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  • richardmitnick 5:18 am on February 10, 2015 Permalink | Reply
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    From phys.org: “Bionic leaf: Researchers use bacteria to convert solar energy into liquid fuel” 

    physdotorg
    phys.org

    1
    Plant cells with visible chloroplasts (from a moss, Plagiomnium affine) Credit: Wikipedia

    Harvesting sunlight is a trick plants mastered more than a billion years ago, using solar energy to feed themselves from the air and water around them in the process we know as photosynthesis.

    Scientists have also figured out how to harness solar energy, using electricity from photovoltaic cells to yield hydrogen that can be later used in fuel cells. But hydrogen has failed to catch on as a practical fuel for cars or for power generation in a world designed around liquid fuels.

    Now scientists from a team spanning Harvard University’s Faculty of Arts and Sciences, Harvard Medical School and the Wyss Institute for Biologically Inspired Engineering at Harvard University have created a system that uses bacteria to convert solar energy into a liquid fuel. Their work integrates an “artificial leaf,” which uses a catalyst to make sunlight split water into hydrogen and oxygen, with a bacterium engineered to convert carbon dioxide plus hydrogen into the liquid fuel isopropanol.

    The findings are published Feb. 9 in PNAS. The co-first authors are Joseph Torella, a recent PhD graduate from the HMS Department of Systems Biology, and Christopher Gagliardi, a postdoctoral fellow in the Harvard Department of Chemistry and Chemical Biology.

    Pamela Silver, the Elliott T. and Onie H. Adams Professor of Biochemistry and Systems Biology at HMS and an author of the paper, calls the system a bionic leaf, a nod to the artificial leaf invented by the paper’s senior author, Daniel Nocera, the Patterson Rockwood Professor of Energy at Harvard University.

    “This is a proof of concept that you can have a way of harvesting solar energy and storing it in the form of a liquid fuel,” said Silver, who is Core Faculty at the Wyss Institute. “Dan’s formidable discovery of the catalyst really set this off, and we had a mission of wanting to interface some kinds of organisms with the harvesting of solar energy. It was a perfect match.”

    Silver and Nocera began collaborating two years ago, shortly after Nocera came to Harvard from MIT. They shared an interest in “personalized energy,” or the concept of making energy locally, as opposed to the current system, which in the example of oil means production is centralized and then sent to gas stations. Local energy would be attractive in the developing world.

    “It’s not like we’re trying to make some super-convoluted system,” Silver said. “Instead, we are looking for simplicity and ease of use.”

    In a similar vein, Nocera’s artificial leaf depends on catalysts made from materials that are inexpensive and readily accessible.

    “The catalysts I made are extremely well adapted and compatible with the growth conditions you need for living organisms like a bacterium,” Nocera said.

    In their new system, once the artificial leaf produces oxygen and hydrogen, the hydrogen is fed to a bacterium called Ralstonia eutropha. An enzyme takes the hydrogen back to protons and electrons, then combines them with carbon dioxide to replicate—making more cells.

    Next, based on discoveries made earlier by Anthony Sinskey, professor of microbiology and of health sciences and technology at MIT, new pathways in the bacterium are metabolically engineered to make isopropanol.

    “The advantage of interfacing the inorganic catalyst with biology is you have an unprecedented platform for chemical synthesis that you don’t have with inorganic catalysts alone,” said Brendan Colón, a graduate student in systems biology in the Silver lab and a co-author of the paper. “Solar-to-chemical production is the heart of this paper, and so far we’ve been using plants for that, but we are using the unprecedented ability of biology to make lots of compounds.”

    The same principles could be employed to produce drugs such as vitamins in small amounts, Silver said.

    The team’s immediate challenge is to increase the bionic leaf’s ability to translate solar energy to biomass by optimizing the catalyst and the bacteria. Their goal is 5 percent efficiency, compared to nature’s rate of 1 percent efficiency for photosynthesis to turn sunlight into biomass.

    “We’re almost at a 1 percent efficiency rate of converting sunlight into isopropanol,” Nocera said. “There have been 2.6 billion years of evolution, and Pam and I working together a year and a half have already achieved the efficiency of photosynthesis.”

    See the full article here.

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    Phys.org™ (formerly Physorg.com) is a leading web-based science, research and technology news service which covers a full range of topics. These include physics, earth science, medicine, nanotechnology, electronics, space, biology, chemistry, computer sciences, engineering, mathematics and other sciences and technologies. Launched in 2004, Phys.org’s readership has grown steadily to include 1.75 million scientists, researchers, and engineers every month. Phys.org publishes approximately 100 quality articles every day, offering some of the most comprehensive coverage of sci-tech developments world-wide. Quancast 2009 includes Phys.org in its list of the Global Top 2,000 Websites. Phys.org community members enjoy access to many personalized features such as social networking, a personal home page set-up, RSS/XML feeds, article comments and ranking, the ability to save favorite articles, a daily newsletter, and other options.

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  • richardmitnick 2:21 pm on February 4, 2015 Permalink | Reply
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    From UCR: “Scientists Reprogram Plants for Drought Tolerance” 

    UC Riverside bloc

    University of California Riverside

    February 4, 2015
    Iqbal Pittalwala

    1
    Sean Cutler’s lab introduced the engineered receptor into transgenic Arabidopsis to establish if it was sufficient to improve survival after drought, one measure of drought tolerance. The transgenic (right) but not non-transgenic plants (left) show improved survival after an extended drought. In this experiment water is withheld for 12 days, which cause severe wilting, and the plants are then re-watered to assess survival. See news release for more details. Photo credit: Sang-Youl Park, UC Riverside.

    Crops and other plants are constantly faced with adverse environmental conditions, such as rising temperatures (2014 was the warmest year on record) and lessening fresh water supplies, which lower yield and cost farmers billions of dollars annually.

    Drought is a major environmental stress factor affecting plant growth and development. When plants encounter drought, they naturally produce abscisic acid (ABA), a stress hormone that inhibits plant growth and reduces water consumption. Specifically, the hormone turns on a receptor (special protein) in plants when it binds to the receptor like a hand fitting into a glove, resulting in beneficial changes – such as the closing of guard cells on leaves, called stomata, to reduce water loss – that help the plants survive.

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    Image shows a representation of the engineered receptor and the agrochemical (shown in yellow) bound inside the receptors ligand binding pocket, as established by X-ray crystallography The grey and blue parts show the parts of the protein that were altered to allow the agrochemical to activate the receptor.Image credit: Sean Cutler, UC Riverside.

    While it is true that crops could be sprayed with ABA to assist their survival during drought, ABA is costly to make, rapidly inactivated inside plant cells and light-sensitive, and has therefore failed to find much direct use in agriculture. Several research groups are working to develop synthetic ABA mimics to modulate drought tolerance, but once discovered these mimics are expected to face lengthy and costly development processes.

    The agrochemical mandipropamid, however, is already widely used in agricultural production to control late blight of fruit and vegetable crops. Could drought-threatened crops be engineered to respond to mandipropamid as if it were ABA, and thus enhance their survival during drought?

    Yes, according to a team of scientists, led by Sean Cutler at the University of California, Riverside.

    The researchers worked with Arabidopsis, a model plant used widely in plant biology labs, and the tomato plant. In the lab, they used synthetic biological methods to develop a new version of these plants’ abscisic acid receptors, engineered to be activated by mandipropamid instead of ABA. The researchers showed that when the reprogrammed plants were sprayed with mandipropamid, the plants effectively survived drought conditions by turning on the abscisic acid pathway, which closed the stomata on their leaves to prevent water loss.

    The finding illustrates the power of synthetic biological approaches for manipulating crops and opens new doors for crop improvement that could benefit a growing world population.

    “We successfully repurposed an agrochemical for a new application by genetically engineering a plant receptor – something that has not been done before,” said Cutler, an associate professor of botany and plant sciences. “We anticipate that this strategy of reprogramming plant responses using synthetic biology will allow other agrochemicals to control other useful traits – such as disease resistance or growth rates, for example.”
    The engineered receptor was introduced into transgenic tomato to establish if it was sufficient to control water use. When plants transpire (release water to the atmosphere) it cools their leaves, so reduced water consumption can be measured by small differences in leaf temperature. The transgenic plants (bottom) show reduced water use when treated with the agrochemical, but not the control non-transgenic plants (top). Photo credit: Sang-Youl Park, UC Riverside.

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    The engineered receptor was introduced into transgenic tomato to establish if it was sufficient to control water use. When plants transpire (release water to the atmosphere) it cools their leaves, so reduced water consumption can be measured by small differences in leaf temperature. The transgenic plants (bottom) show reduced water use when treated with the agrochemical, but not the control non-transgenic plants (top). Photo credit: Sang-Youl Park, UC Riverside.

    Study results appear online Feb. 4 in Nature.

    Cutler explained that discovering a new chemical and then having it evaluated and approved for use is an extremely involved and expensive process that can take years.

    “We have, in effect, circumvented this hurdle using synthetic biology – in essence, we took something that already works in the real world and reprogrammed the plant so that the chemical could control water use,” he said.

    Protein engineering is a method that enables the systematic construction of many protein variants; it also tests them for new properties. Cutler and his co-workers used protein engineering to create modified plant receptors into which mandipropamid could fit and potently cause receptor activation. The engineered receptor was introduced into Arabidopsis and tomato plants, which then responded to mandipropamid as if they were being treated by ABA. In the absence of mandipropamid, these plants showed minimal difference from plants that did not possess the engineered protein.

    Cutler was joined in the research by Sang-Youl Park, Assaf Mosquna and Jin Yao at UCR; and Francis C. Peterson and Brian F. Volkman at the Medical College of Wisconsin.

    UCR’s Office of Technology Commercialization has filed a patent application on the technology described in the research paper.

    The research was supported in part by the National Science Foundation and Syngenta. Mandipropamid, used on a wide range of fruit and vegetable crops for control of various fungal pathogens, is manufactured by Syngenta under the brand name Revus®. Revus® is a registered trademark of a Syngenta Group Company.

    See the full article here.

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  • richardmitnick 8:55 am on January 16, 2015 Permalink | Reply
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    From U Washington: “Tiny plant fossils a window into Earth’s landscape millions of years ago” 

    U Washington

    University of Washington

    January 15, 2015
    Michelle Ma

    Minuscule, fossilized pieces of plants could tell a detailed story of what the Earth looked like 50 million years ago.

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    A 49 million-year-old phytolith. Its curvy, large shape indicate the plant it came from grew in shady conditions. Scale bar is 10 micrometers.Regan Dunn, U of Wash.

    An international team led by the University of Washington has discovered a way to determine the tree cover and density of trees, shrubs and bushes in locations over time based on clues in the cells of plant fossils preserved in rocks and soil. Tree density directly affects precipitation, erosion, animal behavior and a host of other factors in the natural world. Quantifying vegetation structure throughout time could shed light on how the Earth’s ecosystems changed over millions of years.

    “Knowing an area’s vegetation structure and the arrangement of leaves on the Earth’s surface is key for understanding the terrestrial ecosystem. It’s the context in which all land-based organisms live, but we didn’t have a way to measure it until now,” said lead author Regan Dunn, a paleontologist at the UW’s Burke Museum of Natural History and Culture. Dunn completed this work as a UW doctoral student in the lab of Caroline Strömberg, the Estella B. Leopold associate professor in biology and curator of paleobotany at the Burke Museum.

    The findings are published Jan. 16 in the journal Science.

    The team focused its fieldwork on several sites in Patagonia, Argentina, which have some of the best-preserved fossils in the world and together represent 38 million years of ecosystem history (49-11 million years ago). Paleontologists have for years painstakingly collected fossils from these sites, and worked to precisely determine their ages using radiometric dating. The new study builds on this growing body of knowledge.

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    The researchers work in Miocene-aged deposits near Rio Chico in Chubut Province, Argentina.Regan Dunn, U of Wash.

    In Patagonia and other places, scientists have some idea based on ancient plant remains such as fossilized pollen and leaves what species of plants were alive at given periods in Earth’s history. For example, the team’s previous work documented vegetation composition for this area of Patagonia. But there hasn’t been a way to precisely quantify vegetation openness, aside from general speculations of open or bare habitats, as opposed to closed or tree-covered habitats.

    “Now we have a tool to go and look at a lot of different important intervals in our history where we don’t know what happened to the structure of vegetation,” said Dunn, citing the period just after the mass extinction that killed off the dinosaurs.

    “The significance of this work cannot be understated,” said co-author Strömberg. “Vegetation structure links all aspects of modern ecosystems, from soil moisture to primary productivity to global climate. Using this method, we can finally quantify in detail how Earth’s plant and animal communities have responded to climate change over millions of years, which is vital for forecasting how ecosystems will change under predicted future climate scenarios.”

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    Fossil phytoliths from a 40 million-year-old soil from the Sarmiento Formation, Gran Barranca, Chubut, Argentina. At the center is an epidermal phytolith indicative of open habitats by its smaller, less curvy shape. Scale bar is 10 micrometers.Regan Dunn, U of Wash.

    Work by other scientists has shown that the cells found in a plant’s outermost layer, called the epidermis, change in size and shape depending on how much sun the plant is exposed to while its leaves develop. For example, the cells of a leaf that grow in deeper shade will be larger and curvier than the cells of leaves that develop in less covered areas.

    Dunn and collaborators found that these cell patterns, indicating growth in shade or sun, similarly show up in some plant fossils. When a plant’s leaves fall to the ground and decompose, tiny silica particles inside the plants called phytoliths remain as part of the soil layer. The phytoliths were found to perfectly mimic the cell shapes and sizes that indicate whether or not the plant grew in a shady or open area.

    The researchers decided to check their hypothesis that fossilized cells could tell a more complete story of vegetation structure by testing it in a modern setting: Costa Rica.

    4
    Regan Dunn samples for phytoliths from the soil under a dense forest at Rincon de la Vieja National Park, Costa Rica.Melanie Conner, copyright Melanie Conner Photography

    Dunn took soil samples from sites in Costa Rica that varied from covered rainforests to grassy savannahs to woody shrub lands. She also took photos looking directly up at the tree canopy (or lack thereof) at each site, noting the total vegetation coverage.

    5
    This hemispherical photograph shows the tree canopy cover at a site in Santa Rosa National Park, Costa Rica. The corresponding forest profile (modified from Holdridge et al., 1971) gives a side profile of the forest’s density.Regan Dunn, U of Wash.

    Back in the lab, she extracted the phytoliths from each soil sample and measured them under the microscope. When compared with tree coverage estimated from the corresponding photos, Dunn and co-authors found that the curves and sizes of the cells directly related to the amount of shade in their environments. The researchers characterized the amount of shade as “leaf area index,” which is a standard way of measuring vegetation over a specific area.

    Testing this relationship between leaf area index and plant cell structures in modern environments allowed the team to develop an equation that can be used to predict vegetation openness at any time in the past, provided there are preserved plant fossils.

    “Leaf area index is a well-known variable for ecologists, climate scientists and modelers, but no one’s ever been able to imagine how you could reconstruct tree coverage in the past — and now we can,” said co-author Richard Madden of the University of Chicago. “We should be able to reconstruct leaf area index by using all kinds of fossil plant preservation, not just phytoliths. Once that is demonstrated, then the places in the world where we can reconstruct this will increase.”

    When Dunn and co-authors applied their method to 40-million-year-old phytoliths from Patagonia, they found something surprising — habitats lost dense tree cover and opened up much earlier than previously thought based on other paleobotanic studies. This is significant because the decline in vegetation cover occurred during the same period as cooling ocean temperatures and the evolution of animals with the type of teeth that feed in open, dusty habitats.

    The research team plans to test the relationship between vegetation coverage and plant cell structure in other regions around the world. They also hope to find other types of plant fossils that hold the same information at the cellular level as do phytoliths.

    Other co-authors are Matthew Kohn of Boise State University and Alfredo Carlini of Universidad Nacional de La Plata in Argentina.

    The research was funded by the National Science Foundation, the Geological Society of America, UW Biology and the Burke Museum.

    ###

    For more information, contact Dunn at dunnr@uw.edu or 206-685-0374.

    See the full article here.

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    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.

    So what defines us — the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

     
  • richardmitnick 4:02 pm on January 6, 2015 Permalink | Reply
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    From NASA Earth: “Finding Floating Forests” An Amazing Story Complete with Citizen Science 

    NASA Earth Observatory

    NASA Earth Observatory

    December 19, 2014
    By Laura Rocchio Design by Paul Przyborski & Mike Carlowicz

    Giant kelp forests are among Earth’s most productive habitats, and their great diversity of plant and animal species supports many fisheries around the world. The kelp, or Macrocystis, that make up these underwater forests truly are giant. They are the world’s largest marine plants and regularly grow up to 35 meters (115 feet) tall; the largest giant kelp on record stood 65 meters (215 feet) tall. Divers have compared swimming through mature kelp forests to walking through redwood forests.

    k

    Unlike redwoods, giant kelp are ephemeral. They live for seven years at most, and often they disappear before that because of winter storms or over-grazing by other species. As fishermen know, giant kelp forests can appear and disappear from season to season, from year to year. But is there a long-term trend or cycle at work?

    A few years ago, Jarrett Byrnes was in a bit of a quandary over these disappearing forests. As part of his postdoctoral research at the University of California–Santa Barbara (UCSB), he was studying giant kelp at four National Science Foundation-funded sites off the coast. Since 2000, biologists had been using this Long-Term Ecological Research (LTER) site to make monthly in situ measurements of giant kelp. But Byrnes and his colleagues found that they often could not make measurements in winter because rough seas made the diving unsafe.

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    Kelp are the redwoods of the sea. The world’s largest marine plants regularly grow up to 35 meters (115 feet) tall. (Photograph © Phillip Colla / Oceanlight.com)

    “Storms remove quite a bit of the canopy in the winter. Sometimes they even remove whole forests if the storms are large enough,” Byrnes explained. “But getting to those sites with regularity in the winter gets very challenging.” Most of the diving had to wait until summer, and by then the kelp had largely recovered or changed, making it difficult to measure how much damage the storms had done.

    To complicate matters, kelp forests have different seasonality depending on where they are. For instance, the forests along the Central California coast are at their maximum size in the fall; in Southern California, they often reach their peak in the winter and spring. How could these dynamic habitats be monitored more frequently without putting divers at risk?

    Kyle Cavanaugh, then a UCSB graduate student, had an idea. “These forests change so rapidly and on a variety of different time scales—months to years to decades—so we needed a long record with consistent, repeated observations,” Cavanaugh said. He devised a method to use Landsat satellite data to monitor kelp forests.

    A few things made Landsat an obvious resource. Since the 1970s, the satellites have had a regular collection schedule (twice monthly). Their data and images are managed by the U.S. Geological Survey and are reliably stored in an archive that dates back more than forty years. And Landsat’s images are calibrated, or standardized, across different generations of satellites, making it possible to compare data collected across several decades.

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    Landsat 8 can detect near-infrared wavelengths of light that make it easier to spot offshore kelp forests. (NASA Earth Observatory image by Mike Taylor, using Landsat data from the U.S. Geological Survey)

    Landsat measures the energy reflected and emitted from Earth at many different wavelengths. By knowing how features on Earth reflect or absorb energy at certain wavelengths, scientists can map and measure changes to the surface. The most important feature for the kelp researchers is Landsat’s near-infrared band, which measures wavelengths of light that are just outside our visual range. Healthy vegetation strongly reflects near-infrared energy, so this band is often used in plant studies. Also, water absorbs a lot of near-infrared energy and reflects little, making the band particularly good for mapping boundaries between land and water.

    “The near-infrared is key for identifying kelp from surrounding water,” Cavanaugh explained. “Like other types of photosynthesizing vegetation, giant kelp have high reflectance in the near infrared. This makes the kelp canopy really stand out from the surrounding water.”

    For Byrnes, the approach was a breakthrough: “This meant we could see the forests I was analyzing right after storms hit them.”

    Growing Fast and Holding Fast

    Giant kelp are fast growers, and they thrive in cold, nutrient-dense waters, particularly where there is a rocky and shallow seafloor (5 to 30 meters or 15 to 100 feet). They attach to the seafloor with small root-like structures (haptera) also called, appropriately enough, a holdfast. The holdfast supports a stipe, or stalk, and leaf-like blades that float thanks to air-filled pockets (pneumatocysts). The fronds create dense floating canopies on the water surface, yet these massive plants rely on holdfasts barely 60 centimeters (24 inches) wide to keep them rooted and alive.

    Given the right balance of conditions, giant kelp can grow as much as 50 centimeters (1.6 feet) per day, and this robust growth makes it possible for kelp fronds to be commercially harvested. Giant kelp have been plucked from California waters since the early 1900s, and they have long appeared in products like ice cream and toothpaste. At the industry’s peak, large ships using lawnmower-like machinery could harvest more than 200,000 wet tons annually.

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    Kelp fronds create dense floating canopies near the water surface. Kelp have been harvested for a century for commercial products; they also pose trouble for boat propellers. (Photo courtesy of Chad King / NOAA MBNMS)

    “The satellite could definitely see the effects of harvesting, but the kelp recovery was very fast,” said Tom Bell, a UCSB researcher and collaborator with Byrnes and Cavanaugh.

    Today, only a few thousand tons of giant kelp are harvested each year, some by hand and some by mechanical harvesters. The kelp can be trimmed no lower than 4 feet below the water surface, and this sustainable harvesting is the equivalent of humans getting a haircut. Studies have shown that negative affects are negligible, although some fish populations are temporarily displaced.

    7
    Giant kelp thrive in cold, nutrient-dense waters, particularly where there is a rocky, shallow seafloor. The California coast provides ideal habitat. (NASA Earth Observatory image by Mike Taylor, using Landsat data from the U.S. Geological Survey)

    For years, scientists debated whether it was nutrient availability or grazers (not human harvesters, but sea urchins) that had the most influence over kelp forest health, size, and longevity. After using Landsat to look at long-term trends, and comparing those trends to known differences between Central and Southern California waters, Cavanaugh and LTER lead Daniel Reed found that a third force—wave disturbance—was the kingmaker of kelp dynamics. Strong waves generated by storms uproot the kelp from their holdfasts and can devastate the forests far more than any grazer.

    Kelp Research Branches Out

    When giant kelp first brought Byrnes and Cavanaugh together at UCSB, their work was largely California-focused. The data they collected from the LTER study sites off Santa Barbara became a tremendous resource for kelp researchers. But that work covered four discrete locations for a species found all over the world.

    Giant kelp can grow anywhere there are cold, shallow, nutrient-rich waters and a rocky seafloor. Conditions for kelp growth have historically been ideal along the west coast of North America, as well as Chile, Peru, the Falkland Islands, South Africa, and around Australia, New Zealand, and the sub-Antarctic islands.

    More and more often these days, though, the conditions are less ideal. Climate change has brought a trifecta of kelp scourges: warmer waters with fewer nutrients; new invasive species; and severe storms.

    8
    Given the right balance of conditions, giant kelp can grow as much as 50 centimeters (1.6 feet) per day. (Photograph © Phillip Colla / Oceanlight.com)

    After a recent meeting on kelp forests and climate change, Byrnes, Cavanaugh, and other colleagues set out to consolidate all of the available kelp forest data from around the world. They wanted to take a step toward understanding how climate change is affecting kelp globally, but they quickly discovered they had a sparse patchwork of information.

    Byrnes was struck with a thought. They had used Landsat to expand their studies across time, so why not use Landsat to expand their studies around the world? Could Landsat be used to establish global trends in kelp forest extent? The answer was yes, but the problem was eyeballs.

    Unlike research on terrestrial vegetation—which uses Landsat data and powerful computer processing arrays to make worldwide calculations—distinguishing kelp forests requires manual interpretation. While kelp forests pop out to the human eye in near-infrared imagery, computers looking at the data numerically can confuse kelp patches with land vegetation. Programs and coded logic that separate aquatic vegetation from land vegetation can be confounded by things like clouds, sunglint, and sea foam.

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    9
    Natural color (top) and near-infrared (bottom) images from Landsat 8 show the kelp-rich waters around California’s Channel Islands. Clouds, sunglint, and sea foam make it difficult for computer programs to detect the location of forests. So far, human eyes work better. (NASA Earth Observatory image by Mike Taylor and Jesse Allen, using Landsat data from the U.S. Geological Survey)

    “I’ve spent many, many years staring at satellite imagery trying to come up with new ways to extract the kelp signal from that imagery, and it is very time and work intensive,” said Cavanaugh, now based at the University of California–Los Angeles. “But automated classification methods just don’t produce acceptable levels of accuracy yet.”

    Byrnes, now based at the University of Massachusetts–Boston, realized that the best way to study global kelp changes was to turn to citizen scientists. Byrnes and Cavanaugh put together a science team and joined with Zooniverse, a group that connects professional scientists with citizen scientists in order to help analyze large amounts of data. The result was the Floating Forests project.

    Getting Help from a Few Thousand Friends

    The Floating Forest concept is all about getting more eyeballs on Landsat imagery. Citizen scientists—recruited via the Internet—are instructed in how to hunt for giant kelp in satellite imagery. They are then given Landsat images and asked to outline any giant kelp patches that they find. Their findings are crosschecked with those from other citizen scientists and then passed to the science team for verification. The size and location of these forests are catalogued and used to study global kelp trends.

    In addition to examining the California coast, which Byrnes and Cavanaugh know well, the Floating Forests project has also focused on the waters around Tasmania. Tom Bell and collaborators in Australia and New Zealand have noticed dramatic declines in giant kelp forests there over the past few decades. The decline has been so rapid and extensive that giant kelp are only found now in isolated patches.

    1
    2
    Off the east coast of Tasmania, 95 percent of the kelp has disappeared since the 1940s. False-color Landsat images from September 1999 (top) and September 2014 (bottom) provide evidence of recent kelp forest disturbance. (NASA Earth Observatory image by Mike Taylor, using Landsat data from the U.S. Geological Survey)

    Off Tasmania’s east coast, 95 percent of the kelp has disappeared since the 1940s. The loss has been so stark that the Australian government listed Tasmania’s giant kelp forests as an “endangered ecological community“— the first time the country has given protection to an entire ecological community. The loss is so stunning because this was a place where kelp forests were once so dense that they merited mention on nautical charts.

    Cool, subarctic waters once bathed Tasmania’s east coast, but warmer waters (as much as 2.5ºC (4.3ºF) warmer) have brought many invasive species that feast on giant kelp. Compounding the matter, the overfishing of rock lobsters has removed a key predator of the long-spined sea urchins (which eat kelp). The ecosystem’s new protected status could help curb overfishing and restore the lobsters, which would help diminish the threat from sea urchins.

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    This U.S. Hydrographic Service chart from 1925 shows Prosser Bay, Tasmania, and the distribution of giant kelp. (Source: Edyvane at al, 2003)

    Using Landsat to monitor the kelp forests and establish trends may shed more light on what is happening off of Tasmania. “We believe the data from Floating Forests will allow us to better understand the causes of these declines,” said Cavanaugh.

    As of November 2014, more than 2,700 citizen scientists had joined Byrnes and Cavanaugh to look for kelp in 260,000 Landsat images. All combined, the citizen scientists have now made more than one million kelp classifications. The response has exceeded expectations, and the project has been expanded faster than originally planned.

    Already a discovery has been made. A citizen scientist found a large patch of giant kelp on the Cortez Bank, an underwater seamount about 160 kilometers (100 miles) off the coast of San Diego. While giant kelp on this submerged island—which comes within feet of the surface at some points—had been documented by divers and fishermen in the past, the full extent of the kelp beds was unknown.

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    A citizen scientist found satellite evidence of an outlying kelp forest that was previously known only to divers and local fishermen. (NASA Earth Observatory image by Mike Taylor, using Landsat data from the U.S. Geological Survey)

    “The first few months of Floating Forests have been a huge success, and we are hopeful that we will soon be able to expand the project to other regions,” Cavanaugh said. “Our ultimate goal is to cover all the coastlines of the world that support giant kelp forests.”

    To learn how to participate in the Floating Forests project, visit their web page.

    See the full article here.

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    The Earth Observatory’s mission is to share with the public the images, stories, and discoveries about climate and the environment that emerge from NASA research, including its satellite missions, in-the-field research, and climate models. The Earth Observatory staff is supported by the Climate and Radiation Laboratory, and the Hydrospheric and Biospheric Sciences Laboratory located at NASA Goddard Space Flight Center.

     
  • richardmitnick 5:33 am on November 12, 2014 Permalink | Reply
    Tags: , , Biota, Food research,   

    From NOVA: “The Next Green Revolution May Rely on Microbes” 

    PBS NOVA

    NOVA

    12 Jun 2014
    Cynthia Graber

    Ian Sanders wants to feed the world. A soft-spoken Brit, Sanders studies fungus genetics in a lab at the University of Lausanne in Switzerland. But fear not, he’s not on a mad-scientist quest to get the world to eat protein pastes made from ground-up fungi. Still, he believes—he’s sure—that these microbes will be critical to meeting the world’s future food needs.

    Sanders’s eyes widen with delight and almost childlike glee when he talks about a microscopic life form called mycorrhizal fungus, his chosen lifetime research subject. Mycorrhizal fungi live in a tightly wound, mutually beneficial embrace with most plants on the planet. Years of dedication have made Sanders into one of the world’s foremost experts on the genetics of the microbe, and he recently was part of a team that sequenced the first mycorrhizal fungi genome.

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    Mycorrhizal fungi colonize the tip of a root, seen here under magnification.

    Despite his drive, Sanders comes across as light-hearted as he teases and jokes with fellow researchers. But he loses his affable smile as he fires off facts about the upcoming food shortage: The world’s population is expected to increase to between 9 billion and 16 billion people. Five million people per year die of direct causes of malnutrition. Three and a half million of those are children under five. Today, we have the means to grow enough food to feed all those people, but we will most certainly need to produce more in the very near future.

    Sanders may have come up with a way to do just that. He has successfully bred custom varieties of microbes that can help plants produce more food. It’s one of the ultimate goals of farming research—more food with, he hopes, little or no environmental downside.

    We’ve been looking at the wrong set of genes.

    The question of crop productivity is increasingly fraught. People in developed countries eat an enormous amount of food, and people in developing countries are beginning to close the gap. Meanwhile, the world’s population is swelling. By 2030, the UN’s Food and Agriculture Organization predicts food demand will soar by 35%. And then there’s the accelerating impact of climate change: The IPCC’s latest report on the subject, published in March, shows that scientists are predicting a 2% decrease in crop yields per decade over the next century. Higher temperatures and longer, more dramatic swings between drought and rain mean the plants that we rely on will have a hard time weathering the strain.

    According to the FAO, most of the growth in production that we’ll need has to come from increasing yields from crop plants. Selective breeding doesn’t seem to be offering the types of dramatic yield increases seen in the past. Meanwhile, genetic engineering has yet to lead to any significant increase in yields.

    Now, many scientists are saying that we’ve been looking at the wrong set of genes. Instead of in plants, the crucial genes may reside in the galaxy of bacteria and fungi that live in the soil and throughout a plant—the kind that Sanders studies.

    Sanders’ plan is to give existing fungi-plant relationships a boost by breeding better fungi. He’s testing varieties of lab-grown microbes out in the field in tropical Colombia. There, he’s hoping to help cassava plants grow heftier roots, as these potato-like crops are a staple for nearly a billion people around the world. So far, the results show that this approach just might work.

    Belowground Microbiome

    Microbes in the soil function much like the human microbiome, which helps us break down food, access nutrients, and defend against harmful invaders. A plant’s microbiome protects it against malevolent microbes. Microbes can also communicate with one another, flashing chemical alerts that let one plant know when another nearby is under attack. Bacteria and fungi even structure the soil so that it clumps together and doesn’t blow or wash away. And, just as our human cells are outnumbered by our microbial support, the microbial genes in and near the root system alone of a healthy plant greatly eclipse those of the plant itself.

    Plants have depended on microbial assistance since they first edged out of the water onto dry land, about 450 million years ago. They lassoed photosynthetic cyanobacteria and turned them into cellular machines known as chloroplasts, which harvest the sun’s energy. Today, plants are still supported by hundreds of thousands—perhaps millions—of different species of bacteria, fungi, even viruses. In fact, the rhizosphere, the area around a plant’s roots, is considered one of the most ecologically diverse regions on the planet.

    The microbiome in the rhizosphere acts as an extension of plants’ root systems, breaking down nutrients into forms that plants can use. Mycorrhizal fungi have whisper-thin fronds, called hyphae, that reach out past the root tips to access water and nutrients the plant needs to survive. They then trade those for carbohydrates the plant provides. Scientists believe that as much as 30% of the carbon that a plant produces through photosynthesis is pushed into the soil to support an entire city of microbes.

    Though mycorrhizal fungi are just a multitude microbe species in the soil in and around plant roots, they live in symbiosis with about 80–90% of agricultural crops in a relationship hundreds of millions of years old. Mycorrhizal fungi cannot survive without plants, and most plants cannot thrive without mycorrhizal fungi.
    As much as 30% of the carbon that a plant produces supports an entire city of microbes.

    On the most basic level, scientists have known that microbes associate with plants for more than a century, but, even today, many of the details of the interactions are still unknown. Part of the challenge in teasing them out is that they’ve been nearly impossible to study. Scientists estimate that perhaps 1% of all soil microbes can be grown on a petri dish, the conventional model for such research. By only being able to study the thinnest slice of life, we’ve been missing out on a vast, complicated, messy world. It’s like trying to guess what everyone on a city block does during the day by trailing just one person.

    Recently, though, scientists have begun to get a better glimpse. Genetic analyses can help classify and understand newly discovered microbes. Big Data-style techniques, with names like metagenomics, proteomics, and transcriptomics, describe methods by which scientists can take an overall picture of the genetic diversity of life in a given region, and even what genes are active. These types of studies might not be able to describe every individual, but they can give a sense of what genes are in play. Such tools are able to do more, do it more quickly, and do it for less money nearly every year.

    In only the last few years, scientists using these tools have begun to regularly uncover new information about the crucial links between microbes and plants. They’re unraveling clues as to which bacteria, fungus, or virus performs which function. They’re discovering microbes that can help plants withstand heat and drought. And they’re dialing into the genetics to understand how the microbes do what they do, how the plants react, and even what genetic material is exchanged. There’s still a world of research to be done, however. With many millions of individuals packed into every gram of soil, it’s a daunting task.
    tending-cassava-field

    ka
    Tending a cassava field in the Amazon

    Farmers have manipulated the plant-microbe relationship, unknowingly, for thousands of years. Compost, for example, does not simply contain beneficial nutrients—it also teems with living organisms, as does animal manure. Crop rotation, too, can enhance microbial diversity. Stalks and crop remains left on the field or plowed into soil provide microbes with food. And growing particular plants together—such as the traditional grouping of bean-squash-corn in the early Americas—does the same, as each plant likely contributes a complementary set of microbes.

    But, for the most part, the tightly braided relationship hasn’t yet factored into the workings of modern agriculture. Today, if a plant needs more of anything, we just add it—water, nitrogen, phosphorus, manganese, and so on. In the 20th century, this approach produced an abundance of crops and staved off starvation for millions. But it has also soaked groundwater with nitrogen, led to algal blooms in lakes and rivers, and spawned a massive dead zone in the Gulf of Mexico. Studies show that nitrogen fertilizers can also reduce the diversity of microbial life. Pesticides can be more harmful. Even tilling cleaves fungal networks. Until recently, we knew little about how we’ve been inadvertently crippling our crops’ complicated support network.

    “Over the last hundred years in agriculture, we’ve tried to take microorganisms out of the picture. And by doing that—by disrupting the soil with tillage, by using chemical pesticides—we have greatly altered the agricultural biome,” says Rusty Rodriguez, a former microbiologist with the U.S. Geological Survey who’s now head of Adaptive Symbiotic Technologies, a company developing microbial-based seed coatings. “The efficacy of many chemicals is beginning to wane.” Bacteria and fungi, Rodriguez says, “are the next paradigm for agriculture.”
    From Switzerland to Columbia

    Sanders’ Swiss workplace is immaculately clean, and the room where the fungi are taken out for study is scrupulously sterile. Every night, all night, UV lights shine a microbe-killing glare. They destroy anything that could infect his cultures of mycorrhizal fungi.

    Over the course of Sanders’ 26-year career, he’s made a number of key discoveries about fungi genetics and reproduction. He conducted early research that demonstrated that the greater the diversity of mycorrhizal fungi in a given ecosystem, the greater the diversity of plants. And in 2008, as he delved into genetics, he proved that they don’t just reproduce by cloning—they actually exchange genetic material, both in the lab and in the field.

    This gave him an idea. If the microbes created offspring that were different from one another, Sanders thought, “you have a good chance that some will be more effective on plant growth than others.” So he came up with a plan: Take different fungi, breed them, see if any help plants out more than others. In other words, take the approach to farming that breeders have used for thousands of years and use it on fungi.
    Without human intervention, the whole system of microbial support might not be optimally tweaked to match crossbred crops.

    This is where Sanders runs into occasional criticism from some of his microbe-studying colleagues, who say that nature has already bred all the best variety of microbes. “If you use the argument from these researchers,” he counters, “then no one would have produced any plants through plant breeding, because they would have said, ‘Well, nature’s already made the best plants, and we can’t make any more that are any better than what nature has made.’ Now, of course, we know from a few thousand years of agriculture that we can make plants better by crossing them, and we can get varieties that produce bigger yields than that which we see in natural-occurring varieties of those plants in nature.” Without similar human intervention, the whole system of microbial support might not be optimally tweaked to match.

    To test out his idea, Sanders partnered with a colleague in Switzerland who was studying the genetics of the fungi-rice relationship, and who already had conducted research in a university greenhouse set up for rice cultivation. Sanders grew the fungi and allowed them to exchange genetic material and reproduce, creating genetically distinct offspring. Then, he colonized rice with these distinct lines. Sanders used rice as a matter of convenience due to his colleague’s experience, but he also knew that rice, as farmed today, tends to actually grow more poorly when inoculated with mycorrhizal fungi, making it a good test bed. He was stunned when one of the lines produced a five-fold increase in growth over the other fungal lines. “To see such a huge growth increase was very, very surprising,” he says. The greenhouse was an artificial environment, and the microbe-enhanced soil was compared to sterile soil. It in no way mimicked nature. But it proved a point.

    Around that time, Sanders got back in touch with Alia Rodriguez, an agronomist in Colombia who also had expertise in mycorrhizal fungi. They had originally met when he was one of her PhD examiners in England. He was desperate to visit Colombia and see its amazing animal and plant biodiversity for himself, so they decided to try to find a research project together.

    It happened that Colombia offered the perfect field test for his new approach. Mycorrhizal fungi are skilled at helping plants access phosphorus, a key nutrient, which plants in tropical countries have a particular problem securing. The acidity of soil there results in a chemical reaction that ties up most of the phosphate that farmers add to soil. Farmers end up paying precious money to add phosphate that plants mostly can’t use. “I always tell my students, how can we rely on a practice that is so inefficient?” Rodriguez says. “It has to change, because it cannot be sustainable.”
    experimental-cassava-fields.

    fie
    Ian Sanders and Alia Rodriguez’s experimental plots in Columbia

    Colombia is also the home of cassava, a fleshy white root. Cassava is a major staple for nearly a billion people in more than 100 countries, from Brazil to Nigeria to Thailand, who rely on it in much the same way we rely on bread or potatoes. In its various homes and in various languages, it is called cassava, yuca, manioc, balinghoy, kamoteng kahoy, tapoica-root. If you can produce more cassava, then poor communities can eat more food.

    Sanders liked the idea of breeding microbes to increase cassava production. But they still had one major stumbling block ahead. There was no practical way to transport enough pure fungus from his Swiss lab to colonize the cassava trial fields in Colombia.

    This had also been a problem for the early pioneers in the field. In earlier decades, a variety of start-ups had marketed mycorrhizal fungi transported in soil, an imperfect medium that also contained plant roots and a host of other microbes. There was no way to tell whether it contained any live, viable material, let alone a specific species. Plus, transporting enough soil for every plant root on a farm would be heavy and prohibitively expensive.

    Fortunately for Sanders and Rodriguez, a company in Spain named Mycovitro coincidentally announced the culmination of decades of research of their own: a gel that could act as a vehicle for highly concentrated, purified mycorrhizal fungi. With the gel, Sanders would know that he was only transporting the microbes he wanted. A single small bottle could provide enough fungi for an entire field. Even more importantly, the gel base was capable of growing any variation that Sanders bred in his lab. The team partnered with Mycovitro to grow Sanders’ varieties. (The company has no financial connection to Sanders’ and Rodriguez’s research, and neither of the scientists have a stake in the company. The company, however, is providing its services for free, and it will have first right of refusal to commercialize any promising new line that Sanders and Rodriguez develop.)

    With the final piece in place, Sanders and Rodriguez set their research project in motion. They headed down to Columbia to test their varieties by growing hectares of cassava along the edge of the llanos, the country’s lush, damp tropical savannah.

    Catching On

    As the pieces of Sanders and Rodriguez’ research fell into place, the field of commercially-applicable bio products was undergoing a renaissance. A few decades ago, interest in microbes and their use in agriculture flared, but most of the commercial products quickly flickered out. Most of the laboratory successes hadn’t translated to the field. One of the few agricultural microbes that did catch hold was the bacterium Rhizobium, which helps legumes access nitrogen. It’s used extensively on crops such as soy. Other microbes, such as the bacterium Bacillus, are used to protect plants from pathogens. Rhizobium and Bacillus are not the only examples on the market, but the combined market share is still a small fraction of the multibillion dollar agro-chemical industry.

    But new, more effective products have begun to emerge. Marrone Bio Innovations’ most recent pesticide, called Grandevo, was developed from a soil bacterium and is marketed to protect vegetable crops from sucking insects and mites. The company, with more than 150 patents pending, has additional products in the pipeline, including a strain of Bacillus that both controls pathogens and encourages plant growth.

    Dozens of field trials in 14 states around the U.S. are testing microbial products for corn, soybeans, wheat, barley, and rice.

    Rusty Rodriguez (no relation to Alia Rodriguez in Colombia), the head of Adaptive Symbiotic Technologies, got his start in the 1990s when he and his colleagues discovered the symbiosis between plants and fungi in Yellowstone that allowed plants to survive in temperatures as high as 150˚ F. Once he identified and isolated the fungus responsible for the plant’s heat-survival ability, he realized he could use it to help other plants survive extreme heat.

    Rodriguez dove headfirst into extremophiles, sending company employees to collect plants from extreme environments around the U.S. He’s focusing on a number of products—some are single fungi, others are communities working together—that confer a variety of benefits to agricultural plants: drought tolerance, salt tolerance, and the ability to withstand swings in temperature. His company has developed tests that rule out any potential negative impacts of the strains, such as plant damage or toxicity to animals that might snack on them. They have dozens of field trials in place in 14 states around the U.S., working with farmers who are testing their products in corn, soybeans, wheat, barley, and rice.

    Farmers have been willing partners, Rodriguez says, happy to test products that might help what can be a razor thin profit margin. But, overall, the science of applying microbial products in agriculture has been hampered by one major challenge: moving from the lab to the field. “Field work is a lot more difficult to do,” says Rodriguez. “It fails way more often.”

    Sanders and Alia Rodriguez learned the same lesson in Colombia, when the floods came.

    To the llanos

    In Columbia, Sanders and Alia Rodriguez teamed up with an agricultural college named, appropriately, they hoped, Utopia. The professors and students served as field monitors for the crops and the research. Early one morning last July, the sun barely lifting off the flat green fields, I accompanied them and a group of students as they tromped out to visit their plants. Rodriguez poked fun at Sanders’ obsession with snapping photos: “We need to be moving on!” she nudged. “Yes, yes,” he muttered, bending down to focus his lens on a spider whose web spread across the spiny leaves of a pineapple plant.

    cas
    A graduate student tends cassava in an experimental plot.

    Finally we reached the experiment. The cassava looked nearly identical, all about three feet tall, creating a waist-high carpet of broad emerald leaves glittering with droplets misted from the low, grey sky. Despite the plants’ near uniform appearance, Sanders and Rodriguez knew that underground, where the fungi were going to work, the story would be different. There, they had expected to find roots of all sizes.

    The two scientists wandered out, half obscured by foliage: Rodriguez, with tight, dark ringlets woven into a long, single braid and tucked through the back of a salmon-colored baseball cap, and Sanders, whose pale skin clearly marked him as the outsider in the group. Isabel Ceballos, the Colombian PhD student managing the project, pulled a bright pink poncho over her head to ward off the rain.

    Each of the young cassava plants had started out as six-inch sticks. The team had laid them in the earth and covered them with a shallow layer of soil. Three weeks later, when the sticks started to form root buds, the students returned and carefully squeezed a layer of fungus-filled gel beneath a portion of each plant. As the roots stretched into the soil, they pushed down through the gel, inoculating them with mycorrhizae.

    That July day in Colombia, after checking the plants in the field, Sanders, Rodriguez, and I dragged plastic chairs together. They’d cleaned up from the morning’s mud. Rodriguez had changed into a striped cotton top, and her hair cascaded in waves over to the side, revealing beaded lime green and black earrings in the shape of lizards. Sanders’ short-sleeve plaid shirt looked clean and fresh. The sun set over Utopia’s low, red-roofed buildings, and the shrill blur of insects tussled with the frogs’ boggy croaks. The air was thick and warm. Fireflies flashed languidly, slow pulses of glowing and dimming light.

    “It was a good surprise to see the experiments up and running in the field now,” says Rodriguez, relaxing into the chair. “It’s been a process to get things going here. Finally to see it happening—it’s difficult, but it’s achievable. A good feeling.”

    Early on, the team had learned that Mycovitro’s own variety of mycorrhizal fungi increased cassava yields by as much as 20%. Now their own custom, lab-grown microbes were being tested. They had two studies in the field: one in which the cassava were planted in black plastic bags, and a second later one in which the cassava were planted directly in the field, with uninnoculated cassava as a barrier. Each study would take 11 months—the full time for a cassava to reach maturity.

    The first plants in the plastic bags looked a bit sickly; they’d be harvested in October. The second experiment with the plants directly in the ground were flourishing. Those would be harvested the following spring.

    Rodriguez is generally the positive one of the pair, sure that they can find a way to work through all challenges. Sanders tends to be more cautious, more pessimistic. “In Switzerland,” he joked, “we think of every single problem that could happen, and people here in Colombia are extremely optimistic—‘No worry! It will work!’” Rodriguez laughed in response. But things were looking good. Both scientists were pleased—even excited—about what they’d seen. Rodriguez’s optimism appeared justified.

    Her sunny outlook was tested only a few weeks later. The skies of the llanos, often thick and lazy with morning drizzle, turned dark. The clouds unleashed a month’s worth of merciless rain in only 48 hours. Water swept down over the cassava. When the rains finally faded, plant matter was clogging most of the field drains. Liquid mirrors pooled across the research field. Some of the plants, their roots surrounded by water and gasping for oxygen, listed to the side.

    Ceballos, the PhD student in charge of the project, heard the news first. She panicked and ran to Rodriguez to tell her what had happened. Rodriguez panicked as well, thinking, “What are we going to do?” But she quickly regrouped. “We need data,” she told Ceballos, and then called Sanders.

    un
    Unearthing cassava roots

    After a few days, students from Utopia who were dispatched to check on the fields sent back photos. Variation 1, with the older plants trapped in plastic bags, was fine. In the second one with healthier plants, the team received an incredible turn of luck. True, many of the plants were destroyed. But almost none of them had been coated with the fungi. Instead, almost all the dead cassava were just border plants.

    Sanders was relieved. “It would have been a disaster for us,” he says, if the plants had died. It would have set the project back at least a year—and the team’s funding was due to end in the summer of 2014.

    Three months later, in October, it was time to harvest the plants in the plastic bags. Ceballos headed back to Utopia. Each day for a week, she and another graduate student worked with students, crouching down and cutting open the thick black plastic. They shoved aside the soil that clung, damp, to the roots. The cassava poked out, some thicker than others, all with pale, purplish skin, smooth and wet, peeking through the dirt. Their flesh was bright white and oozed milky droplets.

    we
    Utopia students weigh cassava roots in the field.

    The team uncovered more than a thousand roots. All were quickly weighed at Utopia. Then Ceballos hauled the best, least damaged representatives of each cassava plant back to Bogotá, nearly 800 pounds of food. She stored them in a cavernous new freezer the lab bought specifically for this purpose. Over the next few months, she tested each plant’s dry weight and evaluated its fibrousness, starch content, acid content, and other variables that attest to the overall quality.

    Sanders didn’t have high hopes for the first harvest. After all, the crops didn’t look nearly as healthy as the cassava planted straight in the field. But the results thus far have surprised—and delighted—him. The data hasn’t been published in a scientific journal yet, but, he says, “We have actually seen huge differences in the weight of the cassava roots—much larger differences than seen in the rice experiment. We thought it would work but not to such an extent.”

    Into the Mainstream

    Rusty Rodriguez’s approach is proving successful, too. In 2014, his company is releasing two products, one for rice and one for corn, and he plans to have additional products for a wider variety of crops available by 2015. Based on his company’s field research, test plants are able to tolerate more stress from swings in temperature or water availability, and they can defend themselves more effectively against pests. He says his team is now looking at helping farmers decrease the amount of fertilizer they use by employing the fungi. They’re also publishing scientific studies on their research.

    The major agricultural seed and chemical companies are taking notice. In the fall of 2013, Monsanto paid the Danish company Novozymes $300 million to form a partnership called the BioAg Alliance. Novozymes creates what they call “microbial yield and fertilizer enhancers,” among other products in a variety of sectors. The partnership strengthens Monsanto’s role in what they term “sustainable microbial technology.”

    The rest of the field seems to be following suit. The trade journal Agrow: World Crop Protection News, wrote that the biopesticide sector was finally no longer “fringe” in April of 2012, and by 2013 proclaimed that it is now an “intrinsic part of the crop protection industry.” In 2012, Bayer bought the small biopesticide company AgraQuest. Syngenta bought Pasteuria Bioscience, and also has an exclusive international deal to sell a Bacillus-based biofungicide. The FDA is testing the spraying of bacteria on tomatoes that can destroy the human-harming salmonella and prevent other forms of contamination.

    There are plenty of concerns in the field of applied microbes for agriculture. One is whether any product that is successful on one farm will be equally successful on another. Then there’s the concern about releasing microbes into new environments, which means that regulatory agencies are demanding extensive environmental tests before certifying new products.

    The Colombia team is sensitive to this, and they’re studying the existing microbial ecosystems in the presence of the new fungi. They’ve also sent a grad student into the Amazon to collect fungi from wild versions of cassava, fungi that have co-evolved with the cassava for thousands of years, in hopes that they can isolate, grow, and breed these cassava-loving fungi as well.

    film
    Thin filaments of mycorrhizal fungi form a dense network between roots.

    Sanders has an ambitious, seemingly quixotic goal that he figures could be completed in 15 years, maybe 20. He wants to breed enough genetically distinct lines of fungi and try them out with enough crops in enough different environments so that researchers can create what’s called an “association map.” He would start by characterizing the genetics of the fungus and then map them against the crops and the environment. By peering deeply enough into the genetic code, he hopes we can catch a glimpse of which genes make quinoa grow better in Peru, for example. That way scientists could breed a new species of fungus and know in advance which crop it would improve without having to undertake years of trials.

    It seems nearly impossible to do enough studies, with enough crops, in enough farmland around the world to generate such a map. Genetic solutions also frequently seem to dance out of reach. Sanders insists, though, that big, crazy scientific goals in agriculture are crucial. “As one of the senior people in the Food and Agriculture Organization of the United Nations said to me, ‘If scientists don’t do that, then we are in trouble in the future.’ I believe he is right.”

    Sanders and Rodriguez are now setting up studies in Africa, where farmers, like many in Colombia, can find it difficult to pay for fertilizers and suffer from low yields. Cassava is also one of the top crops there. The team has formed partnerships with local research centers to test varieties of fungi on cassava crops in African soil. They’re hoping the research will begin soon, but they’re still searching for funding.

    The scientists believe they’re on their way to achieving their goal of helping farmers grow more food, sustainably. Says Sanders, “We really have to be working extremely hard now to produce the technology that’s going to be used in 10, 15, 20 years’ time. Even if we have something that’s good now, we don’t stop. We have to go for something that’s much better.”

    See the full article here.

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  • richardmitnick 3:45 pm on October 2, 2014 Permalink | Reply
    Tags: , , Biota, ,   

    From Brown- “Invasive species: Darwin had it right” 

    Brown University
    Brown University

    October 2, 2014
    David Orenstein 401-863-1862

    Based on insights first articulated by Charles Darwin, professors at Brown University and Syracuse University have developed and tested the “evolutionary imbalance hypothesis [ETH]” to help predict species invasiveness in ecosystems. The results suggest the importance of accounting for the evolutionary histories of the donor and recipient regions in invasions.

    Dov Sax of Brown University and Jason Fridley of Syracuse University aren’t proposing a novel idea to explain species invasiveness. In fact, Charles Darwin articulated it first. What’s new about Sax and Fridley’s “Evolutionary Imbalance Hypothesis” (EIH) is that they’ve tested it using quantifiable evidence and report in Global Ecology and Biogeography that the EIH works well.

    The EIH idea is this: Species from regions with deep and diverse evolutionary histories are more likely to become successful invaders in regions with less deep, less diverse evolutionary histories. To predict the probability of invasiveness, ecologists can quantify the imbalance between the evolutionary histories of “donor” and “recipient” regions as Sax and Fridley demonstrate in several examples.

    dar
    Survival of the fittest: An iceplant, from a region of high diversity in South Africa, is overtopping and killing a native shrub on the New Zealand coast, a region with far less diversity. Plant lines that have had to struggle against robust competition are strong invaders in areas where native plants have had an easier time. Photo: Jason Fridley

    Darwin’s original insight was that the more challenges a region’s species have faced in their evolution, the more robust they’ll be in new environments.

    “As natural selection acts by competition, it adapts the inhabitants of each country only in relation to the degree of perfection of their associates,” Darwin wrote in 1859. Better tested species, such as those from larger regions, he reasoned, have “consequently been advanced through natural selection and competition to a higher stage of perfection or dominating power.”

    To Sax and Fridley the explanatory power of EIH suggests that when analyzing invasiveness, ecologists should add historical evolutionary imbalance to the other factors they consider.

    “Invasion biology is well-studied now, but this is never listed there even though Darwin basically spelled it out,” said Sax, associate of ecology and evolutionary biology. “It certainly hasn’t been tested before. We think this is a really important part of the story.”

    cd
    Charles Darwin

    The theory was correct. What was missing was quantifiable evidence. That evidence has now been collected.

    Evidence for EIH

    Advancing Darwin’s insight from idea to hypothesis required determining a way to test it against measurable evidence. The ideal data would encapsulate a region’s population size and diversity, relative environmental stability and habitat age, and the intensity of competition. Sax and Fridley found a suitable proxy: “phylogenetic diversity (PD)” , an index of how many unique lineages have developed in a region over the time of their evolution.

    “All else equal, our expectation is that biotas represented by lineages of greater number or longer evolutionary history should be more likely to have produced a more optimal solution to a given environmental problem, and it is this regional disparity, approximated by PD, that allows predictions of global invasion patterns,” they wrote.

    With a candidate measure, they put EIH to the test.

    Using detailed databases on plant species in 35 regions of the world, they looked at the relative success of those species’ invasiveness in three well-documented destinations: Eastern North America, the Czech Republic, and New Zealand.

    They found that in all three regions, the higher the PD of a species’ native region, the more likely it was to become invasive in its new home. The size of the effect varied among the three regions, which have different evolutionary histories, but it was statistically clear that plants forged in rough neighborhoods were better able to bully their way into a new region than those from evolutionarily more “naive” areas.

    Sax and Fridley conducted another test of the EIH in animals by looking at cases where marine animals were suddenly able to mix after they became united by canals. The EIH predicts that an imbalance of evolutionary robustness between the sides, would allow a species-rich region to dominate a less diverse one on the other side of the canal by even more than a mere random mixing would suggest.

    The idea has a paleontological precedent. When the Bering land bridge became the Bering Strait, it offered marine mollusks a new polar path between the Atlantic and Pacific Oceans. Previous research has shown that more kinds of mollusks successfully migrated from the diverse Pacific to the less diverse Atlantic than vice-versa, and by more so than by their relative abundance.

    In the new paper, Sax and Fridley examined what has happened since the openings of the Suez Canal in Egypt, the Erie Canal in New York, and the Panama Canal. The vastly greater evolutionary diversity in the Red Sea and Indian Ocean compared to the Mediterranean Sea and the Atlantic led to an overwhelming flow of species north through the Suez.

    But evolutionary imbalances across the Erie and Panama Canals were fairly small (the Panama canal connects freshwater drainages of the Atlantic and Pacific that were much more ecologically similar than the oceans) so as EIH again predicts, there was a more even balance of cross-canal species invasions.

    Applicable predictions

    Sax and Fridley acknowledge in the paper that the EIH does not singlehandedly predict the success of individual species in specific invasions. Instead it allows for ecosystem managers to assess a relative invasiveness risk based on the evolutionary history of their ecosystem and that of other regions. Take, for instance, a wildlife official in a historically isolated ecosystem such as an island.

    “They already know to be worried, but this would suggest they should be more worried about imports from some parts of the world than others,” Sax said.

    Not all invasions are bad, Sax noted. Newcomers can provide some ecosystem services — such as erosion control — more capably if they can become established. The EIH can help in assessments of whether a new wave of potential invasion is likely to change the way an ecosystem will provide its services, for better or worse.

    “It might help to explain why non-natives in some cases might improve ecosystem functioning,” Sax said.

    But perhaps Darwin already knew all that.

    See the full article here.

    Welcome to Brown

    Rhode Island Hall: Rhode Island Hall’s classical exterior was recently renovated with a modern interiorRhode Island Hall: Rhode Island Hall’s classical exterior was recently renovated with a modern interior

    Located in historic Providence, Rhode Island and founded in 1764, Brown University is the seventh-oldest college in the United States. Brown is an independent, coeducational Ivy League institution comprising undergraduate and graduate programs, plus the Alpert Medical School, School of Public Health, School of Engineering, and the School of Professional Studies.

    With its talented and motivated student body and accomplished faculty, Brown is a leading research university that maintains a particular commitment to exceptional undergraduate instruction.

    Brown’s vibrant, diverse community consists of 6,000 undergraduates, 2,000 graduate students, 400 medical school students, more than 5,000 summer, visiting and online students, and nearly 700 faculty members. Brown students come from all 50 states and more than 100 countries.

    Undergraduates pursue bachelor’s degrees in more than 70 concentrations, ranging from Egyptology to cognitive neuroscience. Anything’s possible at Brown—the university’s commitment to undergraduate freedom means students must take responsibility as architects of their courses of study.

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  • richardmitnick 5:43 pm on September 8, 2014 Permalink | Reply
    Tags: , Biota,   

    From EMSL: “Developing Better Biomass Feedstock” 

    EMSL
    Environmental Molecular Sciences Laboratory (EMSL)

    No Date
    No Writer Credit

    Multi-omics unlocking the workings of plants

    Biomass holds great promise as a fuel source to generate renewable energy to help the United States achieve energy independence. Kim Hixson is applying what she’s learned from a lowly weed to bioengineer better biomass feedstock.

    kh
    Hixson, an EMSL senior research scientist, is collaborating with Norman Lewis, a regents professor and director of the Institute of Biological Chemistry at Washington State University in Pullman. Together they are using EMSL’s multi-omics capabilities to better understand how manipulating the genes in one plant can be applied to other plants to improve their potential as biofuel and biochemical feedstock.

    “Our research is hypothesis driven, but there’s also a lot of discovery,” says Hixson. “The more we study biology, the more we see how interconnected things are in nature.”

    More Than a Weed

    Central to this research is Arabidopsis, a model plant system. A small flowering plant related to cabbage, Arabidopsis makes for an ideal plant model. Its genome has been sequenced and is easy to genetically modify. Hixson calls it the “lab rat of the plant world.”

    ara
    Thale cress (Arabidopsis thaliana)

    two
    Arabidopsis is a small flowering plant related to cabbage and a model organism used to research plant biology. The plant on the left is wild-type Arabidopsis at five weeks. The plant on the right is Arabidopsis at five weeks with ADT-related genes knocked out, reducing the levels of lignin.

    Arabidopsis has a six-member isoenzyme family of arogenate dehydratases, or ADTs. These enzymes are involved in the catalytic reactions that turn arogenic acid, a metabolite, into phenylalanine, an essential metabolite which is incorporated directly into proteins or is further modified into other chemicals such as flavonoids, coumarins, anthocyanins and lignin.

    Hixson’s research found hundreds of different changes occurring in the plant due to the modifications in the ADT composition. The collaborators at WSU discovered that out of the six ADTs in Arabidopsis, five ADTs are seemingly linked to the production of phenylalanine utilized in the phenylpropanoid pathway, which is involved in lignin production. Lignin gives plants their recalcitrance; it’s hydrophobic and difficult to degrade. Lignin is the structural material that makes the sugars in plants difficult to extract when making biofuels.

    “It is well known that a significant amount of the carbon dioxide that Arabidopsis fixes goes into the phenylpropanoid pathway and ultimately ends up as lignin,” says Hixson. “This is very important from the perspective of turning plant material into biofuel.”

    Hixson’s Arabidopsis studies earned her an American Chemical Society Withycombe-Charalambous Graduate Student Symposium Award. At the symposium she presented some of her findings from the multi-omics analysis of the gene knockouts conducted at EMSL. The researchers analyzed several knockout mutants of ADTs, including single, double, triple and quadruple knockout mutants, with each mutant strain producing varying degrees of lignin reduction. They found that knocking out multiple ADTs and specific ADTs leads to a measured reduction of lignin in the plants.

    By knocking out different combinations of the ADT-related genes, the researchers produced plants with various levels of lignin. In the most extreme case where they knocked out four ADT-related genes, the plant was unable to hold its own weight and became vine-like.

    “We knew there were a lot of changes going on in this plant, but we didn’t know at the molecular level what those changes were,” says Hixson. “The questions about what pathways are being changed and what potential points of regulation are being up-regulated or repressed are precisely what transcriptomics coupled with proteomics can answer.”

    Other findings from Hixson’s research showed knocking out ADT genes alters the photosynthesis machinery and pathways in the mutant plants. For reasons not completely understood, knocking out ADT genes causes the mutant plant systems to produce more photosynthetic machinery, potentially fixing more carbon, but an overall increase in plant mass was not observed. Using transcriptomics and proteomics techniques at EMSL, the researchers were able to look at the other pathways and genes that were changed in the mutant plants. They found the photorespiration pathways were also up-regulated. While more carbon was potentially being fixed, more of it was likely being lost or released back into the atmosphere through the photorespiration pathways.

    “This is potentially a very useful discovery,” says Hixson. “In future bioengineering attempts we may need to incorporate strategies to counteract carbon loss via photorespiration which would potentially improve the rates of biomass growth in ADT-altered plants used for biofuels or biochemicals.”

    Applying Their Findings to Poplars

    samples
    Researchers collect samples of mutant poplars to undergo multi-omics analysis to determine if the genetic changes affect other pathways and functions in the tree.
    The research has developed several lines of mutant Arabidopsis by altering the composition of the ADT genes, which ultimately decreases the amount of lignin these plants produce. Questions arise about how much ADT can be lessened and thus how much lignin can be reduced before a plant in a real world setting shows detrimental growth affects. Additionally it is important to understand how these changes alter other pathways and other systems within the plant, and how the changes are altering the plant system as a whole.

    “These are really important questions, not so much in Arabidopsis, which is just a little weed,” says Hixson. “But we’ve started to incorporate some of the same knockouts into poplar trees, which show good potential as a biofuel feedstock.”

    Poplar trees are native to the Pacific Northwest and widely used as a feedstock in the paper industry. The Department of Energy is interested in the poplar as a biofuel. Within the missions of EMSL and the DOE Office of Biological and Environmental Research is a charge to reduce the United States’ dependence on foreign oil and to develop technology for alternative fuel and chemical options.

    Hixson hopes the manipulations in the Arabidopsis translate to other plants, such as poplars. Poplar has a larger and more complex genome than Arabidopsis. She will test the altered poplars at EMSL with multi-omics analysis to see how the transcriptome and proteome changes and if she sees the same types of response in the tree as she saw in the Arabidopsis.

    “I expect a lot of things are going to be similar between the two plants,” Hixson says. “But they are different systems and it will be interesting to see the changes in the poplar compared to the Arabidopsis at the molecular level.”

    The researchers have incorporated the ADT knockouts into poplar trees to test if the amount of lignin can be reduced and how far it can be reduced without damaging effects to the tree as a whole. Hixson recently collected samples of the mutant poplars from a test plot and greenhouse in western Washington. She will use EMSL’s multi-omics capabilities to determine if a change to one pathway affects other pathways and functions in the tree. According to Hixson, proteomics and transcriptomics identify what genes are being affected, either positively or negatively. This information will be useful when bioengineering poplars as a feedstock. The data will also be incorporated into her dissertation for her doctorate in molecular plant sciences from WSU.

    Other Proposals: Where few Have Gone Before

    The study with the poplar trees is an approved EMSL user project. Lewis is the principal investigator and Hixson is a collaborator. Lewis is also Hixson’s faculty advisor.

    Hixson and Lewis have several research proposals they are hoping get approved. In collaboration with Mary Lipton, an integrative omics scientist at Pacific Northwest National Laboratory, and other scientists, they submitted a proposal to NASA. In this study several of the mutant Arabidopsis would be sent into outer space to test what happens to reduced-lignin plants in a microgravity environment.

    “I really hope NASA approves it,” Hixson says. “The findings could be very interesting.”

    In another submission, this one in response to an EMSL internal call, Hixson and Lewis are proposing to study red alder trees as an ideal biofuel source. A red alder grows almost as fast and dense as a poplar, but it forms specialized symbiotic relationships in its root system. These symbiotic relationships produce root nodules which can fix nitrogen, allowing red alders to thrive without added fertilizer and grow on marginal lands. Hixson believes red alder has the potential to be a highly valuable source for biomass feedstock or other wood-based materials.

    For this study, they will apply what they learned from the Arabidopsis and poplar research. The proposal includes a full genetic characterization of the red alder and a multi-omics study of the tree’s association with two ubiquitous root symbionts.

    “Our end goal is to gather enough information throughout multi-omics evaluations to be able to bioengineer the ideal biofuel and biochemical feedstock,” says Hixson. “We’re not there yet, but we’re working on it.”

    See the full article here.

    EMSL is a national scientific user facility that is funded and sponsored by DOE’s Office of Biological & Environmental Research. As a user facility, our scientific capabilities – people, instruments and facilities – are available for use by the global research community. We support BER’s mission to provide innovative solutions to the nation’s environmental and energy production challenges in areas such as atmospheric aerosols, feedstocks, global carbon cycling, biogeochemistry, subsurface science and energy materials.

    A deep understanding of molecular-level processes is critical to gaining a predictive, systems-level understanding of the impacts of aerosols and terrestrial systems on climate change; making clean, affordable, abundant energy; and cleaning up our legacy wastes. Visit our Science page to learn how EMSL leads in these areas, through our Science Themes.

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  • richardmitnick 12:29 pm on September 3, 2014 Permalink | Reply
    Tags: , , Biota   

    From Astrobiology: “Exceptionally well preserved insect fossils from the Rhône Valley” 

    Astrobiology Magazine

    Astrobiology Magazine

    Sep 3, 2014
    No Writer Credit

    First fossil insect discoveries in this area comprise the oldest water treader and traces of activities in sediment and on plants

    fossile
    This is a fossilized aquatic bug from the Orbagnoux outcrop of the Rhone valey: Gallomesovelia grioti (scale bar 1 mm). Credit: Nel Andre

    In Bavaria, the Tithonian Konservat-Lagerstätte of lithographic limestone is well known as a result of numerous discoveries of emblematic fossils from that area (for example, Archaeopteryx).

    arch
    Archaeopteryx Temporal range: Late Jurassic, 150.8–148.5Ma The Berlin specimen (A. siemensii)

    Now, for the first time, researchers have found fossil insects in the French equivalent of these outcrops – discoveries which include a new species representing the oldest known water treader.

    Despite the abundance of fossils in the equivalent Bavarian outcrops, fewer fossils have been obtained from the Late Kimmeridgian equivalents of these rocks in the departments of Ain and Rhône in France. Many outcrops are recorded (for example Cerin and ), but the fauna found there is essentially of marine origin, being made up of crustaceans and fishes. Some layers have provided dinosaur footprints, but until today’s announcement the only known terrestrial organisms were plant remains transported into the ancient lagoons.

    During the course of two field expeditions in 2012 and 2013 French researchers working with the help of two active teams of amateur scientists (Société des Naturalistes et Archéologues de l’Ain and the Group ‘Sympetrum Recherche et Protection des Libellules’) discovered the first insects from the Orbagnoux outcrop, together with traces of activities of these organisms on leaves and in the sediment.

    leaves
    These are insect traces on a Zamites leave. (A) print; (B) counterprint (scale bars 10 mm). Credit: Nel Andre

    The newly discovered insect was described today, in the open access journal PeerJ. The bug was 6 mm long and is the oldest record of the aquatic bug lineage of the Gerromorpha which comprises the water striders and the water measurers. This is the oldest known water treader (Mesoveliidae), the sister group of all other gerromorphan lineages. In a similar manner to some of its recent relatives, this aquatic bug could have lived in brackish environments.

    strider
    Water Strider (Gerridae)

    meas
    Water Measurer (Hydrometridae)

    In addition, traces of insect activity on plants were found, comprising surface feeding traces on Zamites leaves. Such traces are quite rare in the fossil record and in this situation they demonstrate the presence of strictly terrestrial insects on the emerged lands that were surrounded by these Jurassic lagoons.

    The exquisite quality of preservation of the fossils suggests that these rocks are likely to provide new fossil insects of crucial importance for the knowledge of the Upper Jurassic insect fauna, an important transition period in the evolution of the terrestrial environments towards the Lower Cretaceous diversification of the flowering plants.

    See the full article here.

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  • richardmitnick 8:50 am on September 1, 2014 Permalink | Reply
    Tags: , , Biota, ,   

    From Astrobio: “DNA May Have Had Humble Beginnings As Nutrient Carrier” 

    Astrobiology Magazine

    Astrobiology Magazine

    Sep 1, 2014
    Adam Hadhazy

    New research intriguingly suggests that DNA, the genetic information carrier for humans and other complex life, might have had a rather humbler origin. In some microbes, a study shows, DNA pulls double duty as a storage site for phosphate. This all-important biomolecule contains phosphorus, a sometimes hard-to-get nutrient.

    dna

    Maintaining an in-house source of phosphate is a newfound tactic for enabling microorganisms to eke out a living in harsh environments, according to a new study published in the open-access, peer reviewed scientific journal PLOS ONE. The finding bodes well for life finding a way, as it were, in extreme conditions on worlds less hospitable than Earth.

    The results also support a second insight: DNA might have come onto the biological scene merely as a means of keeping phosphate handy. Only later on in evolutionary history did the mighty molecule perhaps take on the more advanced role of genetic carrier.

    “DNA might have initially evolved for the purpose of storing phosphate, and the various genetic benefits evolved later,” said Joerg Soppa, senior author of the paper and a molecular biologist at Goethe University in Frankfurt, Germany.

    Unraveling life’s origins

    Scientists continue to investigate the development of self-replicating, intricate sets of chemistry — in other words, life — from the chemical compounds thought available on early Earth. Out of this mixture of prebiotic chemicals, two nucleic acids — RNA and DNA — emerged as champions.

    early
    Early Earth, in an artist’s impression, where somehow complex, self-replicating chemistry (in other words, life) emerged. Credit: Peter Sawyer / Smithsonian Institution

    Today, these two types of biomolecules serve as the genetic information carriers for all Earthly biota. RNA on its own suffices for the business of life for simpler creatures, such as some viruses. Complex life, like humans, however, relies on DNA as its genetic carrier.

    Astrobiologists want to understand the origin of DNA and its genetic cousin, RNA, because figuring out how life got started here on Earth is key for gauging if it might ever develop on alien planets.

    Many researchers think RNA must have preceded DNA as the genetic molecule of choice. RNA is more versatile, acting as both genetic code and a catalyst for chemical reactions. Explicating the rise of DNA as a genetic material directly from RNA, however, is tricky. Compared to RNA, DNA needs significantly more supporting players for it to work well in a biological setting.

    “The switch from RNA to DNA is not easy because many additional enzymes are required for DNA genomes,” said Soppa.

    This unclear transition from RNA to DNA opens the door for a precursor to DNA possibly having a more mundane job. The new study offers an attractive explanation: that DNA was a fancy way to store nutrients in cells.

    Phosphate depot?

    DNA is chock-full of phosphate. Cells depend on phosphate to form not only DNA and RNA, but also related genetic machinery, such as the ribosome. Phosphate, furthermore, is a must for building the molecule ATP, life’s energy carrier, as well as fatty membrane molecules, certain phospho-proteins and phospho-sugars, and more.

    ds
    The shores of the Dead Sea, which borders Jordan, Palestine and Israel. As the lowest and saltiest lake in the world, it is home to some extreme creatures. Image Credit: Aaron L. Gronstal

    “Phosphate is important for an immense set of biomolecules,” said Soppa.

    Unfortunately for some microbes, ample phosphate is not always available. For example, in salty, nutrient-poor habitats, such as the Dead Sea in the Middle East, an organism called Haloferax volcanii must regularly “eat” ambient DNA to obtain phosphate (plus some other nutritional goodies, such as nitrogen).

    Notably, H. volcanii can still survive and reproduce when phosphorus, the element needed to make phosphate, is lacking. Somehow, then, the microbe must turn to an inner source of phosphate, for otherwise it should cease to grow.

    In their study, Soppa and colleagues from Germany, the United States and Israel sought out this source. The nature of H. volcanii provided some clues. The organism is classified as archaea, one of the three domains of life, in addition to bacteria and eukarya, the latter encompassing all multicellular organisms, from fungi to fruit flies. Many archaea and bacteria — collectively, “prokaryotes”— have just one, circular chromosome. Eukaryotes, like us, on the other hand, can have any number of the chunky pieces of DNA, RNA and proteins. (Humans have 23 pairs of different chromosomes, for the record.) H. volcanii is unusual. It has 20 copies of the same chromosome when it’s growing happily under favorable conditions, and 10 when nutrients are exhausted and it reaches a stationary phase.

    Strength in numbers

    Lots of chromosome copies are good to have in a pinch. So-called polyploidal organisms like H. volcanii use their copious chromosomes to tough it out through bad situations, such as high radiation exposure or total dry-outs, called desiccation. Either scenario causes the strands in chromosomal DNA to break. For single-chromosome species, only a few breaks lead to death because it is impossible to repair a chromosome scattered into fragments.

    But if there are multiple copies of the cracked chromosomes, fragments can fortuitously line up. Rather like how a jigsaw puzzle is easier to put together if there are numerous duplicates of each necessary piece, the chromosome shards can sync up and restore a functional chromosome.

    hv
    H. Volcanii grown in culture. Credit: Yejineun/Wikipedia

    “In polyploid species, the fragments generated from different copies of the chromosome overlap, and it is possible to regenerate an intact chromosome from overlapping fragments,” said Soppa.

    Desperate times, desperate measures

    To investigate if H. volcanii‘s extra chromosomes might help the archaeon survive low phosphate conditions, Soppa and colleagues starved the organism in the lab of the critical substance. The microbe continued to reproduce by splitting one cell apart into two. Interestingly, chromosome counts diminished in the “parent” and the “daughter” cells.

    “From quantifying the number of chromosomes prior to and after growth in the absence of phosphate, we have found that about 30 percent of the chromosomes are ‘missing’ afterwards,” said Soppa.

    The numbers for another potential in-house source of phosphate, H. volcanii‘s ribosomes, however, remained steady. The most likely explanation, then, of the microorganism’s hardiness when facing a phosphate nutrient shortage: H. volcanii simply cannibalizes some of its own chromosomes.

    As further verification, Soppa and colleagues tested the survival skills of H. volcanii cells that contained varying numbers of chromosome copies. Those archaea with just two copies of their chromosome turned out to be more than five times as sensitive to desiccation as those H. volcanii with a hefty complement of 20 chromosomes.

    Life, undaunted

    This newly described benefit of polyploidy in H. volcanii is a fresh demonstration of how life can make do in severe environments. So-called extremophiles have been discovered in recent decades thriving in strongly acidic hot springs, within liquid asphalt, and in other eyebrow-raising niches. Salt-tolerant bacteria and archaea, like H. volcanii, have been found to survive in deserts, simulated Mars conditions, and even the rigors of a space flight. We should not be surprised, perhaps, if life has managed to take hold on formidable worlds.

    rw
    Extremophile microbes have been found that can survive in the polluted Rio Tinto River in Spain. Mining in the river’s vicinity has led to its waters having a high heavy metal content and very low pH, though the bacteria themselves, through their metabolism, also likely contribute to the intense acidity. Image credit: Leslie Mullen

    “The understanding of how harsh the conditions can be that can be survived by some archaea and bacteria helps us to be more optimistic that life could have evolved at very rough and unsuitable places on early Earth or on other planets,” said Soppa.

    The new role ascribed to DNA, as phosphate storage, might help to explain how a completely RNA-dominated primordial era began sharing genetic duties with DNA. Life did not leap from RNA to DNA. Rather, DNA, slowly but surely, learned new tricks.

    “The hypothesis that DNA might have evolved as a storage polymer and became genetic material later, makes the step from RNA to DNA as genetic material easier, because it then would be a two-step and not a one-step process,” said Soppa. “DNA would have been around, and during long time spans additional roles could have been evolved.”

    See the full article here.
    Astrobiology Magazine is a NASA-sponsored online popular science magazine. Our stories profile the latest and most exciting news across the wide and interdisciplinary field of astrobiology — the study of life in the universe. In addition to original content, Astrobiology Magazine also runs content from non-NASA sources in order to provide our readers with a broad knowledge of developments in astrobiology, and from institutions both nationally and internationally. Publication of press-releases or other out-sourced content does not signify endorsement or affiliation of any kind.
    Established in the year 2000, Astrobiology Magazine now has a vast archive of stories covering a broad array of topics.

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