Tag Archives: biology

Conservation versus innovation in the fight against antibiotic resistance (Science)

Pills (Image source: NIH)

(Image source: NIH)

“Antibiotic resistance is a problem of managing an open-access resource, such as fisheries or oil,” writes Ramanan Laxminarayan, a research scholar at Princeton University and the director of the Center for Disease Dynamics, Economics & Policy in Washington, D. C., in today’s issue of the journal Science. He goes on to say that individuals have little incentive to use antibiotics wisely, just as people have little incentive to conserve oil when it is plentiful.

As with many other natural resources, maintaining the effectiveness of antibiotics requires two approaches: conserving the existing resource and exploring new sources, Laxminarayan says. These two approaches are linked, however. “Just as incentives for finding new sources of oil reduce incentives to conserve oil,” Laxminarayan writes, “large public subsidies for new drug development discourage efforts to improve how existing antibiotics are used.” Yet new antibiotics tend to cost more than existing ones due to the expense of clinical trials and the fact that the easiest-to-find drugs may have already been discovered.

Laxminarayan’s analysis reveals that the benefits of conserving existing drugs are significant, and argues that the proposed increases in public subsidies for new antibiotics should be matched by greater spending on conservation of antibiotic effectiveness through public education, research and surveillance.

Ramanan Laxminarayan is a research scholar at the Princeton Environmental Institute. His perspective, “Antibiotic effectiveness: Balancing conservation against innovation,” appeared in the September 12, 2014 issue of Science.

Read the article.

Study resolves controversy over nitrogen’s ocean “exit strategies” (Science)

By Catherine Zandonella, Office of the Dean for Research

Seawater collection device

Princeton University graduate student Andrew Babbin (left) prepares a seawater collection device known as a rosette. The team used samples of seawater to determine how nitrogen is removed from the oceans. (Research photos courtesy of A. Babbin)

A decades-long debate over how nitrogen is removed from the ocean may now be settled by new findings from researchers at Princeton University and their collaborators at the University of Washington.

The debate centers on how nitrogen — one of the most important food sources for ocean life and a controller of atmospheric carbon dioxide — becomes converted to a form that can exit the ocean and return to the atmosphere where it is reused in the global nitrogen cycle.

Researchers have argued over which of two nitrogen-removal mechanisms, denitrification and anammox, is most important in the oceans. The question is not just a scientific curiosity, but has real world applications because one mechanism contributes more greenhouse gases to the atmosphere than the other.

Bess Ward

Bess Ward, Princeton’s William J. Sinclair Professor of Geosciences (Photo courtesy of Georgette Chalker)

“Nitrogen controls much of the productivity of the ocean,” said Andrew Babbin, first author of the study and a graduate student who works with Bess Ward, Princeton’s William J. Sinclair Professor of Geosciences. “Understanding nitrogen cycling is crucial to understanding the productivity of the oceans as well as the global climate,” he said.

In the new study, the researchers found that both of these nitrogen “exit strategies” are at work in the oceans, with denitrification mopping up about 70 percent of the nitrogen and anammox disposing of the rest.

The researchers also found that this 70-30 ratio could shift in response to changes in the quantity and quality of the nitrogen in need of removal. The study was published online this week in the journal Science.

The two other members of the research team were Richard Keil and Allan Devol, both professors at University of Washington’s School of Oceanography.

Research vessel

The researchers collected the samples in 2012 in the ocean off Baja California. Click on the image to read blog posts from a similar expedition that took place the following year.

Essential for the Earth’s life and climate, nitrogen is an element that cycles between soils and the atmosphere and between the atmosphere and the ocean. Bacteria near the surface help shuttle nitrogen into the ocean food chain by converting or “fixing” atmospheric nitrogen into forms that phytoplankton can use.

Without this fixed nitrogen, phytoplankton could not absorb carbon dioxide from the air, a feat which is helping to check today’s rising carbon dioxide levels in the atmosphere. When these tiny marine algae die or are consumed by predators, their biomass sinks to the ocean interior where it becomes food for other types of bacteria.

Test tubes

Researchers added specific amounts and types of nitrogen and organic compounds to test tubes containing seawater, and then noted whether denitrification or anammox occurred.

Until about 20 years ago, most scientists thought that denitrification, carried out by some of these bacteria, was the primary way that fixed nitrogen was recycled back to nitrogen gas. The second process, known as anaerobic ammonia oxidation, or anammox, was discovered by Dutch researchers studying how nitrogen is removed in sewage treatment plants.

Both processes occur in regions of the ocean that are naturally low in oxygen, or anoxic, due to local lack of water circulation and intense phytoplankton productivity overlying these regions. Within the world’s ocean, such regions occur only in the Arabian Sea, and off the coasts of Peru and Mexico.

In these anoxic environments, anaerobic bacteria feast on the decaying phytoplankton, and in the process cause the denitrification of nitrate into nitrogen gas, which cannot be used as a nutrient by most phytoplankton. During this process, ammonium is also produced, although marine geochemists had never been able to detect the ammonium that they knew must be there.

That riddle was solved in the early 2000s by the discovery of the anammox reaction in the marine environment, in which anaerobic bacteria feed on ammonium and convert it to nitrogen gas.

Glove bag

Graduate student Andrew Babbin filling incubation vials under an anoxic atmosphere in a transparent container called a “glove bag.” (Photo courtesy of Andrew Babbin)

But another riddle soon appeared: the anammox rates that Dutch and German teams of researchers measured in the oceans appeared to account for the entire nitrogen loss, leaving no role for denitrification.

Then in 2009, Ward’s team published a study in the journal Nature showing that denitrification was still a major actor in returning nitrogen to the air, at least in the Arabian Sea. The paper further fueled the controversy.

Back at Princeton, Ward suspected that both processes were necessary, with denitrification churning out the ammonium that anammox then converted to nitrogen gas.

To settle the issue, Ward and Babbin decided to look at exactly what was going on in anoxic ocean water when bacteria were given nitrogen and other nutrients to chew on.

They collected water samples from an anoxic region in the ocean south of Baja California and brought test tubes of the water into an on-ship laboratory. Working inside a sturdy, flexible “glove bag” to keep air from contaminating the low-oxygen water, Babbin added specific amounts and types of nitrogen and organic compounds to each test tube, and then noted whether denitrification or anammox occurred.

“We conducted a suite of experiments in which we added different types of organic matter, with variable ammonium content, to see if the ratio between denitrification and anammox would change,” said Babbin. “We found that not only did increased ammonia favor anammox as predicted, but that the precise proportions of nitrogen loss matched exactly as predicted based on the ammonium content.”

The explanation of why, in past experiments, some researchers found mostly denitrification while others found only anammox comes down to a sort-of “bloom and bust” cycle of phytoplankton life, explained Ward.

“If you have a big plankton bloom, then when those organisms die, a large amount of organic matter will sink and be degraded,” she said, “but we scientists are not always there to measure this. In other words, if you aren’t there on the day lunch is delivered, you won’t measure these processes.”

The researchers also linked the rates of nitrogen loss with the supply of organic material that drives the rates: more organic material equates to more nitrogen loss, so the quantity of the material matters too, Babbin said.

The two pathways have distinct metabolisms that turn out to be important in global climate change, he said.  “Denitrification produces carbon dioxide and both produces and consumes nitrous oxide, which is another major greenhouse gas and an ozone depletion agent,” he said. “Anammox, however, consumes carbon dioxide and has no known nitrous oxide byproduct. The balance between the two therefore has a significant impact on the production and consumption of greenhouse gases in the ocean.”

The research was funded by National Science Foundation grant OCE-1029951.

Read the abstract.

Andrew R. Babbin, Richard G. Keil, Allan H. Devol, and Bess B. Ward. Organic Matter Stoichiometry, Flux, and Oxygen Control Nitrogen Loss in the Ocean. Science. Published Online April 10 2014. DOI: 10.1126/science.1248364

 

A more potent greenhouse gas than CO2, methane emissions will leap as Earth warms (Nature)

Freshwater wetlands can release methane, a potent greenhouse gas, as the planet warms. (Image source: RGBstock.com)

Freshwater wetlands can release methane, a potent greenhouse gas, as the planet warms. (Image source: RGBstock.com)

By Morgan Kelly, Office of Communications

While carbon dioxide is typically painted as the bad boy of greenhouse gases, methane is roughly 30 times more potent as a heat-trapping gas. New research in the journal Nature indicates that for each degree that the Earth’s temperature rises, the amount of methane entering the atmosphere from microorganisms dwelling in lake sediment and freshwater wetlands — the primary sources of the gas — will increase several times. As temperatures rise, the relative increase of methane emissions will outpace that of carbon dioxide from these sources, the researchers report.

The findings condense the complex and varied process by which methane — currently the third most prevalent greenhouse gas after carbon dioxide and water vapor — enters the atmosphere into a measurement scientists can use, explained co-author Cristian Gudasz, a visiting postdoctoral research associate in Princeton’s Department of Ecology and Evolutionary Biology. In freshwater systems, methane is produced as microorganisms digest organic matter, a process known as “methanogenesis.” This process hinges on a slew of temperature, chemical, physical and ecological factors that can bedevil scientists working to model how the Earth’s systems will contribute, and respond, to a hotter future.

The researchers’ findings suggest that methane emissions from freshwater systems will likely rise with the global temperature, Gudasz said. But to not know the extent of methane contribution from such a widely dispersed ecosystem that includes lakes, swamps, marshes and rice paddies leaves a glaring hole in climate projections.

“The freshwater systems we talk about in our paper are an important component to the climate system,” Gudasz said. “There is more and more evidence that they have a contribution to the methane emissions. Methane produced from natural or manmade freshwater systems will increase with temperature.”

To provide a simple and accurate way for climate modelers to account for methanogenesis, Gudasz and his co-authors analyzed nearly 1,600 measurements of temperature and methane emissions from 127 freshwater ecosystems across the globe.

New research in the journal Nature found that for each degree that the Earth's temperature rises, the amount of methane entering the atmosphere from microorganisms dwelling in freshwater wetlands — a primary source of the gas — will increase several times. The researchers analyzed nearly 1,600 measurements of temperature and methane emissions from 127 freshwater ecosystems across the globe (above), including lakes, swamps, marshes and rice paddies. The size of each point corresponds with the average rate of methane emissions in milligrams per square meter, per day, during the course of the study. The smallest points indicate less than one milligram per square meter, while the largest-sized point represents more than three milligrams. (Image courtesy of Cristian Gudasz)

New research in the journal Nature found that for each degree that the Earth’s temperature rises, the amount of methane entering the atmosphere from microorganisms dwelling in freshwater wetlands — a primary source of the gas — will increase several times. The researchers analyzed nearly 1,600 measurements of temperature and methane emissions from 127 freshwater ecosystems across the globe (above), including lakes, swamps, marshes and rice paddies. The size of each point corresponds with the average rate of methane emissions in milligrams per square meter, per day, during the course of the study. The smallest points indicate less than one milligram per square meter, while the largest-sized point represents more than three milligrams. (Image courtesy of Cristian Gudasz)

The researchers found that a common effect emerged from those studies: freshwater methane generation very much thrives on high temperatures. Methane emissions at 0 degrees Celsius would rise 57 times higher when the temperature reached 30 degrees Celsius, the researchers report. For those inclined to model it, the researchers’ results translated to a temperature dependence of 0.96 electron volts (eV), an indication of the temperature-sensitivity of the methane-emitting ecosystems.

“We all want to make predictions about greenhouse gas emissions and their impact on global warming,” Gudasz said. “Looking across these scales and constraining them as we have in this paper will allow us to make better predictions.”

Read the abstract.

Yvon-Durocher, Gabriel, Andrew P. Allen, David Bastviken, Ralf Conrad, Cristian Gudasz, Annick St-Pierre, Nguyen Thanh-Duc, Paul A. del Giorgio. 2014. Methane fluxes show consistent temperature dependence across microbial to ecosystem scales. Nature. Article published online before print: March 19, 2014. DOI: 10.1038/nature13164 and in the March 27, 2014 print edition.

Migrating animals add new depth to how the ocean “breathes” (Nature Geoscience)

By Morgan Kelly, Office of Communications

The oxygen content of the ocean may be subject to frequent ups and downs in a very literal sense — that is, in the form of the numerous sea creatures that dine near the surface at night then submerge into the safety of deeper, darker waters at daybreak.

Research begun at Princeton University and recently reported on in the journal Nature Geoscience found that animals ranging from plankton to small fish consume vast amounts of what little oxygen is available in the ocean’s aptly named “oxygen minimum zone” daily. The sheer number of organisms that seek refuge in water roughly 200- to 650-meters deep (650 to 2,000 feet) every day result in the global consumption of between 10 and 40 percent of the oxygen available at these depths.

The findings reveal a crucial and underappreciated role that animals have in ocean chemistry on a global scale, explained first author Daniele Bianchi, a postdoctoral researcher at McGill University who began the project as a doctoral student of atmospheric and oceanic sciences at Princeton.

Migration depth of sea animals

Research begun at Princeton University found that the numerous small sea animals that migrate from the surface to deeper water every day consume vast amounts of what little oxygen is available in the ocean’s aptly named “oxygen minimum zone” daily. The findings reveal a crucial and underappreciated role that animals have in ocean chemistry on a global scale. The figure above shows the various depths (in meters) that animals migrate to during the day to escape predators. Red indicates the shallowest depths of 200 meters (650 feet), and blue represents the deepest of 600 meters (2,000 feet). The black numbers on the map represent the difference (in moles, used to measure chemical content) between the oxygen at the surface and at around 500 meters deep, which is the best parameter for predicting migration depth. (Courtesy of Daniele Bianchi)

“In a sense, this research should change how we think of the ocean’s metabolism,” Bianchi said. “Scientists know that there is this massive migration, but no one has really tried to estimate how it impacts the chemistry of the ocean.

“Generally, scientists have thought that microbes and bacteria primarily consume oxygen in the deeper ocean,” Bianchi said. “What we’re saying here is that animals that migrate during the day are a big source of oxygen depletion. We provide the first global data set to say that.”

Much of the deep ocean can replenish (often just barely) the oxygen consumed during these mass migrations, which are known as diel vertical migrations (DVMs).

But the balance between DVMs and the limited deep-water oxygen supply could be easily upset, Bianchi said — particularly by climate change, which is predicted to further decrease levels of oxygen in the ocean. That could mean these animals would not be able to descend as deep, putting them at the mercy of predators and inflicting their oxygen-sucking ways on a new ocean zone.

“If the ocean oxygen changes, then the depth of these migrations also will change. We can expect potential changes in the interactions between larger guys and little guys,” Bianchi said. “What complicates this story is that if these animals are responsible for a chunk of oxygen depletion in general, then a change in their habits might have a feedback in terms of oxygen levels in other parts of the deeper ocean.”

The researchers produced a global model of DVM depths and oxygen depletion by mining acoustic oceanic data collected by 389 American and British research cruises between 1990 and 2011. Using the background readings caused by the sound of animals as they ascended and descended, the researchers identified more than 4,000 DVM events.

They then chemically analyzed samples from DVM-event locations to create a model that could correlate DVM depth with oxygen depletion. With that data, the researchers concluded that DVMs indeed intensify the oxygen deficit within oxygen minimum zones.

“You can say that the whole ecosystem does this migration — chances are that if it swims, it does this kind of migration,” Bianchi said. “Before, scientists tended to ignore this big chunk of the ecosystem when thinking of ocean chemistry. We are saying that they are quite important and can’t be ignored.”

Bianchi conducted the data analysis and model development at McGill with assistant professor of earth and planetary sciences Eric Galbraith and McGill doctoral student David Carozza. Initial research of the acoustic data and development of the migration model was conducted at Princeton with K. Allison Smith (published as K.A.S. Mislan), a postdoctoral research associate in the Program in Atmospheric and Oceanic Sciences, and Charles Stock, a researcher with the Geophysical Fluid Dynamics Laboratory operated by the National Oceanic and Atmospheric Administration.

Read the abstract

Citation: Bianchi, Daniele, Eric D. Galbraith, David A. Carozza, K.A.S. Milan and Charles A. Stock. 2013. Intensification of open-oxygen minimum zones by vertically migrating animals. Nature Geoscience. Article first published online: June 9, 2013. DOI:10.1038/ngeo1837

This work was supported in part by grants from the Canadian Institute for Advanced Research and the Princeton Carbon Mitigation Initiative.

 

How do bacteria clog medical devices? Very quickly. (PNAS)

stone-figure-2D_540A new study has examined how bacteria clog medical devices, and the result isn’t pretty. The microbes join to create slimy ribbons that tangle and trap other passing bacteria, creating a full blockage in a startlingly short period of time.

The finding could help shape strategies for preventing clogging of devices such as stents — which are implanted in the body to keep open blood vessels and passages — as well as water filters and other items that are susceptible to contamination. The research was published in Proceedings of the National Academy of Sciences.

stone-figure-2D_540

Click on the image to view movie. Over a period of about 40 hours, bacterial cells (green) flowed through a channel, forming a green biofilm on the walls. Over the next ten hours, researchers sent red bacterial cells through the channel. The red cells became stuck in the sticky biofilm and began to form thin red streamers. Once stuck, these streamers in turn trapped additional cells, leading to rapid clogging. (Image source: Knut Drescher)

Using time-lapse imaging, researchers at Princeton University monitored fluid flow in narrow tubes or pores similar to those used in water filters and medical devices. Unlike previous studies, the Princeton experiment more closely mimicked the natural features of the devices, using rough rather than smooth surfaces and pressure-driven fluid instead of non-moving fluid.

The team of biologists and engineers introduced a small number of bacteria known to be common contaminants of medical devices. Over a period of about 40 hours, the researchers observed that some of the microbes — dyed green for visibility — attached to the inner wall of the tube and began to multiply, eventually forming a slimy coating called a biofilm. These films consist of thousands of individual cells held together by a sort of biological glue.

Over the next several hours, the researchers sent additional microbes, dyed red, into the tube. These red cells became stuck to the biofilm-coated walls, where the force of the flowing liquid shaped the trapped cells into streamers that rippled in the liquid like flags rippling in a breeze. During this time, the fluid flow slowed only slightly.

At about 55 hours into the experiment, the biofilm streamers tangled with each other, forming a net-like barrier that trapped additional bacterial cells, creating a larger barrier which in turn ensnared more cells. Within an hour, the entire tube became blocked and the fluid flow stopped.

The study was conducted by lead author Knut Drescher with assistance from technician Yi Shen. Drescher is a postdoctoral research associate working with Bonnie Bassler, Princeton’s Squibb Professor in Molecular Biology and a Howard Hughes Medical Institute Investigator, and Howard Stone, Princeton’s Donald R. Dixon ’69 and Elizabeth W. Dixon Professor of Mechanical and Aerospace Engineering.

“For me the surprise was how quickly the biofilm streamers caused complete clogging,” said Stone. “There was no warning that something bad was about to happen.”

By constructing their own controlled environment, the researchers demonstrated that rough surfaces and pressure driven flow are characteristics of nature and need to be taken into account experimentally. The researchers used stents, soil-based filters and water filters to prove that the biofilm streams indeed form in real scenarios and likely explain why devices fail.

The work also allowed the researchers to explore which bacterial genes contribute to biofilm streamer formation. Previous studies, conducted under non-realistic conditions, identified several genes involved in formation of the biofilm streamers. The Princeton researchers found that some of those previously identified genes were not needed for biofilm streamer formation in the more realistic habitat.

Read the abstract.

Drescher, Knut, Yi Shen, Bonnie L. Bassler, and Howard A. Stone. 2013. Biofilm streamers cause catastrophic disruption of flow with consequences for environmental and medical systems. Proceedings of the National Academy of Sciences. Published online February 11.

This work was supported by the Howard Hughes Medical
Institute, National Institutes of Health grant 5R01GM065859, National Science Foundation (NSF) grant MCB-0343821, NSF grant MCB-1119232, and the Human Frontier Science Program.

Nursing gerbils unravel benefit of multiple mothers in collective mammals (Mammalian Biology)

By Morgan Kelly, Office of Communications

In mammals such as rodents that raise their young as a group, infants will nurse from their mother as well as other females, a dynamic known as allosuckling. Ecologists have long hypothesized that allosuckling lets newborns stockpile antibodies to various diseases, but the experimental proof has been lacking until now.

An in-press report in the journal Mammalian Biology found that infant Mongolian gerbils that suckled from females given separate vaccines for two different diseases wound up with antibodies for both illnesses.

The findings not only demonstrate the potential purpose of allosuckling, but also provide the first framework for further studying it in the wild by using traceable antibodies, said first author Romain Garnier, a postdoctoral researcher in Princeton University’s Department of Ecology and Evolutionary Biology. Garnier conducted the research with Sylvain Gandon and Thierry Boulinier of the Center for Functional and Evolutionary Ecology in France, and with Yannick Chaval and Nathalie Charbonnel at the Center for Biology and Management of Populations in France.

Garnier and his coauthors administered an influenza vaccine to one group of female gerbils, and a vaccine for Borrelia burgdorferi — the bacterial agent of Lyme disease — to another group. Once impregnated, female gerbils from each vaccine group were paired and, as the gerbils do in nature, kept separate from the male gerbils to birth and rear their young. In the wild, females can choose which young to nurse and infant gerbils can likewise choose which female to suckle. In the typical lab, however, one male, one female and their young are housed together, the researchers wrote.

When screened upon birth, all the infant gerbils had no detectable antibodies against influenza while one had antibodies against B. burgdorferi, according to the paper. But after eight days of nursing, all the infants contained high levels of antibodies for both influenza and B. burgdorferi, suggesting that the females nursed the young — their own and those of the other female — evenly. These results suggest that allosuckling is indeed intended to expose newborn animals to a host of antibodies.

This benefit sheds light on a peculiar arrangement in cooperative mammals that ecologists have puzzled over, the authors wrote. In social species, females usually fall into dominant or subordinate groups with the subordinate females typically involved in tending to the young produced by dominant females. Yet, in many cases, subordinate females are “allowed” to breed. Garnier and his colleagues suggest that the potentially larger antibody pool available through nursing might be one of the reasons why.

Cita­tion: Garnier, R., et al., Evidence of cross-transfer of maternal antibodies through allosuckling in a mammal: Potential importance for behavioral ecology. Mammal. Biol. (2012).

Read the abstract.

The implications of “self-boosting” vaccines on herd immunity

Researchers use mathematical models to consider the implications of “self-boosting” vaccines—a class of emerging vaccines that can establish long-term intermittent antigen presentation within a host—on herd immunity.

“Self-boosting vaccines and their implications for herd immunity” by Nimalan Arinaminpathy, et al.
10.1073/pnas.1209683109

Read the abstract