OREGON STATE UNIVERSITY

college of science

Study reveals seven complete specimens of new flower, all 100 million years old

CORVALLIS, Ore. – A Triceratops or Tyrannosaurus rex bulling its way through a pine forest likely dislodged flowers that 100 million years later have been identified in their fossilized form as a new species of tree.

George Poinar Jr., professor emeritus in Oregon State University’s College of Science, said it’s the first time seven complete flowers of this age have been reported in a single study. The flowers range from 3.4 to 5 millimeters in diameter, necessitating study under a microscope.

Poinar and collaborator Kenton Chambers, professor emeritus in OSU’s College of Agricultural Sciences, named the discovery Tropidogyne pentaptera based on the flowers’ five firm, spreading sepals; the Greek word for five is “penta,” and “pteron” means wing.

“The amber preserved the floral parts so well that they look like they were just picked from the garden,” Poinar said. “Dinosaurs may have knocked the branches that dropped the flowers into resin deposits on the bark of an araucaria tree, which is thought to have produced the resin that fossilized into the amber. Araucaria trees are related to kauri pines found today in New Zealand and Australia, and kauri pines produce a special resin that resists weathering.”

This study builds on earlier research also involving Burmese amber in which Poinar and Chambers described another species in the same angiosperm genus, Tropidogyne pikei; that species was named for its flower’s discoverer, Ted Pike. Findings were recently published in Paleodiversity.

“The new species has spreading, veiny sepals, a nectar disc, and a ribbed inferior ovary like T. pikei,” Poinar said. “But it’s different in that it’s bicarpellate, with two elongated and slender styles, and the ribs of its inferior ovary don’t have darkly pigmented terminal glands like T. pikei.”

Both species have been placed in the extant family Cunoniaceae, a widespread Southern Hemisphere family of 27 genera.

Poinar said T. pentaptera was probably a rainforest tree.

“In their general shape and venation pattern, the fossil flowers closely resemble those of the genus Ceratopetalum that occur in Australia and Papua-New Guinea,” he said. “One extant species is C. gummiferum, which is known as the New South Wales Christmas bush because its five sepals turn bright reddish pink close to Christmas.”

Another extant species in Australia is the coach wood tree, C. apetalum, which like the new species has no petals, only sepals. The towering coach wood tree grows to heights of greater than 120 feet, can live for centuries and produces lumber for flooring, furniture and cabinetwork.

So what explains the relationship between a mid-Cretaceous Tropidogyne from Myanmar, formerly known as Burma, and an extant Ceratopetalum from Australia, more than 4,000 miles and an ocean away to the southeast?

That’s easy, Poinar said, if you consider the geological history of the regions.

“Probably the amber site in Myanmar was part of Greater India that separated from the southern hemisphere, the supercontinent Gondwanaland, and drifted to southern Asia,” he said. “Malaysia, including Burma, was formed during the Paleozoic and Mesozoic eras by subduction of terranes that successfully separated and then moved northward by continental drift.”

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Tropidogyne pentaptera

Tropidogyne pentaptera

For bacteria that cheat, food is at the forefront

CORVALLIS, Ore. – If you’ve got plenty of burgers and beers on hand and your own stomach is full, an uninvited guest at your neighborhood barbecue won’t put much strain on you.

But if you’re hungry and food and drink supplies are running low when the moocher shows up, it’s a different story.

New research at Oregon State University indicates bacteria know just how you feel.

Microbes that produce important secretions for use in a community suffer a blow to their own fitness for supplying the non-producing “cheater” bacteria – but only when production requires the same nutrients that would otherwise go into growth and biomass.

Findings were published today in Nature Communications.

Bacteria are important organisms for evolutionary biology research because their fast growth allows scientists to study evolution in real time in the lab. The common, rod-shaped bacteria in the study, Pseudomonas aeruginosa, can lead to infections in humans, and cheater strains are often found among the infection-causing organisms.

“The big picture of this research is a better understanding of how cooperation works and how cooperation evolved,” said corresponding author Martin Schuster. “We can use microbes to study social evolution. Essentially every environment is nutrient limited in some way, and our study allows us to make predictions about what types of environments are conducive to cooperation or cheating.”

The study by Schuster and 2017 Ph.D. graduate Joe Sexton involved P. aeruginosa and a peptide siderophore it secretes, pyoverdine, or PVD.

P. aeruginosa uses PVD to scavenge iron, an essential and hard-to-get nutrient; the cheaters don’t produce PVD but have a receptor to collect the iron the siderophore binds with.

“The secretions benefit everyone, and cheating bacteria don’t participate in the production,” said Schuster, associate professor in OSU’s Department of Microbiology in the colleges of Science and Agricultural Sciences. “In general, cooperation is considered costly; therefore, cheaters can exploit the process by saving on the costs of cooperation.”

Building on earlier studies that showed cooperative behavior in P. aeruginosa can be exploited by mutant cheaters, this research demonstrates that the costs of bacterial cooperation are conditional.

“It’s all contextual and depends on the environment, the available nutrients, the bacterial diet,” Schuster said. “Sometimes cooperation is very costly, other times not at all. And if cooperation isn’t costly, it means that cheating doesn’t provide an advantage.”

In the case of PVD secretion, there’s a fitness cost involved for P. aeruginosa when carbon or nitrogen are in limited supply; those are building blocks for PVD and also necessary for producing cellular biomass.

But shortages of other nutrients – iron, phosphorus and sulfur – don’t result in a fitness cost; thus, the cheaters don’t gain an edge in those scenarios.

“Before, fitness cost was thought to be proportional to how much siderophore was being made,” Sexton said. “We showed that under different nutrient conditions the bacteria were still making the same amount, but the fitness costs varied dramatically.”

The researchers experimentally verified their modeling predictions with a chemostat format, an open system in which fresh nutrients flow in at the same rate spent growth medium flows out; cell density and growth rate are kept constant. In this system, the fitness costs of PVD production were apparent as growth differences between cooperators and cheaters in a mixed culture.

“In addition to fundamental questions about the evolution of cooperation, our work is also relevant to natural populations,” Sexton said. “There are siderophore-negative strains in the soil and the ocean and in human infections. Where did they come from? Did they evolve as cheaters, or for some other reason? Our work provides a new piece of the puzzle to consider in real-world contexts.”

The National Science Foundation and the Alexander von Humboldt Fellowship for Experienced Researchers supported this research.

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Siderophore cross-feeding

Bacterial "cheating"

Diatoms have sex after all, and ammonium puts them in the mood

CORVALLIS, Ore. – New research shows a species of diatom, a single-celled algae, thought to be asexual does reproduce sexually, and scientists learned it’s a common compound – ammonium – that puts the ubiquitous organism in the mood.

The findings, published today in PLOS One, may be a key step toward greater understanding of the evolution of sexual behavior and also have important biotechnology implications.

“Our discoveries solve two persistent mysteries that have plagued diatom researchers,” said corresponding author Kimberly Halsey, a microbiologist at Oregon State University. “Yes, they have sex, and yes, we can make them do it.”

Diatoms hold great potential as a bioenergy source and also for biosensing. In addition, their intricate, silica cell walls offer promising nanotechnology applications for materials chemists and drug-delivery researchers.

There are more than 200,000 species of diatoms, and the organisms are abundant nearly everywhere water is found, forming huge blooms in the spring and fall that help drive the marine carbon cycle.

“Diatoms are amazing; their silica frustules are beautiful and exquisite,” Halsey said. “Now that we can control their sexual pathway, that should open the door to being able to make crosses between different diatoms with different characteristics. We should be able to breed them just like we do with corn or rice or strawberries to select for traits that are really desirable.”

Halsey and collaborators in botany and statistics from OSU’s colleges of Science and Agricultural Sciences studied the “centric” Thalassiosira pseudonana species of diatom, a model organism for researchers; it’s one of two diatoms, the other being the “pennate” diatom Phaeodactulum tricornutum, to have had its genome sequenced.

Centric diatoms are radially symmetrical – think of them as shaped like a soup can, Halsey says – and pennate diatoms are bilaterally symmetrical: elongated in the manner of a pea pod.

“Everybody said Thalassiosira pseudonana was asexual, because they’d never seen anything else,” Halsey said. “The general thinking was that it just lost the ability or need to go through sex.”

Other scientists, Halsey notes, had showed T. pseudonana retained genes necessary for meiosis, a type of genetic replication specific to sexual reproduction, and concluded the diatom wasn’t using those genes.

“But we started seeing very different morphologies,” changes in cell structure, Halsey said, in this case related to sexual activity. “We also saw genes expressed that are involved in flagellar structures and assembly, which would only happen with sperm cells.”

Graduate student Eric Moore, lead author on the research, was astonished to learn “these single-celled organisms can differentiate into male and female cells, completely changing their morphologies.”

“In fact, I was convinced my cultures were contaminated before I realized what was actually going on,” he said.

Previous work by other researchers studying different types of centric diatoms showed that growth stress – interruptions of light, changes in salinity, shifts in nutrients – can sometimes, but not reliably, cause cells to become sexual.

“Lab efforts to induce sex in centric diatoms have ranged from sweet talk to torture,” Halsey said.

But manual, microscopic analysis by Halsey’s team found that ammonium, a common compound that’s a metabolic waste product of animals, reliably caused two strains of T. pseudonana and two other centric diatoms to change their cell structures, making eggs and sperm; ammonium caused the diatoms to get ready for sex when at least one other cell growth factor – such as light, phosphorus or silica – was in short supply.

In addition, RNA sequencing showed more than 1,200 diatom genes that changed in activity when ammonium lit the algae’s sexual fires. Halsey suggests that in nature, the protists that graze on the diatom blooms excrete the ammonium that triggers the diatoms’ sexualization.

“The specific collection of environmental factors that make diatoms have sex aren’t yet known,” she said. “But identifying ammonium as a sexuality inducer potentially opens the door to new avenues of research into breeding and genetic modification to control important traits.”

Collaborators also included Brianna Bullington of OSU’s Department of Microbiology, Alexandra Weisberg of the Department of Botany and Plant Pathology, and Yuan Jiang of the Department of Statistics.

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Thalassiosira pseudonana

New approach improves ability to predict metals’ reactions with water

CORVALLIS, Ore. – The wide reach of corrosion, a multitrillion-dollar global problem, may someday be narrowed considerably thanks to a new, better approach to predict how metals react with water.

Researchers at Oregon State University and the University of California, Berkeley, have developed a new computational method that combines two techniques to make predictions faster, less costly and more effective.

The findings, published in Nature Communications, could have a wide range of applications, including in the design of bridges and aircraft engines, both of which are susceptible to corrosion.

Every metal except precious metals like gold and silver reacts with water, said Doug Keszler, distinguished professor of chemistry in Oregon State’s College of Science.

“We’d like to predict the specific reactions of metals and combinations of metals with water and what the products of those reactions are, by computational methods first as opposed to determining them experimentally,” said Keszler, who also serves as director of the Center for Sustainable Materials Chemistry at OSU.

Traditionally, Keszler noted, when looking at metals dissolved in water, the chemical assumption has been that a metal dissolves to form a simple salt. That’s not always what happens, however.

“In many cases, it initially dissolves to form a complex cluster that contains many metal atoms,” he said. “We can now predict the types of clusters that exist in solution, therefore furthering the understanding of metal dissolution from a computational point of view.”

Studying aqueous metal oxide and hydroxide clusters from Group 13 elements – aluminum, gallium, indium and thallium – scientists coupled quantum mechanical calculations with a “group additivity” approach to create Pourbaix diagrams, the gold standard for describing dissolved metal species in water. 

“Applying this new approach, we arrive at a quantitative evaluation of cluster stability as a function of pH and concentration,” said study co-author Paul Ha-Yeon Cheong, associate professor of chemistry at OSU.

Understanding clusters is critical because of the role they play in chemical processes ranging from biomineralization to solution-deposition of thin films for electronics applications. And characterizing corrosion stems from being able to depict metals’ stable phases in water.

“If you’re designing a new steel for a bridge, for example, you’d like to include the potential for corrosion in a computational design process,” Keszler said. “Or if you have a new metal for an aircraft engine, you’d like to be able to determine if it’s going to corrode.”

These examples are not merely hypothetical. Just last summer, a Japanese airline had to refurbish all 100 Rolls-Royce engines on its fleet of Boeing 787 Dreamliners after a series of engine failures caused by the corrosion and cracking of turbine blades. The engines sell for $20 million each.

“Most Pourbaix diagrams do not include these metal clusters and hence our understanding of metal dissolution and reaction with water has been lacking,” said study co-author Kristin A. Persson, professor of materials science at UC Berkeley. “We have now uncovered a fast and accurate formalism for simulating these clusters in the computer, which will transform our abilities to predict how metals react in water.”

The National Science Foundation partially supported this research.

Lindsay Wills, I-Ya Chang and Thomas Mustard of the OSU Department of Chemistry were co-authors of the research, as was Xiaohui Qu of the University of California, Berkeley. 

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Coos Bay bridge

Coastal bridge

Alloying materials of different structures offers new tool for controlling properties

CORVALLIS, Ore. – New research into the largely unstudied area of heterostructural alloys could lead to greater materials control and in turn better semiconductors, advances in nanotechnology for pharmaceuticals and improved metallic glasses for industrial applications.

Heterostructural alloys are blends of compounds made from materials that don’t share the same atom arrangement. Conventional alloys are isostructural, meaning the compounds they consist of, known as the end members, have the same crystal structure.

“Alloys are all around us,” said study co-author Janet Tate, a physicist at Oregon State University. “An example of an istostructural alloy is an LED; you have a semiconductor like aluminum gallium arsenide, dope it with a particular material and make it emit light, and change the color of the light by changing the relative concentration of aluminum and gallium.”

Structure and composition are the two means of controlling the behavior of materials, Tate said. Combining materials gives the alloy properties between those that the end members have individually.

“If two materials have different structures, as you mix them together it’s not so clear which structure will win,” said Tate, the Dr. Russ and Dolores Gorman Faculty Scholar in the College of Science. “The two together want to take different structures, and so this is an extra way of tuning an alloy’s properties, a structural way. The transition between different crystal structures provides an additional degree of control.”

Tate and collaborators from around the world, including the National Renewable Energy Laboratory, published their findings in Science Advances.

“This is a very interesting piece of materials science that represents a somewhat uncharted area and it may be the beginning something quite important,” Tate said. “The heterostructural alloy concept had been known before, but it’s different enough that it hadn’t really been explored in a detailed phase diagram – the mapping of exactly how, at what temperature and what concentration, it goes from one structure to another.

“This paper is primarily the NERL’s theoretical work being supported by other collaborators’ experimental work,” Tate said. “Our involvement at OSU was in making one of the kinds of heterostructural alloys used in the research, the combination of tin sulfide and calcium sulfide.”

Tate and graduate student Bethany Matthews have been focusing on the semiconductor application.

“Tin sulfide is a solar cell absorber, and the addition of calcium sulfide changes the structure and therefore the electrical properties necessary for an absorber,” Tate said “Combining tin sulfide with calcium sulfide makes it more isotropic – properties being the same regardless of orientation – and that’s usually a useful thing in devices.”

In this study, thin-film synthesis confirmed the metastable phases of the alloys that had been predicted theoretically.

“Many alloys are metastable, not stable – if you gave them enough time and temperature, they’d eventually separate,” Tate said. “The way we make them, with pulsed laser deposition, we allow the unstable structure to form, then suppress the decomposition pathways that would allow them to separate; we don’t give them enough time to equilibrate.”

Metastable materials – those that are thermodynamically stable provided they are not subjected to large disturbances – are in general understudied, Tate said.

“When theorists predict properties, they tend to work with materials that are stable,” she said. “In general the stable compounds are easier to attack. The idea here with heterostructural alloys is that they give us a new handle, a new knob to turn to change and control materials’ properties.”

In addition to scientists at the National Renewable Energy Laboratory, the collaboration included researchers at the University of Colorado, the Colorado School of Mines, the SLAC National Accelerator Laboratory, and Harvard University.

The U.S. Department of Energy supported this research.

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OSU researcher part of $14 million NSF program for improved genomic tools

CORVALLIS, Ore. – Coral researcher Virginia Weis of Oregon State University is one of eight researchers selected for a new $14 million National Science Foundation program aimed at helping scientists better understand the relationship between gene function and the physical and functional characteristics of organisms.

Weis, head of the Department of Integrative Biology in OSU’s College of Science, will use her $1.875 million EDGE program award to further study the microscale cellular, molecular and genetic mechanisms that underpin the symbiosis between corals and algae.

EDGE stands for Enabling Discovery through Genomic Tools. The NSF’s Biological Sciences Directorate administers the program, which funds projects that seek to develop new tools and teach researchers how to use them.

“It’s a tremendous honor to be selected for this important new program,” Weis said.

Corals are made up of interconnected animal hosts called polyps that house microscopic algae inside their cells, Weis said. The coral-algal symbiosis, or partnership, is the foundation of the entire coral reef ecosystem; the polyps receive food from the algae, and the polyps in turn provide nutrients and protection to the algae.

“Coral reefs are profoundly important, diverse ecosystems that are threatened worldwide by environmental variation and stress,” Weis said. “While a great deal of attention has been focused on the environmental threats to corals, there remains only a partial understanding of the regulation of the symbiosis, and more knowledge will provide a stronger foundation for studies of coral health and coral stress, such as coral bleaching, in which the host polyps lose their symbiotic algae.”

Weis’ project will bring together coral biologists, cell biologists and geneticists from Stanford University, the Carnegie Institution and Florida International University to study a small sea anemone that serves as a proxy for corals. Corals do not survive well in a laboratory setting, are slow growing and are difficult to collect.

The fast-growing, weedy sea anemone Aiptasia will allow researchers to make quick progress on the study of coral symbiosis.

“This award is focused on technique development and swift dissemination of results through online communication platforms to both the scientific community and the public,” Weis said. “A variety of genetic techniques will be developed, including gene editing in both partners, to be able to test hypotheses about the involvement of specific genes in coral health and stress. This award will contribute to the training of scientists and expose school-aged children and others in the general public to coral reef and symbiosis science.”

Oregon Health & Science University, the University of Texas, Massachusetts Institute of Technology, Michigan State University, Penn State, Virginia Tech and Boyce Thompson Institute are the home institutions of the other EDGE award recipients.

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Virginia Weis

Virginia Weis

International science team: Marine reserves can help mitigate climate change

CORVALLIS, Ore. – An international team of scientists has concluded that “highly protected” marine reserves can help mitigate the effects of climate change and suggests that these areas be expanded and better managed throughout the world.

Globally, coastal nations have committed to protecting 10 percent of their waters by 2020, but thus far only 3.5 percent of the ocean has been set aside for protection – and less than half of that (1.6 percent) is strongly protected from exploitation. Some scientists have argued that as much as 30 percent of the ocean should be set aside as reserves to safeguard marine ecosystems in the long-term. 

Results of the study, which evaluated 145 peer-reviewed studies on the impact of marine reserves, is being published this week in Proceedings of the National Academy of Sciences.

“Marine reserves cannot halt or completely offset the growing impacts of climate change,” said Oregon State University’s Jane Lubchenco, former National Oceanic and Atmospheric Administration (NOAA) Administrator and co-author on the study. “But they can make marine ecosystems more resilient to changes and, in some cases, help slow down the rate of climate change. 

“Protecting a portion of our oceans and coastal wetlands will help sequester carbon, limit the consequences of poor management, protect habitats and biodiversity that are key to healthy oceans of the future, and buffer coastal populations from extreme events,” Lubchenco said. “Marine reserves are climate reserves.”

The scientists say marine reserves can help protect ecosystems – and people – from five impacts of climate change that already are taking place: ocean acidification, rising sea levels, an increase in the severity of storms, shifts in the distribution of species, and decreased ocean productivity and availability of oxygen.

Lead author Callum Roberts, from the University of York, said that many studies already have shown that marine reserves can protect wildlife and support productive fisheries. The goal of this peer-reviewed literature-study was to see whether the benefits of marine reserves could ameliorate or slow the impacts of climate change. 

“It was soon quite clear that they can offer the ocean ecosystem and people critical resilience benefits to rapid climate change,” Roberts said.

The benefits are greatest, the authors say, in large, long-established and well-managed reserves that have full protection from fishing and mineral extraction, and isolation from other damaging human activities. 

The study notes that ocean surface waters have become on average 26 percent more acidic since pre-industrial times, and by the year 2100 under a “business-as-usual” scenario they will be 150 percent more acidic. The authors say coastal wetlands – including mangroves, seagrasses and salt marshes – have demonstrated a capacity for reducing local carbon dioxide concentrations because many contain plants with high rates of photosynthesis.

“Unfortunately,” Lubchenco said, “these ecosystems are some of the most threatened coastal areas and have experienced substantial reductions in the past several decades. Wetland protection should be seen as a key element in achieving greater resilience for coast communities.” 

Coastal wetlands, along with coral and oyster reefs, kelp forests and mud flats, can help ameliorate impacts of rising sea levels and storm surge. The average global sea level has risen about seven inches since 1900, and is expected to increase nearly three feet by the year 2100, threatening many low-lying cities and nations. The dense vegetation in coastal wetlands can also provide protection against severe storms, which are increasing in intensity in many parts of the world.

Climate change already is having a major impact on the abundance and distribution of marine species. Phytoplankton communities are changing in response to warming, acidification and stratifying oceans, and upper trophic level species are being affected, threatening global food security. Climate change interacts with and exacerbates other stressors like overfishing and pollution, the researchers say.

Reducing some stressors can increase the resilience of species and ecosystems to impacts of other stressors. 

“We have seen how marine reserves can be a haven for some species that are under duress from over-fishing or habitat loss, and as a ‘stepping-stone’ for other species that are recolonizing or moving into new areas,” Lubchenco said. “Reserves also promote genetic diversity and provide protection for older fish and other marine organisms. In short, reserves are one of the most powerful tools in our adaptation toolbox. Reserves enhance the resilience of marine ecosystems, and thus our resilience.”

Lubchenco, who recently completed a two-year term as the first U.S. Science Envoy for the Ocean, has been involved in research at Oregon State on the interactions between people and marine ecosystems. She has led pioneering studies on coastal hypoxia (so-called “dead zones”) and innovative ways to achieve sustainable fishing and other uses of the ocean. 

The authors point out that effectiveness of marine reserves is often challenged by lack of staff, equipment and funding; inconsistent management; lack of communication with industry and local communities; and concerns about displacing fishing activities. But, they point out, these challenges can be resolved. Their findings that reserves enhance the resilience of marine ecosystems suggests that reserves may offer the best hope to adapt to a changing climate.

“Marine reserves will not halt, change or stop many of the threats associated with climate change affecting communities within their boundaries,” they write. “We contend, however, that existing and emerging evidence suggests that (marine reserves) can serve as a powerful tool to help ameliorate some problems resulting from climate change, slow the development of others, and improve the outlook for continued ecosystem functioning and delivery of ecosystem services.”

Lubchenco is a distinguished professor in the College of Science at Oregon State and marine studies adviser to OSU President Ed Ray.

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Jane Lubchenco, 541-737-5337, lubchenco@oregonstate.edu

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Photo at left: Marine life around Palau. Photo by Richard Brooks

Acidified ocean water widespread along North American West Coast

CORVALLIS, Ore. – A three-year survey of the California Current System along the West Coast of the United States found persistent, highly acidified water throughout this ecologically critical nearshore habitat, with “hotspots” of pH measurements as low as any oceanic surface waters in the world.

The researchers say that conditions will continue to worsen because the atmospheric carbon dioxide primarily to blame for this increase in acidification has been rising substantially in recent years.

One piece of good news came out of the study, which was published this week in Nature Scientific Reports. There are “refuges” of more moderate pH environments that could become havens for some marine organisms to escape more highly acidified waters, and which could be used as a resource for ecosystem management.

“The threat of ocean acidification is global and though it sometimes seems far away, it is happening here right now on the West Coast of the United States and those waters are already hitting our beaches,” said Francis Chan, a marine ecologist at Oregon State University and lead author on the study.

“The West Coast is very vulnerable. Ten years ago, we were focusing on the tropics with their coral reefs as the place most likely affected by ocean acidification. But the California Current System is getting hit with acidification earlier and more drastically than other locations around the world.”

A team of researchers developed a network of sensors to measure ocean acidification over a three-year period along more than 600 miles of the West Coast. The team observed near-shore pH levels that fell well below the global mean pH of 8.1 for the surface ocean, and reached as low as 7.4 at the most acidified sites, which is among the lowest recorded values ever observed in surface waters.

The lower the pH level, the higher the acidity. Previous studies have documented a global decrease of 0.11 pH units in surface ocean waters since the beginning of the Industrial Revolution. Like the Richter scale, the pH scale in logarithmic, so that a 0.11 pH unit decrease represents an increase in acidity of approximately 30 percent.

Highly acidified ocean water is potentially dangerous because many organisms are very sensitive to changes in pH. Chan said negative impacts already are occurring in the California Current System, where planktonic pteropods – or small swimming snails – were documented with severe shell dissolution.

“This is about more than the loss of small snails,” said Richard Feely, senior scientist with the National Oceanic and Atmospheric Administration’s Pacific Marine Environmental Laboratory. “These pteropods are an important food source for herring, salmon and black cod, among other fish. They also may be the proverbial ‘canary in the coal mine’ signifying potential risk for other species, including Dungeness crabs, oysters, mussels, and many organisms that live in tidepools or other near-shore habitats.”

Previous studies at OSU have chronicled the impact of acidified water on the Northwest oyster industry.

Chan said the team’s observations, which included a broad-scale ocean acidification survey via ship by NOAA, did not vary significantly over the three years – even with different conditions, including a moderate El Niño event.

“The highly acidified water was remarkably persistent over the three years,” Chan said. “Hotspots stayed as hotspots, and refuges stayed as refuges. This highly acidified water is not in the middle of the Pacific Ocean; it is right off our shore. Fortunately, there are swaths of water that are more moderate in acidity and those should be our focus for developing adaptation strategies.”

The researchers say there needs to be a focus on lowering stressors to the environment, such as maintaining healthy kelp beds and sea grasses, which many believe can partially mitigate the effects of increasing acidity.

Further, the moderately acidified refuge areas can be strategically used and managed, Chan pointed out.

“We probably have a hundred or more areas along the West Coast that are protected in one way or another, and we need to examine them more closely,” he said. “If we know how many of them are in highly acidified areas and how many are in refuge sites, we can use that information to better manage the risks that ocean acidification poses.”

Managing for resilience is a key, the researchers conclude.

“Even though we are seeing compromised chemistry in our ocean waters, we still have a comparably vibrant ecosystem,” Chan said. “Our first goal should be to not make things worse. No new stresses. Then we need to safeguard and promote resilience. How do we do that? One way is to manage for diversity, from ensuring multiple-age populations to maintaining deep gene pools.

“The greater the diversity, the better chance of improving the adaptability of our marine species.”

Chan, a faculty member in the College of Science at Oregon State University, was a member of the West Coast Ocean Acidification and Hypoxia Panel appointed by the governments of California, Oregon, Washington and British Columbia.

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Francis Chan, 541-737-9131, chanft@science.oregonstate.edu

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ocean acidification 2

Acidification is threatening tidepool organisms

ocean sensors 2

A sensor at the Oregon coast.

Blocking TB germs’ metabolic ‘escape pathways’ may be key to better, shorter treatment

CORVALLIS, Ore. – New research suggests the bacteria that cause tuberculosis alter their metabolism to combat exposure to antimicrobials, and that these metabolic “escape pathways” might be neutralized by new drugs to shorten the troublesome duration of therapy.

The findings are important because the respiratory disease kills nearly 2 million people a year worldwide, and its long treatment regimen leads to poor compliance and, in turn, drug-resistant germs.

Oregon State University scientist Luiz Bermudez estimated that decreasing the time of treatment from six months to three weeks would likely eliminate many of the compliance problems.

His research may be a key step toward that shorter therapy.

About one-third of the global population is infected with the bacteria that cause TB – Mycobacterium tuberculosis, or Mtb – though only a small percentage will develop the actual disease. For those who do, treatment is basically the same now as it was a half-century ago: taking a combination of drugs for six months because the germs do not die easily or quickly.

As Bermudez notes, anyone who’s ever had trouble sticking with a 10-day antibiotic regimen for an ear infection can understand the hurdles in taking multiple medicines for a couple of dozen weeks – especially given the numerous side effects of the TB drugs.

Another compliance issue is that tuberculosis is particularly prevalent in impoverished countries in which patients often live great distances from pharmacies and other medical facilities.

“Because of problems with compliance, you have resistance becoming more and more of an issue,” said Bermudez, a physician and a faculty member in OSU’s College of Veterinary Medicine. “And the second line of drugs is much more toxic than the first line of drugs.”

Bermudez and collaborators at the veterinary college, as well as researchers at Oregon State’s colleges of science and pharmacy and Oregon Health & Science University, took a biology-driven approach to learn how Mtb prolongs survival following exposure to bactericidal concentrations of antimicrobials.

Researchers investigated how the bacteria reacted to each class of anti-TB drug with the goal of making headway toward developing a more-reasoned combination therapy.

They studied the proteomic responses of the bacteria to five compounds – isoniazid, rifampicin, moxifloxacin, mefloquine and bedaquiline – and discovered escape pathways and enzymes associated with changes in metabolic state.

“When we looked at the enzymes carefully, we realized the enzymes being synthesized by the bacteria were enzymes connecting several different metabolic pathways,” Bermudez said. “Then we came up with the idea that maybe what the bacteria were trying to do, in the presence of a bactericidal compound that was threatening their way of living, was use other ways to survive. One of the things we saw, for example, was a shift to an anaerobic metabolism, which makes a lot of drugs inactive and incapable of killing bacteria. 

“The gene inactivation of some of these enzymes results in improved drug efficacy against Mtb,” he said. “The identified proteins may provide powerful targets for development of synergistic drugs aimed to accelerate bacterial killing.”

Bermudez said that using a combination of drugs to treat tuberculosis arose as an attempt to prevent antibiotic resistance.

“But the antibiotics used were never a rational combination of drugs and in some cases they could antagonize each other,” he said. “If we can use another compound that inhibits bacteria from shifting metabolic pathways, then we get a more reliable and desirable synergy of therapy. That might have a significant impact on reducing the time needed for therapy and improving compliance and, consequently, reducing the emergence of resistance.”

Findings were published recently in Antimicrobial Agents and Chemotherapy. The National Institutes of Health supported this research.

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Luiz Bermudez

Luiz Bermudez

Study provides detailed glimpse of predators’ effects on complex, subtidal food web

CORVALLIS, Ore. – Research using time-lapse photography in the Galapagos Marine Reserve suggests the presence of a key multilevel “trophic cascade” involving top- and mid-level predators as well as urchins and algae.

The findings are important because they include detailed information about interactions in a complex food web. Such information is crucial to knowing how to cause, prevent or reverse population changes within the web.

In the rocky, species-rich subtidal area off the Galapagos Islands, scientists from Oregon State University and Brown University examined the relationships among predatory fishes, urchins, the algae that the urchins graze on, and how the interactions among them were influenced by sea lions and sharks at the top of the food chain.

The key question: Do predators high up in the chain affect the abundance of the “primary producers” at the bottom – in this case algae – thus causing a trophic cascade?

Trophic level refers to a species’ position in the chain, and the cascade describes the series of effects that can occur.

Using GoPro cameras, the researchers made a number of key findings regarding triggerfish, Spanish hogfish, pencil urchins, the larger green urchins and algae, including:

  • Among a diverse guild of predatory fishes, triggerfish can control the abundance of pencil urchins and thus also the abundance of algae the urchins eat; the experiments showed grazing on algae was eliminated when the pencil urchins were exposed to triggerfish predation, meaning triggerfish are a candidate for protection because of their strong effects on ecosystem function.
  • Green urchins eat more algae than pencil urchins yet are not the urchin prey of choice for predatory fish. That suggests those fish aren’t controlling green urchin populations and thus that green-urchin barrens in the Galapagos – areas where the urchins have stripped the sea floor of algae – are not the result of the overfishing of predatory fish.
  • Spanish hogfish are not major predators of urchins as earlier, survey-based research had suggested. Hogfish mainly eat the smaller pencil urchins and also interfere with triggerfish feeding on large pencil urchins; the hassling hogfish cause triggerfish to spend more time to eat an urchin and in some cases force a fumble.
  • Statistical modeling of predation on pencil urchins indicates that two types of interference behavior – the hogfish harassing the triggerfish, and sea lions and sharks startling the triggerfish – could slow the rate of triggerfish predation on pencil urchins.

The researcher who did the modeling, Mark Novak of the College of Science at Oregon State, noted that historically, ecologists believed complex food webs typical of the tropics were more immune to trophic cascades than the simpler food webs of higher latitudes; the Galapagos straddle the equator.

Studies such as this one now suggest that is not the case, and that the dynamics of complex food webs can be as predictable as simpler ones provided you understand who the relevant players are.

“When the backbone of the system is strong, you can connect the top of the food chain to the bottom despite all of the indirect effects and the complexities of the system,” said Novak, assistant professor of integrative biology.

“It’s important to know individual species identity when you’ve got a suite of consumers,” Novak said. “The hogfish, the triggerfish, they all feed on very similar things, yet one of the two is most important, the one that drove that first link. And an urchin isn’t just an urchin – one was more immune to consumption from triggerfish, the other more susceptible. And one urchin was important for grazing, and another was not.”

Merely lumping species together at trophic levels would have caused researchers to miss a lot of the subtleties that the photographic study uncovered.

“If you just put urchins out and see how quickly they disappear, you can’t attribute that to any given predator,” Novak said. “We were able to identify those species that were responsible for transmitting the cascade.”

Findings were recently published in PLOS One. The National Science Foundation supported this research.

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Triggerfish, top, and hogfish