The Current | Winter/Spring 2013

current THE

research and happenings from rhode island nsf epscor | winter/spring 2013

Cultivating Collaboration The STAC & EPSCoR Issue Rhode Island salt marshes, gateways to the sea page 6 A Rhode Islander’s path to science education: From installing air conditioners to dissecting mussels page 9 Cultivating collaboration page 11 Studying algae blooms, for the health of the bay and the economy page 14

mission Sara K. MacSorley

invited commentary

editor and project administrator

Basics Group design

Basics Group Joe Giblin Mary Grady Dr. Breea Govenar Dr. Serena Moseman-Valtierra photography

Copyright © 2012 The Current.

All rights reserved.

Our Mission is to provide a platform to promote collaboration and cooperation among Rhode Island’s institutions of higher education (IHE) and to enable alignment of our efforts with the needs of the state to increase research competitiveness, especially in marine life science and affiliated sciences.

We believe this will improve the employment rate, provide more attractive employment opportunities, create new businesses, and preserve and strengthen our connection to Narragansett Bay, its watersheds, Rhode Island Sound, and the Atlantic Ocean.

Greetings from the Rhode Island State EPSCoR Director

Rhode Island EPSCoR

Peter Alfonso, Ph.D. program director

facilities

Jennifer Specker, Ph.D. principal investigator

Edward Hawrot, Ph.D. co-principal investigator

Charlie Cannon, M. ARCH. co-principal investigator

Mary Sullivan, Ed.D.

co-principal investigator

Shelley Hazard

scientific research grant assistant

Rhode Island NSF EPSCoR supports three core research facilities to help discover the effect of climate variability on marine life. Each facility is open to researchers and students statewide. An inventory of available equipment and expertise can be found at www.riepscor.org.

Proteomics Center, Brown University, Providence Instrumentation for the physical characterization of biological macromolecules

The Current, Rhode Island NSF EPSCoR Coastal Institute, Suite 21 University of Rhode Island Narragansett Bay Campus 215 South Ferry Road Narragansett, RI 02882 (401) 874-6880

Genomics & Sequencing Center, URI, Kingston

our website has a new look check out http://riepscor.org

Instrumentation for robotic sample preparation, fragment analysis, rt-qPCR, bioanalyzer

Marine Life Science Facility URI, Narragansett Flowing seawater with temperature control, instrumentation for preparing organisms for analyses, BD Influx Flow Cytometer

Become a fan of Growing STEM in the Ocean State www.facebook.com/RhodeIslandEPSCoR

we are rhode island nsf epscor

Please join me in congratulating and celebrating the winners of the 2012 Collaborative Grants Program with this issue of The Current. In the pages that follow, we highlight the winning projects that are tackling the pressing issues of marine life science and climate change — the core research of the Rhode Island NSF EPSCoR program.

These awards illustrate the value of our investment in the integration of teaching and research.

The scientists featured within these pages stand as models of collaboration and student training.

They are preparing the next generation of scientists to win jobs and to be fully prepared for their careers in research.

In addition to the remarkable gains in research and education, these collaborative grants also enhance the state’s economy with follow-on funding and growth of our job base. They help drive competitive efforts to secure strong partnerships while providing for the future success of our citizens, schools, businesses and industries.

If you haven’t already, take a look back at our Current issues to date. The newsletter provides insight on the impressive track record of Rhode Island NSF EPSCoR as we look to our fourth year of funding.

From collaboration in the lab and field to an overhaul of our fiber optic capabilities, our stories explore how we are engaging young schoolchildren in the science and technology fields, providing unparalleled research opportunities for undergraduate and graduate students, and helping build a 21st Century workforce for Rhode Island.

Sincerely,

On the Cover: An escaped oyster that didn’t make it from a working oyster farm in Wareham, Mass.

02 //

Peter Alfonso, Ph.D. Rhode Island State EPSCoR Director Vice President for Research and Economic Development University of Rhode Island Dr. Jennifer Specker

Dr. Edward Hawrot

Mary Sullivan, Ed.D.

Charlie Cannon

RI NSF EPSCoR Principal Investigator University of Rhode Island

RI NSF EPSCoR Co-Principal Investigator Brown University

RI NSF EPSCoR Co-Principal Investigator Rhode Island STEM Center Rhode Island College

RI NSF EPSCoR Co-Principal Investigator Rhode Island School of Design

// 03

From NSF EPSCoR Principal Investigator Jennifer Specker

From STAC Executive Director Christine M.B. Smith

With this note to the readers of The Current, we at the Rhode Island NSF EPSCoR Office say farewell to Sara K. MacSorley, project administrator since 2010 and communications coordinator since 2008. Sara is now the director of Green Street Arts Center and Project to Increase Mastery in Mathematics and Science at Wesleyan University, Connecticut.

For nearly a decade, the Rhode Island Science and Technology Advisory Council (STAC) and Rhode Island NSF EPSCoR have been working together to build research infrastructure here in the Ocean State.

A fond farewell to Sara MacSorley, NSF ESCoR Project Administrator.

In instituting The Current newsletter, Sara carefully laid out the inner machinations of the NSF EPSCoR effort here in Rhode Island. Through The Current’s issues — all catalogued here http://web.uri.edu/rinsfepscor/thecurrent-2/ — Sara communicated the value of EPSCoR’s collaborative efforts to advance the academic research capacity within Rhode Island and create a fertile, well-funded landscape for scientists to conduct cutting edge work. She introduced Current readers to the Summer Undergraduate Research Fellowship (SURF) program and gave them an inside look at the ongoing research and the individuals behind the experiments.

As detailed by the Current’s Winter 2012 issue, a collaborative effort by Rhode Island NSF EPSCoR and other organizations saw the improved connection between our colleges, libraries, grade schools and other anchor institutions via 350 miles of fiber optic cable. The high speed, multi-lane, technical infrastructure makes the transmission of large amounts of information almost instantaneous. In some areas, the new fiber network provides up to 100 times the previous bandwidth, allowing researchers to share massive amounts of new data with their peers across the state and around the world, speeding up the analysis necessary for new discoveries.

Readers of The Current learned about the Rhode Island NSF EPSCoR Academy’s efforts to engage more students from diverse backgrounds in science and technology, and build a 21st Century workforce grounded in the disciplines of science, technology, engineering and math (STEM). Other Current stories explored the EPSCoR partnership with the Rhode Island Educational Talent Search (ETS) that engages middle and high school students in science and technology programs and the variety of programming available at the undergraduate and graduate levels on the state’s public and private campuses.

Sara also consistently shined a bright and well-deserved light on the talented individuals conducting exciting research and their discoveries, whether seasoned professors or budding scientists mentored in our many labs.

And, she helped establish the relevant connection between science and art, detailing the partnership with the Rhode Island School of Design and the unique opportunities of interdisciplinary discovery. Together, science and art provide us with the powerful ability to explore and appreciate, preserve and promote life on earth.

Christine M. B. Smith, Executive Director, RI Science & Technology Advisory Council.

An important part of this partnership has been the Collaborative Research Grant program. These grants support teams that are at a catalytic stage of inter-organizational, inter-disciplinary, collaborative research. Funded projects clearly demonstrate how the combined efforts of the institutions can lead to results that could not be achieved by either alone, focus on building research capacity across institutions and advance the competitiveness of the team members to secure additional funding. Since inception of the program, STAC has invested nearly $8 million in 46 teams representing 117 researchers from 38 public and private institutions. To date, awardees have attracted $36 million in follow-on funding from public and private sources, proof of the catalytic nature of these grants.

In the following pages, I hope you enjoy reading some examples of how the 2012 Collaborative Research Grant recipients have been busy at work exploring new knowledge and pioneering our future through novel technologies and innovations. From marine genomics to aquaculture to coastal management, these teams have made collaboration and the convergence of multiple disciplines the key to tackling diverse challenges and complex issues.

Christine M.B. Smith Executive Director Rhode Island Science & Technology Advisory Council

Student research The Summer Undergraduate Research Fellowship symposium showcased 133 student research projects.

We awarded our first complete graduate student cohort at Brown University, Rhode Island College, and the University of Rhode Island.

Science communication in action Dr. Jennifer Specker Rhode Island NSF EPSCoR Principal Investigator University of Rhode Island

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news

Sara proved herself to be a leader as an undergraduate in the Marine Biology Program at the University of Rhode Island. She served as president of the Marine Science Society. She also took advantage of a semester at the Bermuda Institute of Ocean Sciences. Sara transitioned to Rhode Island’s NSF-funded Experimental Program to Stimulate Competitive Research a few weeks after graduating with her bachelor’s degree. While working with us, she pursued her master’s in business administration. She founded “Growing STEM in the Ocean State” on the social networking platforms of Facebook and Twitter, and interned with the Metcalf Institute for Marine and Environmental Reporting.

Rhode Island has a strong reputation in marine science research, is home to the country’s first and most active University Sea Grant program and has a historically ocean-based economy. We also enjoy a compact geography and densely connected networks among our research institutions, government agencies and the business community.

So it is only natural that through our federal-state partnership, we have built on these core assets and our ability to collaborate. Utilizing the rich coastal and ocean environment provided by the Narragansett Bay estuary and watershed as our laboratory, we have made major strides in strengthening our statewide research platform with the goal of increasing the competitiveness of our investigators for funding, engaging and training students and enhancing R&D-related economic development activity.

Dr. Susanne Menden-Deuer’s research on plankton — the first time a plant has been observed evading a predator — hit it big with news outlets like Science360 and NPR. The story was covered in 31 media articles (and 7 podcasts) in 8 countries in 6 languages. She attributed her preparedness and confidence to handle that deluge to the Metcalf Institute workshops.

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Rhode Island salt marshes, gateways to the sea By: Sara MacSorley

If you’ve spent any time in Rhode Island, you realize it is a state known for its beaches and its unexpected connections between people. Two new faculty members — Dr. Breea Govenar at Rhode Island College and Dr. Serena Moseman-Valtierra at the University of Rhode Island — are learning about those connections firsthand while studying salt marshes.

Crossing paths In graduate school at Pennsylvania State University, Dr. Breea Govenar studied deep-sea hydrothermal vent communities. One day she received an email about her work from another graduate student 2,500 miles away at the Scripps Institution of Oceanography, the now Dr. Serena Moseman-Valtierra. Dr. Moseman-Valtierra was interested in Dr. Govenar’s experiments on tubeworms at deep-sea vents and what they were revealing about marine community structure and function (topics she was exploring in salt marshes). Their common interest in communities at the bottom of the ocean brought them together at ocean meetings around the globe and then again in Woods Hole, MA, as postdoctoral fellows.

When Moseman-Valtierra arrived at the University of Rhode Island last year to start her tenure track faculty position, she had her first “only in Rhode Island” moment. A student mentioned a recent seminar at the University of Rhode Island about salt marshes presented by Govenar who accepted a faculty position at Rhode Island College the year before. Upon hearing this, Moseman-Valtierra emailed Govenar at her new address to congratulate her and convey happiness that both were beginning their new careers in Rhode Island.

When the grant was awarded, the two gathered up their students, yanked on their hip-high boots, and waded into the local salt marshes.

“Serena is interested in greenhouse gas emissions and I’m interested in the diets of invertebrates. Together we wondered if microbial diets of invertebrates could be contributing to gas emissions in the marsh,” says Govenar.

“We are focusing on the marsh sediments because that is where a lot of the greenhouse gases are being produced or consumed,” says Moseman-Valtierra. It’s the microbes in the sediment producing and consuming the gases. The molecular work will show who the major bacterial players are in the marsh sediments and in the gut contents of invertebrates. The team is using tools at the NSF EPSCoR-supported Genomics and Sequencing Center (URI) and the Center for Computation and Visualization (Brown). Next generation DNA sequencing will help identify the microbial communities in the marsh sediments with very high levels of detail.

06 //

Why salt marshes?

Salt marshes release methane and hydrogen sulfide, which tends to smell like rotten eggs. The marshes also emit nitrous oxide which is the worst culprit of the greenhouse gases. The release of nitrous oxide may increase with nitrogen loading from human activities and with higher temperatures. This is relevant for Narragansett Bay with its nitrogen gradient and the changing climate.

So, why should you care about a smelly salt marsh?

Salt marshes are critical for a healthy coastline in the Ocean State, all 400 miles of coastline. They act as buffers, purifiers, and nurseries.

“Salt marshes are buffers between the sea and the backyard for many people in Rhode Island,” says MosemanValtierra. They stabilize the shoreline during storms.

Collaborating When the call for STAC Collaborative Grant proposals was posted, Govenar and Moseman-Valtierra officially connected and submitted a proposal. The scientists wanted to use the well-documented nitrogen gradient in Narragansett Bay — higher levels in the northern reaches of the Bay — to test whether human impacts and climate change may be switching salt marshes from carbon sinks to sources (see explainer, page 08). Nitrogen loading and warming can stimulate microbial communities that release potent greenhouse gases. Govenar had strengths in benthic communities and food web dynamics that complemented Moseman-Valtierra’s strengths in biogeochemical cycling of nutrients. They were a perfect match.

Dr. Serena Moseman-Valtierra collects porewater, soil and plant samples in Waquoit Bay, MA.

Salt marshes act as nature’s water filter. “Marshes collect a lot of pollutants and metals and can start to recycle them over time,” says Govenar. The scientists want to see how these ecosystem functions may shift with climate change. A clean bay supports the local economy through fisheries, attractive beaches, and ecotourism.

Economically important shellfish and finfish use salt marshes as nursery grounds. The salt marshes create a safe haven for small fish, such as mummichogs, crabs, and the local favorite filter feeder and appetizer, the quahog (or the “stuffie” found on seafood restaurant menus).

Dr. Breea Govenar, kneeling, at computer, works in the field with students, from left, Melanie Garate (URI), Janis Hall (RIC), Cindy Cesar (RIC), CJ Pickett (RIC)

The STAC-sponsored research may also contribute to a newly recognized economic value of salt marshes —

voluntary carbon markets. The marshes could be critical players in reducing greenhouse gases and marsh restoration could therefore help offset carbon footprints.

Moseman-Valtierra and multiple colleagues working on the adjacent Waquoit Bay, MA, are addressing this possibility through a National Estuarine Research Reserve Science Collaboration. The STAC research in Narragansett Bay offers an opportunity to add important additional sites and explore this idea in Rhode Island.

Mentoring the next generation In addition to cooperative spirits, Govenar and MosemanValtierra share a strong passion for teaching and student mentoring. They knew from the beginning they wanted to design a STAC project that heavily involved students, especially in a way that exposed students to both college campuses.

The one-year project involves about a dozen students, mostly undergraduates from the University of Rhode Island, Rhode Island College, the University of Massachusetts at Amherst, and one student from Brown University as part of the Woods Hole Partnership Education Program. The students’ backgrounds range from biology to secondary education and one currently teaches at a local high school.

“I think about how eye-opening and empowering real research is,” says Govenar. “Students get to experience the entire arc of the scientific process from making observations and generating hypotheses to collecting, analyzing and presenting data.” (continued on page 08)

// 07

Communicating science “Building confidence through communication is key,” says Govenar. Students in both labs have already made presentations at science conferences. “The students are able to speak to a variety of students at different stages as well as to faculty at other institutions.”

What is a Carbon Sink?

Hint: You won’t find it in your kitchen.

Moseman-Valtierra agrees, “The strongest avenue for getting the word out about our research is with education, by having the students be advocates for the results and by letting them present to the broader community.”

Her favorite part of working with students is modeling the process of science. She is teaching them how to plan an experimental design and how to clearly communicate results as appropriate for science in society.

The students are gaining valuable research skills and learning about other life issues that will support them through a research career. “It has been really nice to emphasize the value of collaboration,” says MosemanValtierra. “The students in my lab can see the other students, meet in the field and see that we all have our own sets of tools but that we’re working together to try to answer complementary questions.”

explainer

(continued from page 07)

A carbon atom trapped in the right environment can slow the process of global warming.

By: Rebecca Helm

Four hundred million years ago an ocean covered New York State. This sea teemed with bizarre, alien-like creatures: giant fish, squidlike ammonoids, heavily armored trilobites, and algae. As these creatures ate, reproduced, and died; their bodies and waste fell to the seafloor and got buried under sediment. The sea retreated northward and this sandy tomb, called the Marcellus Shale, is now land. Through heat and pressure, the animals transformed over time into the oily substance known as fossil fuel.

Carbon is the major building block of life. When the creatures of the Marcellus Shale were entombed, so was the carbon in their bodies. The shale is a “carbon sink” because it takes carbon out of the environment and stores it away for a long time.

Analyzing greenhouse gas fluxes and measuring environmental properties in New England salt marshes, are (back row, from left): Dr. Serena Moseman-Valtierra, Kate Morkeski (research assistant, Marine Biological Laboratory), Jessica Eason (undergraduate, Brown University), Rose Martin (graduate student, URI); (front row, from left) Shirlie Yang (MBL undergraduate intern), Melanie Garate (graduate student, URI) and Katharine Egan (undergraduate, URI Coastal Fellow).

Women and minorities in science Moseman-Valtierra had some powerful advice for young women interested in getting into the sciences. “It’s important for students to be aware that others like them have succeeded. There are fantastic role models for women and minorities in science and if those models aren’t visible, we should do what we can to help make them more visible.” Rhode Island NSF EPSCoR supports women in science and is proud to feature these two new shining salt marsh stars.

08 //

We drill into the shale for fossil fuels. The process of burning fossil fuels releases carbon into the atmosphere and the fossil fuels then become a “carbon source.” Whereas a carbon sink like the Marcellus Shale removes carbon from the environment, a source, like the burning of fossil fuels, releases carbon into the atmosphere.

The processes that trapped carbon in the Marcellus Shale are still at work today. Marine ecosystems like salt marshes (page 06) take in carbon from the atmosphere. When the animals and plants that live there die and are buried, this carbon gets trapped.

This process, like the growth of trees in terrestrial ecosystems, removes atmospheric carbon added by human use of fossil fuels. Protecting carbon sinks is critical to slowing the rate of global climate change because they remove carbon (as the gas carbon dioxide) from our atmosphere.

// student spotlight //

A Rhode Islander’s path to science education: From installing air conditioners to dissecting mussels By: Sara MacSorley

Mike Martel pursues his passion for science with hands-on work in the field as part of his biology studies at Rhode Island College.

Meet Mike Martel, a local Rhode Islander who spends his spare time enjoying being outside in nature and digging for quahogs. After a dozen years as a technician in the heating and air conditioning industry, Mike experienced two major life events. He, like many Rhode Islanders, lost his job. Soon after, his wife gave birth to twin girls.

In Rhode Island, you can apply for a tuition waiver at the public colleges if you lose your job. Mike decided to take advantage of the opportunity to pursue his real passion for teaching and the environment.

He now studies elementary education with a focus in biology at Rhode Island College. “I was always interested in teaching and was excited to come back and take some science courses,” he says. “I like the education part but I love the science. It’s awesome to get into the lab and actually get to work with the organisms.”

Mike’s first lab experience was helping a graduate student with a pharmacology project on yeast. He learned how to grow cultures and run gels using electrophoresis. While he enjoyed the work, it was hard to find time to volunteer in the lab between going to school full time, working part time, and raising two small children.

However, the secondary education program requires credit in research. This allowed Mike to get back into the lab, and this time he also got into the field, researching the ecology of salt marshes, with Dr. Breea Govenar (page 06).

The project explores how ribbed mussel populations are responding to varying amounts of nitrogen in the marshes.

Excess nitrogen comes from fertilizers people use on their lawns and from sewage treatment plants and creates a nitrogen gradient running from north (high) to south (low) in Narragansett Bay. The research team collected ribbed mussels from the local salt marshes and brought them back to the lab.

There, Mike dissected the mussels, and measured their

wet weight and shell volume. His favorite part of the project, however, was going on the collection trips. “I like getting my hands dirty,” he says.

Mike also brought his skills from the heating and air industry to the team. Dr. Govenar wanted to use a respirometer to measure oxygen consumption by the mussels, but they were having trouble removing the air introduced into the system by the pump and the valves.

Not only did Mike fix the tubing system and help get the machine up and running, but he and Dr. Governar also created a waterproof casing so it could be used in the field!

Mike describes Dr. Govenar as a great mentor, “I wish I could get into the lab more to work with her. She obviously loves what she does.” You know you’re a scientist when you get excited about the biomass of mussels.

Studying the Bay is important to Mike because Rhode Island is home. “I’ve lived in New England my whole life.

It was great to actually get to see where the mussels live and the surrounding area in Narragansett Bay. It gives us a better idea of how the Bay and people interact.”

After one more semester of classes and a semester of student teaching, Mike plans to become a science teacher.

His passion for nature will make him a great addition to our community of educators.

“I love science because it is all around us,” he says.

“Everywhere you look there are trees and other plants.

If you look a little deeper there are organisms running around on them.” We can imagine how much fun his girls have exploring their backyard with their dad.

The most important lesson Mike will take away is about the connection between people and nature, not only how people can affect environment, but also how the environment can affect them. “I want to inspire students to explore the world around them.”

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Cultivating collaboration: Three projects measuring the impact of change in the marine environment By: Mary Grady

Collaborative funding by STAC and Rhode Island NSF EPSCoR has produced amazing results in the marine science field. Here, we highlight three great projects — with real and measurable impact — that are taking place right now.

New tools and mechanisms to combat aquaculture diseases Collaborators: David Rowley, Ph.D., University of Rhode Island; Marta Gomez-Chiarri, Ph.D., University of Rhode Island; David Nelson, Ph.D., University of Rhode Island; Dale Leavitt, Ph.D., Roger Williams University; Roxanna Smolowitz, DVM, Roger Williams University Oyster aquaculture is an important and growing part of Rhode Island’s economy. When juvenile oysters are raised in outdoor nurseries, lethal outbreaks of bacterial borne disease can be devastating. “With climate change, warmer waters carry less oxygen and may harbor more bacteria, making the oysters even more susceptible to disease,” says University of Rhode Island pathologist Dr. Marta Gomez-Chiarri.

Gomez Chiarri warns that antibiotics are not an economical solution and that it’s not a good idea to introduce them into aquatic ecosystems where they might have undesirable side effects. “Another option is probiotics which are beneficial bacteria that don’t harm the oysters and naturally protect them from pathogens,” says Gomez-Chiarri.

Gomez-Chiarri, microbiologist Dr. David Rowley, and Dr. David Nelson, a microbiologist and director of the NSF EPSCoR-subsidized Genomics and Sequencing Center at URI, designed lab experiments to figure out exactly how the probiotics prevent disease. “Perhaps the biofilm formed by the probiotics provides a physical barrier that protects the shellfish from pathogens, or maybe they produce a specific protective chemical, or it could be that they boost the oysters’ immunity,” says Nelson. Perhaps some combination of these effects provides the best protection. “It’s probably more complex than you want to think, but you have to approach it in a reductionist fashion,” Nelson says.

“Our data suggest that protection involves both biofilm formation and production of a protective antibiotic chemical, with some involvement of the oyster immune system.”

Two probiotic bacteria that occur naturally in Narragansett Bay are being tested in the research hatchery at Roger Williams University. At the hatchery, a team of students and faculty work to design protocols to deliver the probiotics and measure the results. A dozen tanks filled with millions of tiny oyster larvae, each one smaller than a pinhead, provide the venue for experimentation.

It’s a labor-intensive process, requiring attention to detail to develop the best methodology. Students care for the larvae, apply the probiotics, collect and count the larvae, and analyze the data. “It’s all-hands-on-deck for counting days,” says technician Kate Markey, who works in the Aquatic Diagnostic Laboratory with Roxanna Smolowitz. “We have six microscopes working and, in addition to counting, we take size measurements.”

The researchers confirmed that the probiotics do protect the larvae from disease. They also learned that the probiotics do not damage the larvae or affect their growth, says Gomez-Chiarri. The larvae must be treated every day with the probiotics to be effective, and now the researchers are figuring out the optimum dose and the best management practices to maximize survival.

“We’ve gone a long way toward beginning to understand the mechanisms involved,” says Gomez-Chiarri. The team plans to test what happens if the temperature or acidity of seawater changes, as might happen in a warming climate.

Probiotics may be able to help the oysters cope by moderating or neutralizing the impact of that change.

“We will also be figuring out how to develop these probiotics into products for use in commercial hatcheries,” says Gomez-Chiarri. The collaborators will expand the research to test the probiotics with hatchery-raised scallops and clams — other economically important marine species in Narragansett Bay. The project embodies the EPSCoR spirit of collaboration. “This is a highly interdisciplinary effort that involves experts in marine microbiology, chemistry, pathology, and shellfish aquaculture,” says collaborator David Rowley. “It’s wonderful that we’ve been able to assemble a team of scientists from right here in Rhode Island to tackle a problem that affects shellfish farming in this state and beyond.” (continued on page 12)

010 //

// 11

Nitrogen and climate change in narragansett bay Collaborators: Bethany Jenkins, Ph.D., University of Rhode Island, and Chris Deacutis, Ph.D., Narragansett Bay Estuary Program On a hot summer day in Rhode Island, with no wind to stir Narragansett Bay, a complex chain of interacting events can deplete the waters of oxygen and cause the stress or even death of economically important fish and other animals that live there. Understanding this process is key to learning how to better manage the Bay and to support healthy ecosystems, says Dr. Chris Deacutis, chief scientist with the Narragansett Bay Estuary Program.

Catherine Grimm, front, worked with Dr. Roxanna Smolowitz, Roger Williams University, as a SURF student fellow last summer. Grimm and Whitney Jaillet, center, received URE funds to work with Dr. Smolowitz this past academic year.

Kate Markey, rear, is a technician at Roger Williams University.

One well-known factor precipitating low dissolved oxygen, or hypoxia, is nitrogen entering the Bay from sewage treatment plants, says Deacutis. The nitrogen acts as fertilizer for algae near the surface, and when those algae die they are consumed by bacteria. The bacteria use up the available oxygen and degrade the ecosystem.

(continued from page 11)

Understanding coastal environmental change past, present, and future Collaborators: Timothy Herbert, Ph.D., Brown University; Linda Amaral-Zettler, Ph.D.; Brown University and Marine Biological Laboratory; Tatiana Rynearson, Ph.D., University of Rhode Island To geologist Dr. Timothy Herbert, the sediments beneath Narragansett Bay represent a library filled with information that can help him reconstruct the past. Herbert and his students at Brown University can detect soil erosion from Colonial farms and noxious heavy metals from the early Industrial Revolution by examining sediment cores collected from the bottom of the Bay. They use a number of molecular methods to reconstruct the past and create a time line of events, but when it comes to documenting historical water temperatures they could only make rough estimates until recently. A new method, based on molecular clues left behind in the sediments by algae that grow in the Bay, may provide the solution.

Dr. Linda Amaral-Zettler prepares to collect a marine sediment sample in Mt. Hope Bay.

relation to water temperature. When these biomarkers are found in the geologists’ sediment samples, they can be measured to determine what the water temperature was when the algae were alive.

If he could determine those temperature changes over time, Herbert could help resource managers better predict how the Bay’s ecosystem will react to future variations in climate. Part of the solution is collaboration. “Biologists bring a different set of skills and knowledge that can help measure past temperatures much more precisely than geologists can,” says Herbert. “These new biological tools tell us things we never could see before.”

Lipid-producing algae that live in the open ocean are well known, but until this study, the algae found in the brackish water of Narragansett Bay had not been studied before. Amaral-Zettler is working with algae from Narragansett Bay to determine if they are closely genetically related to the open-ocean species that make the same biomarkers. “If the lipids behave differently here, that might affect our interpretation of the data,” says Amaral-Zettler. But if her experiments work as expected “We’ll have a very nice thermometer that can accurately determine past temperatures,” says Herbert.

This is the goal of their STAC project.

Dr. Linda Amaral-Zettler, a biologist working jointly with Brown and the Marine Biological Lab at Woods Hole, says algae can provide a clue to past temperatures. “Some algae produce certain lipids in their cells that can be measured precisely in the lab,” says Amaral-Zettler. The proportion of lipids varies in

Estuaries like Narragansett Bay are sensitive to climate change, says Herbert. If scientists can reconstruct past temperature changes in the Bay, “That will help us understand the Bay’s history a lot better,” he said. The more we understand changes of the past, the better we can manage change in the future.

12 //

Research at the University of Rhode Island has revealed that some bacteria in the Bay absorb nitrogen gas directly from the atmosphere, adding even more fertilizer to the process. “This is something that wasn’t previously thought to happen in the Bay,” says URI microbiologist Dr. Bethany Jenkins. These nitrogen-fixing bacteria thrive in low-oxygen waters, so it may be that as hypoxic events increase, they create a niche for these bacteria that didn’t exist locally in the past. “This project is focused on trying to cultivate and grow those bacteria in the lab under lowoxygen conditions and characterize their biology,” says Jenkins.

Jenkins and her students are using high-throughput DNA sequencers at URI’s NSF EPSCoR-supported Genomics and Sequencing Center to study the genomes of these bacteria. “This — in a very quick way — will give us a rapid overview of their metabolism,” says Jenkins. The work will reveal if the bacteria can metabolize substances such as iron, sulfur, or uranium, which could make them useful for removing those pollutants from the environment. The bacteria also could potentially be used to power fuel cells. “So, there’s a real applied aspect to what we’re doing,” says Jenkins.

These experiments will help managers better understand the nitrogen-fixing bacteria’s role in the Bay’s ecology, and also could find a way to turn those bacteria into an asset for the state’s economy.

For Deacutis, the payoff from this project will be improved management practices for the Bay. “Managers now are being told they need to control nitrogen,” he says. “They thought they knew all the inputs of nitrogen, but this nitrogen-fixing bacteria is a new source.

We didn’t even know this was happening until recently.

So we’re trying to understand it, and this project is going to make a huge contribution. We’re going to learn a lot from these organisms about how to manage hypoxia.”

Kate Markey, a technician from Roger Williams, takes a break from working in the university’s oyster hatchery.

// 13

// research in focus //

Studying algae blooms, for the health of the Bay and the economy By: Sara MacSorley

Algae are a bigger part of your life than you probably realize. Many everyday products like toothpaste, cosmetics, and ice cream use algal ingredients. Scientists are even working to turn algae into alternative fuel sources. Who knew that green slimy stuff that gets stuck between your toes at the beach might someday gas up your car?

A team of scientists in Rhode Island is looking closer at local algal species to see how algal blooms may be affected during climate change. The blooms are a cause for concern — ecologically and economically.

Algal blooms can cause a lot of problems for Rhode Island. The algae wash up on our beaches affecting local tourism and get stuck in fishing nets. When the blooms die, they sink, causing hypoxic events in Narragansett Bay. These low oxygen environments can kill other marine species and interrupt food webs. Macroalgae, like salt marshes (see page 06), act as protective nursery grounds for small fish and invertebrates that are important food for larger animals in the Bay. “Most of the energy in the ocean comes from a primary producer,” says Dr. Carol Thornber, and algae — whether it be microscopic phytoplankton or macroalgae — are primary producers. “In Rhode Island, the commercial and recreational fisheries are dependent on primary production at some point in the food chain.”

Believe it or not, blooms are also of interest to the military. There is a lot of satellite work going on to better understand algae blooms. Part of the reason is that algae can get caught in sonar and cause problems. If we can learn to control blooms, the military may also be able to use algae as cover for submarines.

Algae + berries = collaboration Thornber, an algal ecosystem expert at the University of Rhode Island, has been researching algal blooms in Narragansett Bay since 2005. She identified two local forms of Ulva, a green macroalgae, with a prior STAC award. In her next research questions, she wanted to learn more about how the Ulva algal blooms formed.

At a fateful EPSCoR meeting last year, Thornber met Dr. JD Swanson, a new faculty member at Salve Regina 14 //

University. The two started talking weekly about how their research interests might complement each other.

Swanson came to Rhode Island from the University of Central Arkansas, where he was known for his work on berries. His research brings a new tool kit to the table.

“People pigeon hole themselves too much. I bring a good set of tools that can be applied to any organism,” Swanson says. “The question that drives me is what controls cell growth and development.”

Very little is known about the population biology of Ulva blooms. This project brings molecular tools and ecology together to find answers. “If we understand the causes and can detect blooms, we can prevent them,” says Swanson.

The scientists developed a project and submitted a few proposals. The STAC Collaborative Award came through.

The STAC research will allow the team to collect preliminary data and show that they have developed techniques that work for the Ulva species. This proof of concept work will be favorably viewed when Thornber and Swanson resubmit a proposal to NSF’s Biological Oceanography Division.

“We have different skill sets but neither one of us could do this by ourselves,” says Thornber. She knows the algae and Swanson knows the genomics. “It’s exactly what it’s supposed to be,” says Swanson. “It’s a collaboration. We’re greater than the sum of our parts by using the strengths of both universities.”

Breaking down the bloom The project has three parts. First, the team will determine how individual algae in the blooms are related. This is tricky because algae can reproduce sexually or by cloning depending on the stage of their life cycle. This molecular work will examine microsatellites — small variable repeat regions of DNA that can be used to fingerprint individuals

Left: Square plots of algal bloom samples in Greenwich Bay allow researchers to determine species coverage. Center: Research assistant Amy Battocletti, left, and graduate student Elaine Potter, right, look at algal samples in Greenwich Bay as part of their work with Dr. Carol Thornber. Right: Emily Bishop, a research assistant in the Thornber laboratory, checks on experimental tanks on URI’s Narragansett Bay Campus.

— using equipment at the EPSCoR-supported Genomics and Sequencing Center.

being able to coordinate and direct people doing research with me. All research projects are team endeavors.”

Second, they will determine which phase of the algae life cycle is causing the blooms. This is virtually unknown for algae in estuarine systems around the world. The scientists will use flow cytometry — a technique that lets you look at single cells — to see how much DNA is in each cell. Algal individuals that are haploid (one copy of each chromosome) have less DNA than diploid individuals (two copies of each chromosome).

The students get to experience real collaboration at work.

Thornber and Swanson designed the project so there would be cross-fertilization between the two schools. The students do field work together and URI students are learning about DNA fingerprinting techniques at Salve.

Students gain perspective by working with a research institution and a primarily undergraduate institution. They get to see how different labs operate and they get insight into what might be a good fit for their own careers.

Third, the scientists will extract the RNA to look at the transcriptomes — blueprints of what genes are on and what genes are off. Recent advances in DNA sequencing allow scientists to look specifically at what genes are turned on and off and by how much in one sample. The next generation sequencing for this project will be done at Washington University and Brown University. The University of Rhode Island will provide bioinformatics support to analyze the data.

“Basically, when a bloom occurs, there are genes that signal the algae to start dividing really fast,” says Swanson.

“We are trying to find the link between the genes that get turned on and the environment that turns them on.”

An education in algae Thornber and Swanson wanted to use their STAC award to give research opportunities to undergraduates.

Thornber has been mentoring students since she was a student in graduate school. “One of the most enjoyable and rewarding parts of being a scientist is mentoring the next generation,” she says.

There are a dozen students working on the project learning technical skills in ecology and molecular biology.

They are also learning skills that go beyond the lab to prepare them for their future careers in research, like organizational skills. For example, a recent graduate from Thornber’s lab just started a Master’s at the University of Alaska, Fairbanks. “The biggest things she gained was experience in organizing and managing,” says Thornber.

“One of the most important skills for me as a researcher is

“It’s useful for the students to see which type of career path may be good for them,” says Thornber. One of her former students who worked on another algae project with Brian Wysor from Roger Williams University learned she wanted a more student-focused institution.

She is now working at Sacred Heart University in Connecticut, a primarily undergraduate institution.

“Experiential learning is the way to go,” says Swanson. “The key part that is absolutely irreplaceable is the idea that students know how science is done from conception to completion. And they have ownership of the research. It’s our project. It’s equally mine, Thornber’s, and all the students.”

Doing science also includes communicating science.

Both scientists have relationships with local high schools that they plan to partner with as the project moves forward. “The best public outreach we have is through getting the students out to communicate about the research,” says Swanson. He considers teaching students how to communicate science effectively part of his role as an educator. “We want to get the spotlight on the undergrads because they are the stars of the show.”

Learn more about Dr. Swanson’s research at http://swanson.salvereginablogs.com Learn more about Dr. Thornber’s research at http://cels.uri.edu/Thornber/ // 15

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The Science & Technology Advisory Council ensures fidelity to the Science

Charlie Cannon

Eric Roberts

Rhode Island School of Design

Rhode Island College

and Technology Infrastructure Plan (2009) for Rhode Island. One major role of STAC is to be a catalyst for integrating academic research with state priorities and thereby advise on innovation policies that promote economic growth.

Edward Hawrot

Sheila Adamus Liotta

Brown University

Providence College

Mary Sullivan

Neal Overstrom

Rhode Island STEM Center

Rhode Island School of Design

Dr. Peter Alfonso is the Director of Rhode Island EPSCoR. He and Dr. Clyde Briant, Vice President for Research at Brown University, serve as Co-Chairs of STAC.

The Steering Committee promotes collaboration, guides research infrastructure development and use, and seeks competitive funding opportunities for Rhode Island’s institutes of higher education.

Jennifer Specker University of Rhode Island

Christine Smith

Lonnie Guralnick

Science and Technology Advisory Council

Roger Williams University

Pamela Swiatek

Brown University

Brown University

David Rand Richard D. Horan

The Partner Liaisons foster

Slater Technology Fund

research training of students, communicate to their colleagues the new infrastructure and equipment available, assist in the reporting requirements of NSF, and, ultimately, serve their institutions in developing goals and strategies for continued excellence in student mentoring.

Dan McNally Bryant University

Peter Woodberry Community College of Rhode Island

Lisa A. Zuccarelli Salve Regina University

Carol Thornber University of Rhode Island