Creation of National Microbiome Initiative

May 13th, 2016 @

Today, the White House Office of Science and Technology Policy announced a new, National Microbiome Initiative, and senior scientists Zoe Cardon and David Mark Welch represented the MBL, and Jack Gilbert represented the new UChicago/Argonne/MBL Microbiome Center, at the event in Washington, DC. The National Microbiome Initiative has emerged over the last several years from the growing recognition that microbes are at the core of organismal health and ecosystem services sustaining humanity world-wide.


Photo Credit: Suzanne Thomas and Francois Thomas

Over the past two decades, building on collaboration between John Hobbie (Ecosystems Center) and Mitch Sogin (Bay Paul Center), the MBL has fostered an uncommon synergy, combining in-depth microbial, genomic, and bioinformatic expertise with organismal and ecosystems research. Created by scientists drawn year-round to Woods Hole and the far-flung research sites the MBL spearheads, this growing microbiomes community is now examining microbial activities in ecosystems from deep mid-ocean ridges to the coastal and polar frontlines of global climate change. The power of field and lab experiments is being combined with the clarity of evolutionary, ecological, and thermodynamic theory to identify commonalities uniting microbiome function. These commonalities -- new paradigms – will provide the framework for new solutions to real-world problems, from improving diagnostic tools for ecosystem, organismal, and human health, to developing novel strategies for environmental resilience and remediation.

For more information about the initiative, please see:
MBL's Press Release
White House Briefing
Related Publications:

Blaser M, Cardon ZG, Cho M, Dangl J, Donohue J, Green J, Knight R, Maxon M, Northern T, Pollard K, Brodie E. (2016) Towards a predictive understanding of Earth's microbiomes to address 21st Century challenges. mBio 7(3):e00714-16, doi: 10.1128/mBio.00714-16

Biteen JS, Blainey PC, Cardon ZG, Chun M, Church G, Dorrestein PC, Fraser SE, Gilbert J, Jansson JK, Knight R, Miller JF, Ozcan A, Prather KA, Taha S, Ven den Engh G,  Quake S, Ruby EG, Silver P, Weiss PS, Wong GCL, Wright AT, Xie XS, Young TD (2016) Tools for the Microbiome: Nano and Beyond. ACS Nano, 10:6-37. DOI: 10.1021/acsnano.5b07826

Alivisatos AP et al. (2015) A unified initiative to harness Earth’s microbiomes. Science 350:507-508. (45 authors in Unified Microbiome Initiative Consortium.)

Arctic Scientists Gather at MBL

April 8th, 2016 @

More than 65 ecologists and earth system scientists gathered at MBL April 6 and 7 for the annual Arctic LTER All-Scientists meeting. The Arctic LTER, led by Ecosystems Center Senior Scientist Gus Shaver, investigates the dynamics of the tundra, lake and stream ecosystems on the North Slope of Alaska and is based at Toolik Field Station.

The Arctic LTER All-Scientists meeting attracts a collaborative mix of senior investigators, post docs and graduate students who take advantage of the long-term experiments and ecological datasets that the LTER develops, maintains and makes available to the broader scientific community.

Ecosystems Center Senior Scientist Edward Rastetter explains the planned transition of the Arctic LTER project to new leadership.

Ecosystems Center Senior Scientist Edward Rastetter explains the planned transition of the Arctic LTER project to new leadership.

Later this year, Ecosystems Center Senior Scientist Edward Rastetter will assume leadership of the Arctic LTER project. Ed led the writing of the 2016 LTER renewal and developed a new theoretical framework for the project that will test the open or closed nature of element cycles and species movements in coupled tundra, stream and lake ecosystems. It will also predict how rapid Arctic climate change will alter these cycles and species rearrangements.

Global study of tundra to desert plants shows leaves respond to warming in remarkably similar ways

March 25th, 2016 @

Mary Heskel, MBL Postdoctoral Scientist

Plants from all over the globe respond to temperature changes in remarkably similar ways. That’s the finding of a new study led by MBL Ecosystems Center postdoctoral researcher Mary Heskel and published in the Proceedings of the National Academy of Sciences.

Mary, along with a large team of researchers, measured the respiration rates of vegetation at eighteen remote sites around the world that represented seven different types of plant habitat. It was the most comprehensive study of plant respiration responses to temperature ever conducted.

The team found that the sensitivity of respiration to temperature decreases as plants warm.

“The findings have important consequences for estimating carbon storage in vegetation, and for predicting concentrations of atmospheric carbon dioxide and future surface temperatures," Heskel said.

The finding points to universally conserved controls of temperature responsiveness across the world’s plant life.

The study looked at a wide range of plants growing in contrasting environments, from the arid woodlands of Western Australia, to the deciduous forests of New York, the arctic tundra in Alaska, the boreal forests of Sweden and the tropical forests of Costa Rica and Peru, according to Owen Atkin, Professor at the Australian Research Council Centre of Excellence in Plant Energy Biology at the Australian National University (ANU) in Canberra.

“We saw that in the cold, respiration is more sensitive to temperature than previously thought and that the sensitivity of respiration declines at higher temperatures.  Amazingly, these patterns were remarkably uniform across all the habitats and plant types studied,” Atkin said.

Odhran O’Sullivan, a postdoctoral researcher involved in the study who is now at the University of Sheffield, conducted fieldwork at the Arctic LTER site at the Toolik Field Station, which played an important role in defining responses at the cold end of the temperature spectrum experienced by plants.

Mary’s previous work in the Arctic LTER during her PhD improved understanding of the photosynthesis of arctic plants and resulted in several recent papers.

Respiration is the set of metabolic reactions used by plants to make usable energy for growth and cell maintenance. Plants release carbon dioxide during respiration as a by-product of converting sugars into energy.

The finding has important implications for the way that the temperature sensitivity of plants is incorporated into global ecosystem models that predict how ecosystems will respond to climate change. Heskel worked with Atkin at ANU before coming to the Ecosystems Center in November 2014 as a Rosenthal Postdoctoral Scholar.

The reality that respiration is more temperature sensitive that previously assumed and becomes less sensitive as the temperature rises is important for creating accurate climate models.

Plant respiration contributes a large amount of carbon to the atmosphere and plays a key role in the global carbon cycle. Climate models predict how warm the Earth will be later this century. Central to this is the prediction of carbon flows between plants and the atmosphere.

See other media coverage of this article.

IIC Brazil Summer Policy Lab

February 23rd, 2016 @

Aerial photograph of the Xingu Indigenous Reserve in eastern Mato Grosso. The Xingu Reserve is one of the largest protected rainforest areas in the world but extensive croplands in the Reserve’s headwaters threaten water quality and regional climate. Photo credit: Marcia Macedo.

The Ecosystems Center will partner with the University of Chicago’s International Innovation Corps (IIC) in the Harris School of Public Policy to create a Brazil Summer Policy Lab to link Amazon ecosystem science to forest and biodiversity conservation policy.

This summer, eight to ten University of Chicago graduate students will live and work in the Brazilian capital of Brasilia from June to August and collaborate with scientists from MBL and the MBL’s partners in Amazon research at the Woods Hole Research Center (WHRC) and the Institute for Amazon Environmental Research (IPAM) to link Amazon science to conservation policy recommendations.

Students will develop policy prescriptions for sustaining forest protected area, reducing fire and protecting streamside riparian forest and water quality using data derived from science conducted by MBL, WHRC, IPAM and other partners in Mato Grosso and other places in the Amazon. Participants will be drawn from the Harris School and across the University.

The program is funded by a USAID grant to the University of Chicago. Policy fellows will spend several days in Woods Hole in late June before they depart for Brazil.

The Ecosystems Center’s Chris Neill and Linda Deegan worked with IIC Director of Operations Phoebe Holtzman and colleagues at WHRC and IPAM to develop the program.

Applications for the program and more information may be found online at:

Download the program brochure (pdf).

Ecosystems Center scientists investigate effects of climate change on important arctic plants

November 17th, 2015 @
Eriophorum vaginatum_cottongrass

Eriophorum vaginatum (cottongrass)

A new project of Ecosystems Center Postdoctoral Scientist Thomas Parker and Associate Scientist Jim Tang investigates the impacts climate change will have on different populations of the dominant arctic sedge, cottongrass (Eriophorum vaginatum) and whether populations of cottongrass adapted to specific local arctic conditions will survive under climate warming. This work tests whether warm-adapted species will be able to track climate change and move north and how this will affect ecosystem processes such as releases of greenhouse gases and carbon storage in tundra soils. Drs. Parker and Tang collaborate with Dr. Ned Fetcher from Wilkes University and Dr. Michael Moody of the University of Texas at El Paso.

The team worked at Toolik Lake Field station on the North Slope of Alaska during the summer of 2015 and will return in 2016. The team transplants cottongrass to sites farther north and south within the species’ wide range and combines transplants with warming experiments (pictured) to simulate warming over the next century. This NSF-funded project will improve our understanding of future vegetation of a warmer arctic and how this will affect the carbon balance of this globally-important ecosystem.

Tom Parker (right) and Wilkes University student Stephen Forney (left) measure cotton grass abundance and cover at the southern-most experimental site at Coldfoot, Alaska. Photo credit: Darrel Dech, Wilkes University.

Tom Parker (right) and Wilkes University student Stephen Forney (left) measure cottongrass abundance and cover at the southern-most experimental site at Coldfoot, Alaska. Photo credit: Darrel Dech, Wilkes University.

Research assistant Mahalia Clark tags an Eriophorum vaginatum tussock for long-term monitoring. Photo credit: Dr. Joanna Carey, MBL Postdoctoral Scientist.

Research assistant Mahalia Clark tags an Eriophorum vaginatum tussock for long-term monitoring. Photo credit: Dr. Joanna Carey, MBL Postdoctoral Scientist.

Researchers set up open top chambers to increase air temperature over potentially vulnerable cottongrass at Toolik Field Station, Alaska. This plant currently covers vast expenses of tundra in northern Alaska.

Researchers set up open top chambers to increase air temperature over potentially vulnerable cottongrass at Toolik Field Station, Alaska. This plant currently covers vast expenses of tundra in northern Alaska.

The Ecosystems Center and a Century of ESA

September 11th, 2015 @

It’s the 100th birthday of the Ecological Society of America, and Ecosystems Center scientists and their work are being featured in the celebration. Formed in 1915 through the vote of several members of the American Association for the Advancement of Science, the ESA is now the largest professional society devoted to the science of ecology, with more than 10,000 members.

As part of the centennial activities, ESA has identified “Notable Papers of the Last Century”, and among those listed are two published by Ecosystems Center scientists:

Melillo JM, Aber JD, and Muratore JF. (1982) Nitrogen and Lignin Control of Hardwood Leaf Litter Decomposition Dynamics. Ecology, 63(3): 621-626.

Chapin III FS, Shaver GR, Giblin AE, Nadelhoffer KJ, Laundre JA. (1995) Responses of Arctic Tundra to Experimental and Observed Changes in Climate. Ecology, 76(3): 694-711.

Also, at the recent ESA national meeting in Baltimore, MD, the ESA Science Committee presented a celebratory “Ignite” session, where eight speakers were invited to provide their vision of a roadmap for key advances, frontiers, challenges, and applications of ecology over the next 100 years. “Got Organisms?” was the title of Zoe Cardon’s talk in the session. Over the last several decades, she says, there has been an explosion of research in biological science at the two ends of the biological spectrum—genes and ecosystems. “But where did the organisms go?” she asks. “Organismal ecology links genes with ecosystems,” Cardon says. The expression of genes “packaged” within organisms has to be carefully orchestrated for organisms to survive. At the same time, organisms (whether microbial, plant, or animal) carry out many of the large-scale environmental functions upon which humanity depends, such as cleansing wastewater and recycling nutrients in soil. Understanding organismal biology, Cardon says, helps bridge knowledge at the two ends of the biological spectrum—and that’s especially important in the face of rapid global change.

A ciliate active in sludge from the Falmouth, MA wastewater processing plant. Credit: Suzanne Thomas (MBL) and Ruby An (Metcalf intern, University of Chicago, and MBL SES student).

Rachel Chelsea Nagy Defends Thesis on Amazon Land Use Change

September 11th, 2015 @

Rachel Chelsea Nagy, a student in the Brown-MBL Graduate Program in Biological and Environmental Sciences, successfully defended her Ph.D. dissertation entitled “Ecological and Biogeochemical Consequences of Land Use Change in the Brazilian Amazon” on August 6 at Brown University. Nagy, a student in the Ecology and Evolutionary Biology Department at Brown, was co-advised by MBL Senior Scientist and Ecosystems Center Director Chris Neill and Steven Porder, Associate Professor of Ecology and Evolutionary Biology at Brown.

This month, Nagy began a post-doctoral position with Jennifer Balch in the Dept. of Geography at the University of Colorado-Boulder. She is studying the links between fire distribution and anthropogenic activities across the United States.

Chelsea Nagy installing a temperature/ humidity logger to monitor microclimate conditions in riparian forests in the summer of 2013 on the Tanguro ranch in Mato Grosso, Brazil.

Chelsea Nagy installing a temperature/ humidity logger to monitor microclimate conditions in riparian forests in the summer of 2013 on the Tanguro ranch in Mato Grosso, Brazil.

Nagy’s doctoral research compared the structure, composition, and diversity of plant species in intact riparian forests (adjacent to rivers or streams) to riparian forests that were isolated by clearing for agriculture. She found that the size distribution, number of dead trees, mortality, biomass and carbon storage of altered riparian forests surrounded by agriculture were similar to that of intact riparian forests. However, riparian fragments had fewer seedlings and saplings that indicated reduced potential for forest regeneration. Agricultural fragments also had lower tree species diversity and a different species composition than intact riparian forests.

Nagy's other projects looked at carbon storage in agricultural soils and regrowing secondary forests. Her work showed that the widespread conversion of forests to intensive soybean production did not lead to large reductions in soil carbon despite relatively large changes in microclimate that accompany the land conversion. She developed a mass balance biogeochemical model to understand how different disturbance and land use practices, such as land clearing, shape nutrient limitation and biomass recovery in tropical secondary forests. Her model indicated that nitrogen limits growth of young secondary forests but that this limitation progresses to phosphorus as the forest ages. These results show the importance of retaining nutrients, particularly phosphorus, in order to fully recover from the disturbance of forest clearing.

Nagy’s doctoral committee also included Ed Rastetter, Senior Scientist at the MBL Ecosystems Center and Susan Trumbore, Professor of Earth System Science at the University of California, Irvine, and Director of the Max Planck Institute for Biogeochemistry.

Chelsea Nagy conducting a forest inventory of woody plants, seedlings, and saplings in Mato Grosso, Brazil

Chelsea Nagy conducting a forest inventory of woody plants, seedlings, and saplings in Mato Grosso, Brazil

Funding for Nagy’s doctoral research was supported by an EPA’s STAR graduate fellowship, a NSF grant to Chris Neill and Michael Coe (Woods Hole Research Center), with additional grant support from Steven Porder. Nagy also earned a Dissertation Development Grant (DDG) from the Dept. of Ecology and Evolutionary Biology at Brown and a Center for Latin American and Caribbean Studies (CLACS) award for research in Brazil.

Nagy, R.C., Porder, S.; Neill, C., Brando, P.; Quintino, R.M., Nascimento, S.A. (2015). Structure and composition of altered riparian forests in an agricultural Amazonian landscape. Ecological Applications 25(6): 1725-1738.

2015 Summer Undergraduates

June 25th, 2015 @

The Ecosystems Center is mentoring a record number of undergraduate students this year! All of the students are working with Center scientists and are fully participating in laboratory exercises and activities. While some are working here on the MBL campus, others are working at the Toolik Field Station in Alaska, the Marshview Field Station in Plum Island, MA, and one will be off to the Tanguro Field Station in Brazil! It's shaping up to be a great summer!

Biological Discovery in Woods Hole REU Program
Jasmine Prat, University of California, Santa Barbara (Tang)

Brown-MBL LINK Awardees
Jonathan Ang, Brown University (Tang)
Lena Champlin, Brown University (Neill)
Jon Gewirtzman, Brown University (Tang)
Sarah Skelton, Brown University (Valiela)

Cornell University Visiting Undergraduate Intern
Jeanne Powell, Cornell University (Howarth)

Linton-Jefferson Fellow
Kassandra Baron, Washington & Jefferson College (Deegan)

National Science Foundation REUs
Lindsay Arick, University of Central Florida (Giblin)
Vanessa Cabrera, University of California, Santa Cruz (Neill)
Andrew Collins, University of New England (Deegan)
Emily Maness, University of Tampa (Conte)
Nathalie Moore, William & Mary (Deegan)
Levi Simmons, Utah State University (Shaver)
Kate Yuhas, University of Michigan (Shaver)

Naushon Island Summer Research Program
Luke O'Brien, Boston College (Neill)

Metcalf Summer for Undergraduate Research
Ruby An, University of Chicago (Vallino)
Eva Kinnebrew, University of Chicago (Neill)
Jonathan Michelsen, University of Chicago (Tang)
Caroline Owens, University of Chicago (Valiela)
Leonard Shaw, University of Chicago (Conte)

The Woods Hole Partnership Educational Program (PEP)
Camila Fishtahler, William & Mary (Tang)
Wyntin Goodman, University of Maryland, Eastern Shore (Foreman)



Toolik Field Station, North Slope, Alaska

June 17th, 2015 @

Research assistants for the Arctic Long-Term Ecological Research project collect water from lakes in the foothills of the Brooks Range. Since 1975, this project has tracked nutrient fluxes and water chemistry to study ecosystem dynamics in the rapidly changing Alaskan arctic.

1 Toolik North Slope

Photo by Sarah Nalven (click for larger image)


Fazendo Tanguro, Mato Grosso, Brazil

June 17th, 2015 @

A rainstorm approaches a soybean field in Amazonian Brazil. Ecosystems Center scientists conduct experiments on this working farm to study how agricultural practices alter water and nutrient cycles.

Neill Amazon soybean field

Photo by Chris Neill (click for larger image)