Citizen scientists’ contributions a boon to snowpack modeling, OSU research shows

Peer-Reviewed Publication

OREGON STATE UNIVERSITY

 

IMAGE: OSU CIVIL ENGINEERING PROFESSOR DAVID HILL CHECKS SNOWPACK DEPTH. view more 

CREDIT: KENDRA SHARP, OSU

CORVALLIS, Ore. – Data gathered by backcountry skiers, avalanche forecasters and other snow recreationists and professionals has the potential to greatly improve snowpack modeling, research by the Oregon State University College of Engineering indicates.

Findings, published in the journal Hydrology and Earth System Sciences, stem from a NASA-funded project known as Community Snow Observations, or CSO, part of NASA’s Citizen Science for Earth Systems program.

The paper is the first documentation of CSO’s power to make snowpack modeling better through “organic, opportunistic” data – a notable outcome, said researcher David Hill.

“We have shown citizen scientist contributions are very valuable and that we can do great things in the absence of observational network infrastructure,” said Hill, professor of civil engineering at OSU. “In this study, we used a new data set collected by CSO participants in coastal Alaska to improve snow depth and snow-water equivalent outputs from a snow process model.”

In western North America, snow’s role in ecosystem function and water resource management is critical, the scientists say, and around the world more than a billion people live in watersheds where snow is a major component of the hydrologic system.

“Snowpack dynamics in the mountains have a big role in connecting atmospheric processes and the hydrologic cycle with downstream water users,” said Chris Cosgrove, an OSU graduate student during the research. “At our Alaska field site, hydroelectric power generation is the principal concern, but in the lower 48, many agricultural producers and municipal water systems rely on seasonal snow.”

In 2017, NASA enlisted Hill and doctoral student Ryan Crumley, as well as researchers at the University of Washington, the University of Alaska Fairbanks and the Alaska Division of Geological & Geophysical Surveys, to recruit citizen scientists and incorporate their data into computer models that generate important snowpack information for scientists, engineers and land and watershed managers.

Community Snow Observations kicked off in February 2017 and since then thousands of data entries have been made. Led by Hill, Gabe Wolken of Alaska Fairbanks and Anthony Arendt of the University of Washington, the project first focused primarily on Alaskan snowpacks. Researchers then recruited citizen scientists in the Pacific Northwest and in the Rocky Mountain region.

The work is ongoing and getting involved in Community Snow Observations is easy. A smartphone, the free Mountain Hub application and an avalanche probe with graduated markings in centimeters are the only tools needed.

As citizen scientists make their way through the mountains, they use their avalanche probes to take snow depth readings that they then upload into Mountain Hub, an app for the outdoor community.

That’s all there is to it.

“We’ve now taken our modeling work operational,” Hill said. “We serve up real-time grids on snow information at many sites across the United States, including the central Cascades in Oregon, at mountainsnow.org. The general public can go there and view real-time information on snow, snow changes and other things like satellite measurements of snow.”

In the recently published research, Hill and Crumley, who’s now at the Los Alamos National Laboratory, teamed with Wolken, Arendt, Cosgrove and OSU graduate student Christina Aragon to look at how snowpack models for the Thompson Pass region of Alaska’s Chugach Mountains improved when citizen science measurements were incorporated.

“Improvements were seen in 62% to 78% of the simulations depending on the model year,” Aragon said. “Our results suggest that even modest measurement efforts by citizen scientists have the potential to improve efforts to model snowpack processes in high mountain environments.”

Information about snow distribution reaches scientists from many sources, including telemetry stations and remote sensing via light detection and ranging, or LIDAR, but the simplicity of the citizen science data gathering approach allows for many gaps to be filled, the scientists say.

“Snow depth measurements can be made accurately and quickly by anyone with a measuring device,” Crumley said. “The potential of mobilizing a new type of data set collected by people like snowshoers and snow machiners is significant because those folks often go to remote mountain environments where so far there haven’t been many observations recorded. All of those people can gather data at scales much greater than the capacity of a small group of scientists.”

Also collaborating on this research was Katreen Jones of the Alaska Division of Geological and Geophysical Surveys.

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JOURNAL

Hydrology and Earth System Sciences

DOI

10.5194/hess-25-4651-2021 

METHOD OF RESEARCH

Computational simulation/modeling

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Assimilation of citizen science data in snowpack modeling using a new snow data set: Community Snow Observations

ARTICLE PUBLICATION DATE

31-Aug-2021

COI STATEMENT

The authors declare that they have no conflict of interest.

Project aims to improve accuracy of climate change models

Grant and Award Announcement

CORNELL UNIVERSITY

ITHACA, N.Y. - There’s broad scientific consensus that, because of climate change, the western U.S. will have less water and the northeastern U.S. will have more. But how much less and how much more is deeply uncertain, presenting a critical challenge for the scientists, policymakers and public servants tasked with ensuring the nation’s water supply.

Flavio Lehner, assistant professor of earth and atmospheric sciences at Cornell University, is working to reduce that uncertainty, by improving the climate models on which future water projections are based. Lehner won a three-year, $500,000 grant from the National Oceanic and Atmospheric Administration (NOAA) to do that work, beginning this fall.

Dan Barrie, a program manager in NOAA’s Climate Program Office, said Lehner’s work will improve NOAA’s climate models and enable the agency to make better short-term predictions of floods and droughts and better long-term projections of how surface water systems will evolve in the 21st century.

“The United States is experiencing profound changes in its regional water resources,” Barrie said. “It is more urgent than ever to have the best modeling tools to provide a vision of these future changes so that we can take cost-effective measures now to mitigate and adapt to them.”

Lehner’s research, which will improve climate modeling globally, was based on similar research he began in the Colorado River. Current estimates predict that for every degree Celsius of global warming, the Colorado River will lose between 3 to 15% of its streamflow.

Lehner compared the differences in climate models to the disparity in human reactions to COVID-19 – assessing whether an individual has COVID-19 is relatively simple, but predicting how sick the virus will make each person is much more difficult. A similar principle is at play in climate modeling, he said.

“For example, for the Colorado River, all of the numbers point in the same direction – in a warmer climate, there will be less water. But the big uncertainty is how much less,” Lehner said.

To test the sensitivity of climate models, Lehner’s group is studying 70 years of data on precipitation, temperature and streamflow, to assess how well current models would have predicted what actually happened.

“The most important question to us is: How sensitive are these models to changing environmental factors, such as changes in temperature and atmospheric greenhouse gases? And is their sensitivity consistent with what we see in reality?” he said.

The models Lehner and colleagues are using are more complicated and ultimately more useful because they take into account multiple interacting systems. Rather than just measuring rainwater or groundwater, Lehner is examining how atmospheric, terrestrial and hydrologic systems interplay, in the presence of increasing temperatures and atmospheric greenhouse gases. For example, there is now 40% more carbon dioxide in the air today than there was 100 years ago, and the earth is 1 degree Celsius warmer.  Even if precipitation remained neutral, those changes would cause plants to alter their behavior – consuming more groundwater to prevent parching, and thus leaving less to become stream runoff available to humans. But with added complexity comes added uncertainty.

“We already have a sizable uncertainty because we don’t know how much precipitation is going to change, but if you go one step further and say, how does runoff or streamflow change? The uncertainty becomes even larger,” Lehner said.

Modern climate modeling expanded dramatically in the 1980s and has provided useful and accurate information to help scientists and policymakers plan and adapt, Barrie said. Since 1980, the U.S. has experienced an average of 7.1 major weather or climate disasters per year, each causing losses of more than $1 billion. But in the past five years, the annual average of major disasters has jumped to 16.2, according to NOAA.

“Improving climate models is one step to ensuring that equitable adaptation efforts can be implemented to minimize net negative impacts on people and the economy. The cost of investments like Dr. Lehner's research project pales in comparison to the magnitude of the potential benefits,” Barrie said.

###

Waters off French coast in winter may be a deadly trap for small, foraging turtles

The movement of turtles rescued from the French coast suggests they are visiting to forage for food, but small individuals may get trapped there in colder months

Peer-Reviewed Publication

FRONTIERS

The documented habitat boundaries of the loggerhead, Kemp’s ridley and green turtles are questioned by a new study suggesting that stranded turtles rescued from European French Atlantic and Channel waters could be visiting the area to forage for food. Published in Frontiers in Marine Science, satellite tracking data reveals that while some turtles may be able to return home, after their rehabilitation and release to Florida in the US, or Cape Verde off the African coast, younger individuals are at risk of being trapped in the region.

“Stranded turtles that were tracked swimming westwards presumably towards their birth homes, after their rescue and release from the Atlantic coast of France, were older and more developed than those that remained in the Bay of Biscay region,” said Dr Philippine Chambault, first author of this study, based at the Aquarium La Rochelle, France. “Turtles that remained in the area were much smaller, possibly trapped in the winter, as they are not able to regulate their body temperature and get lethargic with decreasing sea temperatures.”

“These findings have important turtle conservation implications,” added Florence Dell'Amico, co-author of the study, who oversees the Center of Studies, and cares for the sea turtles at the Aquarium La Rochelle. “Maps of their ecological range need to be updated, and these study findings can help to plan effective rehabilitation and release strategies for turtles rescued from this area.”

Rescue and rehabilitation

The Aquarium La Rochelle has rescued and rehabilitated more than 200 turtles from the east Atlantic coast of France in the past 40 years. To ensure the turtles they were caring for had the best chance of survival after their reintroduction back into the wild, the center wanted to understand where they travelled to after their release.

“Were the turtles returning to their natal beaches or staying within the Bay of Biscay region? To find out, we glued miniaturized satellite transmitters to the shells of some rescued turtles, which would track their movements over several months,” said Dell'Amico.

“In addition, we used the Copernicus Marine Service to obtain information on the currents, water temperatures and prey abundance along turtles’ trajectories. This enabled us to link turtle movement patterns to these oceanic factors, as well as the size and mass of the turtles,” explain Dr Philippe Gaspar, co-author of the study based at Mercator Ocean, France.

Too cold for small turtles?

“The Bay of Biscay waters are especially cold during wintertime, less than 10°C, and so this area is assumed to be outside the geographical range for turtles. Our observations suggest that while the turtles could be visiting this area to forage for food, it may be an ecological trap for very small turtles that may suffer from hypothermia in the cold months,” said Gaspar. “A turtle’s body temperature is largely controlled by the temperature of the environment, and temperatures below 10oC are often lethal.”

The team hope to satellite track more turtles in the region to confirm the surprising movement patterns they observed in this study.

“Future work should also focus on genetic analysis and computerized simulations of turtle movement across oceans to compare their routes back to their birth home to their natal origin. Simulations of juvenile turtle dispersal from the beaches that they were born should also be conducted to assess the proportion of individuals that reach western Europe,” concluded Chambault.

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JOURNAL

Frontiers in Marine Science

DOI

10.3389/fmars.2021.736604 

METHOD OF RESEARCH

Observational study

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

Ecological trap or favorable habitat? First evidence that immature sea turtles may survive at their range-limits in the North-East Atlantic

ARTICLE PUBLICATION DATE

26-Oct-2021

COI STATEMENT

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

An international team of scientists, lead by researchers at UC Santa Barbara, will investigate how elephants shape their environment even after death

The nutrients from the giant mammals could be crucial to the character of the African savanna

Grant and Award Announcement

UNIVERSITY OF CALIFORNIA - SANTA BARBARA

 

IMAGE: AN ELEPHANT CARCASS IN KRUGER NATIONAL PARK. THE BARE AREA OF SOIL WAS CREATED BY CARCASS DECOMPOSITION AND DISTURBANCE FROM SCAVENGERS. view more 

CREDIT: DERON BURKEPILE

Big animals have a big impact on the environment. Whales, elephants, bison: They’re the movers and shakers of their ecosystems. But what happens when they die?

An international team of researchers, led by professors at UC Santa Barbara, will investigate how these animals’ carcasses affect their ecosystems. With a three-year grant totaling more than $1.3 million, they will survey Kruger National Park in South Africa, studying the impact of elephant carcasses on the landscape.

“People focus on the role of big animals in ecosystems for obvious reasons. But almost everybody focuses on the role these animals play while they’re alive; their role once they’re dead is really underappreciated,” said Deron Burkepile, an ecology professor at UC Santa Barbara and the project’s principal investigator.

Kruger National Park is about the area of Massachusetts, and among the largest reserves in Africa. Rangers patrol sections of the park and record elephant carcasses, marking the locations with GPS coordinates. They’ve amassed around 30 years of data so far.

In summer 2022, the research team will survey the park by helicopter with the goal of finding 50 carcasses of varying ages in areas with different rain patterns and soil regimes. They’ll begin collecting data the following year to build up their understanding of the communities and conditions around an elephant carcass.

The scientists will sample the soil for nutrients and microbial activity, the plants growing around the body, the bone from the remains themselves, and any animal scat around each site. They also plan to survey the plant and herbivore communities around the site of each carcass. The team will repeat all the surveys and sampling at a control area about 50 meters away from each carcass.

What’s more, the park staff tallies a census of the number and distribution of live elephants on a yearly basis. The scientists also have a good estimate of the animals’ annual mortality rate. With these data, the team can develop a simple model of how many carcasses there should be and where they may be clustered. They can then combine the insights from their fieldwork with the information from the census to create a model showing how elephant carcasses impact the Kruger ecosystem at the landscape scale.

In addition to the researchers at UCSB, the project will include scientists from Utah State University, Marquette University, South African National Parks, and the South African Environment Observation Network. “This research is really only possible because we’re working with people on the ground: The scientists in South Africa in Kruger National Park that have been compiling these data on elephant carcasses,” Burkepile said.

The landscape of Kruger National Park is relatively flat, and its soils are quite old. “They’ve been sitting there exposed — leaching nutrients, weathering and developing for millennia without having enough erosion to bring new resources to the surface,” explained UC Santa Barbara soil scientist Joshua Schimel, who is a co-principal investigator on the project. As a result, the soils are quite nutrient poor.

“A dead elephant is, essentially, one heaping pile of fertilizer,” he continued. In fact, it’s not too different from fortifying a garden. “Bone meal is a standard substance used as an organic fertilizer in a vegetable garden. Bloodmeal for nitrogen and bone meal for phosphorous.”

After an elephant dies, there’s a huge influx of organic carbon, nitrogen and phosphorous as a result of scavenger activity and the decomposition of soft tissues. Despite the flood of nutrients, the site of a fresh elephant carcass can be barren for some time. Scavengers rip up existing vegetation and high levels of nutrients prevent plants from reestablishing.

The influx of nitrogen is actually so intense that it likely makes the area uninhabitable for plants in the short term. “It’s just like when we put too much fertilizer on our tomatoes,” Burkepile said. “Those tomato plants burn. We imagine the same thing would be happening around really fresh elephant carcasses.”

In contrast, the carcass is a windfall for the soil microbiota. “Microbes get first dibs on almost everything,” Burkepile remarked. The researchers anticipate seeing a spike in microbial respiration as the soil bugs feast on the glut of organic carbon and nitrogen. Then, as some of the nitrogen is processed, they expect to see plants recolonize the area.

A carcass actually contains two pools of phosphorus, the researchers explained. Molecules like DNA and ATP in soft tissues will release a quick pulse of the element as the animal decays. Meanwhile, the phosphorous in teeth and bones takes much longer to break down, leading to a more sustained release.

Burkepile expects to see a surge in plant biomass three to four years after the animal’s death, with a peak around five years, once the nitrogen toxicity has declined and phosphorus has begun percolating into the soil. At this point, the process will likely begin affecting the local wildlife directly, especially herbivores.

The extra nutritious patch of land may well attract herbivores from all around, fostering a thriving community. As animals graze and hunt, eat and excrete, they spread seeds and aggregate nutrients from other parts of the savannah. This could then create a feedback loop where elephants frequent these spots to feed, potentially fostering these patches when they ultimately die, Schimel proposed.

As Burkepile put it: “The legacies of these animals don’t stop when they die.”

'I’m melting, melting' — environmentally hazardous coal waste diminished by harmless citric acid

Sandia innovation frees rare-earth metals from coal ash for smartphones, computers

Business Announcement

DOE/SANDIA NATIONAL LABORATORIES

 

IMAGE: A COMPARISON OF SANDIA NATIONAL LABORATORIES METHOD FOR EXTRACTING RARE-EARTH METALS TO EXISTING METHODS SHOWS HOW USING CITRIC ACID IS MORE EFFICIENT. view more 

CREDIT: (IMAGES COURTESY OF GUANGPING XU

In one of nature’s unexpected bounties, a harmless food-grade solvent has been used to extract highly sought rare-earth metals from coal ash, reducing the amount of ash without damaging the environment and at the same time increasing an important national resource.

Coal ash is the unwanted but widely present residue of coal-fired power. Rare-earth metals are used for a variety of high-tech equipment from smartphones to submarines.

The separation method, which uses carbon dioxide, water and food-grade citric acid, is the subject of a Sandia National Laboratories patent application.

“This technique not only recovers rare-earth metals in an environmentally harmless manner but would actually improve environments by reducing the toxicity of coal waste dotting America,” said Guangping Xu, lead Sandia researcher on the project.

“Harmless extraction of rare-earth metals from coal ash not only provides a national source of materials essential for computer chips, smart phones and other high-tech products — including fighter jets and submarines — but also makes the coal ash cleaner and less toxic, enabling its direct reuse as concrete filler or agricultural topsoil,” he said.

The method, if widely adopted, could make coal ash, currently an environmental pariah, into a commercially viable product, Xu said.

Environmentally friendly method for mining rare-earth metals

The most common acids used as chemical separators in mining — nitric, sulfuric or phosphoric acids — also are able to extract rare-earth metals from coal ash but produce large amounts of acid waste, leaving the environment in worse shape than before, Xu said. “Environmentally harmful acids would raise clean-up costs beyond economic feasibility in the United States.”

The Sandia process, which uses citric acid as a carrier for rare-earth metals, so they separate from coal ash, the host material, was implemented by Xu. The extraction process is facilitated by using supercritical carbon dioxide solvent. Xu’s Sandia colleague Yongliang Xiong suggested citric acid, a commonly used and environmentally friendly chemical for holding metals in solution.

Xu found that in less than a day, at 158 degrees Fahrenheit (70 degrees Celsius) and 1,100 pounds per square inch pressure (about 70 times ordinary atmospheric pressure), the method extracted 42% of rare-earth metals present in coal waste samples.

Chinese mines, where 95% of the world’s resources of rare-earth metals are located, achieve less efficient separation while using environmentally damaging methods.

“Theoretically, an American company could use this technique to mine coal and coal byproducts for rare-earth metals and compete with Chinese mining,” said Xu. Furthermore, for U.S. national security purposes “it is probably reasonable to have alternate sources of rare-earth metals to avoid being at the mercy of a foreign supply.”

Detoxifying coal ash for reuse alone should be worth the effort, Xu said. There’s no shortage of coal ash as a raw material. According to a paper published in 2016 in the journal Environmental Science & Technology, “Approximately 115 million metric tons of coal combustion products are generated annually, and this sum includes 45 million tons of fly ash,” the lightest kind of coal ash.

These numbers remain of interest today, said Xu.

“If we don’t detoxify and reuse the coal ash, then it will be abandoned in ponds and landfills and cost billions of dollars to clean up over the long term,” he said. To help make that outcome less likely, “We expect tests of our extraction techniques at larger volumes and on a variety of coal-based sources in the near future.”  

 

CAPTION

Sandia National Laboratories researcher Guangping Xu adds coal ash into a citric acid mixture. This solution will be fed into a reactor — operating at about 70 times atmospheric pressure — where supercritical carbon dioxide aids citric acid in extracting rare-earth metals.

CREDIT

Rebecca Lynne Gustaf

Carbon sequestration also a possibility

This technology also could open a new avenue for carbon-dioxide reutilization and sequestration, said Xu’s Sandia colleague Mark Rigali, who with Xu is exploring the use of citric acid and supercritical carbon dioxide to mine metals from oil and gas shales that are often rich in metals.

“Using existing oil and gas fracking wells, the citric acid and supercritical carbon dioxide can be used cost-effectively to mine metals while disposing of carbon dioxide below ground,” Rigali said.

Subsurface storage of the carbon dioxide should keep it from entering the atmosphere and contributing to climate change, Rigali said.

The work is supported by Sandia’s Laboratory Directed Research and Development program.

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Sandia National Laboratories is a multimission laboratory operated by National Technology and Engineering Solutions of Sandia LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration. Sandia Labs has major research and development responsibilities in nuclear deterrence, global security, defense, energy technologies and economic competitiveness, with main facilities in Albuquerque, New Mexico, and Livermore, California.

Scientists reveal genetic secrets of stress-tolerant mangrove trees

Mangrove trees use changes in gene activity, including the activity of parasitic ‘jumping genes’, to increase their resilience to stress, a new study finds.

Peer-Reviewed Publication

OKINAWA INSTITUTE OF SCIENCE AND TECHNOLOGY (OIST) GRADUATE UNIVERSITY

 

IMAGE: (LEFT) MANGROVE TREES GROWING NEAR THE OCEAN EXPERIENCE HIGH LEVELS OF SALINITY AND ARE SMALL IN STATURE. (RIGHT) MANGROVE TREES GROWING UPRIVER HAVE LESS SALINE, BRACKISH CONDITIONS AND GROW TALLER, WITH THICKER TRUNKS AND LARGER LEAVES. THESE TREES WERE SURVEYED BY DR. MATIN MIRYEGANEH (PICTURED) AND HER COLLEAGUES, AS PART OF A NEW STUDY FEATURED IN THE PRESS RELEASE, “SCIENTISTS REVEAL GENETIC SECRETS OF STRESS-TOLERANT MANGROVE TREES.” view more 

CREDIT: OIST

• Mangrove trees live in harsh environments and have evolved a remarkable resilience to stres
• Researchers have now decoded the genome of the mangrove tree, Bruguiera gymnorhiza, which contains 309 million base pairs with an estimated 34,403 genes
• The genome is larger than other known mangrove trees, with a quarter of the genome composed of parasite ‘jumping genes’ called transposons
• The researchers also compared gene activity between mangrove trees grown in environments with high salinity to those grown in conditions with low salinity
• Mangrove trees grown in more stressful, high saline conditions suppressed the activity of the transposons and increased the activity of stress-response genes

Mangrove trees straddle the boundary between land and ocean, in harsh environments characterized by rapidly changing levels of salinity and low oxygen. For most plants, these conditions would mark a death sentence, but mangroves have evolved a remarkable resistance to the stresses of these hostile locations.

Now, researchers from the Okinawa Institute of Science and Technology Graduate University (OIST) have decoded the genome of the mangrove tree, Bruguiera gymnorhiza, and revealed how this species regulates its genes in order to cope with stress. Their findings, published recently in New Phytologist, could one day be used to help other plants be more tolerant to stress.

“Mangroves are an ideal model system for studying the molecular mechanism behind stress tolerance, as they naturally cope with various stress factors,” said Dr. Matin Miryeganeh, first author of the study and a researcher in the Plant Epigenetics Unit at OIST.

Mangroves are an important ecosystem for the planet, protecting coastlines from erosion, filtering out pollutants from water and serving as a nursery for fish and other species that support coastal livelihoods. They also play a crucial role in combating global warming, storing up to four times as much carbon in a given area as a rainforest.

Despite their importance, mangroves are being deforested at an unprecedented rate, and due to human pressure and rising seas, are forecast to disappear in as little as 100 years. And genomic resources that could help scientists try to conserve these ecosystems have so far been limited.

The mangrove project, which was initially suggested by Sydney Brenner, one of the founding fathers of OIST, began in 2016, with a survey of mangrove trees in Okinawa. The scientists noticed that the mangrove tree, Bruguiera gymnorhiza, showed striking differences between individuals rooted in the oceanside, with high salinity, and those in the upper riverside, where the waters were more brackish.

“The trees were amazingly different; near the ocean, the height of the trees was about one to two meters, whereas further up the river, the trees grew as high as seven meters,” said senior author, Professor Hidetoshi Saze, who leads the Plant Epigenetics Unit. “But the shorter trees were not unhealthy – they flowered and fruited normally – so we think this modification is adaptive, perhaps allowing the salt-stressed plant to invest more resources into coping with its harsh environment.”

Unlike long-term evolutionary adaptation, which involves changes to the genetic sequence, adaptations to the environment that take place over an organism’s lifespan occur via epigenetic changes. These are chemical modifications to DNA that affect the activity of different genes, adjusting how the genome responds to different environmental stimuli and stresses. Organisms like plants, which can’t move to a more comfortable environment, rely heavily on epigenetic changes to survive.

Before focusing in on how the genome was regulated, the research team first extracted DNA from the mangrove tree, Bruguiera gymnorhiza, and decoded the genome for this species. They found that the genome contained 309 million base pairs, with a predicted 34,403 genes – a much larger genome than those for other known mangrove tree species. The large size was due to, for the most part, almost half of the DNA being made up of repeating sequences.

When the research team examined the type of repetitive DNA, they found that over a quarter of the genome consisted of genetic elements called transposons, or ‘jumping genes.’

Prof. Saze explained: “Active transposons are parasitic genes that can ‘jump’ position within the genome, like cut-and paste or copy-and-paste computer functions. As more copies of themselves are inserted into the genome, repetitive DNA can build up.”

Transposons are a big driver of genome evolution, introducing genetic diversity, but they are a double-edged sword. Disruptions to the genome through the movement of transposons are more likely to cause harm than provide a benefit, particularly when a plant is already stressed, so mangrove trees generally have smaller genomes than other plants, with suppressed transposons.

However, this isn’t the case for Bruguiera gymnorhiza, with the scientists speculating that as this mangrove species is more ancestral than others, it may not have evolved to have an efficient means of suppression.

CAPTION

Researchers from the OIST Plant Epigenetics Unit grew mangrove trees under controlled conditions in the laboratory to see the effect of different salinity levels. Their findings were part of a new study featured in the press release “Scientists reveal genetic secrets of stress-tolerant mangrove trees.”

CREDIT

OIST

The team then examined how activity of the genes, including the transposons, varied between individuals in the oceanside location with high salinity, and individuals in the less saline, brackish waters upriver. They also compared gene activity for mangrove trees grown in the lab, under two different conditions that replicated the oceanside and upriver salinity levels.

Overall, in both the oceanside individuals and those grown in high salinity conditions in the lab, genes involved in suppressing transposon activity showed higher expression, while genes that normally promote transposon activity showed lower expression. In addition, when the team looked specifically into transposons, they found evidence of chemical modifications on their DNA that lowered their activity.

“This shows that an important means of coping with saline stress involves silencing transposons,” said Dr. Miryeganeh.

The researchers also saw increases in the activity of genes involved in stress responses in plants, including those that activate when plants are water-deprived. Gene activity also suggested the stressed plants have lower levels of photosynthesis.

In future research, the team plan to study how seasons, changes in temperature and rainfall, also affect the activity of the mangrove tree genomes.

“This study acts as a foundation, providing new insights into how mangrove trees regulate their genome in response to extreme stresses,” said Prof. Saze. “More research is needed to understand how these changes in gene activity impact molecular processes within the plant cells and tissues and could one day help scientists create new plant strains that can better cope with stress.”

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JOURNAL

New Phytologist

DOI

10.1111/nph.17738 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

De novo genome assembly and in natura epigenomics reveal salinity-induced DNA methylation in the mangrove tree Bruguiera gymnorhiza

ARTICLE PUBLICATION DATE

16-Sep-2021

Tiny microscopic hunters could be a crystal ball for climate change

Simple measurements of these obscure organisms can help predict future CO2 emissions for warming ecosystems, study finds

Peer-Reviewed Publication

DUKE UNIVERSITY

 

IMAGE: SCIENTISTS SAY A FEW SIMPLE MEASURES OF A PROTIST’S CELL SIZE AND SHAPE CAN BE POWERFUL PREDICTORS OF HOW THEY MIGHT RESPOND TO GLOBAL WARMING. view more 

CREDIT: COURTESY OF DAN WIECZYNSKI.

DURHAM, N.C. -- It’s hard to know what climate change will mean for Earth’s interconnected and interdependent webs of life. But one team of researchers at Duke University says we might begin to get a glimpse of the future from just a few ounces of microbial soup.

Every drop of pond water and teaspoon of soil is teeming with tens of thousands of tiny unicellular creatures called protists. They’re so abundant that they are estimated to weigh twice as much as all the animals on Earth combined.

Neither animals nor plants nor fungi, the more than 200,000 known species of protists are often overlooked. But as temperatures warm, they could play a big role in buffering the effects of climate change, said Jean Philippe Gibert, an assistant professor of biology at Duke.

That’s because of what protists like to eat. They gobble up bacteria, which release carbon dioxide into the air when they respire, just like we do when we breathe out. But because bacteria account for more of the planet's biomass than any other living thing besides plants, they are among the largest natural emitters of carbon dioxide — the greenhouse gas most responsible for global warming.

In a study published Oct. 19 in Proceedings of the National Academy of Sciences, Gibert, postdoctoral researcher Dan Wieczynski and colleagues tested the effects of warming on bacteria-eating protists by creating mini ecosystems -- glass flasks each containing 10 different species of protists going about the business of eating and competing and reproducing.

The flasks were kept at five temperatures ranging from 60 degrees to 95 degrees Fahrenheit. Two weeks later, the researchers looked to see which species had survived at each temperature and measured how much CO2 they gave off during respiration.

“To me, the question was a simple one in nature,” Gibert said. “Is there something to be measured on living organisms, today, that may allow us to predict their response to increasing temperature, tomorrow?”

The answer was yes. The researchers were surprised to find that each species’ response to temperature could be predicted from just a few simple measurements of their size, shape and cell contents. And together, these factors in turn influenced respiration rates for the community as a whole.

They also found that by taking measurements such as cell size and shape and plugging them into a mathematical model, they could get very close to how things played out in their mini ecosystems in reality.

“We can actually use what we know about the relationship between traits and temperature responses at the species level, and scale it all the way up to a whole ecosystem level,” Wieczynski said.

The work is important because it sheds light on “how climate change will alter microbial communities and how this will feed back to influence the pace of climate change,” Wieczynski said.

This research was supported by a grant from the U.S. Department of Energy (DE-SC0020362).

CITATION: “Linking Species Traits and Demography to Explain Complex Temperature Responses Across Levels of Organization," Daniel J. Wieczynski, Pranav Singla, Adrian Doan, Alexandra Singleton, Zeyi Han, Samantha Votzke, Andrea Yammine, Jean P. Gibert. Proceedings of the National Academy of Sciences, Oct. 19, 2021. DOI:  10.1073/pnas.2104863118

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JOURNAL

Proceedings of the National Academy of Sciences

DOI

10.1073/pnas.2104863118 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Cells

ARTICLE TITLE

Linking Species Traits and Demography to Explain Complex Temperature Responses Across Levels of Organization

ARTICLE PUBLICATION DATE

19-Oct-2021

That primate’s got rhythm!

Peer-Reviewed Publication

MAX PLANCK INSTITUTE FOR PSYCHOLINGUISTICS

 

VIDEO: RESEARCHERS FROM THE UNIVERSITIES OF TURIN, LYON/SAINT-ÉTIENNE AND THE MAX PLANCK INSTITUTE FOR PSYCHOLINGUISTICS IN NIJMEGEN STUDIED INDRIS, THE ‘SINGING PRIMATES’ FROM MADAGASCAR view more 

CREDIT: ANDREA RAVIGNANI

Songbirds share the human sense of rhythm, but it is a rare trait in non-human mammals. An international research team led by senior investigators Marco Gamba from the University of Turin and MPI’s Andrea Ravignani set out to look for musical abilities in primates. “There is longstanding interest in understanding how human musicality evolved, but musicality is not restricted to humans”, says Ravignani. “Looking for musical features in other species allows us to build an ‘evolutionary tree’ of musical traits, and understand how rhythm capacities originated and evolved in humans.”

To find out whether non-human mammals have a sense of rhythm, the team decided to study one of the few ‘singing’ primates, the critically endangered lemur Indri indri. The researchers wanted to know whether indri songs have categorical rhythm, a ‘rhythmic universal’ found across human musical cultures. Rhythm is categorical when intervals between sounds have exactly the same duration (1:1 rhythm) or doubled duration (1:2 rhythm). This type of rhythm makes a song easily recognisable, even if it is sung at different speeds. Would indri songs show this “uniquely human” rhythm?

CAPTION

Indri songs recorded in the wild have rhythmic categories similar to those found in human music.

CREDIT

Filippo Carugati

Ritardando in the rainforest

Over a period of twelve years, the researchers from Turin visited the rainforest of Madagascar to collaborate with a local primate study group. The investigators recorded songs from twenty indri groups (39 animals), living in their natural habitat. Members of an indri family group tend to sing together, in harmonised duets and choruses. The team found that indri songs had the classic rhythmic categories (both 1:1 and 1:2), as well as the typical ‘ritardando’ or slowing down found in several musical traditions. Male and female songs had a different tempo but showed the same rhythm.

According to first author Chiara de Gregorio and her colleagues, this is the first evidence of a ‘rhythmic universal’ in a non-human mammal. But why should another primate produce categorical ‘music-like’ rhythms? The ability may have evolved independently among ‘singing’ species, as the last common ancestor between humans and indri lived 77.5 million years ago. Rhythm may make it easier to produce and process songs, or even to learn them.

CAPTION

Finding common musical traits across species may shed light on the biology and evolution of rhythm and music.

CREDIT

Filippo Carugati

Endangered species

“Categorical rhythms are just one of the six universals that have been identified so far”, explains Ravignani. “We would like to look for evidence of others, including an underlying ‘repetitive’ beat and a hierarchical organisation of beats—in indri and other species.” The authors encourage other researchers to gather data on indri and other endangered species, “before it is too late to witness their breath-taking singing displays.”

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JOURNAL

Current Biology

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

Categorical rhythms in a singing primate

ARTICLE PUBLICATION DATE

25-Oct-2021