Wetlands provide solutions for agricultural runoff


When a dry spell made their intended experiments impossible, researchers made a serendipitous discovery: a novel biochemical reaction that could help clean up wastewater and remediate wetlands. (Photo by Peter Jaffe)

A PATCHWORK OF SMALL LAKES, forests and marshes surrounded by farms and suburbs, the Assunpink Wildlife Management Area in central New Jersey is an ideal place to track the effects of agricultural nitrogen runoff on wetland soil chemistry. Princeton professor Peter Jaffe and his students arrived at the study site in 2004, along with an ecology research group from Rutgers University.

But a drought made their intended experiments impossible; they couldn’t study the wetlands when they had dried out. Instead, Jaffe, a professor of civil and environmental engineering, asked his students to take soil samples back to the lab, where they added different sources of nitrogen to the samples and analyzed changes in their chemistry.

In some of the samples, the researchers observed something unexpected: in the absence of oxygen, a polluting form of nitrogen called ammonium was transformed into harmless nitrogen gas. In these samples, electrons — charged particles — were moving from ammonium, which comes from fertilizer runoff, to iron, a plentiful metal in the soil. Jaffe’s group documented this reaction for the first time.

Although Jaffe’s original goal was to examine how nitrogen runoff from fertilizer affects metal transport in wetland ecosystems, he wondered if this newly discovered natural phenomenon could be useful for cleaning up nitrogen pollution. To investigate it further, he secured funding from the National Science Foundation and Princeton’s Project X, a program that funds risky but promising projects, and returned to the site in 2011 with postdoctoral research associate Shan Huang. “My first fear was that we wouldn’t see anything,” Jaffe said. “But our findings were reproducible.”

Huang and Jaffe brought fresh soil samples back to the lab. To mimic the underground environment at the field site, Huang placed the small bottles of mud in a chamber without oxygen and bathed them in water spiked with ammonium. She monitored levels of ammonium and forms of iron in the samples and found that the ammonium was indeed being converted into nitrite, a precursor of nitrogen gas.

As Huang monitored the reaction, she noticed something intriguing. “After six months, the reaction became more and more efficient,” she said. “We thought there should be some bacteria responsible for the reaction.” When Huang sterilized the soil by heating it under high pressure, the ammonium removal stopped, suggesting that microorganisms were the force behind the chemical transformations.

Those microorganisms were carrying out a reaction, now known as Feammox, that oxidizes ammonium — takes the electrons from it — and transfers the electrons to iron (Fe is the symbol for the element iron). The oxidized ammonium became nitrite, and other bacteria converted the nitrite to nitrogen gas.

Since the Jaffe team’s initial discovery of Feammox, two other groups have observed the process, in a laboratory sewage treatment reactor and in soil from a Puerto Rican rainforest. But Jaffe and Huang were the first to identify the bacterium that carries out the reaction. Huang isolated this bacterial species from the others present in the soil. “We tried hundreds of different growth conditions, and finally got a pure culture,” she said. “It was 50 percent hard work and 50 percent luck.” The winning recipe had an acidic pH, similar to the soil environment where the bacteria were found.

The bug, which belongs to a family of soil microbes called Acidimicrobiaceae, functions without oxygen and at a relatively low temperature — about 68 degrees Fahrenheit, compared with 86 degrees for other microbes that oxidize ammonium in the absence of oxygen. “This is really good when you think about applying this in wastewater treatment plants,” said Melany Ruiz-Urigüen, a graduate student who is working to optimize the Feammox reaction. “It means you wouldn’t have to heat the water, and that saves a lot of energy.”

Ruiz-Urigüen is also testing whether the bacteria can use inexpensive sources of iron, such as scrap metal. The Feammox reaction requires iron oxide, which is found on rusty steel — a plentiful industrial waste. For Ruiz-Urigüen’s latest experiments, she uses steel wool pads purchased from a home improvement store. She sprays the metal mesh with a salty solution and lets it rust for two weeks before adding it to a reactor.

In the wetland environment, Feammox bacteria likely depend on plants to supply oxidized iron for the reaction. Oxygen leaks out of plant roots, forming orange nodules where it reacts with iron in the soil; this natural rust can seep into areas without oxygen, where Feammox bacteria thrive. To investigate how the Feammox process might work in an engineered wetland, graduate student Zheyun Zhang is monitoring the reaction in greenhouse pots planted with cattails and bulrushes. “We want to use the plants to recycle the iron,” Zhang said. “Plants are very cheap. And it’s a natural process.”

Jaffe and his team hope to improve the Feammox process and harness it to clean up pollution — not only of nitrogen runoff, but perhaps also of certain toxic metals that may act as stand-ins for iron. The success of this fortuitous discovery gives the researchers confidence as they strive to turn Feammox into a useful technology.

–By Molly Sharlach

The City Lost and Found: Exhibition examines creative responses to urban changes in ’60s, ’70s America

Chicago 1969

Kenneth Josephson, “Chicago,” 1969. Photo collage. The Art Institute of Chicago. Gift of the School of the Art Institute of Chicago. Copyright Kenneth Josephson.

THE AMERICAN CITY OF THE 1960S AND 1970S witnessed seismic physical changes and social transformations, including shifting demographics and political protests as well as the aftermath of decades of urban renewal. In this climate of uncertainty, a host of different actors — including photographers, architects, filmmakers, planners and activists — transformed these conditions of crisis into provocative and visually compelling statements about the culture, urban landscape and politics of New York, Chicago and Los Angeles.

A groundbreaking exhibition, The City Lost and Found: Capturing New York, Chicago and Los Angeles, 1960-1980, examines creative responses to dramatic urban changes through the intersection of photography, film, architecture and urban planning. On view from Feb. 21 to June 7, 2015, at the Princeton University Art Museum, the show focuses on the interconnections of art practices and lived realities in these three major American cities, with accompanying print and digital materials.


The exhibition is accompanied by a richly illustrated 272-page catalogue, with contributions from more than 20 noted scholars in art history, urban planning, architecture and cultural studies.

More than 150 objects — including photographs, photo-based work, film, architectural renderings, planning documents and publications — are highlighted across four galleries in the museum. The exhibition reframes work by renowned artists and architects, such as Martha Rosler, Paul Rudolph, Ed Ruscha, Mierle Laderman Ukeles, Garry Winogrand and the firm of Skidmore, Owings and Merrill, while also showcasing pivotal works by underrepresented artists, including Ralph Arnold, Oscar Castillo, Jonas Dovydenas, Arthur Tress and Shadrach Woods.

Though arranged by city, the exhibition focuses on major themes framing common directions of creative response and artistic engagement, including demonstration, preservation and renewal. For example, The New York Times photographer Barton Silverman captured protestors at the 1968 Democratic National Convention in Chicago occupying the public space in Grant Park opposite the convention hotel and taking over a public monument. The speed at which such images circulated in print and in television news coverage resonates with the use of social media in documenting contemporary life.

The exhibition is organized in collaboration with the Art Institute of Chicago, where it opened in October 2014. Katherine Bussard, the Peter C. Bunnell Curator of Photography at the Princeton University Art Museum, coorganized the show with Alison Fisher, the Harold and Margot Schiff Assistant Curator of Architecture and Design at the Art Institute of Chicago, and Greg Foster-Rice, associate professor of film at Columbia College Chicago.

A major scholarly catalogue accompanies the exhibition to further explore the connections between critical practices in art and architecture and the political, social and geographic realities of American cities during this transformational period. For example, Bruce Davidson’s two-year study of a single block, East 100th Street (1966- 68), and Romare Bearden’s photo collage The Block II (1971-72) reveal complex portraits of race, poverty and community in Harlem. With more than 300 illustrations, the book features contributions from more than 20 scholars in art history, urban planning, architecture and cultural studies. The catalogue is published by the Princeton University Art Museum and distributed by Yale University Press.

As a digital component, self-guided walking tours of each city are available to view online and access on mobile devices. Each walking tour connects up to 10 objects from the exhibition with their respective sites of engagement in the city. For example, on the New York City tour, users are directed to the former residence of artist Vito Acconci in Greenwich Village. There, starting at the front stoop, Acconci performed the conceptual work Following Piece for a month in 1969 to “follow [a] different person every day until person enters private place.” In this way users can see and experience firsthand how vital these cities were and remain to artistic and everyday life.

Visit artmuseum.princeton.edu/the-city

–By Erin Firestone

Striking resemblance: A physical law may govern very different biological activities


FLOCKS OF BIRDS FLY ACROSS THE SKY in shifting configurations. In the retina of an eye, millions of neurons ignite in ever-changing combinations, translating light into meaningful images. Yet both of these seemingly random behaviors have an underlying order that can be described by mathematics.

Like these cells and birds, when atoms and molecules come together they can display coordinated behaviors that are more than the sum of their parts. At a critical point, such as the boundary between liquid and gas, local interactions between molecules propagate through an entire material, changing its essential properties.

Princeton biophysicist William Bialek thinks criticality may also underlie collective behaviors in living organisms, and he’s using real-world data to test this hypothesis. Recently, Bialek and his colleagues have analyzed the flocking behaviors of birds, the genetic networks of fruit fly embryos and the activation patterns of salamander neurons.

“In physics, we use the same mathematical language to describe many seemingly different behaviors,” said Bialek, the John Archibald Wheeler/Battelle Professor in Physics and the Lewis-Sigler Institute for Integrative Genomics. “So we understand that the emergence of collective behavior from all the individual interactions has a kind of universality.”

To explore the possibility that this universality might extend to living systems, Bialek made use of a large dataset on the changing positions and velocities of thousands of individual birds in a flock of starlings. A group of Italian physicists used multiple cameras to record the birds and calculate their exact locations over time in three dimensions — “a technical triumph,” according to Bialek.

The researchers, including former Princeton postdoctoral fellows Thierry Mora and Aleksandra Walczak, analyzed the deviations of each bird from the flock’s average speed and direction of movement. They found not only that these variations were correlated between nearby birds, but also that the fluctuations from the average propagated through the group over long distances. This pattern of rapid, remote signal transmission echoes the changes that occur among molecules during a phase change from solid to liquid or liquid to gas. At a critical point, this could allow information to spread swiftly through the group, enabling the whole flock to nimbly change direction.

“The model you build just by keeping track of what each bird does relative to its neighbors predicts what happens throughout the entire flock,” Bialek said. “And it does so with an accuracy that is beyond what we had any reason to expect. It’s really a very precise prediction.”

Other biological examples of criticality play out on a microscopic scale. Bialek has an ongoing collaboration with Princeton’s Squibb Professor in Molecular Biology Eric Wieschaus, a Howard Hughes Medical Institute researcher and Nobel Prize winner, who has uncovered many of the genes involved in the embryonic development of the fruit fly — a model biological system.

Bialek has found signatures of criticality in gene activation patterns during the first few hours of fly embryo development. The synchronized actions of “gap genes” establish the fly’s 14-segment body plan. Mutations in these genes lead to gaps between segments, whose effects are reflected in the names of the genes: two examples are “hunchback” and “giant.”

Recently, Thomas Gregor, an assistant professor of physics and also a member of the Lewis-Sigler Institute, has developed experimental tools to precisely measure the activity of many gap genes at once, all along the halfmillimeter length of the fly embryo. These measurements allowed Bialek and physics graduate student Dmitry Krotov to test whether the patterns of gene activity across the embryo fit a model of criticality. Indeed, using data from 24 embryos, they found that fluctuations from the average level of gene activity at each point along the embryo were correlated between certain pairs of gap genes, which regulate one another’s activity like on/off switches. They mapped the locations of these switch points, which appear to act like signals that spread over long distances, just as changes in velocity are correlated in a flock of birds.

Bialek has also looked for signatures of criticality among the activation patterns in a patch of 160 nerve cells from a salamander retina, a model system for studying this light-sensing layer of the eye. In collaboration with Michael Berry, an associate professor of molecular biology and the Princeton Neuroscience Institute, Bialek and his colleagues showed how the coordinated activity of the neurons could be tuned to a critical state.

Bialek thinks critical systems may be common features of life that have repeatedly evolved in different organisms and at different levels — both molecular and behavioral. This could explain why, though systems of cells or groups of organisms could be organized in any number of possible ways, networks with similar properties continue to emerge.

“Is there anything special about the way nature has organized things in living systems?” Bialek wondered. He said much more work is necessary to claim criticality as a general biological principle. “But I do think we’re seeing in the data, somehow, signs of that specialness — things that it seems you can only get if the system has been set up in particular ways and not in others,” he said. “That I find very appealing.”

This work was supported in part by the National Science Foundation, the National Institutes of Health, the Howard Hughes Medical Institute, the W.M. Keck Foundation and the Swartz Foundation.

–By Molly Sharlach

Africa’s poison ‘apple’ provides common ground for elephants and livestock


The tall and bushy plant known as the Sodom apple has overrun vast swaths of East African savanna and pastureland, including parts of Kenya’s Amboseli National Park. New research suggests that certain animals, including elephants and impalas, could keep this invasive plant in check. (Photo courtesy of Rob Pringle)

AFRICAN WILDLIFE OFTEN RUN AFOUL of ranchers securing food and water resources for their animals, but the interests of fauna and farmer might finally be unified by the “Sodom apple,” a toxic invasive plant that has overrun vast swaths of East African savanna and pastureland.

Not a true apple, Solanum campylacanthum is a relative of the eggplant that smothers native grasses with its thorny stalks, while its striking yellow fruit provides a deadly temptation to sheep and cattle.

New research suggests, however, that certain wild animals, particularly elephants, could be a boon to human-raised livestock because of their voracious appetite for the Sodom apple. A fiveyear study led by Princeton University researchers found that elephants and impalas, among other wild animals, can not only safely gorge themselves on the plant, but also can efficiently regulate its otherwise explosive growth.

Just as the governments of nations such as Kenya prepare to pour millions into eradicating the plant, the findings present a method for controlling the Sodom apple that is cost-effective for humans and beneficial for the survival of African elephants, explained first author Robert Pringle, a Princeton assistant professor of ecology and evolutionary biology.


An elephant prepares to uproot a Solanum campylacanthum plant in the upland savanna of central Kenya. Although this woody shrub is toxic to many mammal species, large browsers such as elephants can eat it, and in so doing help to reduce its abundance.

“The Holy Grail in ecology is these win-win situations where we can preserve wildlife in a way that is beneficial to human livelihoods,” Pringle said “Elephants have a reputation as destructive, but they may be playing a role in keeping pastures grassy.”

The findings are important given the threats to elephants from poaching, Pringle said. “We need to understand to what extent these threatened animals have unique ecological functions.”

Elephants and impalas can withstand S. campylacanthum’s poison because they belong to a class of herbivores known as “browsers” that subsist on woody plants and shrubs, many species of which pack a toxic punch, Pringle said. On the other hand, “grazers” such as cows, sheep and zebras primarily eat grass, which is rarely poisonous. These animals easily succumb to the Sodom apple, which causes emphysema, pneumonia, bleeding ulcers, brain swelling and death.

An unexpected feast Pringle was roughly three years into a study about the effects of elephants on plant diversity when he noticed that the Sodom apple was conspicuously absent from some experiment sites. He and other researchers had set up 36 exclosures — which are designed to keep animals out rather than in — totaling nearly 89 acres (36 hectares) at the Mpala Research Centre in Kenya, a multi-institutional research preserve with which Princeton has been long involved.

There were four types of exclosure: one type open to all animals; another where only elephants were excluded; one in which elephants and impalas were excluded; and another off limits to all animals.

It was in the sites that excluded elephants and impala that the Sodom apple particularly flourished, Pringle said, which defied everything he knew about the plant.

“I had always thought that these fruits were horrible and toxic, but when I saw them in the experiment, I knew some animal was otherwise eating them. I just didn’t know which one,” Pringle said. “The question became, ‘Who’s eating the apple?”

Using the exclosures, Pringle and his coauthors documented the zest with which wild African browsers will eat S. campylacanthum. Pringle worked with Corina Tarnita, a Princeton mathematical biologist and assistant professor of ecology and evolutionary biology, as well as with collaborators from the University of Wyoming, University of Florida, University of California-Davis, Mpala Center and University of British Columbia.

The researchers specifically observed the foraging activity of elephants, impalas, smalldog- sized antelopes known as dik-diks, and rodents. Using cameras, they captured about 30,000 hours of foraging, and discovered that elephants and impalas were the primary eaters of the plants.

There is a catch to the elephants’ and impalas’ appetite for the Sodom apple: When fruit goes in one end, seeds come out the other. Though some seeds are destroyed during digestion, most reemerge and are potentially able to germinate.

Pringle and Tarnita developed a mathematical model to conduct a sort of cost-benefit analysis of how the Sodom apple’s ability to proliferate is affected by being eaten. The model weighed the “cost” to the plant of being partially consumed against the potential benefit of having healthy seeds scattered across the countryside in an animal’s droppings.

While elephants ate an enormous amount of Solanum seeds, they also often destroyed the entire plant, ripping it out of the ground and stuffing the whole bush into their mouths. The model showed that to offset the damage an elephant wreaks on a plant, 80 percent of the seeds the animal eats would have to emerge from it unscathed. On top of that, each seed would have to be 10-times more likely to take root than one that simply fell to the ground from its parent.

Impalas, on the other hand, can have a positive overall effect on the plants, the researchers found. Impalas ate the majority of the fruit consumed — one impala ate 18 fruit in just a few minutes. But they do not severely damage the parent plant while feeding and also spread a lot of seeds in their dung. Of the seeds eaten by an impala, only 60 percent would need to survive, and those seeds would have to be a mere three-times more likely to sprout than a seed that simply fell from its parent.

“A model allows you to explore a space you’re not fully able to reach experimentally,” said Tarnita, who uses math to understand the outcome of interactions between organisms. “This model helped us conclude that although it is theoretically possible for elephants to benefit the plant, that outcome is extremely unlikely.”

The study was published in the June 22, 2014, edition of the Proceedings of the Royal Society B. The work was supported by the National Science Foundation, the National Sciences and Engineering Research Council of Canada, the Sherwood Family Foundation, and the National Geographic Committee for Research and Exploration.

–By Morgan Kelly