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Egghead is a blog about research by, with or related to UC Davis. Comments on posts are welcome, as are tips and suggestions for posts. General feedback may be sent to Andy Fell. This blog is created and maintained by UC Davis University Communications, and mostly edited by Andy Fell.

How antibiotics open door to “bad” gut bacteria: more oxygen

By Carole Gan

Antibiotics are essential for fighting bacterial infection, but they can also make the body more prone to infection and diarrhea. Exactly how do antibiotics foster growth of disease-causing microbes – and how can resident “good” microbes in the gut protect against pathogens, such as Salmonella?

Now research led by Andreas Bäumler, professor of medical immunology and microbiology at UC Davis Health System, has identified the chain of events that occur within the gut lumen of mice after antibiotic treatment that allow “bad” bugs to flourish.

This has profound implications, expanding the current view of how microbes interact with each other at the gut surface, wrote the authors of an accompanying commentary that appeared online with the study April 13 in the journal Cell Host Microbe. It could lead to new strategies to prevent side effects of antibiotic treatment.

According to Bäumler, the process begins with antibiotics depleting “good” bacteria in the gut, including those that breakdown fiber from vegetables to create butyrate, an essential organic acid that cells lining the large intestine need as an energy source to absorb water. The reduced ability to metabolize fiber prevents these cells from consuming oxygen, increasing oxygen levels in the gut lumen that favor the growth of Salmonella.

Less fiber breakdown by bacteria, more oxygen

“Unlike Clostridia and other beneficial microbes in the gut, which grow anaerobically, or in the complete absence of oxygen, Salmonella flourished in the newly created oxygen-rich micro environment after antibiotic treatment,” Bäumler said. “In essence, antibiotics enabled pathogens in the gut to breathe.”

Other research has linked low levels of butyrate-producing microbes with inflammatory bowel disease, but additional research is needed to determine if these findings are limited to butyrate and growth of Salmonella or if similar mechanisms underlie interactions that influence human health.

Other authors on the research paper include Fabian Rivera-Chavez, Lillian F. Zhang, Franziska Faber, Christopher A. Lopez, Mariana X. Byndloss, Erin E. Olsan, Eric M. Velazquez, Gege Xu and Carlito B. Lebrilla, all of UC Davis; and Sebastian E. Winter at the University of Texas Southwestern Medical Center.

The research study is entitled, “Depletion of Butyrate-Producing Clostridia from the Gut Microbiota Drives an Aerobic Luminal Expansion of Salmonella.” It was supported by Public Health Service grants AI096528 (A.J.B.), AI112949 (A.J.B.), AI103248 (S.E.W.), AI112241 (C.A.L.), OD010931 (E.M.V.) and AI060555 (E.M.V. and F.R.-C).

More information: A version of this story is also available here.

Carole Gan writes about basic sciences for UC Davis Health System Public Affairs.

Microbe studies zoom in on effects of HIV in the gut

By Pat Bailey

The curtain cloaking how AIDS and HIV (human immunodeficiency virus) impact the human digestive and immune systems has been drawn back a bit further, thanks to a team of researchers from UC Davis’ departments of Food Science and Technology and Medical Microbiology and Immunology.

The small intestine­ is extremely difficult to study because of its location in the body but plays a critical role in human health. Its inner lining offers both a portal for absorbing nutrients and a barrier against toxins or invasive microbes.

Using rhesus macaque monkeys as a research model, the scientists examined gene expression of both naturally occurring gut bacteria and an introduced probiotic bacterium, Lactobacillus plantarum, in the small intestine.

Figures: Microbial gene expression lights up in green in the small intestine of SIV-infected monkeys without (left) and with (right) Lactobacillus. Images by Lauren Hirao and Irina Grishna.

SIV lactoSIV

They then compared the gene activity of those bacteria in healthy animals to that of the same bacteria during the first few days of infection with SIV (simian immunodeficiency virus), the monkey version of HIV.

Their findings are reported online in the open-access journal Nature Scientific Reports.

“This is a new approach to investigating how bacteria interact with the small intestine during times of health and disease,” said study co-author Maria Marco, a microbiologist in the Department of Food Science and Technology, who studies the effects of ‘beneficial’ bacteria.

By looking at their gene expression patterns, Marco and colleagues found that both the native and introduced bacteria appeared to be consuming sugars produced by the intestinal cells.

The researchers also showed that both L. plantarum and the native microbes responded the same way in the small intestine of healthy rhesus macaques as they did in the small intestine of macaques in the very early stage of SIV infection. This indicates that the transcriptomes—the entire collections of mRNA sequences in a cell—for these bacteria are not altered shortly after SIV infection.

“The effects of SIV infection were clearly very minor for both types of bacteria,” Marco said.

She noted, however, that in a study published last year, co-author Satya Dandekar, professor of medical microbiology and immunology and colleagues showed that L. plantarum was able to reverse some of the damage to the small intestine’s epithelium, or thin inner lining, which had been caused by SIV infection only a few days after exposure to the virus. That study also used rhesus macaques as an animal model.

“Such discoveries related to how bacteria adapt to the small intestine, help us to develop a clearer picture of how the lining of the small intestine is impacted during chronic HIV infection and, we hope, will lead to new strategies for manipulating native gut microbes to alleviate such intestinal damage,” she said.

Collaborating with Marco and Dandekar were co-authors Benjamin Golomb, formerly of the Department of Food Science and Technology, and Lauren A. Hirao Department of Medical Microbiology and Immunology.

The cross-campus collaborative effort was largely initiated by the UC Davis RISE (Research Investments in the Sciences and Engineering) grant program.  Funding for the study was provided by the National Institutes of Health, the U.S. Department of Agriculture – National Institute of Food and Agriculture, and the California HIV/AIDS Research Program.

Pat Bailey writes about agricultural and veterinary sciences for UC Davis Strategic Communications. Follow her on Twitter @UCDavis_Bailey.

Livestock and Climate Change: Facts and Fiction

By Frank Mitloehner

As the November 2015 Global Climate Change Conference COP21 concluded in Paris, 196 countries reached agreement on the reduction of fossil fuel use and emissions in the production and consumption of energy, even to the extent of potentially phasing out fossil fuels out entirely.

Dairy cows eat hay

Holstein cows eat lunch at the Dairy Cattle Facility at UC Davis. Credit: Gregory Urquiaga, UC Davis

Both globally and in the U.S., energy production and use, as well as the transportation sectors, are the largest anthropogenic contributors of greenhouse gasses (GHG), which are believed to drive climate change. While there is scientific consensus regarding the relative importance of fossil fuel use, anti animal-agriculture advocates portray the idea that livestock is to blame for a lion’s share of the contributions to total GHG emissions.

Divorcing Political Fiction from Scientific Facts

One argument often made is that U.S. livestock GHG emissions from cows, pigs, sheep and chickens are comparable to all transportation sectors from sources such as cars, trucks, planes, trains, etc. The argument suggests the solution of limiting meat consumption, starting with “Meatless Mondays,” to show a significant impact on total emissions.

When divorcing political fiction from scientific facts around the quantification of GHG from all sectors of society, one finds a different picture.

Leading scientists throughout the U.S., as well as the U.S. Environmental Protection Agency have quantified the impacts of livestock production in the U.S., which accounts for 4.2 percent of all GHG emissions, very far from the 18-51 percent range that advocates often cite.

Comparing the 4.2 percent GHG contribution from livestock to the 27 percent from the transportation sector, or 31 percent from the energy sector in the U.S. brings all contributions to GHG into perspective. Rightfully so, the attention at COP21 was focused on the combined sectors consuming fossil fuels, as they contribute more than half of all GHG in the U.S.

Graphic of greenhouse gas emissions by sector

Greenhouse gas emissions by sector.


GHG Breakdown by Animal Species

Breaking down the 4.2 percent EPA figure for livestock by animal species, shows the following contributors: beef cattle, 2.2 percent; dairy cattle, 1.37 percent; swine, 0.47 percent; poultry, 0.08 percent; sheep, 0.03 percent; goats, 0.01 percent and other (horses, etc.) 0.04 percent.

It is sometimes difficult to put these percentages in perspective, however. If all U.S. Americans practiced Meatless Mondays, we would reduce the U.S. national GHG emissions by 0.6 percent.

A beefless Monday per week would cut total emissions by 0.3 percent annually. One certainly cannot neglect emissions from the livestock sector but to compare them to the main emission sources would put us on a wrong path to solutions, namely to significantly reduce our anthropogenic carbon footprint to reduce climate change.

lightbulb graphic U.S. Population Replace Incandescent with Energy Star bulbs = 1.2 percent GHG savings




Meatless Monday globeU.S. Population “Meatless Monday” = 0.6 percent GHG savings 


In spite of the relatively low contributions to total GHG emissions, the U.S. livestock sector has shown considerable progress during the last six-plus decades and commitment into the future, to continually reduce its environmental footprint while providing food security at home and abroad. These environmental advances have been the result of continued research and advances in animal genetics, precision nutrition, as well as animal care and health.

U.S. Dairy and Beef Production Carbon Footprint Reduced 

Since the 1950s, the carbon footprint of the U.S. beef and dairy sector has shrunk as production increased or stayed the same.                              


• 1950: 22 million dairy cows produced 117 million tons milk

• 2015: 9 million dairy cows produced 209 million tons of milk. (Fifty-nine percent fewer cows produced 79 percent more milk than they did in 1950.)


• 1970: 140 million head of cattle produced 24 million tons of beef

• 2015: 90 million (36 percent fewer) head of cattle produce 24 million tons of beef

Globally, the U.S. is the country with the relatively lowest carbon footprint per unit of livestock product produced (i.e. meat, milk, or eggs). The reason for this achievement largely lies in the production efficiencies of these commodities. Fewer animals are needed to produce a given quantity of animal protein food, as the following milk production example demonstrates:

• The average dairy cow in the U.S. produces 22,248 lbs. milk/cow/year. In comparison, the average dairy cow in Mexico produces 10,500 lbs. milk/cow/year, so it requires more than two cows in Mexico to produce the same amount of milk as one cow in the U.S.

• India’s average milk production per cow is 2,500 lbs. milk/cow/year, increasing the methane and manure production by a factor of nine times compared to the U.S. cow. As a result, the GHG production for that same amount of milk is much lower for the U.S. versus the Mexican or Indian cow.

Production efficiency is a critical factor in sustainable animal protein production and it varies drastically by region.

Graphic of milk produced per cow, by country

Improvements in livestock production efficiencies are directly related to reductions of the environmental impact. Production efficiencies and GHG emissions are inversely related—when the one rises, the other falls.

The 2050 challenge to feeding the globe is real. Throughout our lifetime, the global human population will have tripled from three to more than nine billion people without concurrent increases of natural resources to produce more food.

Our natural resources of land, water and minerals (fertilizer) necessary for agricultural production have not grown but in fact decreased. As a result, agriculture will have to become much more efficient worldwide and engage in an efficient path similar to the one it has traveled down in U.S. livestock production in recent decades.

UN’s FAO Committee Develops Global Benchmarking Method 

How can emissions accurately and fairly be assessed to lay ground for a path for solutions?

In its quest to identify a sustainable, scientific path toward fulfilling the future global food demand, the Food and Agriculture Organization of the United Nations (FAO) has formed an international partnership project to develop and adopt a “gold standard” life cycle assessment (LCA) methodology for each livestock specie and the feed sector.

The ‘Livestock Environmental Assessment and Performance Partnership’ (LEAP), engaged with more than 300 scientists from the world’s most prestigious academic institutions in this unprecedented effort to develop a global benchmarking methodology.

The first three-year phase project was finalized in December 2015 with six publically available LCA guidelines. This globally harmonized quantification methodology will not only allow the accurate measurement by livestock species and production regions across the globe today, but will also identify opportunities for improvement and the ability to measure that progress in each region going forward.

Efficiency and Intensification Key to Low-Carbon Livestock Sector

Addressing the 2050 challenge of supplying food to a drastically growing human population can sustainably be achieved through intensification of livestock production. Indeed, intensification provides large opportunities for climate change mitigation and can reduce associated land use changes such as deforestation. Production efficiencies reduce environmental pollution per unit of product.

The U.S. livestock, poultry and feed industries are one of the most efficient and lowest environmental impact systems in the world. The research, technologies and best practices that have been developed and implemented over time in the U.S. can also be shared with other production regions around the world.

It is important to understand that all regions have unique demands and abilities, and so require regional solutions. However, the advances in the U.S. agriculture and food system can be adapted within these regional solutions.  These significant environmental advances and benefits are in addition to the well-documented human health and developmental value of incorporating animal protein in the diets of the growing population.

The livestock sector is committed to continuous improvement of their environmental impact in North America, and to doing its part in transferring knowledge, technologies and best practices to enhance global environmental livestock impact by region.

Now is the time to end the rhetoric and separate facts from fiction around the numerous sectors that contribute emissions and to identify solutions for the global food supply that allow us to reduce our impact on the planet and its resources.

Frank Mitloehner is a professor of Animal Science and Air Quality Specialist at UC Davis. He recently concluded chairing a Food and Agriculture Organization of the United Nations committee to measure and assess the environmental impact of the livestock industry.





UC Davis Physicist Will Illuminate Black Holes In Inaugural Ko Lecture

Update May 4: This event is now free of charge for all. RSVPs are requested.

By Becky Oskin

The first lecture in new Winston Ko Frontiers in Mathematical and Physical Sciences Public Lecture series will take place May 9. Veronika Hubeny will discuss modern understanding of black holes, and the remaining mysteries. Her talk, “Illuminating Black Holes,” begins at 5 p.m. on Monday, May 9, in the UC Davis Conference Center.Public lecture on black holes, May 9, UC Davis Conference Center

Veronika Hubeny, a professor of physics at UC Davis, is one of the experts probing the nature of black holes and gravity. Hubeny is a key member of the new Center for Quantum Mathematics and Physics, or QMAP, an initiative aimed at fostering a vibrant research environment exploring the forefront of modern theoretical physics and mathematics. QMAP researchers work in concert to tackle questions such as the origin of space and time, quantum gravity and string theory.

The Ko Lecture series was endowed by former dean Winston Ko upon his retirement from the UC Davis Division of Mathematical and Physical Sciences. The gift is part of a challenge grant to establish a Professorship in Science Leadership to recognize an outstanding faculty member in the division. Fundraising for the Winston Ko Professorship in Science Leadership continues — we welcome contributions of any size toward this goal. Make a gift.

Purchase tickets online or at the UC Davis Ticket Office (located at Aggie Stadium North). Tickets are free for students with ID at the box office, $10 advance, and $12 day of event. Tickets will not be sold at the door.

More information

View this event on the UC Davis events calendar 

Becky Oskin writes for the Division of Mathematical and Physical Sciences, College of Letters and Science. Follow her on Twitter @beckyoskin.


West Coast Scientists Recommend Immediate Action Plan to Combat Ocean Acidification

By Kat Kerlin

Global carbon dioxide emissions are triggering permanent changes to ocean chemistry along the West Coast. Failure to act on this fundamental change in seawater chemistry, known as ocean acidification, is expected to have devastating ecological consequences for the West Coast in the decades to come, warns a multistate panel of scientists, including two from UC Davis Bodega Marine Laboratory.

Their report, issued this week, urges immediate action and outlines a regional strategy to combat the alarming global changes underway. Inaction now will reduce options and impose higher costs later, the report said.

P20 - Bob Wick:Creative Commons License

Global carbon dioxide emissions is changing ocean chemistry, particularly along the West Coast. Credit: Bob Wick/Creative Commons

“The work of the panel has brought the threat of ocean acidification and hypoxia to the fore, and has provided specific guidance on next steps for West Coast managers and decision makers,” said UC Davis professor Tessa Hill, a member of the West Coast Ocean Acidification and Hypoxia Science Panel, which authored the report, and associate director of the UC Davis Coastal and Marine Sciences Institute. “In being proactive, the West Coast will serve as a model for other coastal regions on how to tackle this global problem at a regional scale. Decisions that we make now matter a great deal — and there is a cost to inaction.”

West Coast affected more so than other regions
Atmospheric carbon dioxide emissions from human activities affect not only global climate change, but are also absorbed by the world’s oceans. That can lead to ocean acidification and hypoxia, a term referring to low dissolved oxygen levels. Ocean acidity is expected to continue in lockstep with rising atmospheric CO2 emissions.

Because of the way the Pacific Ocean circulates, the West Coast is exposed to disproportionately high volumes of seawater at elevated acidity levels. Already, West Coast marine shelled organisms are having difficulty forming protective outer shells, and the West Coast shellfish industry is seeing high mortality rates during early life stages when shell formation is critical.

Developing shellfish

West Coast shellfish already have difficulty forming their protective shells due to ocean acidification. Credit: Nina Bednarsek

Strategies to combat ocean acidification
The panel’s report outlines potential management actions the governments of California, Oregon, Washington and British Columbia can immediately take to mitigate the economic and ecological impacts of ocean acidification.

Their recommendations include:

  • Explore using seagrass to remove CO2 from seawater.
  • Develop new benchmarks for improving water quality that take into account protecting marine organisms from ocean acidification.
  • Identify strategies to reduce the amount of pollution entering coastal waters from the land.
  • Strengthen a West Coast-wide monitoring network that informs coastal ecosystem management plans.
  • Support approaches that help marine organisms cope with acid acidification.

“Our panel dug deep into new research and debated intensely on what is more or less likely to occur,” said panel member and UC Davis professor John Largier. “We sought local solutions to local impacts. But we also recognize that underlying those impacts is a global phenomenon due to carbon dioxide emissions that requires urgent global attention.”

The West Coast Ocean Acidification and Hypoxia Science Panel was convened for a three-year period in 2013 to explore how West Coast government agencies could work together with scientists to combat the effects of ocean acidification and hypoxia. The panel’s report, “Major Findings, Recommendations and Actions,” can be read at

Discovery links Brucella infection, inflammation, chronic diseases

By Carole Gan

Researchers at UC Davis have discovered an unexpected link between how the immune system sounds an alarm when its cells are taken over by pathogens during an infection and how an inflammatory response is triggered.

The finding of this novel link, published in the journal Nature on March 23, is important because it helps researchers understand how a cell senses bacterial or viral infection, and how these pathways are linked to inflammatory diseases, such as inflammatory bowel disease, diabetes and atherosclerosis.


Image shows a human cell  invaded by Brucella bacteria (red) which is growing within the endoplasmic reticulum (blue). The green label shows lysosomes, which normally degrade bacteria, are unable to eliminate Brucella. Reprinted with permission from journal mBio (vol. 4 no. 1 e00418-12.)

“Some bacteria are able to hijack the cell’s own manufacturing machinery to gain nutrients and grow within our cells,” said Mariana Byndloss, co-author of the study and postdoctoral scholar in the Department of Medical Microbiology and Immunology at the UC Davis School of Medicine.

“However, our cells can sense this disruption and trigger an alarm that leads to inflammation,” she said. “We have found that the same two proteins involved in alerting the immune system to bacterial infection, NOD1 and NOD2, are also involved in how a cell responds to cellular stress.”

The cell’s manufacturing processes take place in a specialized organelle in the cell, called the endoplasmic reticulum (ER), and are critical to making many components needed to maintain and repair cells. During a hostile takeover of the cell by bacteria or viruses, these manufacturing processes are disturbed, and the assembly line for producing these components becomes backed up. This condition is known as ER stress, which triggers an alarm that causes the cell to shut down production to try and resolve the problem. It also triggers a host response, termed inflammation, which is designed to fight infection.

In this study, UC Davis researchers studying the response to infection with the bacterial pathogen Brucella, a cause of chronic febrile illness, discovered a novel link between ER stress and the innate immune response to bacterial infection. Two proteins, NOD1 and NOD2, which were already known to sense bacterial infection, turned out also to be involved in sensing ER stress, whether it was caused by infection with bacteria, such as Brucella and Chlamydia, or by chemicals that disrupt the endoplasmic reticulum’s function.

“ER stress in various cells plays an important role in the pathogenesis of several diseases, including obesity, diabetes, cancer, and intestinal bowel and airway diseases,” Byndloss said. “Moreover, it has been suggested that ER stress-induced inflammation contributes substantially to disease progression. But it was not known how this response was linked to infection until now.”

The discovery that the NOD1/NOD2 and ER stress pathways are linked helps researchers understand how a cell senses bacterial or viral infection, and how these pathways are linked to inflammatory diseases.

The title of the journal paper is “NOD1 and NOD2 signalling links ER stress with inflammation.”

Other authors include: A. Marijke Keestra-Gounder, Núbia Seyffert, Briana M. Young, Alfredo Chávez-Arroyo, April Y. Tsai, Stephanie A. Cevallos, Maria G. Winter, Tobias Kerrinnes, Connor R. Tiffany, Marteen F. deJong, Andreas J. Bäumler and Renée M. Tsolis at UC Davis Department of Medical Microbiology and Immunology; and Oanh H. Pham, Resmi Ravindran, Paul A. Luciw and Stephen J. McSorley at the UC Davis Center for Comparative Medicine.

The research is supported with grants from the U.S. Public Health Service (USPHS A/112258, A/109799, A/044170, A/076246, A/096528, A/076278, A/117303,  and GM056765) the American Heart Association (12SDG12220022) and a CAPES Science without Borders fellowship.

Carole Gan writes about basic sciences for UC Davis Health System Public Affairs.

Magneto-ionics could be a new alternative to electronics

Our electronic devices are based on what happens when different materials are layered together: “The interface is the device,” as Nobel laureate Herbert Kroemer famously claimed over 40 years ago. Right now, our microchips and memory devices are based on the movement of electrons across and near interfaces, usually of silicon, but with limitations of conventional electronics become apparent, researchers are looking at new ways to store or process information. These “heterostructures” can also find applications in advanced batteries and fuel cells.

Now physicists at UC Davis have observed what’s going on at some of these interfaces as oxygen ions react with different metals, causing drastic changes in magnetic and electronic properties.

Ionic and electronic effects

Electronic devices operate, as the name implies, on the movement of electrons. But ions – here atoms with extra electrons and negative charges – can also move in and near interfaces and take part in magnetoelectric effects.

“Typically, the electronic structure is dominant, but now we’re realizing that the movement of ions is also important,” said Kai Liu, professor of physics at UC Davis and corresponding author on the paper published March 21 in Nature Communications. “If we can get a handle on ion movement, then we can get insight into how we alter the chemistry of these structures and their properties.”

But these effects are hard to measure, because the ions are buried beneath the interface.

The magnetic properties of the layers in this gadolinium-iron/nickel-cobalt oxide interface are influenced by chemistry.

The magnetic properties of the layers in this gadolinium-iron/nickel-cobalt oxide interface are influenced by chemistry.

Liu’s graduate students Dustin Gilbert (now a postdoctoral scientist at the National Institute of Standards and Technology, NIST), Justin Olamit and Randy Dumas studied thin films of gadolinium iron alloy, which is magnetic, placed over nickel-cobalt oxide, which is an antiferromagnet (with two opposite sets of magnetic moments). When these materials are put together, the antiferromagnet “pins” the moments in the magnetic material in place so they cannot move freely, allowing realization of desired magnetic configurations. This effect, called exchange bias, is widely used in devices such as hard disk drive read heads and magnetic random access memory.

But when the antiferromagnet oxide is layered with another magnetic metal with strong oxygen affinity, such as gadolinium iron, a chemical reaction occurs where the oxygen is pulled towards the gadolinium, drastically changing the pinning effect the original oxide has on the metal.

Liu’s group and collaborators were able to track down the origin of these unusual behaviors to physical processes occurring at the buried interface.

“We can study the oxygen migration across the interface through changes in the magnetic properties of the films,” Liu said.

New layer influences entire structure

The team used X-rays from the Advanced Light Source at the U.S. Department of Energy’s Lawrence Berkeley Laboratory to probe the interfacial magnetic signatures. They found elemental nickel and cobalt, showing that part of the nickel/cobalt oxide had been chemically reduced (lost oxygen). Using neutron scattering at the NIST Center for Neutron Research, they were able to show that these elements were at the interface between the two original materials. This new layer of nickel and cobalt, a result of the oxygen migration, can couple to both the magnetic gadolinium-iron and antiferromagnetic nickel/cobalt oxide and influence the behavior of the entire structure.

“This tells us what oxygen migration does in such a system, and it means that now we can design structures to take advantage of this effect,” Liu said. Devices based on this “magneto-ionics” principle could use much less energy, and therefore generate less heat, than conventional electronics, Liu said.

Other authors on the study were Brian Kirby, Alexander Grutter, Brian Maranville and Julie Borchers at the NIST Center for Neutron Research, Gaithersburg, MD, and Elke Arenholz at the Advanced Light Source, Lawrence Berkeley Laboratory. The work was supported by the National Science Foundation, NIST and the Department of Energy, Office of Basic Energy Sciences.

More information

Read the paper (open access)

Tide pools at the front line of ocean acidification

By Becky Oskin

Beloved by beach goers, tide pools are also important ecological zones that provide shelter and food for many plants and animals.

Marine life living in tide pools are vulnerable to rising acid levels in seawater, according to new research from UC Davis, the Carnegie Institution for Science and UC Santa Cruz published March 18 in the journal Scientific Reports.

“The animals living in tide pools are already in a very stressful environment,” said study co-author Tessa Hill, an associate professor in the Department of Earth and Planetary Sciences and at the UC Davis Bodega Marine Laboratory, and associate director of the UC Davis Coastal and Marine Sciences Institute. “In the future, as ocean conditions change, tide pool organisms will spend more time in pools that are acidic enough to dissolve shells,” Hill said.

Study co-authors Lester Kwiatkowski and Yana Nebuchina taking samples from a rocky tide pool on the UC Bodega Marine Reserve. Photo credit: Ken Caldeira

Study co-authors Lester Kwiatkowski and Yana Nebuchina taking samples from a rocky tide pool on the UC Bodega Marine Reserve. Photo credit: Ken Caldeira

The world’s oceans are growing more acidic because of the sharp rise in atmospheric carbon dioxide during the past 200 years, a result of emissions from human activity. Increasing ocean acidity makes life difficult for organisms such as mussels, oysters and coralline algae, which build their shells and exoskeletons out of calcium carbonate. However, some marine life seems to thrive in more acidic waters, including tide pool predators such as sea stars and crabs.

How Tide Pools May Adapt to Ocean Acidification

In the study, the researchers document the effects of natural pH swings on marine life in rocky tide pools near the UC Davis Bodega Marine Laboratory. The team found carbon dioxide used during daytime photosynthesis helps balance ocean acidity, creating a favorable water environment for shell-builders. But at night, when plants and animals respire (and there is no photosynthesis), releasing carbon dioxide, the water’s pH level quickly becomes acidic.

During low tide at night, when the tide pools are cut off from the ocean, shells and skeletons may even start to dissolve, the study reports. The findings suggest increasing ocean acidity will put tide pools at risk by exacerbating these natural pH variations.

“This indicates that the first response to ocean acidification may be at nighttime in these restricted, coastal environments,” Hill said.

The protected lands of the Bodega Marine Reserve, part of the UC Natural Reserve System, have been instrumental in ocean acidification research at UC Davis. The reserve provides isolation from outside impacts, such as people walking among the tide pools. The new study is the most extensive set of ocean acidification measurements ever made in tide pools, the researchers said.

Tide pool animals may be the first at risk from ocean acidification

Tide pool animals may be the first at risk from ocean acidification.

Climate Change Threat

Separate research suggests the average ocean pH is three times more acidic than pre-industrial levels. Predictions by the Intergovernmental Panel on Climate Change (IPCC) the pH will continue to drop (become more acidic) through 2100. The conditions seen in nighttime tide pools during the study could occur up and down the Pacific coast by 2100.

“Unless carbon dioxide emissions are rapidly curtailed, we expect ocean acidification to continue to lower the pH of seawater,” said lead study author Lester Kwiatkowski, a postdoctoral researcher at the Carnegie Institution for Science in Washington, D.C. “If what we see happening along California’s coast today is indicative of what will continue in the coming decades, by the year 2050 there will likely be twice as much nighttime dissolution as there is today. Nobody really knows how our coastal ecosystems will respond to these corrosive waters, but it certainly won’t be well.”

Other Carnegie authors include Yana Nebuchina, Marine Sesboü and Ken Caldeira. Co-authors from UC Davis include Brian Gaylord, Jessica Hosfelt, Aaron Ninokawa, Ann Russell and Emily Rivest. Other co-authors include UC Santa Cruz professor Kristy Kroeker.

More information

Read the paper

More photos from the study

UC Davis Bodega Marine Laboratory

Becky Oskin writes for the Division of Mathematical and Physical Sciences, College of Letters and Science. Follow her on Twitter @beckyoskin.

Not so sweet: Why Pollinators Forage on Toxic or Bitter Nectar

By Kathy Keatley Garvey

Nectar doesn’t always taste so sweet, but honeybees and other pollinators still feed on it. Now UC Davis community ecologist Rachel Vannette has discovered why pollinators continue to forage on “toxic” or bitter-tasting nectar, despite what should be a deterrent.

In newly published research in the journal Ecology, Vannette notes that floral nectar is produced by many plants to reward pollinators, but this sugary secretion often contains chemical compounds that are bitter tasting or toxic, which should deter pollinators. Plants including citrus, tobacco (Nicotiana), milkweed (Asclepias), turtlehead (Chelone), Catalpa, and others produce nectar containing bioactive or toxic compounds.

“This poses a paradox of toxic nectar: why are deterrent or harmful compounds present in a resource intended to attract pollinators?” she said. “One hypothesis is that these compounds reduce microbial growth, which could otherwise spoil the nectar resource.”

A foraging honeybee. Photo  by Kathy Keatley Garvey.

A foraging honeybee. Photo by Kathy Keatley Garvey.

Vannette, an assistant professor in the UC Davis Department of Entomology and Nematology, and Tadashi Fukami, associate professor at Stanford University, tested this hypothesis by growing yeasts and bacteria in sugar solutions spiked with chemical compounds found in nectar.

Contrary to expectations, the chemical compounds only weakly inhibited microbial growth in most cases. Some microorganisms even grew better in the presence of plant compounds such as nicotine. But most surprising, they found that microbial growth reduced the concentration of the toxic chemical compounds in nectar solutions.

These microbial effects on nectar, in turn, actually increased consumption of nectar by honeybees, she said.

“We found that microorganisms in nectar can both reduce the concentration of some plant compounds in nectar and increase consumption of nectar that does contain these compounds. This indicates that although ‘toxic nectar’ does not strongly inhibit microbial growth, microbes modify the palatability of nectar to pollinators, which can change foraging behaviors and may reduce selection on this trait,” Vannette said.

Nectar microbes bring more pollinators

Another hypothesis for why some plants have bad-tasting compounds in nectar is that it might keep the nectar exclusive to a few pollinators, keeping down micro-organisms and deterring other non-pollinators looking for a sweet treat. The new work, however, shows the opposite: microbes aren’t much affected by the secondary compounds, and microbe growth actually seems to encourage more pollinators to visit flowers.

The research, “Nectar Microbes Can Reduce Secondary Metabolites in Nectar and Alter Effects on Nectar Consumption by Pollinators,” appears in the journal Ecology.

The research was funded by the Gordon and Betty Moore Foundation, the National Science Foundation, and Stanford University.

Future work will examine how microbial modification of nectar traits influences floral attractiveness, how microbial growth may modify the specificity of plant-pollinator interactions, and if microbial effects vary among plant species.

Vannette joined UC Davis in September 2015. “I am interested in understanding and predicting how microbial communities influence interactions between plants and insects,” she said. “In the Vannette lab, we use tools and concepts from microbial ecology, chemical ecology, and community ecology to better understand the ecology and evolution of interactions among plants, microbes and insects.”

Kathy Keatley Garvey writes about all things insect-related for the UC Davis Department of Entomology and Nematology and UC Division of Ag and Natural Resources. For more insect news, follow her Bug Squad blog. 


Multitasking? “Digital archaeology” shows up to five projects is optimal

How many projects can you work on at the same time, before losing efficiency? There are many reasons to get involved in multiple projects – impress your boss, gain personal satisfaction, help out colleagues or just because you’re interested. But at some point, there must be one project too many.

“There is a limit,” said Bogdan Vasilescu, postdoctoral researcher in the DECAL lab at the UC Davis Department of Computer Science. “Multitasking fills time that’s otherwise unused, but there is a limit at four or five projects in a week.”

UC Davis researchers are using the behavior of programmers on GitHub to study multitasking. This figure shows the activity of one programmer over a year, with deeper colors showing more projects per day. (Bogan Vasilescu, UC Davis)

UC Davis researchers are using the behavior of programmers on GitHub to study multitasking. This figure shows the activity of one programmer over a year, with deeper colors showing more projects per day. (Bogan Vasilescu, UC Davis)

That estimate comes from what Vasilescu and and computer science professor Vladimir Filkov call “digital archaeology,” conducted on the vast amounts of data within the collaborative open-source programming site, GitHub. Vasilescu, Filkov and their colleagues excavated GitHub’s records of how individual programmers contributed to different pieces of software to reach their conclusions, which will be presented at the International Conference on Software Engineering in Austin, Texas this May. The paper is available online.

GitHub was founded in 2008, and Vasilescu has been studying it since 2012. The site now includes over 12 million contributors who self-organize around millions of different projects, creating billions of lines of code that anyone can use.

“Your GitHub profile is a programmer’s resume now,” Vasilescu said.

Because GitHub records everything, Vasilescu and Filkov could measure how individual programmers work: how many projects they work on during a week, how many projects they switch between in a day, how much they focus on any single project, and how repetitive is their day-to-day behavior. Then, they statistically analyzed which working styles associate with increases in the number of lines of code written per week — one of the facets of programming productivity.

“Over four of five GitHub projects per week, your attention becomes too fragmented, regardless of how you schedule working on them,” Vasilescu said. The results are in good agreement from studies by psychologists, Filkov noted.

The researchers plan to keep digging through GitHub for more treasures. For example, what mix of people creates an effective team? What trade-offs are programmers making with their privacy, when they give away information about themselves by participating in collaborative projects?

It’s a new way of doing science by mining vast amounts of data, Filkov said. “This model of research is here to stay. Software engineering datasetsof this size have never been available before.”

Additional coauthors are: Casey Casalnuovo and Premkumar Devanbu at UC Davis;  Kelly Blincoe, University of Auckland, New Zealand;  Qi Xuan, Zhejiang University of Technology, Hangzhou, China; and Daniela Damian, University of Victoria, Canada. The work was received support from the National Science Foundation, NSERC Canada and NSF China.