

How does nutrient cycling compare between urbanized waterfronts and water bodies more removed from human activity?

Scott Nixon, Professor, URI Graduate School of Oceanography) focuses on better understanding nutrient cycling—for a suite of organic nutrients—between bottom sediments and the water column in Rhode Island’s bay and coastal water ecosystems.

The study has been designed to allow comparison, over a two-year period, of nutrient cycling along a gradient from the highly human-influenced Providence River estuary to Rhode Island Sound, which is less impacted by humans.

The findings of this research will help us better understand how Narragansett Bay and connected waterbodies recycle available nutrients, and how and perhaps why they recycle nutrients differently from each other. It will also help us understand what impact, if any, management measures to reduce nutrients in wastewater are having on the ecology of Narragansett Bay and Rhode Island Sound.


  • The addition of these data to the national database is now available for use in improving summer hypoxia models used by resource managers to assess fishable/swimmable status of coastal waters.
  • The data will also be available for use by other researchers so that broader understanding of status and trends of U.S. coastal waters can be gained, and so that national trends resulting from changing climate and impacts to nutrient dynamics can be better understood.

Related Publications:

Coupled biogeochemical cycles: eutrophication and hypoxia in temperate estuaries and coastal marine ecosystems



[toggle title=”Looking at Climate Change through Nitrogen Transport”]

Climate change can have unexpected effects on fundamental nutrient cycling in coastal ecosystems.

Robinson Fulweiler, assistant professor and researcher at Boston University, focuses on the mechanics of how nitrogen is being transported between bottom sediments and the water column.

Recent research in Narragansett Bay conducted by Fulweiler and collaborators has highlighted, for the first time, how climate change can have unexpected effects on fundamental nutrient cycling in coastal ecosystems.

Their findings suggest that a new model for nitrogen cycling in coastal systems may be emerging—instead of removing nitrogen and storing it in bottom sediments, nitrogen is being released into the water column.

The bottom line is that some estuaries may no longer provide the nitrogen removal services they once did. Instead, they may become a source of nitrogen to coastal waters.

The currently funded research will look closely at this “twist” in nitrogen cycling in Narragansett Bay and will sample Rhode Island Sound to see if a similar change is taking shape, and will consider the potential ecological ramifications.


  • The data set created for nitrogen dynamics in Narragansett Bay has become one of the best in existence. These data provide researchers with extensive knowledge of annual sediment cycles for nitrogen gas and nitrous oxide.
  • Preliminary analysis of data has shown that sediments in Narragansett Bay act as both source and sink for nitrogen, dependent upon season.
  • The Providence River is a major source of nitrous oxide, especially during summer months and also shows the highest fluxes of nitrogen gas throughout the Narragansett Bay estuary.
  • Scientific results have also shown Rhode Island and Block Island Sounds as significant sites for denitrification on a consistent basis, showing little spatial or temporal variation.
  • Based on samples from Narragansett Bay, Rhode Island Sound, and Block Island Sound, a negative correlation between anammox N gas production and temperature has been observed, with anammox production be more significant in cooler waters. This may imply altered nitrogen dynamics and nitrogen cycling in coastal marine ecosystems with warming temperatures; determination of environmental impacts are, however, beyond the scope of the present study.

+Read full publication


[toggle title=”Anaerobic Ammonium Oxidation New Nitrogen Pathway”]

Newly discovered driver of nitrogen transport from sediment to water column.

Anaerobic ammonium oxidation—anammox—is a newly discovered mechanism by which nitrogen moves between bottom sediments and the water column, mediated by anaerobic bacteria, which don’t need oxygen to sustain life.

Jeremy Rich, assistant professor at Brown University, looks into this process that has recently been found to occur across broad geographical areas, and is being noted as a very significant component of nitrogen cycling in marine systems, accounting for up to 67 percent of nitrogen loss in some areas.

This research will describe, for the first time, the role that anammox plays in nutrient cycling in Narragansett Bay and Rhode Island Sound, and how that alters our view of the ecological functioning of these marine ecosystems.


  • Anammox appears to play a small role in Narragansett Bay, accounting for less than 2% of nitrogen gas production. In the offshore waters of Rhode Island and Block Island Sound however, anammmox accounts for 10-40% of nitrogen gas production, making it an important part of the nitrogen cycle in these ecosystems.
  • Several analytical methods are being trialed to determine accuracy before more can be said with surety; earlier reports of seasonality of the anammox pathway are still being explored but may be related to methodology used. Furthermore, bioturbation appears to play a role in the anammox pathway, and further sampling is being conducted to clarify these interactions.

Related Publications:


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New Imaging Technologies for Detailed View of Seafloor

[toggle title=”BayMap Habitat Mapping Project”]

In 2004, John King, Professor of Oceanography at the URI Graduate School of Oceanography, submitted to Rhode Island Sea Grant a very ambitious proposal to map the entire seafloor and the benthic ecological habitats of Narragansett Bay and the south shore lagoon ecosystems (salt ponds).

Six years later, King has nearly finished the BayMap Habitat Mapping Project and Rhode Island Sea Grant is assisting in seeing the work through to completion. Along the way, King has garnered substantial outside funding to expand coverage and improve image resolution. He has also parlayed the expertise built during this project into assisting federal agencies in developing national standards and baselines for seafloor mapping.

His work has also located many archaeologically important sites, one of them being the possible finding of the Endeavour, the ship Captain James Cook used in his early explorations of the New World. The real treasures from this ongoing project, however, are the three-dimensional maps of Rhode Island coastal benthic habitats that have been created and posted online that others are now using in a variety of ways.

Resource managers are using these maps to help them better plan for and manage the state’s natural resources, while shellfish growers are using them to identify the best habitats for raising shellfish. Guiding the creation of national benthic habitat mapping standards, discovering important archaeological sites, and providing significant economic assistance to aquaculture are all unanticipated benefits generated by funding what might have been envisioned as simply making maps.


  • Availability of these maps has allowed for rapid preliminary assessment of sites for more detailed study and analysis, shortening the learning curve and associated expenses for aquaculture entrepreneurs, habitat and restoration ecologists, and coastal resources management personnel.
  • Existing aquaculture businesses are using these benthic habitat maps to plan for expansion, and potential aquaculture startups are using them for site suitability purposes.
  • Furthermore, all data are compliant with the NOAA Coastal and Marine Ecological Classification Standard, Version III national standards, and will, therefore, be directly usable by any and all other researchers utilizing the new national standards.
  • Protocols developed by BayMap were directly applicable to Rhode Island Ocean SAMP marine spatial planning project. We are currently further developing these protocols as part of a National Oceanographic Partnership Program project for the Bureau of Ocean Energy Management, Regulation and Enforcement.
  • An additional Bay-wide dataset was collected to assess benthic habitat quality changes due to reductions in nutrient inputs and other environmental/anthropogenic changes over the past twenty years.

Related Publications:


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Fitting a piece into the circulation puzzle

Rhode Island Sound is an important local resource, supporting valuable commercial and recreational fisheries, providing passage for vessels ranging from sailboats to cruise ships to oil tankers, and potentially being a site for offshore wind power generation. Although much is understood about the dynamics of water circulation in neighboring Long Island Sound, Block Island Sound, and the Massachusetts shelf, surprisingly little is known about circulation patterns in Rhode Island Sound. Modeling studies have hypothesized the existence of a current flowing counter-clockwise in Rhode Island Sound, but there are no data available to verify or disprove this idea.

[toggle title=”How Water Behavior Influences Ecology “]

A research and modeling study, “Observations of Rhode Island Sound Circulation and Hydrography: Interaction with Massachusetts Shelf Waters,” conducted by David Ullman, a researcher at the URI Graduate School of Oceanography, is designed to collect information in areas where little or none currently exist.

The research team will place continuous-recording instrument arrays along the border of Rhode Island Sound and the Massachusetts shelf, and in several locations within Rhode Island Sound.

The data, collected in three-month periods, will then be fed into circulation models to create a more accurate picture of how currents behave in Rhode Island Sound.

This information will aid scientists in better understanding how Rhode Island Sound interacts with adjacent water bodies, and how these interactions influence the ecology of the region as a whole.

Results of this research will feedback directly into ongoing research, benefitting the regional research community at large.


  • Researchers have identified a large counter-clockwise gyre in Rhode Island Sound, validating a pattern that was suspected to exist based on largely circumstantial evidence.
  • This observed gyre is seasonal in its nature, forming during the summer and then broken apart during winter by shifting wind patterns.
  • Continental Shelf water was not found to intrude into Rhode Island Sound at any time during 2011, leading researchers to believe that such an event is non-regular in nature, and does not appear to be seasonal in nature.

Related Publications:


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Reconstructing Climate in the Past

Sediment pours into Narragansett Bay daily from rivers, streams, and runoff coming directly over the landscape, while pollen, dust, and windblown particles end up in surface waters on the bay. Eventually, all these particles end up sinking to the bottom and becoming incorporated into the sediments. Fortunately, all of the particles carry chemical clues to their origins and to the conditions of the environment during the time when they entered the bay ecosystem. This allows scientists to extract cores from the bay bottom that they can use to reconstruct an environmental history for Narragansett Bay and its watershed that reaches back centuries.

[toggle title=”Climate Change Trends”]

Warren Prell, professor of geological sciences and researcher at Brown University is utilizing a multi-proxy reconstruction of anthropogenic-induced productivity and spatial coupling in Narragansett Bay using sediment cores.

Prell is reconstructing history—over a 500-year time span—in terms of biological response to recent global warming trends, the urbanization and industrialization of the bay watershed, and the onset of major land-use changes. Comparison of sediment cores taken from the urbanized upper bay, mid-bay, and more rural lower bay will help tell a story of human impact to Narragansett Bay. More importantly for ecologists, however, a story of ecosystem alteration as a result of changing climate may emerge that will help them better comprehend the interplay of human domination and climate change impacts on not only the Narragansett Bay ecosystem but also at regional, if not global, scales.



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Urbanization and water quality in upper Narragansett Bay

Estuarine modeling is a tool commonly used to guide water quality management in urban areas. Because of the complexities involved in modeling estuarine waters—a blend of freshwater and saltwater—the models are often overly simplistic. Furthermore, urban estuaries are often highly engineered, with hardened shorelines, dredged channels, and other manmade features that influence current flows in very complicated ways. The problem is that while models are helpful in understanding what is going on, they often don’t mimic reality very well. Models can be improved, but it takes sophisticated effort and determination to do so.

[toggle title=”Role of Environmental Forcing and Local Geometry on Flushing and Water Quality in Urban Marine Environments”]

Christopher Kincaid, a professor and researcher at the URI Graduate School of Oceanography, is working to improve modeling capabilities for management of water quality in upper Narragansett Bay, particularly the Providence River and Greenwich Bay. This is a timely project in that current management schemes are targeted at significantly reducing nutrient inputs to the bay to improve water quality—fewer algae blooms and less hypoxic (reduced oxygen content) water, for instance—with ecosystem health being enhanced as a result.

The resulting model can be used by resource management professionals to better understand, and perhaps predict, cause-and-effect scenarios in the urban Narragansett Bay marine ecosystem, such as what impacts nutrient reduction programs will have.


  • Model outputs incorporating wind data allow for the model to simulate flushing more accurately, and in particular, to differentiate between inner and outer sections of the bay where wind influence differs markedly over similar time frames.
  • The Narragansett Bay Regional Ocean Monitoring System (ROMS) model has now been improved to high enough resolution, and to a high enough degree of accuracy, that point source pollutant discharges can be accurately modeled.
  • Such “forensic oceanographic” use of the model has shown that wind is the most important factor in determining pollutant transport routes, and model outputs have now entered the dialog and decision-making process for managing upper Narragansett Bay water quality.
  • Application of the high-resolution ROMS has shown that previous models — and those currently being used by resource managers — overestimate flushing in the Providence River and Greenwich Bay to be between three and ten times faster than actual flushing processes within the Bay. This high degree of error could pose risks to beach-goers and other resource users.

Related Publications:


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Combating marine disease outbreaks

Aquaculture is fast becoming a major source of protein for an ever-growing human population. One of the biggest challenges to increase aquaculture production is bacterial disease outbreaks, which limit production and result in an annual loss of millions of dollars to growers. Pharmaceuticals are most often used to combat disease outbreaks in aquaculture operations, but they are expensive solutions and can have significant environmental consequences.

[toggle title=”Role of Interspecies Interactions in Mitigating Diseases of Marine Animals”]

David Rowley, associate professor of biomedical sciences at the University of Rhode Island, will explore natural pathways for combating disease outbreaks in crustaceans and in bivalves. Researchers will study how various species of bacteria interact with one another, specifically looking for interactions that prevent infections and their subsequent spread, and then devise ways to exploit these interactions at scales that are practical for application in aquaculture operations, particularly with regard to oyster culture.

Findings from this research study have clear implications in the growing field of probiotics—using live microorganisms to confer health benefits to host organisms. Research findings will also provide insight into the biology and ecology of the various microorganisms being studied, which will, in turn, be useful to others researching new ways to combat marine diseases. Research results will have use close to home as well—as climate changes, marine diseases once restricted to southern areas are expanding their range to the north, and oyster growers are concerned.

Results from this research just might help them find ways to keep our marine waters disease free and keep Rhode Island as a leading producer of top quality oysters.


  • One probiotic candidate has been refined and tested and has shown increased survival in larval oysters.
  • The probiotic response reduces pathogen load while increasing oyster survival, and this unique outcome is being further investigated as to its potential application for oyster husbandry.

Related Publications:


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Helping coastal communities cope with climate change

[toggle title=”Human Behavior and Climate Change Adaptation”]

In a collaborative approach to addressing the problem, Linking Natural, Behavioral, and Communication Sciences to Enhance Coastal Community Wellbeing in the Face of Climate Change (Pamela Rubinoff, URI Coastal Resources Center/Rhode Island Sea Grant), is bringing experts from different fields together to assist Rhode Island communities in finding a way forward.

The collaborative team will gather the latest and best science available on changing climate and its impacts, and will work with communities to help them understand the science, the projected impacts, and the uncertainty involved in both. Faced with uncertainty, individuals, and the communities they make up, are often unwilling to commit to a path of action because of the risk involved.

The collaborative team will address this issue by implementing a process of shaping and changing behaviors, at both individual and community levels, that will address the issue of risk and help people enter an action-taking phase. Such an undertaking is a risk in itself, but the benefits— Rhode Island communities that are implementing actions to address impacts of changing climate—is well worth it.


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