Building a Better Weather Forecast? SMAP May Help

SMAP's soil moisture measurements will help with forecasts of precipitation and temperature. Image credit: UCAR

If you were trying to forecast tomorrow's weather, you would probably look up at the sky rather than down at the ground. But if you live in the U.S. Midwest or someplace with a similar climate, one key to a better weather forecast may lie beneath your feet.

Precipitation and temperature are part of every weather forecast. Precipitation comes from clouds, clouds are formed of airborne water vapor, and vapor comes from evaporating soil moisture -- so soil moisture governs precipitation. Evaporating soil moisture also makes air cooler, so it affects temperature. In certain kinds of climate, scientists believe, soil moisture is so influential that better observations of it might improve weather forecasts. These climates are transitional: not too humid and not too dry. For example, the agriculturally productive states of the U.S. Midwest fall into that category.

"Better soil moisture observations lead to better land-atmosphere interaction in weather forecasting models and ultimately to a better prediction of temperature and precipitation," said Michael Ek, leader of the Land Hydrology Team at the Environmental Monitoring Center of the National Oceanic and Atmospheric Administration (NOAA). "Weather models need good initial observations of the land surface, or you're starting from the wrong place."

Better soil moisture observations are just what the Soil Moisture Active Passive (SMAP) mission will provide. Scheduled for launch on Jan. 29, SMAP will collect the most accurate and highest-resolution soil moisture measurements ever made from a satellite SMAP will cover the entire globe in two to three days. Ek is a member of one of five groups in SMAP's Early Adopter program that have been working for several years on the question of how best to incorporate the new data into national weather forecasting models.

Forecasts will not improve, however, the moment SMAP starts collecting data. U.S. Department of Agriculture research scientist Wade Crow, a member of SMAP's science team, explained that, since closely spaced global soil moisture measurements have never existed before, the mathematical models used in weather forecasting are not configured to include them directly. Getting the best use out of the new observations has been a subject of active research for several years and will require some significant changes in how soil moisture data are assimilated into the models.

Data assimilation is necessary because weather forecasting models all drift a bit, like cars. If you're driving on a perfectly straight road, you still need to keep a hand on the steering wheel or you'll run off the edge sooner or later. Data assimilation in a model serves the same purpose as the slight movements of your hands that keep your car on course.

Drift is not a fatal flaw for a weather forecasting model any more than it is for a car. It is simply a sign that the Earth system is too vast and complicated to model perfectly with the resources available today. To steer forecasts toward greater realism, models ingest, or assimilate, real-world data and use them in sophisticated mathematical techniques. Each time updated observations become available, they are assimilated to improve the starting point for the next forecast.

Closely spaced and highly accurate global measurements are an important part of the process. For soil moisture, however, current observations are not on a fine enough scale to meet the needs of weather forecasting models directly. "Modelers compensate for the lack of direct observations of soil moisture by using more indirect measures, such as estimating it from observations of temperature and precipitation," Crow explained. "As a consequence, modeled soil moisture tends to diverge from reality. SMAP will be directly observing the state that they want, so they won't have to back it out from proxy measurements."

JPL scientist Eni Njoku is working with researchers at another forecasting center, the European Centre for Medium-Range Weather Forecasts (ECMWF) in Reading, England. Njoku said, "SMAP will provide benefits of higher soil moisture accuracy and spatial resolution than have previously been available from satellites. This could lead potentially to improved regional and global weather forecasts by ECMWF." Environment Canada, the branch of the Canadian government responsible for weather forecasting in that nation, is also working on assimilating SMAP data into its models.

"The numerical weather prediction centers are adapting to the new availability of soil moisture information and thinking of ways they can exploit it," Crow summarized. "It will be really exciting to see what they find."

SMAP is managed for NASA's Science Mission Directorate in Washington by the agency's Jet Propulsion Laboratory in Pasadena, California, with instrument hardware and science contributions made by NASA's Goddard Space Flight Center in Greenbelt, Maryland. JPL is responsible for project management, system engineering, radar instrumentation, mission operations and the ground data system. Goddard is responsible for the radiometer instrument. Both centers collaborate on science data processing and delivery to the Alaska Satellite Facility, in Fairbanks, and the National Snow and Ice Data Center, at the University of Colorado in Boulder, for public distribution and archiving. NASA's Launch Services Program at the agency's Kennedy Space Center in Florida is responsible for launch management. JPL is managed for NASA by the California Institute of Technology in Pasadena.

Source: Nasa

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Scientists call for soil mapping program to help Indian agriculture

Delegates to the University's agriculture workshop at Kharagpur

Scientists attending an agriculture workshop in India organised by the University of Sydney have called for a detailed soil mapping program to help policy makers and farmers draw up effective land management proposals.

The Soil and Water National Networking Workshop, organised jointly with the Indian Institute of Technology at Kharagpur, involved 40 scientists from India and Australia.

They discussed key issues including soil security, digital soil mapping, India's participation in the Global Soil Map project, national level spectral libraries, soil data requirement in crop simulations, soil health mapping, hydrological model behaviour, and using soil digital and satellite data for hydrologic models.

A number of speakers urged India to participate in the Global Soil Map and accelerate the provision of fine scale information on soil fertility and conditions in India. The information could also be used to monitor and understand the change over time in soil nutrients.

The workshop's soil group was led by Professor Budiman Minasny, Professor Bhabani Das and Dr Kanika Singh from the University of Sydney. The hydrology group was led by A/Professor Willem Vervoort from Sydney, Dr Rajib Maity and Mr Dipangkar Kundu.

The workshop was launched with a welcome video by Professor Alex McBratney, the Dokuchaev award winner in Soil Science, who is actively involved with the Global Soil Map.

Dr Singh said: "The workshop was a great success; the Indian scientists showcased high quality research and are open to future collaboration in the Global Soil Map effort.

"The director of IIT Kharagpur in his speech talked about a joint collaboration between India and Australia for a comprehensive digitisation of soil information contributing to soil security and sustainable productivity. The Assistant Director General of the Indian Council of Agricultural Research is also keen to developIndian collaboration in the Global Soil Map effort.

"We look forward to long-term collaboration with IIT Kharagpur and other such organisations in India to achieve collaborative research."

The workshop was sponsored by the Australia-India Council.

Contact: Richard North
Phone: 02 9351 3191
Email: richard.north@sydney.edu.au

 Source: THE UNIVERSITY OF SYDNEY

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Body weight heavily influenced by gut microbes: Genes shape body weight by affecting gut microbes

Body sizes (stock image). New research shows that our genetic makeup influences whether we are fat or thin by shaping which types of microbes thrive in our body. Credit: © olly / Fotolia

Our genetic makeup influences whether we are fat or thin by shaping which types of microbes thrive in our body, according to a study by researchers at King's College London and Cornell University.

By studying pairs of twins at King's Department of Twin Research, researchers identified a specific, little known bacterial family that is highly heritable and more common in individuals with low body weight. This microbe also protected against weight gain when transplanted into mice.

The results, published today in the journal Cell, could pave the way for personalised probiotic therapies that are optimised to reduce the risk of obesity-related diseases based on an individual's genetic make-up.

Previous research has linked both genetic variation and the composition of gut microbes to metabolic disease and obesity. Despite these shared effects, the relationship between human genetic variation and the diversity of gut microbes was presumed to be negligible.

In the study, funded by National Institutes of Health (NIH), researchers sequenced the genes of microbes found in more than 1,000 fecal samples from 416 pairs of twins. The abundances of specific types of microbes were found to be more similar in identical twins, who share 100 per cent of their genes, than in non-identical twins, who share on average only half of the genes that vary between people. These findings demonstrate that genes influence the composition of gut microbes.

The type of bacteria whose abundance was most heavily influenced by host genetics was a recently identified family called 'Christensenellaceae'. Members of this health-promoting bacterial family were more abundant in individuals with a low body weight than in obese individuals. Moreover, mice that were treated with this microbe gained less weight than untreated mice, suggesting that increasing the amounts of this microbe may help to prevent or reduce obesity.

Professor Tim Spector, Head of the Department of Twin Research and Genetic Epidemiology at King's College London, said: 'Our findings show that specific groups of microbes living in our gut could be protective against obesity -- and that their abundance is influenced by our genes. The human microbiome represents an exciting new target for dietary changes and treatments aimed at combating obesity.

'Twins have been incredibly valuable in uncovering these links -- but we now want to promote the use of microbiome testing more widely in the UK through the British Gut Project. This is a crowd-sourcing experiment that allows anyone with an interest in their diet and health to have their personal microbes tested genetically using a simple postal kit and a small donation via our website (www.britishgut.org). We want thousands to join up so we can continue to make major discoveries about the links between our gut and our health.'

Ruth Ley, Associate Professor at Cornell University in the United States, said: 'Up until now, variation in the abundances of gut microbes has been explained by diet, the environment, lifestyle, and health. This is the first study to firmly establish that certain types of gut microbes are heritable -- that their variation across a population is in part due to host genotype variation, not just environmental influences. These results will also help us find new predictors of disease and aid prevention.'

Source: King's College London

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NASA Goddard instrument makes first detection of organic matter on Mars

MSL Curiosity rover at "John Klein" drill site. This self-portrait of NASA's Mars rover Curiosity combines dozens of exposures taken by the rover's Mars Hand Lens Imager on Feb. 3, 2013 plus three exposures taken May 10, 2013 to show two holes (in lower left quadrant) where Curiosity used its drill on the rock target "John Klein". Credit: NASA/JPL-Caltech/MSSS

The team responsible for the Sample Analysis at Mars (SAM) instrument suite on NASA's Curiosity rover has made the first definitive detection of organic molecules at Mars. Organic molecules are the building blocks of all known forms of terrestrial life, and consist of a wide variety of molecules made primarily of carbon, hydrogen, and oxygen atoms. However, organic molecules can also be made by chemical reactions that don't involve life, and there is not enough evidence to tell if the matter found by the team came from ancient Martian life or from a non-biological process. Examples of non-biological sources include chemical reactions in water at ancient Martian hot springs or delivery of organic material to Mars by interplanetary dust or fragments of asteroids and comets.

The surface of Mars is currently inhospitable to life as we know it, but there is evidence that the Red Planet once had a climate that could have supported life billions of years ago. For example, features resembling dry riverbeds and minerals that only form in the presence of liquid water have been discovered on the Martian surface. The Curiosity rover with its suite of instruments including SAM was sent to Mars in 2011 to discover more about the ancient habitable Martian environment by examining clues in the chemistry of rocks and the atmosphere.

The organic molecules found by the team were in a drilled sample of the Sheepbed mudstone in Gale crater, the landing site for the Curiosity rover. Scientists think the crater was once the site of a lake billions of years ago, and rocks like mudstone formed from sediment in the lake. Moreover, this mudstone was found to contain 20 percent smectite clays. On Earth, such clays are known to provide high surface area and optimal interlayer sites for the concentration and preservation of organic compounds when rapidly deposited under reducing chemical conditions.

While the team can't conclude that there was life at Gale crater, the discovery shows that the ancient environment offered a supply of reduced organic molecules for use as building blocks for life and an energy source for life. Curiosity's earlier analysis of this same mudstone revealed that the environment offered water and chemical elements essential for life and a different chemical energy source.

"We think life began on Earth around 3.8 billion years ago, and our result shows that places on Mars had the same conditions at that time -- liquid water, a warm environment, and organic matter," said Caroline Freissinet of NASA's Goddard Space Flight Center in Greenbelt, Maryland. "So if life emerged on Earth in these conditions, why not on Mars as well?" Freissinet is lead author of a paper on this research submitted to the Journal of Geophysical Research-Planets.

The organic molecules found by the team also have chlorine atoms, and include chlorobenzene and several dichloroalkanes, such as dichloroethane, dichloropropane and dichlorobutane. Chlorobenzene is the most abundant with concentrations between 150 and 300 parts-per-billion. Chlorobenzene is not a naturally occurring compound on Earth. It is used in the manufacturing process for pesticides (insecticide DDT), herbicides, adhesives, paints and rubber. Dichloropropane is used as an industrial solvent to make paint strippers, varnishes and furniture finish removers, and is classified as a carcinogen.

It's possible that these chlorine-containing organic molecules were present as such in the mudstone. However, according to the team, it's more likely that a different suite of precursor organic molecules was in the mudstone, and that the chlorinated organics formed from reactions inside the SAM instrument as the sample was heated for analysis. Perchlorates (a chlorine atom bound to four oxygen atoms) are abundant on the surface of Mars. It's possible that as the sample was heated, chlorine from perchlorate combined with fragments from precursor organic molecules in the mudstone to produce the chlorinated organic molecules detected by SAM.

In 1976, the Gas Chromatograph Mass Spectrometer instrument on NASA's Viking landers detected two simple chlorinated hydrocarbons after heating Martian soils for analysis (chloromethane and dichloromethane). However they were not able to rule out that the compounds were derived from the instrument itself, according to the team. While sources within the SAM instrument also produce chlorinated hydrocarbons, they don't make more than 22 parts-per-billion of chlorobenzene, far below the amounts detected in the mudstone sample, giving the team confidence that organic molecules really are present on Mars.

The SAM instrument suite was built at NASA Goddard with significant elements provided by industry, university, and national and international NASA partners.

For this analysis, the Curiosity rover sample acquisition system drilled into a mudstone and filtered fine particles of it through a sieve, then delivered a portion of the sample to the SAM laboratory. SAM detected the compounds using its Evolved Gas Analysis (EGA) mode by heating the sample up to about 875 degrees Celsius (around 1,600 degrees Fahrenheit) and then monitoring the volatiles released from the sample using a quadrupole mass spectrometer, which identifies molecules by their mass using electric fields. SAM also detected and identified the compounds using its Gas Chromatograph Mass Spectrometer (GCMS) mode. In this mode, volatiles are separated by the amount of time they take to travel through a narrow tube (gas chromatography -- certain molecules interact with the sides of the tube more readily and thus travel more slowly) and then identified by their signature mass fragments in the mass spectrometer.

The first evidence for elevated levels of chlorobenzene and dichloroalkanes released from the mudstone was obtained on Curiosity Sol 290 (May 30, 2013) with the third analysis of the Cumberland sample at Sheepbed. The team spent over a year carefully analyzing the result, including conducting laboratory experiments with instruments and methods similar to SAM, to be sure that SAM could not be producing the amount of organic material detected.

"The search for organics on Mars has been extremely challenging for the team," said Daniel Glavin of NASA Goddard, a co-author on the paper. "First, we need to identify environments in Gale crater that would have enabled the concentration of organics in sediments. Then they need to survive the conversion of sediment to rock, where pore fluids and dissolved substances may oxidize and destroy organics. Organics can then be destroyed during exposure of rocks at the surface of Mars to intense ionizing radiation and oxidants. Finally, to identify any organic compounds that have survived, we have to deal with oxychlorine compounds and possibly other strong oxidants in the sample which will react with and combust organic compounds to carbon dioxide and chlorinated hydrocarbons when the samples are heated by SAM."

As part of Curiosity's plan for exploration, an important strategic goal was to sample rocks that represent different combinations of the variables thought to control organic preservation. "The SAM and Mars Science Laboratory teams have worked very hard to achieve this result," said John Grotzinger of Caltech, Mars Science Laboratory's Project Scientist. "Only by drilling additional rock samples in different locations, and representing different geologic histories were we able to tease out this result. At the time we first saw evidence of these organic molecules in the Cumberland sample it was uncertain if they were derived from Mars, however, additional drilling has not produced the same compounds as might be predicted for contamination, indicating that the carbon in the detected organic molecules is very likely of Martian origin."

Source: nasa

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Martian meteorite yields more evidence of the possibility of life on Mars

Is there, or was there once, life on Mars? Credit: NASA/JPL/MSSS

A tiny fragment of Martian meteorite 1.3 billion years old is helping to make the case for the possibility of life on Mars, say scientists.

The finding of a 'cell-like' structure, which investigators now know once held water, came about as a result of collaboration between scientists in the UK and Greece. Their findings are published in the latest edition of the journal Astrobiology.

While investigating the Martian meteorite, known as Nakhla, Dr Elias Chatzitheodoridis of the National Technical University of Athens found an unusual feature embedded deep within the rock. In a bid to understand what it might be, he teamed up with long-time friend and collaborator Professor Ian Lyon at the University of Manchester.

Professor Lyon, based in Manchester's School of Earth, Atmospheric and Environmental Sciences explains: "In many ways it resembled a fossilized biological cell from Earth but it was intriguing because it was undoubtedly from Mars. Our research found that it probably wasn't a cell but that it did once hold water, water that had been heated, probably as a result of an asteroid impact."

These findings are significant because they add to increasing evidence that beneath the surface, Mars does provide all the conditions for life to have formed and evolved. It also adds to a body of evidence suggesting that large asteroids hit Mars in the past and produce long-lasting hydrothermal fields that could sustain life on Mars, even in later epochs, if life ever emerged there.

As part of the research, the feature was imaged in unprecedented detail by Dr Sarah Haigh of The University of Manchester whose work usually involves high resolution imaging for next generation electronic devices ,which are made by stacking together single atomic layers of graphene and other materials with the aim of making faster, lighter and bendable mobile phones and tablets. A similar imaging approach was able to reveal the atomic layers of materials inside the meteorite.

Together their combined experimental approach has revealed new insights into the geological origins of this fascinating structure.

Professor Lyon said: "We have been able to show the setting is there to provide life. It's not too cold, it's not too harsh. Life as we know it, in the form of bacteria, for example, could be there, although we haven't found it yet. It's about piecing together the case for life on Mars -- it may have existed and in some form could exist still."

Now, the team is using these and other state-of-the-art techniques to investigate new secondary materials in this meteorite and search for possible bio signatures which provide scientific evidence of life, past or present. Professor Lyon concluded: "Before we return samples from Mars, we must examine them further, but in more delicate ways. We must carefully search for further evidence."

Source: Manchester University

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Earth-like soils on Mars? Ancient fossilized soils potentially found deep inside impact crater suggest microbial life

Rover image from Gale Crater reveals soil features similar to paleosols on Earth. Credit: NASA

Soil deep in a crater dating to some 3.7 billion years ago contains evidence that Mars was once much warmer and wetter, saysUniversity of Oregon geologist Gregory Retallack, based on images and data captured by the rover Curiosity.

NASA rovers have shown Martian landscapes littered with loose rocks from impacts or layered by catastrophic floods, rather than the smooth contours of soils that soften landscapes on Earth. However, recent images from Curiosity from the impact Gale Crater, Retallack said, reveal Earth-like soil profiles with cracked surfaces lined with sulfate, ellipsoidal hollows and concentrations of sulfate comparable with soils in Antarctic Dry Valleys and Chile's Atacama Desert.

His analyses appear in a paper placed online this week by the journal Geology in advance of print in the September issue of the world's top-ranked journal in the field. Retallack, the paper's lone author, studied mineral and chemical data published by researchers closely tied with the Curiosity mission. Retallack, professor of geological sciences and co-director of paleontology research at the UO Museum of Natural and Cultural History, is an internationally known expert on the recognition of paleosols -- ancient fossilized soils contained in rocks.

"The pictures were the first clue, but then all the data really nailed it," Retallack said. "The key to this discovery has been the superb chemical and mineral analytical capability of the Curiosity Rover, which is an order of magnitude improvement over earlier generations of rovers. The new data show clear chemical weathering trends, and clay accumulation at the expense of the mineral olivine, as expected in soils on Earth. Phosphorus depletion within the profiles is especially tantalizing, because it attributed to microbial activity on Earth."

The ancient soils, he said, do not prove that Mars once contained life, but they do add to growing evidence that an early wetter and warmer Mars was more habitable than the planet has been in the past 3 billion years.

Curiosity rover is now exploring topographically higher and geologically younger layers within the crater, where the soils appear less conducive to life. For a record of older life and soils on Mars, Retallack said, new missions will be needed to explore older and more clayey terrains.

Surface cracks in the deeply buried soils suggest typical soil clods. Vesicular hollows, or rounded holes, and sulfate concentrations, he said, are both features of desert soils on Earth.

"None of these features is seen in younger surface soils of Mars," Retallack said. "The exploration of Mars, like that of other planetary bodies, commonly turns up unexpected discoveries, but it is equally unexpected to discover such familiar ground."

The newly discovered soils provide more benign and habitable soil conditions than known before on Mars. Their dating to 3.7 billion years ago, he noted, puts them into a time of transition from "an early benign water cycle on Mars to the acidic and arid Mars of today." 

Life on Earth is believed to have emerged and began diversifying about 3.5 billion years ago, but some scientists have theorized that potential evidence that might take life on Earth farther back was destroyed by plate tectonics, which did not occur on Mars.

In an email, Malcolm Walter of the Australian Centre for Astrobiology, who was not involved in the research, said the potential discovery of these fossilized soils in the Gale Crater dramatically increases the possibility that Mars has microbes. "There is a real possibility that there is or was life on Mars," he wrote.

Retallack noted that Steven Benner of the Westheimer Institute of Science and Technology in Florida has speculated that life is more likely to have originated on a soil planet like Mars than a water planet like Earth. In an email, Benner wrote that Retallack's paper "shows not only soils that might be direct products of an early Martian life, but also the wet-dry cycles that many models require for the emergence of life."

Source: University of Oregon

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Native fungus suggested as another tool for restoring ghostly whitebark pine forests

Siberian slippery jack is a native fungus that may help in the effort to restore whitebark pine forests.
Credit: Cathy Cripps

Cathy Cripps doesn't seem to worry about the grizzly bears and black bears that watch her work, but she is concerned about the ghosts and skeletons she encounters.

The ghosts are whitebark pine forests that have been devastated by mountain pine beetles and white pine blister rust, said the Montana State University scientist who studies fungi that grow in extreme environments. The skeletons are dead trees that no longer shade snow or produce pine cones. The round purple pine cones hold the seeds that feed bears, red squirrels and Clark's nutcracker birds. Shade at the top of watersheds keeps snow from melting too fast in the spring, preventing trout streams from drying up too early in the summer.

Fortunately, she has found hope in a native fungus called Siberian slippery jack, or Suillus sibiricus, said Cripps, a mycologist in MSU's Department of Plant Sciences and Plant Pathology.

Cripps conducted a three-year study in collaboration with Waterton Lakes National Park in Canada that showed a 10 to 15 percent increase in the survival rate of whitebark pine seedlings when Siberian slippery jack spores are injected into the soil around them. The injection takes place in nurseries before the seedlings are transplanted in the mountains.

That increase is significant and good news for those trying to reinstate whitebark pine trees to the north-central Rocky Mountains and Pacific Northwest, Cripps said. The whitebark pine is a keystone species that grows at high elevations where other trees cannot, but it has been declared an endangered species in Canada and awaits the designation in the United States.

"That (jump in survival rates) might not sound like a big difference, but a small amount is a big deal considering the labor-intensive process," Cripps said.

Cyndi Smith, scientist emeritus at Waterton, said "The positive results have encouraged Waterton Lakes National Park to continue inoculating both whitebark and limber pine seedlings, to give them the best opportunity we can to establish and survive to maturity."

Participants in the research project, in addition to Cripps' and Smith's teams, were the U.S. Forest Service, National Park Service and volunteers from the United States and Canada.

Explaining how the collaboration began, Smith said, "Cathy gave a presentation on some of her Yellowstone work at the annual science meeting of the Whitebark Pine Ecosystem Foundation in Hailey, Idaho, in 2006. I was really taken with the idea that the ecosystem may have lost the beneficial fungi because our forests have been dead and dying for so long and that perhaps there was a way to reverse that trend so I approached Cathy with the idea.

"I'm a big believer in collaboration, whether locally or internationally, but certainly working with someone of Cathy's academic stature has been very helpful when I have applied for funding for whitebark and limber pine projects," Smith said, adding that, "Cathy's enthusiasm is very infectious, and it is a delight to work with her."

To carry out the research project, the participants placed cages around whitebark pine trees to collect pine cones without interference from wildlife. Then they tested the cones to see if they were resistant to white pine blister rust, removed seeds by hand from the resistant cones, grew the seeds into seedlings and shipped them to the nursery in Glacier National Park.

Cripps and former graduate student Erin Lonergan drove to Waterton Lakes 

National Park and throughout the Greater Yellowstone area, hiked to the tops of mountains and collected the Siberian slippery jack and other fungi from whitebark pine forests. Then they returned to MSU where they used a coffee grinder to process the spongy outer layer of the fungi. They added water to create a spore slurry, stored the mixture at MSU and later injected about 3 million spores into the soil around each seedling temporarily housed at the Glacier National Park nursery.

A few months later, volunteers planted more than 1,000 seedlings into MSU's test plots. Most of those test plots were located in Waterton, while others were in the neighboring Glacier National Park. The two parks together comprise Waterton-Glacier International Peace Park.

Two years into the study, Lonergan, Cripps and Smith reported success in the journal, American Forests. One year later, they announced their final results in the spring/summer 2014 issue of Nutcracker Notes, a small journal hosted by the Whitebark Pine Ecosystem Foundation.

"We wanted to get the word out that results after three years showed that inoculation with these native fungi significantly improved the survival of rust resistant seedlings, especially when inoculated seedlings were planted in burned areas near shelter objects such as stumps and logs," Cripps said.

High nitrogen fertilizations and fungicides prevent the inoculations from working, Cripps said. The age of the seedlings is important because they need to grow plenty of side roots before being inoculated.

When successful, the injected fungi slip like tiny socks over the ends of every root of the whitebark pine seedling and form a relationship that benefits both the tree and the fungi, Cripps said. The fungi help the seedling take in more nutrients and water from the soil. The tree produces the sugars that feed the fungi.

"Instead of being bad guys, these fungi are beneficial," Cripps said of the Siberian slippery jack. "They help plants take up nitrogen and phosphorus from the soil. That's a big deal."

Her study is one of many research projects involving whitebark pine forests, but it's unique because it focuses on beneficial native fungi, Cripps said. She added that land managers might want to incorporate MSU's findings into their overall strategy for restoring whitebark pine forests. She noted that large-scale inoculations are already planned for nurseries in Canada. She said inoculating beneficial fungi into nursery stock is common in Europe.

"As we work to save the vital whitebark pine from disappearing from the landscape, it is essential to use all available tools," Cripps said. "Ectomycorrhizal fungi are an integral part of forest integrity, ecology and health. Showing respect for these mighty microbes might just mean the difference between the restoration and death of a forest."

"Ectomycorrhizal fungi" refers to beneficial fungi that form a symbiotic relationship with the roots of trees. Siberian slippery jack is one of those fungi, and it only associates with five-needle pines. White pine blister rust is another type of fungus, one of the "bad guys."

Source: Montana State University

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The science behind swimming: From whales to larvae, common principles at work in swimming

Whale and diver (stock illustration). Using simple hydrodynamics, researchers were able to show that a handful of principles govern how virtually every animal -- from the tiniest fish to birds to gigantic whales propel themselves though the water. Credit: © James Thew / Fotolia

At nearly 100 feet long and weighing as much as 170 tons, the blue whale is the largest creature on the planet, and by far the heaviest living thing ever seen on Earth. So there's no way it could have anything in common with the tiniest fish larvae, which measure millimeters in length and tip the scales at a fraction of a gram, right?

Not so fast, says L. Mahadevan, the Lola England de Valpine Professor of Applied Mathematics, of Organismic and Evolutionary Biology, and of Physics.

Using simple hydrodynamics, a team of researchers led by Mahadevan was able to show that a handful of principles govern how virtually every animal -- from the tiniest fish to birds to gigantic whales propel themselves though the water. The study is described in a September 14 paper in Nature Physics.

"What we wanted to investigate was how the speed of an organism changes as a function of how large it is, how quickly it moves and how much it moves," Mahadevan said. "To resolve that in detail, however, is very complex, because there is a great deal of differences in morphology and what parts of the body different creatures use to swim. The question is: Is there anything in common across all these organisms? The answer, we found, is yes."

In an effort to uncover those common principles, Mahadevan working with a postdoctoral fellow in his group , Mattia Gazzola, and a colleague Mederic Argentina from the University of Nice, began by trying to unpack the physics of how different creatures swim.

"The traditional approach to swimming phenomena is to take a certain specimen and accurately characterize it via experiments and/or simulations, and try to generalize from there, but it is very hard to strip out specific biological effects from general principles," Gazzola said. "We instead thought that while swimmers exhibit a huge diversity in shapes and kinematics, at the end of the day they all live in the same media, water.

"Therefore we thought that if a unifying mechanistic principle existed, it had to lie in the constraints that the flow environment poses to all its inhabitants," he continued. "And this is a purely physical problem, much easier to solve since it is not affected by biological vagaries. What I like about this paper is that in one line of algebra we derived a compact formula that accounts for 50 years of experiments. This is an example of how powerful minimal modeling can be."

"The basic relationship we wanted to understand was how the input variables -- namely the size of the organism, the amount an organism moves and how quickly it moves -- control the output variable, which is effectively the speed at which it moves," Mahadevan explained. "What we found is that there is a specific relationship, which can be described by in terms of a simple scaling law with two limits."

The first, which corresponds to creatures moving at intermediate speeds, describes situations where the bulk of the resistance is caused by skin friction, because water "sticks" to the organism's body. At faster speeds, Mahadevan said, the resistance organisms face largely comes from pressure that builds up in front of and around them, which is described by the second limit.

"While it wasn't a surprise that the resistance changed at organisms moved faster, the fact that those challenges could be so simply described was interesting and provocative, because we are talking about organisms that range in size from a few millimeters to the size of a blue whale," Mahadevan said.

Armed with those observations, Mahadevan and colleagues turned to a host of empirical observations that had been made over the past 50-plus years. When those data were plotted on a graph, the researchers found that the swimming speed of virtually every organism, from fish larvae to frogs to birds, amphibians and even whales, could be described by one of the two equations.

The same also held true, Mahadevan said, when Gazzola created complex computer models to solve the governing equations of fluid dynamics to describe how different organisms swim.

"What is particularly interesting is that all the organisms essentially reach the hydrodynamic limits of performance," he said. "Our simple theory, which doesn't distinguish in any detailed way between something like a blue whale and fish larvae, except in the parameters of how large you are, much you move and how quickly you move, can describe all this diversity. That suggests there are general principles at work here."


Source: Harvard University

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Soil mineral surfaces linked to key atmospheric processes

Pictured are, from left, are David Bish, Melissa Donaldson and Jonathan Raff. Credit: Indiana University

Research by Indiana University scientists finds that soil may be a significant and underappreciated source of nitrous acid, a chemical that plays a pivotal role in atmospheric processes such as the formation of smog and determining the lifetime of greenhouse gases.

The study shows for the first time that the surface acidity of common minerals found in soil determines whether the gas nitrous acid will be released into the atmosphere. The finding could contribute to improved models for understanding and controlling air pollution, a significant public health concern.

"We find that the surfaces of minerals in the soil can be much more acidic than the overall pH of the soil would suggest," said Jonathan Raff, assistant professor in the School of Public and Environmental Affairs and Department of Chemistry. "It's the acidity of the soil minerals that acts as a knob or a control lever, and that determines whether nitrous acid outgasses from soil or remains as nitrite."

The article, "Soil surface acidity plays a determining role in the atmospheric-terrestrial exchange of nitrous acid," will be published this week in the journal Proceedings of the National Academy of Sciences. Melissa A. Donaldson, a Ph.D. student in the School of Public and Environmental Affairs, is the lead author. Co-authors are Raff and David L. Bish, the Haydn Murray Chair of Applied Clay Mineralogy in the Department of Geological Sciences.

Nitrous acid, or HONO, plays a key role in regulating atmospheric processes. Sunlight causes it to break down into nitric oxide and the hydroxyl radical, OH. The latter controls the atmospheric lifetime of gases important to air quality and climate change and initiates the chemistry leading to the formation of ground-level ozone, a primary component of smog.
Scientists have known about the nitrous acid's role in air pollution for 40 years, but they haven't fully understood how it is produced and destroyed or how it interacts with other substances, because HONO is unstable and difficult to measure.

"Only in the last 10 years have we had the technology to study nitrous acid under environmentally relevant conditions," Raff said.

Recent studies have shown nitrous acid to be emitted from soil in many locations. But this was unexpected because, according to basic chemistry, the reactions that release nitrous acid should take place only in extremely acidic soils, typically found in rain forests or the taiga of North America and Eurasia.

The standard method to determine the acidity of soil is to mix bulk soil with water and measure the overall pH. But the IU researchers show that the crucial factor is not overall pH but the acidity at the surface of soil minerals, especially iron oxides and aluminum oxides. At the molecular level, the water adsorbed directly to these minerals is unusually acidic and facilitates the conversion of nitrite in the soil to nitrous acid, which then volatilizes.

"With the traditional approach of calculating soil pH, we were severely underestimating nitrous acid emissions from soil," Raff said. "I think the source is going to turn out to be more important than was previously imagined."

The research was carried out using soil from a farm field near Columbus, Ind. But aluminum and iron oxides are ubiquitous in soil, and the researchers say the results suggest that about 70 percent of Earth's soils could be sources of nitrous acid.

Ultimately, the research will contribute to a better understanding of how nitrous acid is produced and how it affects atmospheric processes. That in turn will improve the computer models used by the U.S. Environmental Protection Agency and other regulatory agencies to control air pollution, which the World Health Organization estimates contributes to 7 million premature deaths annually.

"With improved models, policymakers can make better judgments about the costs and benefits of regulations," Raff said. "If we don't get the chemistry right, we're not going to get the right answers to our policy questions regarding air pollution."

Source: Indiana University

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'Probiotics' for plants boost detox abilities; untreated plants overdose and die

The Doty lab conducts work to see how plants treated with naturally occurring endophytes might handle soils contaminated with a variety of pollutants. Graduate student Robert Tournay, for example, is interested in how the plants handle arsenic. Credit: M Levin/U of Washington

Scientists using a microbe that occurs naturally in eastern cottonwood trees have boosted the ability of two other plants -- willow and lawn grass -- to withstand the withering effects of the nasty industrial pollutant phenanthrene and take up 25 to 40 percent more of the pollutant than untreated plants.

The approach could avoid the regulatory hurdles imposed on transgenic plants -- plants with genes inserted from or exchanged with other plant or animal species -- that have shown promise in phytoremediation, the process of using plants to remove toxins from contaminated sites, according to Sharon Doty, associate professor of environmental and forestry sciences and corresponding author on a paper about the new work in Environmental Science & Technology.

"Our approach is much like when humans take probiotic pills or eat yogurt with probiotics to supplement the 'good' microbes in their guts," she said.

The microbe from the cottonwood was encouraged to colonize the roots of willows simply by dipping rooted and trimmed cuttings in solutions with the microbe. Grasses were treated with microbes in solution as seeds sprouted in soil. Once integrated into the plants, the microbe supplemented their own microbial defenses.

Microbes that take up residence in the inner tissue of plants and don't cause negative symptoms are called endophytes. In nature, endophytes have a welcomed, symbiotic relationship with plants. In polluted soil, for instance, if the right endophytes are present they consume toxins coming up through plant roots. The endophytes get fed and the plant gets help neutralizing pollutants that could kill it.

That's been one challenge of phytoremediation: plants removing pollutants can, all too quickly, succumb to the toxins.

"When the endophyte in these experiments was given to willow and grasses, it reduced the phytotoxic effects of phenanthrene compared to the control plants that did not receive the endophyte and died," said lead author Zareen Khan, a UW research scientist in environmental and forest sciences.

Phenanthrene is carcinogenic, on the Environmental Protection Agency's priority pollutants list and belongs to a class of polycyclic aromatic hydrocarbons that get deposited into the environment via fossil fuel combustion, waste incineration or as byproducts of industrial processes. Soils that become contaminated can be capped with layers of uncontaminated soil or dug up and removed for cleaning at soil remediation facilities or storage at waste disposal facilities.

In their search, UW researchers tested six different endophytes from cottonwood and willow varieties and found one -- lab name PD1 -- from the eastern cottonwood to be superior at breaking down phenanthrene.

They introduced this endophyte into willow cuttings and lawn grass. Willows were chosen because some varieties have already proven adept at removing toxins and the shrubs have extensive root systems, take up a lot of water and grow rapidly. Lawn grass was included because it also grows fast and could be useful in parks and open-space areas.

In lab experiments, the willow cuttings with added endophyte protection continued to grow, kept their leaves and had denser root systems. Untreated plants wilted, lost leaves and their roots turned brown. When soils were analyzed, the treated willows took up 65 percent of the phenanthrene compared with untreated plants that removed 40 percent, an improvement of 25 percent.

Grass seed planted in contaminated soils and watered with solutions containing the PD1 endophyte germinated five days quicker, grew taller and had 100 more tillers, or new offshoots, after 13 days. Treated grass removed 50 percent of the phenanthrene from the soil, compared with untreated grass that removed 10 percent, an improvement of 40 percent.

In phytoremediation, plants that take up pollutants but don't degrade them have to be removed and treated as hazardous waste or otherwise disposed of safely. The willows treated in the UW experiment appear to have degraded some 90 percent of the phenanthrene to harmless components. The researchers said they'd like to determine if that promising finding holds up in mass-balance studies and want to examine the possible effects on bugs or animals that might bite the plants processing the toxins and other environmental considerations. Interestingly, other studies have shown that bugs can smell similar semi-volatile pollutants and avoid eating the plants containing them, Doty said.

The work was funded by a Small Business Innovation Research grant from the National Institute of Environmental Health Sciences and by funds provided through the Byron and Alice Lockwood Endowed Professorship that Doty holds. The other four co-authors on the paper were undergraduate volunteers: David Roman and Trent Kintz have since graduated while May delas Alas and Raymond Yap are still working on their bachelor's degrees.
Just down the road from UW is Seattle's Gas Works Park, a site Doty thinks is a prime candidate for the approach her lab reported. Contaminants in the soil, including phenanthrene, are from a now-dismantled gasification plant. Soils have been covered with uncontaminated soil.

"The idea of leaving a known carcinogen in a public place is not right," she said. "What about problems of erosion? We should do what we can to remove it. We spend so much money treating cancer, I'd like us to take steps to prevent it instead."

Source: University of Washington

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Earthworms, ants, termites: The real engineers of the ecosystem

The contribution of home gardens in the preservation of biodiversity, economics and human health prompted a multidisciplinary group at the South Border College (Ecosur) in Mexico to work on a project in Tabasco, a south state of the country, with the aim to improve the production and environmental management of these plantations. Credit: Image courtesy of Investigación y Desarrollo

The contribution of home gardens in the preservation of biodiversity, economics and human health prompted a multidisciplinary group at the South Border College (Ecosur) in Mexico to work on a project in Tabasco, a south state of the country, with the aim to improve the production and environmental management of these plantations.

Although the research was conducted from different perspectives, head of research Esperanza Huerta Lwanga focused on the study of soil invertebrates because they are indicators of its quality.

"These organisms fulfill various functions,like allowing the soil to absorb processed organic matter such as leaves, wood, trunks and branches and with this nourishing crops; they also maintain an ecological balance capable of preventing the invasion of pests and provide greater fertility without using chemicals. This happens when growing different types of plants, allowing the existence of a wide variety of soil invertebrates" the researcher explains.

The project, which began in 2009 and was funded by the Ministry of Energy, Natural Resources and Environmental Protection (SERNAPAM), arises because home gardens are places where there is a wealth of soil. In total, the research team worked in 50 home gardens located in different physiographic regions of the state: mountains, coast, floodplain and hillocks.

"During the fieldwork I realized that the orchards whose owners had family harmony, were characterized by a rich vegetation and greater diversity of soil invertebrates was found. However, in other orchards we observed garbage instead vegetation and organisms, revealing a gap between people and nature, " relates Huerta Lwanga.

An important finding of this project was when the researcher found a anecic earthworm, initially thought to be a new species, however, it was only a new entry in the state of Tabasco. "Such organism is characterized by its vertical movements, thereby creating tunnels, helping to integrate the organic matter in the soil, aerating it and forming its structure," the researcher says.

Other species were also identified, like earthworms, ants, termites, centipedes, beetles, grasshoppers, cockroaches and woodlice, which may also be called "ecosystem engineers" (specifically earthworms, termites and some ants) because their activities modify the soil, enriching its productivity.

According to the researcher, it is important to note that the presence of such organisms does not mean that the garden is infested with pests. "If you let me live there, they fulfill their tasks and at the same time control their population because the variety of invertebrates generates food chains."

The pest problem, she says, appears when the land is handled as a monoculture. In these cases only one type of organisms thrives and rapidly increases in number and , because nobody eats them, they become a threat to the plantations.

The research results revealed that the coastal region was the one with more garbage, followed by the hillocks. "In the mountains we found healthy vegetation and a great variety of crops, high diversity of invertebrates and greater earthworm biomass, which was estimated at more than 33 grams per square meter," highlights Huerta Lwanga.

That amount is important because according to previous studies it was established that if biomass is equal or greater than 30 grams per square meter germination induction and plant growth are achieved.

Additionally, this project included environmental education, which was given by mini-workshops and training in the production of vermi-compost.

"At Ecosur, we designed a box for composting, which is equiped with a small mill and worms, where we place the fresh waste to be processed. A device like this was given to all farmers, but was only accepted by 47 percent of them," she sadly concludes.

Source: Investigación y Desarrollo

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Live fast, die young: Soil microbes in a warmer world

Aerial view of the Northern Minnesota landscape including numerous conifer peatlands, deciduous uplands and lakes. Credit: USDA Forest Service Northern Research Station

Warmer temperatures shorten the lifespan of soil microbes and this may affect soil carbon storage, according to a new NSF-funded study published in Nature Climate Change this week.

A research team led by Shannon Hagerty and Paul Dijkstra from Northern Arizona University measured two key characteristics of soil microbes that determine their role in the soil carbon cycle: how efficiently they use carbon to grow and how long they live. "Higher temperatures make microbes grow faster, but they also die faster," said Hagerty, who conducted the research as part of her master's degree and was lead author on the study.

Soil microbes consume organic carbon compounds in soil, use some of it to make more microbes and release the rest to the atmosphere as carbon dioxide. The efficiency with which microbes use their food to make new microbes affects how much carbon remains in soil, and how much is released back to the atmosphere. The accepted idea before this study was that microbes would become less efficient at warmer temperatures.

The scientists incubated soil from a peatland and a forest in Minnesota at different temperatures and measured the efficiency with which microbes grew. They used a new method to measure microbial efficiency: they added small amounts of sugar and tracked how individual atoms in this sugar were turned into carbon dioxide.

"Microbes process sugars in similar ways as we do," says Paul Dijkstra. "We know very well how these processes work in laboratory studies, and can predict which carbon atoms in sugar molecules end up as carbon dioxide, and which are used to build new microbes. We applied this knowledge to the microbes living in soil."

The researchers found, contrary to expectation, that temperature had no effect on how microbes utilized their food, but instead boosted microbial death. "We don't yet know why microbes are dying faster at higher temperatures. Maybe they are eaten by nematodes or mites, or they die because of viruses," said Hagerty. "We need to know more about how temperature affects microbial death."

To explore what these new findings could mean for soil carbon storage in a warming world, the team compared output from a soil model that includes the effect of temperature on microbial lifespan to models unaffected by temperature change. "Models are used to predict how soil processes change, for example, in response to climate change," said Steve Allison, coauthor from the University of California, Irvine. "If we want to predict the future correctly, we'd better use models that accurately describe these microbial processes."

Including a temperature-dependent lifespan to the model increased the amount of carbon retained in soils at warmer temperatures compared to estimates from traditional models. The study concludes that incorporating this new insight into soil models will improve our understanding of how soils influence atmospheric carbon dioxide levels and global climate.

Does this mean that with climate change, more carbon will stay in the soil? "Too early to tell," said Bruce Hungate, Director of the Center for Ecosystem Science and Society at NAU. 

"The results suggest that the biochemistry of the microbes remains the same with warmer temperature, but that predation and death become more important. This laboratory study is just the first step, identifying a potential mechanism. Now we need to study how, in the real world, and in the long-term, the processes of biochemical efficiency and lifespan will change. And nobody has done that yet."

Source: Northern Arizona University

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Sunlight, not microbes, key to carbon dioxide in Arctic

Terrestrial organic matter is shown spilling into a lake. Credit: Image courtesy of Oregon State University

The vast reservoir of carbon stored in Arctic permafrost is gradually being converted to carbon dioxide (CO2) after entering the freshwater system in a process thought to be controlled largely by microbial activity.

However, a new study -- funded by the National Science Foundation and published this week in the journal Science -- concludes that sunlight and not bacteria is the key to triggering the production of CO2 from material released by Arctic soils.

The finding is particularly important, scientists say, because climate change could affect when and how permafrost is thawed, which begins the process of converting the organic carbon into CO2.

"Arctic permafrost contains about half of all the organic carbon trapped in soil on the entire Earth -- and equals an amount twice of that in the atmosphere," said Byron Crump, an Oregon State University microbial ecologist and co-author on the Science study. "This represents a major change in thinking about how the carbon cycle works in the Arctic."

Converting soil carbon to carbon dioxide is a two-step process, notes Rose Cory, an assistant professor of earth and environmental sciences at the University of Michigan, and lead author on the study. First, the permafrost soil has to thaw and then bacteria must turn the carbon into greenhouse gases -- carbon dioxide or methane. While much of this conversion process takes place in the soil, a large amount of carbon is washed out of the soils and into rivers and lakes, she said.

"It turns out, that in Arctic rivers and lakes, sunlight is faster than bacteria at turning organic carbon into CO2," Cory said. "This new understanding is really critical because if we want to get the right answer about how the warming Arctic may feedback to influence the rest of the world, we have to understand the controls on carbon cycling.

"In other words, if we only consider what the bacteria are doing, we'll get the wrong answer about how much CO2 may eventually be released from Arctic soils," Cory added.

The research team measured the speed at which both bacteria and sunlight converted dissolved organic carbon into carbon dioxide in all types of rivers and lakes in the Alaskan Arctic, from glacial-fed rivers draining the Brooks Range to tannin-stained lakes on the coastal plain. Measuring these processes is important, the scientists noted, because bacteria types and activities are variable and the amount of sunlight that reaches the carbon sources can differ by body of water.

In virtually all of the freshwater systems they measured, however, sunlight was always faster than bacteria at converting the organic carbon into CO2.

"This is because most of the fresh water in the Arctic is shallow, meaning sunlight can reach the bottom of any river -- and most lakes -- so that no dissolved organic carbon is kept in the dark," said Crump, an associate professor in Oregon State's College of Earth, Ocean, and Atmospheric Sciences. "Also, there is little shading of rivers and lakes in the Arctic because there are no trees."

Another factor limiting the microbial contribution is that bacteria grow more slowly in these cold, nutrient-rich waters.

"Light, therefore, can have a tremendous effect on organic matter," University of Michigan's Cory pointed out.

The source of all of this organic carbon is primarily tundra plants -- and it has been building up for hundreds of thousands of years, but doesn't completely break down immediately because of the Arctic's cold temperatures. Once the plant material gets deep enough into the soil, the degradation stops and it becomes preserved, much like peat.

"The level of thawing only gets to be a foot deep or so, even in the summer," Crump said. "Right now, the thaw begins not long before the summer solstice. If the seasons begin to shift with climate change -- and the thaw begins earlier, exposing the organic carbon from permafrost to more sunlight -- it could potentially trigger the release of more CO2."

The science community has not yet been able to accurately calculate how much organic carbon from the permafrost is being converted into CO2, and thus it will be difficult to monitor potential changes because of climate change, they acknowledge.

"We have to assume that as more material thaws and enters Arctic lakes and rivers, more will be converted to CO2," Crump said. "The challenge is how to quantify that."

Some of the data for the study was made available through the National Science Foundation's Arctic Long-Term Ecological Research project, which has operated in the Arctic for nearly 30 years.

Source:  Oregon State University

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