Research 2016–2018

Research Projects 2016–2018
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For this funding period, Rhode Island Sea Grant is placing research emphasis on improved understanding of shellfish (bivalve and gastropod) stock assessment and population dynamics with resource management implications, as well as impacts of changing climate on finfish and shellfish population dynamics in Rhode Island waters, with special interest on Narragansett Bay species and fisheries.

The selected projects began February 1, 2016.

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Lobster Shell Disease impacts the outer shell. While it doesn't harm the meat, it does harm its marketability.Finding New Probiotic to Fight Lobster Shell Disease Outbreak

PI: Kathleen Castro, URI
Affiliates: Marta Gomez-Chiarri, David Rowley, David Nelson, URI

Southern New England lobster (Homarus americanus) stocks are being severely impacted by epizootic shell disease, which also appears to be increasing in Maine. The disease is “characterized by moderate to deep erosions on the carapace, which in severe cases may spread to the other parts of the lobster.” Heavily affected animals literally can be covered with a rotted, weakened shell that leaves them more vulnerable to bacterial infections.

Although it is not considered harmful for consumption, the unattractive appearance of infected shells makes it hard to sell this species that supports one of the largest shellfish fisheries in the world, estimated at more than $400 million.

There are currently no tools to deal with wild stocks, leaving some fishermen culling infected lobsters in the hope that it would reduce the spread causing loss of reproductive females and sub-legal animals to the stock and loss of yield to the fishery.

Dr. Kathleen Castro and her team will be investigating bacteria that could act as probiotics against those associated with epizootic shell disease (ESD) in lobsters, and will test effects of treatment on progression of the disease on live lobsters in the hopes of providing a method to control the disease. This probiotic treatment approach, a safe and economical alternative to treatment with antibiotics, takes a step towards providing a tool and will help determine the potential feasibility of using probiotics to treat lobsters on fishing boats before lobsters are returned back to the water. By slowing down the disease progression, lobsters may be able to recover and reduce direct and indirect mortality caused by the disease.

An Ounce of Prevention: Probiotics Hold Potential for Shellfish Disease

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Three teams from the University of Rhode Island FAVS, Microbiology, and Pharmacy departments worked in isolating bacteria, sequencing genomes, culturing, challenge with pathogens, and testing.

Exposure of lobster post-larvae to five of the candidate strains isolated from lobsters and a probiotic isolated from the eastern oyster, Crassostrea virginica (Phaeobacter inhibens S4) showed that, with the exception of one isolate (a Loktanella species) these isolates did not negatively impact growth, survival, or molting frequency of the lobster larvae, but may protect them against challenging environmental conditions (temperature and water quality stress).

Adult lobsters with moderate to severe Epizootic Shell Disease exposed to weekly treatments with probiotics showed no effect on mortality, molting, growth, or disease progression.

Ultimately, seven candidates of probiotic strains (Bacillius pumilus, Loktanella maritima, YPC210, and Loktanella maritima YPC 211, Aquimarina macrocephalii, Thallosobius) isolated from lobsters have been identified for testing to develop probiotics to help treat harmful bacteria. If the correct probiotics are found to treat Epizootic Shell Disease, the lobster fishery in Rhode Island will benefit.

A model for further testing of the effect of bacterial isolates on lobster performance and health has been developed, as well as the development of protocols for effective testing of probiotic treatments that will assist future researchers in experimental design and methods.

The information from this project has also been shared with stakeholders, such as lobster fishers. These fishermen have contributed innovative ideas on how these probiotics could be incorporated into fishing practices.



flounderEffects of Climate on Declining Winter Flounder in Narragansett Bay

PI: Jeremy Collie, URI
Affiliates: Mark Gibson, RI Fish and Wildlife

Winter flounder has historically been a dominant species in Narragansett Bay that has supported commercial and recreational fisheries. However, populations have recently declined to historically low levels. Several factors may be attributed to this such as overfishing and predation, but warming water temperatures resultant of climate change may also be restricting the population.

Dr. Jeremy Collie and Mark Gibson will be investigating the life-cycle stages of winter flounder that have experienced increased mortality (as a result of climate change) in order to identify stressors, such as temperature, and changes in key habitats for spawning.

It is unclear to what extent survival can be enhanced to support sustainable fisheries, and which life stages to target, but this project will aim to identify which life-history stage(s) are the bottlenecks for winter flounder survival and whether they have remained the same over time, and which habitats to protect in order to sustain a winter flounder population in Narragansett Bay

The results should also be applicable to the Southern New England – Mid Atlantic stock complex of winter flounder.


The Murder Mystery of Narragansett Bay’s Winter Flounder


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The project team conducted year two of a fish larval survey in Narragansett Bay, continuing a larval-fish survey that had been conducted by Rhode Island Department of Environmental Management Division of Fish and Wildlife from 2001 to 2008. After a gap of eight years, the team found that the Providence River is still the most important spawning area, despite a continued decline in winter flounder abundance. Spawning habitat has contracted to upper Narragansett Bay.

Numerous larval and age-one Atlantic cod larvae were also found in Narragansett Bay. These larvae were likely
spawned offshore and advected into Narragansett Bay. These preliminary results suggest that there is a local, self-reproducing sub-population of Atlantic cod.

Preliminary results suggest that warming water temperatures may be shortening the spawning season for winter flounder, restricting the species’ overall habitat in Narragansett Bay and food availability, as well as potentially introducing more predators.

Researchers also identified that the early life-history stages, from egg-to-larvae, larvae-to-juvenile, and the second winter between  age 1 in the fall to age 2 in spring were most indicative of the species’ resilience to fishing pressure and other stresses that include striped sea robin, which showed the most negative effect on survival during the larval-to-juvenile stage compared to predation by summer flounder and scup.

Other stress factors indicated in winter flounder survival are most vulnerable during the first summer, high summer temperatures, low dissolved oxygen, and high cormorant abundance, which has helped researchers to distinguish between external stressors (ocean temperatures) and stressors that are within the jurisdiction of local managers (e.g. abundance of predator species). 

Researchers have also ruled out a suite of stressors that have been hypothesized to be important such as power plants, sewage treatment plants, seal predation.



oyster_baggingWhat is the Limit for Oysters in RI Waters Now and in the Future?

PI: Robinson Fulweiler, Boston University

The rapid growth of the oyster aquaculture industry in Rhode Island has raised questions about how many oyster farms Narragansett Bay and the state’s salt ponds can support. And while past research has shown that there is room to grow, Narragansett Bay has already seen significant decreases in productivity in the mid-Bay. With current nitrogen reductions, it is likely that productivity will decrease in the Providence River Estuary. While it is unlikely that oyster populations are food limited today, in the future, this may not always be the case.

Since food availability is key to understanding the ecological carrying capacity, Dr. Robinson Fulweiler will be investigating food sources and abundance to determine what dominates oyster diets in the Bay across seasonal changes.

Determining the diet of oysters in Rhode Island waters will inform models for oyster ecological carrying capacity, as well as shellfish management strategies. In addition, Fulweiler will be measuring sediment metabolism at six oyster-dominated habitats to determine how nutrients are recycled to the water column or removed through denitrification across oyster habitat types, which may highlight what types of habitats remove nutrients most efficiently thus providing information for aquaculturists who wish to partake in future nitrogen trading credit plans.

[toggle title=”Results”]Researchers have developed a complete record of sediment metabolism at all studied sites that will help to better understand how oyster habitats alter their environment, and found that natural reefs were better than aquaculture sites at removing excess nitrogen from urban outputs but that overall, all of the sites were found to be removing nitrous oxide – a powerful greenhouse gas. This highlighting an additional service provided by these habitats.

These data will underscore the importance of examining both inorganic nitrogen fluxes as well as denitrification – and the balance between them highlights which sites are best at removing nitrogen. These data will help oyster farmers, restoration ecologists, and managers better describe the ecological impact of oysters and the potential ecosystem benefits they provide.




Pathogens, Nitrogen, and Changing Climate Impacts on Narragansett Bay Shellfish 

PI: Serena Moseman-Valtierra, URI
Affiliates: Marta Gomez-Chiarri, URI

The eastern oyster (Crassostrea virginica) and blue mussel (Mytilus edulis) are commercially, culturally, and ecologically significant shellfish in New England. In response to stakeholder interest on the potential effects of environmental change on shellfish populations, Dr. Moseman-Valtierra will lead research investigating how two key drivers of coastal ecosystems –nitrogen and warming– impact the health and function of C.virginica and M. edulis.

Shellfish perform significant nitrogen cycling functions but are potentially overlooked as major sources (or sinks) of nitrous oxide due to microbial associates in their guts and on their shells.

This project will examine potential relationships among nitrogen loading, nitrous oxide emissions, and shellfish disease to help sustain local aquaculture and evaluate their effectiveness at nitrogen remediation, as well as minimize potential feedback from managed and natural shellfish populations on global climate.

Field experiments at Point Judith Pond will directly involve Rhode Island shellfishermen and will incorporate a high quality, time series of environmental data made available via the URI Watershed watch laboratory and the Rhode Island Salt Ponds Coalition.

Results may reveal the potential of shellfish in nutrient control, as well as help identify pathogens of the greatest threat to two major bivalve species and at what thresholds of nitrogen and/or warming shellfish populations may be severely impacted by disease.

[toggle title=”Results”]Climate and Nutrient Loading Strains Shellfish Ecosystem Services

Findings showed that a combination of warming and nutrient loading led to a shift in the rates of nitrogen removal and nitrous oxide production in oysters due to changes in the microbial community, suggesting that environmental stress due to human activity can affect these ecosystem services.

Nitrogen cycling in oysters is performed by microbes associated with the oyster tissues. In order to understand the mechanisms driving changes in nitrogen cycling of oysters in response to temperature and nutrient loading, researchers characterized the microbial communities of oysters from one of the field experiments using metagenomics.  Oyster samples from Point Judith Pond showed a diverse bacterial community, with variability observed within and between treatments.

Although several of the most abundant genera were shared between sites, treatments, and sample types, patterns of relative abundance were different, and a few phyla were characteristic of certain sample types and treatments. These analysis identified bacterial phyla in the oyster samples that appear to be were associated with denitrification or nitrous oxide production.

This was an additional accomplishment, complementing the aims included in the proposal, that extends the original aims of the proposal by characterizing the effect of temperature and nitrogen loading on the microbial community in oysters exposed to a variety of environmental conditions. This preliminary analysis will allow for insights into mechanisms of nitrogen cycling in oysters through metagenomics analysis.

Blue mussels were shown to generally support net denitrification (nitrogen removal) in all tested scenarios of nitrogen availability and temperature, which indicates a greater role of N removal than previously reported, as most past studies have focused solely on sedimentary denitrification.

This information can be used by resource managers and groups interested in coastal restoration.



quahog_boatFishermen-Based Research Fleet for Quahog Management 

PI: Anna Malek, Commercial Fisheries Research Foundation
Affiliates: Dale Leavitt (Roger Williams University), Anna Malek (Commercial Fisheries Research Foundation), Jeffrey Mercer (RI DEM), Frederick Mattera (Commercial Fisheries Research Foundation)

[toggle title=”Read More”]The primary goal of this project is to blend fishermen knowledge and science in a more formal way that will initiate a new collaborative management approach for the quahog fishery in Narragansett Bay.

In order to do this, a research fleet must be equipped with knowledge, tools, and validity to contribute to the current RI-DEM quahog stock assessment data collection program. This will help support the sustainable management of the quahog (northern hard clam, Mercenaria mercenaria) fishery, the single most valuable fishery in Narragansett Bay, by addressing the need to reduce uncertainties in the current quahog stock assessment that are attributable to data limitations and spatial gaps. If successful, a new model will be available for industry-based data collection that can be duplicated in other fisheries and regions, as well as greater capacity for Rhode Island shellfishermen involvement in coastal monitoring and other types of marine research.

Anna Malek of Commercial Fisheries Research Foundation and her team will be investigating whether bullrake and hydraulic dredge sampling are appropriate for stock assessments and whether bullraking data significantly impacts estimates of quahog abundance and spatial distribution.

Additional results will also help yield answers as to whether sampling at fishermen-selected stations (fishery-dependent data) vs. assigned sampling stations (fishery-independent data) reveal distinct distributions/abundances of quahogs throughout Narragansett Bay.

Quahog Research Fleet Video Release

[toggle title=”Results”] The Quahog Research Fleet consisted of five commercial fishermen who were equipped with modern technology to collect environmental and biological data year-round through routine fishing practices, which improved both their understanding of how survey data are used by scientists and the working relationship between industry and managers and illustrated the type of survey and data structures needed to properly conduct science.

A data collection app for Android tablets (On Deck Data – Quahog) was developed to streamline data collection by the Fleet. The app strengthens and empowers fishermen to contribute to science by providing scientifically rigorous data to back up anecdotal observations. Data from more than 50,000 quahogs from over 1,000 transects, which will be applied to the state’s stock assessment.

The Fleet has improved efficiency estimates for the dredge survey and helped address the fishing industry’s long-standing concern regarding the dredge’s ability to fish, and developed a new protocol utilizing the bullrake sampling method that has proven to be a viable means of assessing quahog populations. 

The dredge efficiency estimates and pair-wise sampling conducted provided insight into the efficiency of a hydraulic dredge survey and what other gear types may be suitable for assessing the quahog stock via supplementary fisheries-independent data or an industry-based index of abundance (e.g. catch per unit effort.). This includes utilizing a bullrake sampling method, which in the hands of an experienced fisherman averaged over 95% (StDev +2.9%).

The high level of catch efficiency and the low level of variability in the individual catch data have demonstrated that the bullrake is a viable means to assess standing stock of quahog populations. The improved efficiency estimates for the dredge survey helped address the fishing industry’s long-standing concern regarding the dredge’s ability to fish and helped improve the working relationship between managers and shellfishermen. 

As a result, a new protocol was developed in Rhode Island for evaluating the catch efficiency of bullrake sampling, finding it over 95 percent efficient – adding another assessment tool for the state fisheries management agency that is being considered by Connecticut, New Jersey, and Louisianna as a component to their stock assessment protocols



Photo: Robert Rheault, Flickr

Where is Vibrio Now and Where is it Going?
Protecting the health of oysters and consumers

PI: Roxanna Smolowitz, Roger Williams University
Affiliates: Dale Leavitt and Tim Scott (RWU), Robert Rheault (East Coast Shellfish Growers Assoc.)

As filter feeders, eastern oysters can accumulate nutrients and pathogens present in the water column. And while most are harmless some pathogens are not, such as Vibrio parahaemolyticus, a bacteria that can cause gastrointestinal illness for consumers of raw oysters, and in rare cases, death for those with compromised immune systems.

Rhode Island aquaculture has not yet suffered from closures due to human infections and the industry has taken important preventative handling steps, but as sea temperatures increase, it is likely that the accumulation of Vibrio parahaemolyticus will increase in aquacultured oysters.

Dr. Roxanna Smolowitz and her team will investigate current levels of Vibrio parahaemolyticus and pathogenic genes in aquacultured animals under different culture conditions commonly used in Rhode Island, as well as whether certain diseases increase the likelihood of Vibrio parahaemolyticus accumulation in tissues, which could support the use of different types of oysters that are disease resistant for aquaculture.

Results will provide guidance for depuration or probiotic treatment methods currently being discussed in order to protect consumers and maintain healthy seafood in the state.

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How oysters are cultured may determine the abundance of the harmful bacterium, Vibrio parahaemolyticus.

Findings suggest that the type of culture method used for growing the Eastern oyster plays a larger role in Vp abundance than water temperature, highlighting the need to identify the appropriate method to reduce or eliminate Vp accumulation.

The results also provide evidence that the abundance of Vp in cultured oysters in the northeast is generally very low and may not be the prime driver behind human disease occurring as a result of eating raw oysters.

Additionally, the strain O4 K12 is not a prominent component in Vp identified in oysters in this study and its occurrence is very low in the Northeast.

Findings also show that since the most viable forms of Vp are associated with the surfaces of the mantle and gill of an oyster, and are within the lumen of the stomach, that depuration for short periods of time for animals in the Northeast may be an effective method of clearing Vp from the oysters before sale.



Program Development projects 2016-2018:

  • Values of Recreational Boating Activities Associated with the Block Island Wind Farm
    PI: Tracey Dalton, University of Rhode Island
    Few studies have explored how on-the-water users will be affected by social and ecological impacts of wind farms, like perceived safety risks associated with boating near turbines and changes in catch availability of targeted organisms. Rhode Island provides an ideal setting to study preferences of wind farms, as the nation’s first offshore wind farm is in its state waters with another much larger wind farm planned for development near RI and MA state waters in the next few years. This project will provide knowledge on how recreational boaters might respond to potential social and ecological impacts of the Block Island wind farm.

    • RESULTS:
      Findings show that owners of relatively large recreational boats in Rhode Island do not mind seeing a wind farm in the distance during a boating trip, but they would prefer not to get close or within 100 feet of the turbines. They also tend to prefer boating in coastal waters, like those near Newport and Block Island, to offshore areas near active lease sites for offshore wind farms. Those boaters who primarily go boating to fish, however, are not affected by a wind farm nearby or off in the distance. They might be affected by potential changes in fish abundance near the wind turbines as their utility is enhanced by catching fish.
      + Read full paper in Frontiers in Marine Science 

  • Understanding, Predicting, and Mitigating Beach Erosion in Rhode Island
    PI: Reza Hashemi, University of Rhode Island
    Beach profile surveys and aerial photographs show an accelerated erosion rate of sandy beaches and dunes, especially along Rhode Island’s southern coast. Recent climate models simulating various sea-level rise and global warming scenarios predict an increasing frequency of larger and more damaging tropical and extra-tropical cyclones, which could worsen this alarming erosional trend not only in Rhode Island but along the U.S. eastern coastline.  The focus of this project is to better understand the physics of shoreline recession in relation to sea-level rise and storm intensification, which is not well understood, by develope a comprehensive quantitative framework to assess and predict storm-induced shoreline erosion in the context of climatic change.

      A quantitative and physical-based model has been developed to understand and predict the response of the beach to coastal storms, which existing tools are not adequately able to do. Initial results showed for the 100-year storm utilized by FEMA, there is a large alongshore variability in erosion and onshore deposition of sediment, and multiple breaching of storm channels and inlets. Additionally, vegetated dunes appear to be more resistant to storm damage. Research is ongoing to determine vegetation effects for overwash and inundation and whether reinforced dune protections can withstand various degrees of storm energy.
  • Marine Resource User Response to Ecological Impacts of Offshore Wind Energy
    PI: Julia Livermore, Rhode Island Department of Environmental Management
    The Block Island wind farm presents the first opportunity to identify biological and marine environmental changes to the local ecosystem caused by an offshore wind farm in U.S. waters and to determine human response to these changes. This project looks to determine how the wind farm is impacting the local ecosystem to gain a deep understanding of how humans will be impacted, and how future wind projects may affect Rhode Islanders.

    • RESULTS:
      A case study of the Block Island Wind Farm was developed to illustrate the perceptions of associated changes to the wind farm, providing for mutually beneficial situations between different communities-at-sea, and in using transdisciplinary innovation and creative thinking to propose solutions that decrease the harm of both carbon dioxide emissions and offshore structures to fishers. The paper is being used for planning and workshop facilitation by offshore wind farm companies.
  • Consumer Preferences and Purchasing Trends of Local Seafood
    PI: Lori Pivarnik, University of Rhode Island
    The Department of Environmental Management is looking toward local seafood branding as a way to bolster seafood harvested and landed in Rhode Island, however, little is known about consumer preference, perceptions, and understanding of local alternatives. This project seeks to further understand consumer attitudes, concerns, and knowledge of local seafood options to assess current purchasing choices in order to more effectively promote a local seafood industry in Rhode Island.

      Survey results indicate that consumers have not seen or are unaware of the local seafood brand designation. Some participants expressed a willingness to pay more if they knew seafood was local or try new local species.
  • Scup: Consumption of Underutilized Local Seafood in Rhode Island
    PI: Elin Torell, University of Rhode Island
    This project responds to the need to understand the “flow” of seafood from the dealer to destinations locally, regionally, and beyond. While fish landing data are available to the public, there is no database or requirement for reporting where seafood goes once dealers purchase it. More specifically, the market potential for underutilized species such as scup, butterfish, and mackerel—which are in healthy states of abundance in the ecosystem—is not clear. As a result, groups such as the Rhode Island Seafood Marketing Collaborative, the Northwest Atlantic Marine Alliance, and the Rhode Island Department of Environmental Management have requested research to better understand the flow of seafood landed in Rhode Island and to promote these products (or tailor promotional efforts) to consumers. Additionally, this project will investigate finding additional local markets for underutilized species to communities that desire these products.

    • RESULTS:
      With less than 1/3 of the total scup quota being utilized, this project identified a potential for economic gains through direct sales by fishermen and wholesalers to restaurants and informal markets such as farmers’ markets and street vendors, finding that regulatory constraints must be addressed to allow entry into new markets.
      Anecdotal evidence suggests that scup sold whole in local retail markets commands a higher price than in regional markets (where at least 90 percent of scup landed in Rhode Island is sold). Access to more scup, especially as a whole fish, could also provide increased cultural benefits to recent immigrants who prefer whole to fish fillets for their own preparation and consumption.
  • Relative Sea-Level Changes in Rhode Island and Land Subsidence
    PI: Simon Engelhart, University of Rhode Island
    As projections of relative sea-level rise rapidly increase, significantly impacting Rhode Island’s low-lying coastline, more information regarding sea level rise changes in the past (prior to 1930) is needed to help coastal managers build a resilient coastline in the face of accelerated sea-level rise. Rhode Island Sea Grant-funded Engelhart to support a project investigating relative sea-level rise during the last 3000 years in Rhode Island, focusing on the time of acceleration and spatial variability in land subsidence related to deglaciation. Initial findings analyzing various salt marsh peat cores suggest that the current rate of relative sea-level rise in Rhode Island is faster than at any point in the last 3300 years and that Rhode Island is sinking about 1 millimeter annually, which has an impact on current nuisance flooding events near the coast.

A Sinking State and a Rising Sea: Salt Marshes Provide the Answer

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