2012 Annual Report


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Fifty years after it was established as one of the original science departments at WHOI, and more than eighty years after the first WHOI biologists began to study life in the oceans, the Biology Department continues to be a home for cutting-edge research on marine organisms and their interactions with the environment. The department in 2012 included 32 scientific staff and 44 highly skilled research and technical staff, supported by a vital administrative team. Approximately 20 postdoctoral researchers and 25 students in the WHOI/MIT Joint Graduate Program in Oceanography/Applied Ocean Science and Engineering participated in the research, as did dozens of visiting researchers who collaborated with members of the department. 

WHOI biologists study the diversity of life in the oceans, including bacteria and archaea, viruses, protists, phytoplankton and zooplankton, other invertebrates, fish, seabirds, and whales. As diverse as the organisms they study, members of the Biology Department include oceanographers, as well as scientists who trained initially in other fields, such as zoology, mathematics, biochemistry, genetics, microbiology, toxicology, animal behavior, or engineering. All came to WHOI to apply their skills to better understand the biology of the oceans. Research in the department ranges from molecules and cells to communities and ecosystems; it occurs at sea all over the world, in the laboratory, and on computers.

In 2012, WHOI biologists reported their findings in nearly 150 published papers.

Several papers involved the effects of climate change:  Stephanie Jenouvrier and Hal Caswell, combining long-term population data with climate models, found that the loss of sea ice caused by global warming threatens emperor penguins in the Antarctic. Rubao Ji, Carin Ashjian, Cabell Davis, and colleagues published an important paper in which they used computer models of physical and biological processes to predict the impact of future climate change on zooplankton populations in the Arctic. Also in the Arctic, John Dacey and collaborators found that algae living in sea ice participate in rapid recycling of dimethylsulfide, an important atmospheric gas that affects clouds and climate.

Tim Shank and colleagues in MC&G, using WHOI’s deep-sea robotics fleet, discovered that oil from the Deepwater Horizon spill had affected deep-water corals in the Gulf of Mexico.

Several papers were led by current or former Joint Program (JP) students:  Shank and Joint Program student Santiago Herrera published a paper describing patterns of genetic diversity and population connectivity in deep-sea corals.  Recent JP graduate Kelton McMahon, advised by Simon Thorrold, used new isotopic methods to study the movement of coral reef fishes between juvenile and adult habitats.  Another recent JP graduate, Maya Yamato, and her advisor Darlene Ketten, described the role of fats in hearing in baleen whales. Former JP student Kelly Sutherland and her advisor Larry Madin were part of a team that published a paper evaluating the evidence for a recent increase in jellyfish populations.

Julie Kellner applied a multi-species bio-economic model to a Caribbean coral reef community to better understand the trade-offs involved in adopting ecosystem-based management of fisheries.

New Assistant Scientist Neel Aluru and colleagues described how exposure of fish embryos to environmental contaminants can disrupt microRNAs, a recently discovered type of nucleic acid with important roles in embryonic development.

Several projects ongoing in 2012 promise to yield exciting results in the future:

Mark Baumgartner and Ann Tarrant, with colleagues in Norway, conducted an ambitious project combining laboratory and field research to understand the role of gene expression in helping copepods (small crustaceans) prepare for diapause, a state of dormancy used to survive adverse conditions.

Cabell Davis, with Rubao Ji, traveled to Indonesia to develop an international collaborative project to explore the diversity and productivity of the Halmahera Sea, in the region known as the global epicenter of marine biodiversity. 

Stefan Sievert sequenced the genomes (complete DNA) of 11 individual cells from bacteria living at deep-sea hydrothermal vents, the first time single-cell sequencing has been accomplished on vent microorganisms.

In a study of northern elephant seals, Gareth Lawson and colleagues deployed a new animal-borne acoustic system for detecting zooplankton and fish. These “sonar tags” allow the researchers to study the behavior of the animals in relation to prey abundance and distribution.

And as part of the NSF-supported Arctic Observing Network, Sam Laney and colleagues in the WHOI Physical Oceanography Department used a novel fluorescent sensor mounted on an ice-tethered profiler (ITP) to obtain the first high-resolution (daily), full-year record of under-ice phytoplankton in the Arctic Ocean.

In 2012, more than fifty new research grants from external funding sources were awarded to WHOI Biologists.  Some examples:

Matthew Johnson and colleagues in MC&G received an award from the Gordon and Betty Moore Foundation’s Marine Microbiology Initiative to study the role of chemical communication among microbial cells in carbon and nutrient cycling in the North Atlantic.

Tim Shank and a group of collaborators received funding from NSF for the Hadal Ecosystem Studies (HADES) program to study deep ocean trenches.

Scott Gallager received funding from the new Okinawa Institute of Science and Technology (OIST) to develop and build a series of cabled underwater observatories, similar to ones he has installed in Panama, to provide long-term measurements relative to effects of ocean acidification off the coast of Japan. 

Two multidisciplinary programs received renewed funding for another five years.  Led by Don Anderson with strong support from Judy Kleindinst and others, the Cooperative Institute for the North Atlantic Region (CINAR) was rated “outstanding” in its 5-year review. As a result, CINAR will continue to serve as a mechanism for coordinating and supporting research of relevance to the mission of the U.S. National Oceanic and Atmospheric Administration (NOAA). The Woods Hole Center for Oceans and Human Health (WH-COHH) received a 5-year renewal to study the dynamics of harmful algal blooms in the Gulf of Maine and coastal Cape Cod and the effects of low-level exposure to algal toxins on embryonic development. Led by John Stegeman, the center also includes Don Anderson, Mark Hahn, and Neel Aluru from Biology and Dennis McGillicuddy from the AOPE Department.

WHOI Biologists also were involved in research translation and communication, making sure that WHOI research has broader impacts beyond the scientific community. For example:

Rob Olson and Heidi Sosik successfully licensed the manufacture of their Imaging FlowCyotobot, an instrument for automated visualization of phytoplankton and zooplankton in the ocean.

Amber York and Scott Gallager launched a new citizen science web site “Seafloor Explorer” that allows the public to identify organisms in images taken by HabCam, an underwater vehicle for mapping seafloor habitats.

Don Anderson and colleagues in AOP&E continued to provide annual forecasts of the potential for “red tides” (harmful algal blooms, or HABs) in the Gulf of Maine.

Gareth Lawson’s research on ocean acidification and pteropods inspired sculptures on these “charismatic microfauna” that were exhibited at a Manhattan art gallery. The exhibit has been selected for display at the Sant Ocean Hall of the Smithsonian National Museum of Natural History.

Andrea Bogomolni participated in the Northwest Atlantic Seal Research Consortium (NASRC), a group of researchers, managers, and fisherman interested in understanding the ecological roles of seals along the coast of New England. As part of the consortium, Becky Gast is studying the possible contribution of fecal bacteria from gray seals to beach closures on Cape Cod.

Bob Groman, Peter Wiebe and colleagues in Marine Chemistry and Geochemistry continue to operate the NSF-supported Biological and Chemical Oceanography Data Management Office (BCO-DMO), working closely with NSF-funded scientists and others to manage the data and information produced during their research.

Judy McDowell chaired a committee of the U.S. National Research Council (part of the National Academy of Sciences) that produced a report on "Assessing Risks to Endangered and Threatened Species from Pesticides."

The research of several WHOI Biologists was featured in Oceanus magazine.

Education continued to be a high priority for the Biology Department, involving the WHOI/MIT Joint Graduate program, postdoctoral researchers, and undergraduate summer fellows. This year saw a major revision in the Joint Program curriculum in Biological Oceanography and a new exam format that will foster interdisciplinary research. Simon Thorrold stepped down as chair of the Joint Committee for Biological Oceanography (JCBO). He was replaced by Mike Neubert, who turned over his role as Biology Education Coordinator to Becky Gast

Biology department personnel received recognition in 2012 through awards and promotions:  

Darlene Ketten was elected as a Fellow of the American Association for the Advancement of Science (AAAS).

Sam Laney and Heidi Sosik were members of a team of researchers that received the NASA Group Achievement Award for their work on the ICESCAPE (Impacts of Climate on the Eco-Systems and Chemistry of the Arctic Pacific Environment) project.

The Biology Department recognized excellence in research by promoting Stefan Sievert and Tim Shank to Associate Scientist with Tenure.

Neel Aluru and Joel Llopiz were hired as new Assistant Scientists.  Aluru studies environmental epigenetics – the mechanisms by which animals adapt to environmental changes without altering their “DNA blueprint.” Llopiz studies the ecology of larval fishes and their roles in marine food webs. 

As we begin our second 50 years, the WHOI Biology Department remains an exciting and vibrant center for research on life in the oceans.

Mark Hahn, Department Chair

Last updated: September 6, 2013