Image source - fastcoexist.com

For the past several months, Principal Research Scientist Stephanie Dutkiewicz and researcher Oliver Jahn have been consultants for staff at San Francisco’s Exploratorium science museum on the development of a new and exciting interactive exhibit designed to provide a hands-on experience with microscopic sea life.

In a hybrid of Darwin vizualisations with the museum’s traditional hands-on philosophy, staff at the museum have embedded interactive images of plankton distributions from the MIT project in a table-top, putting them in reach of small (and not so small) hands equipt with hand-held viewers for feasting on microscopic detail embedded in the exhibit.

The Exploratorium reopened Wednesday on a new nine-acre campus by the San Francisco Bay: Might be worth a visit next time you’re in town…

Below is an exerpt from In New Home, Exploratorium Widens Its Interactive Appeal (New York Times)

The potential can be seen clearly in a tabletop exhibit in the East Gallery, which focuses on living systems, that maps the world’s plankton species.

“We frame something that is always around you from the natural world and let you do the verbs of science — test, explore, observe,” said Jennifer Frazier, a cell biologist who is a staff scientist at the Exploratorium.

The availability of giant scientific data sets has proved to be both a challenge and an opportunity for the museum.

“It gives us access to a whole new phenomenon,” Dr. Frazier said, “and for me in particular it gives us access to a whole new scientific tool.”

Dr. Frazier came to the idea of observing the world’s plankton on a global scale while she was hunting for visualization information on even smaller life forms. While exploring the idea of an exhibit on the work that Craig Venter has done in charting the diversity of DNA in the world’s oceans, she learned about a Massachusetts Institute of Technology project that offered a vast plankton census.

The undertaking, known as the Darwin Project, is a giant supercomputer-based simulation of the world’s microscopic ocean life, which produces half the world’s oxygen and absorbs more carbon dioxide than all the forests on earth. This virtual ocean is based on sensor data from satellites and buoys. And with the help of scientific visualization experts at the University of California, Davis, the Exploratorium has translated that into an exhibit that is both visual and interactive.

The result is a “social” table that creates an experience that can be shared simultaneously by multiple viewers. Visitors can manipulate microscopelike rings that make it possible to peer into the virtual ocean and see the microscopic plankton.

“My first concern was that when people approached this, they would get an experience that felt like it belonged in the Exploratorium,” said Eric Socolofsky, one of the Exploratorium’s media designers. “Something like a big touch screen could be great, but it is a place where people are expecting to be engaging with things and operating things with their hands and their bodies and where they need tangible feedback. A touch screen by itself isn’t sufficient.”

When San Francisco’s Exploratorium moves into its new building on the waterfront next year, it promises to use technologies in ways never before seen in a museum. One of those experiences will be an interactive ocean, the product of a collaboration between scientists at UC Davis and MIT’s Darwin Project. Read more

Schematic of a sample marine ecosystem model - source: Dutkiewicz (2012)

In this article, featured in the July issue of Microbe magazine, Darwin Project researcher Stephanie Dutkiewicz explains how, when used properly, models provide valuable insights into complex systems and sometimes yield surprising, even counterintuitive outcomes.

Read more.

Modeling Marine Microbes

Diverse microorganisms undergoing growth and reproduction. As organisms evolved from simple prokaryotes to unicellular eukaryotes to multicellular organisms their strategies for internal energy partitioning dramatically changed as illustrated by a recent mathematical model. Image courtesy of Mari Kempes

Population growth rate is a fundamental ecological and evolutionary characteristic of living organisms, but individuals must balance the metabolism devoted to biosynthesis and reproduction against the maintenance of existing structure and other functionality. Chris Kempes, Stephanie Dutkiewicz and Mick Follows have developed a mathematical model relating metabolic partitioning to the form of growth. The research is published in the Dec. 26 issue of the Proceedings of the National Academy of Sciences.

Read more at MIT News

Limiting nutrients and abundance of nitrogen fixers in the Pacific Ocean.

Nitrogen is an essential component of all cells. It is used to make the amino acid building blocks of proteins, and is also required in the nucleic acids of DNA and RNA. Although nitrogen extremely abundant in the open ocean, it is mostly found in dissolved N₂ molecules that cannot be used by most phytoplankton, who require nitrogen in its reduced, or “fixed” forms, such as nitrate or ammonium.

Fixed nitrogen is rare across large tracts of the ocean, and phytoplankton abundance is closely tied to its availability. There are however a small but important group of marine microbes who can bypass the need for reduced nitrogen, by fixing their own.

These organisms are known as diazotrophs, a term that derives from the Greek words dis, azōos, and trophikos. The diazo- suffix is in this case drawn from the scientific shorthand for a paired nitrogen bond, but azōos and trophikos literally mean “non-living”, and “nutrition”. Diazotrophs use the inert nitrogen gas that is dissolved in the ocean to make new organic compounds, significantly increasing productivity across large areas of the ocean where other forms of nitrogen are in short supply.

Working with scientists at MIT and the University of Bristol, we have been investigating the large scale distribution of diazotrophs in the Pacific Ocean. We know that there are many thousands of different species of phytoplankton that compete and coexist together in the ocean, but by reducing the system down to a number of key equations, we have been able to show that iron is the dominant limiting factor controlling the distribution of nitrogen fixers in the Pacific.

The model equations broke down in a way that clearly explained the behaviour of a much more complex and realistic model, and we found that the Pacific Ocean can be divided up into three key provinces. Over the much of the equatorial, and Southern Pacific, phytoplankton are strongly limited by a lack of mineral iron, which is essential for growth. The diazotrophs in particular need a lot of this essential micronutrient, and where it is scarce they are outcompeted by the regular phytoplankton.

Further north, iron is added to the ocean as large amounts of mineral rich dust is carried in the winds blowing off Asia and Australia. This addition of iron to the ocean quickly relieves the iron limitation among the regular phytoplankton. This allows them to grow more, but in doing so they quickly become nitrogen limited instead.

In theory, this is where the nitrogen fixers should come in to there own. They can fix their own nitrogen, and are known to thrive where other phytoplankton are starved of of this nutrient. Our analysis reveals that while this is true, it is not quite the whole story.

The high iron content of nitrogen fixing enzymes means that diazotrophs need more iron than most other phytoplankton. Consequently, there are large patches of the Pacific where iron levels are still too low to support this group, when the other phytoplankton have abundant iron. In the figure above, the boundary between iron and nitrogen limitation for the regular phytoplankton is shown with a dotted line, but we can see that this does not mark out the regions where the diazotrophs are able to grow (shown with a solid black line). Only when the iron supply was noticeably higher where the diazotrophs able to survive.

We found that diazotroph ecology is more closely governed by the ratio of iron to nitrogen supplied to the ocean surface, rather than to the absolute concentrations. The theoretical study has helped us to better understand the factors that control the growth of these important marine microbes. By adding fixed nitrogen, diazotrophs play a potentially significant role in regulating the biological uptake of carbon by the ocean. We hope that by breaking the complex marine system down into its component parts, we will be better able to understand how it has changed in the past, and how it might respond in the future.

This study is currently under peer-review with Global Biogeochemical Cycles:

Dutkiewicz, S., Ward, B.A., Monteiro, F. and Follows, M.J. Interconnection of nitrogen fixers and iron in the Pacific Ocean: Theory and numerical simulations. (in review)

New model predicts maximum tree height across the United States; gives information about forest density, carbon storage - image: MIT News

Knowing how tall trees can grow in any given region can give ecologists a wealth of information, from the potential density of a forest and size of its tree canopy to the amount of carbon stored in woodlands and the overall health of an ecosystem. Now grad student Chris Kempes, along with colleagues at the University of Maryland and the Santa Fe Institute in New Mexico, has come up with a simple model to predict the maximum tree height in different environments across the United States. The researchers’ results have been published in the journal PLoS One. Read more.

Modeled diazotroph biomass (log10, μmolP per litre)

In this study, Fanny Monteiro, Stephanie Dutkiewicz and Mick Follows, interpret the environmental controls on the global ocean diazotroph biogeography in the context of a three-dimensional global model with a self-organizing phytoplankton community. As is observed, the model’s total diazotroph population is distributed over most of the oligotrophic warm subtropical and tropical waters, with the exception of the southeastern Pacific Ocean. This biogeography broadly follows temperature and light constraints which are often used in both field-based and model studies to explain the distribution of diazotrophs. However, the model suggests that diazotroph habitat is not directly controlled by temperature and light, but is restricted to the ocean regions with low fixed nitrogen and sufficient dissolved iron and phosphate concentrations. The team interpret this regulation by iron and phosphate using resource competition theory which provides an excellent qualitative and quantitative framework. You can read more about this work in Monteiro et al, 2011.

Monteiro F.M., S. Dutkiewicz and M. J. Follows, 2011
Biogeographical controls on the marine nitrogen fixers, Global Biogeochemical Cycles, Vol. 25, GB2003, 8 pp., doi:10.1029/2010GB003902

]]> http://darwinproject.mit.edu/?feed=rss2&p=426 0 http://darwinproject.mit.edu/?p=416 http://darwinproject.mit.edu/?p=416#comments Tue, 21 Jun 2011 19:47:38 +0000 admin http://darwinproject.mit.edu/?p=416 Using an idealized model of cell physiology and community competition, Darwin project researchers identify one mechanism by which mixotrophs can effectively outcompete specialists for nutrient elements]]>

Mixotrophic organisms combine autotrophic and heterotrophic nutrition and are abundant in both freshwater and marine environments

Mixotrophic organisms combine autotrophic and heterotrophic nutrition and are abundant in both freshwater and marine environments. Recent observations indicate that mixotrophs constitute a large fraction of the biomass, bacterivory, and primary production in oligotrophic environments. While mixotrophy allows greater flexibility in terms of resource acquisition, any advantage must be traded off against an associated increase in metabolic costs, which appear to make mixotrophs uncompetitive relative to obligate autotrophs and heterotrophs. Using an idealized model of cell physiology and community competition, Ben Ward and co-workers identify one mechanism by which mixotrophs can effectively outcompete specialists for nutrient elements. At low resource concentrations, when the uptake of nutrients is limited by diffusion toward the cell, the investment in cell membrane transporters can be minimized. In this situation, mixotrophs can acquire limiting elements in both organic and inorganic forms, outcompeting their specialist competitors that can utilize only one of these forms. This advantage can be enough to offset as much as a twofold increase in additional metabolic costs incurred by mixotrophs. This mechanism is particularly relevant for the maintenance of mixotrophic populations and productivity in the highly oligotrophic subtropical oceans. You can read more about this work in Ward et al., 2011