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The DOE Science News Source is a Newswise initiative to promote research news from the Office of Science of the DOE to the public and news media.
  • 2018-01-22 11:05:09
  • Article ID: 688257

Researchers Reveal How Microbes Cope in Phosphorus-Deficient Tropical Soil

  • Credit: Melanie Mayes and Andy Sproles/Oak Ridge National Laboratory, U.S. Dept. of Energy

    An Oak Ridge National Laboratory-led research team found genes for production of phytase enzymes that would be released by tropical soil microbes. Phytase enzymes will attack phytate molecules, releasing much needed phosphate molecules for the microbes’ survival. The soil samples were collected in phosphorus-rich and -poor experimental sites at the Smithsonian Tropical Research Institute in the Republic of Panama.

  • Credit: Melanie Mayes/Oak Ridge National Laboratory, U.S. Dept. of Energy

    Soil scientists from Oak Ridge National Laboratory uncovered how certain microbes cope in a phosphorus-poor environment to survive in a tropical ecosystem.

OAK RIDGE, Tenn., Jan. 22, 2018 – A team led by the Department of Energy’s Oak Ridge National Laboratory has uncovered how certain soil microbes cope in a phosphorus-poor environment to survive in a tropical ecosystem. Their novel approach could be applied in other ecosystems to study various nutrient limitations and inform agriculture and terrestrial biosphere modeling.

Phosphorus is a critical nutrient for global biological processes, such as collecting the sun’s energy during photosynthesis and degrading plant debris and soil organic matter. Most tropical ecosystems endure long-term weathering that leaches phosphorus from soil.

The ORNL-led team set out to discover how soil microbial communities respond to the lack of phosphorus and other nutrient deficiencies at the molecular level.

They collected soil samples at the Smithsonian Tropical Research Institute in the Republic of Panama, an experimental field site with phosphorus-rich plots and unfertilized control plots.

“This was the perfect place to test the optimal foraging theory, which is a model that helps predict an organism’s behavior when searching for resources,” said Chongle Pan, ORNL senior staff scientist and joint associate professor at the University of Tennessee. “We learned how this theory plays out when applied to microbial communities as they compete for nutrients.”

The team analyzed the behaviors of many genes and proteins, and in the phosphorus-deficient, untreated soil, they found an increased number of genes responsible for producing phosphorus-acquiring enzymes. They also discovered more than 100 genes that work to pull phosphorus from phytate, which is a complex organic compound found in plant tissue.

“Finding so many genes to break apart and transport such a complex molecule tells us that microbes are hungry for phosphorus in untreated soil,” said Melanie Mayes, an ORNL senior staff scientist who studies multi-scale environmental processes.

Conversely, she noted that when phosphorus was plentiful, more genes needed to acquire complex carbon compounds were present. “The microbial community prioritizes the breakdown of the most needed nutrients, focusing efforts on the most limiting element to balance their overall nutritional needs,” she said.

The team ran each soil sample through a series of rigorous and comprehensive analyses. The DOE Joint Genome Institute conducted deep sequencing of the soils’ metagenomes, or genetic material recovered directly from the soil. ORNL then used mass spectrometry and metaproteomics to identify more than 7,000 proteins in each sample.

ORNL’s Titan supercomputer quickly analyzed the large amounts of metagenomics and metaproteomics data, comparing microbial activities in phosphorus-rich and -poor soils. Environmental Molecular Sciences Laboratory scientists further characterized the soils’ organic matter at Pacific Northwest National Laboratory.

These unique tools working together enabled one of the deepest proteogenomics studies done on soil microbial communities, according to Pan.

The ORNL-led team plans to continue their research to characterize the ecology and evolution of soil microbial communities in nutrient-poor environments, which has applications in agriculture and terrestrial biosphere modeling worldwide. Additionally, Mayes and her team are incorporating metagenomics information into nutrient cycling models under a DOE Early Career Research Program Award.

Results from their three-year study titled, “Community Proteogenomics Reveals the Systemic Impact of Phosphorus Availability on Microbial Functions in Tropical Soil,” were published in Nature Ecology & Evolution.

The paper’s coauthors included Qiuming Yao, Zhou Li, Yang Song, Melanie A. Mayes and Chongle Pan of ORNL; S. Joseph Wright and Benjamin L. Turner of the Smithsonian Tropical Research Institute; Terry C. Hazen, University of Tennessee-ORNL Governor’s Chair for Environmental Biotechnology; Xuan Guo of UT; Susannah G. Tringe of the DOE Joint Genome Institute; and Malak M. Tfaily and Ljiljana Paša-Tolic of Pacific Northwest National Laboratory.

The research was supported by the Laboratory Directed Research and Development program at ORNL. Metagenomic sequencing was conducted by the DOE Joint Genome Institute and soil organic matter analyses were performed using Fourier-transform ion cyclotron resonance mass spectrometry by PNNL’s Environmental Molecular Sciences Laboratory, both DOE Office of Science User Facilities. This work also leveraged the Oak Ridge Leadership Computing Facility, a DOE Office of Science User Facility.

ORNL is managed by UT-Battelle for DOE’s Office of Science. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit http://science.energy.gov/.

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Lawrence Livermore Issues Combined State-by-State Energy and Water Use Flow Charts

For the first time, Lawrence Livermore National Laboratory (LLNL) has issued state-by-state energy and water flow charts in one location so that analysts and policymakers can find all the information they need in one place.

Battery's Hidden Layer Revealed

An international team led by Argonne National Laboratory makes breakthrough in understanding the chemistry of the microscopically thin layer that forms between the liquid electrolyte and solid electrode in lithium-ion batteries. The results are being used in improving the layer and better predicting battery lifetime.

Ramp Compression of Iron Provides Insight into Core Conditions of Large Rocky Exoplanets

A team of researchers from Lawrence Livermore National Laboratory (LLNL), Princeton University, Johns Hopkins University and the University of Rochester have provided the first experimentally based mass-radius relationship for a hypothetical pure iron planet at super-Earth core conditions. This discovery can be used to evaluate plausible compositional space for large, rocky exoplanets, forming the basis of future planetary interior models, which in turn can be used to more accurately interpret observation data from the Kepler space mission and aid in identifying planets suitable for habitability.

Getting Magnesium Ions to Pick Up the Pace

Magnesium ions move very fast to enable a new class of battery materials.

Valleytronics Discovery Could Extend Limits of Moore's Law

Research appearing today in Nature Communications finds useful new information-handling potential in samples of tin(II) sulfide (SnS), a candidate "valleytronics" transistor material that might one day enable chipmakers to pack more computing power onto microchips. 

Scientists Use Machine Learning to Speed Discovery of Metallic Glass

SLAC and its collaborators are transforming the way new materials are discovered. In a new report, they combine artificial intelligence and accelerated experiments to discover potential alternatives to steel in a fraction of the time.

Seeing How Next-Generation Batteries Power-Up

Scientists directly see how the atoms in a magnesium-based battery fit into the structure of electrodes.

A Heavyweight Solution for Lighter-Weight Combat Vehicles

Researchers at Pacific Northwest National Laboratory have developed and successfully tested a novel process - called Friction Stir Dovetailing - that joins thick plates of aluminum to steel. The new process will be used to make lighter-weight military vehicles that are more agile and fuel efficient.

How to Turn Light Into Atomic Vibrations

Converting laser light into nuclear vibrations is key to switching a material's properties on and off for future electronics.

Could Holey Silicon Be the Holy Grail of Electronics?

Electronics miniaturization has put high-powered computing capability into the hands of ordinary people, but the ongoing downsizing of integrated circuits is challenging engineers to come up with new ways to thwart component overheating.


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Argonne Selects Innovators From Across Nation to Grow Startups

Argonne announces second cohort of Chain Reaction Innovations.

Brookhaven Lab Materials Physicist Yimei Zhu Receives 2018 Distinguished Scientist Award from the Microscopy Society of America

How do complex atomic and electronic interactions impact material properties? Using electron microscopy instrumentation and methods he developed, Yimei Zhu has been investigating this question for the past 30 years. The Microscopy Society of America is now recognizing his contributions.

SLAC Produces First Electron Beam with Superconducting Electron Gun

Accelerator scientists at the Department of Energy's SLAC National Accelerator Laboratory are testing a new type of electron gun for a future generation of instruments that take snapshots of the atomic world in never-before-seen quality and detail, with applications in chemistry, biology, energy and materials science.

U.S., India Sign Agreement Providing for Neutrino Physics Collaboration at Fermilab and in India

Earlier today, April 16, 2018, U.S. Secretary of Energy Rick Perry and India's Atomic Energy Secretary Dr. Sekhar Basu signed an agreement in New Delhi to expand the two countries' collaboration on world-leading science and technology projects. It opens the way for jointly advancing cutting-edge neutrino science projects under way in both countries: the Long-Baseline Neutrino Facility (LBNF) with the international Deep Underground Neutrino Experiment (DUNE) hosted at the U.S. Department of Energy's Fermilab and the India-based Neutrino Observatory (INO).

Nanomaterials Expert Ganpati Ramanath Named Fellow of Materials Research Society

Nanomaterials expert Ganpati Ramanath, the John Tod Horton '52 Professor of Materials Science and Engineering at Rensselaer Polytechnic Institute, has been named a fellow of the Materials Research Society (MRS) "for developing creative approaches to realize new nanomaterials via chemically directed nanostructure synthesis and assembly and for tailoring interfaces in electronics and energy applications using molecular nanolayers."

Doing the Neutron Dance

Two materials scientists, Suzanne te Velthuis and Stephan Rosenkranz, have been named fellows of the Neutron Scattering Society of America (NSSA).

Hirohisa Tanaka Joins SLAC to Push Limits of Neutrino Physics

Accomplished neutrino physicist Hirohisa Tanaka has joined the Department of Energy's SLAC National Accelerator Laboratory as a professor of particle physics and astrophysics. He oversees a group at the lab that is preparing for research with the future Deep Underground Neutrino Experiment (DUNE) at the Long-Baseline Neutrino Facility (LBNF). The experiment will give scientists unprecedented opportunities to learn more about neutrinos - fundamental particles with mysterious properties that could play crucial roles in the evolution of the universe.

University Teams to Compete in Department of Energy's 2018 National Cyber Defense Competition

The U.S. Department of Energy is proud to announce the 29 university teams selected to compete in the third annual Cyber Defense Competition (CDC), taking place April 6-7, 2018.

Jefferson Lab Announces May 19 Public Open House

The free event is open to the public and offers an opportunity for people of all ages to spend the day exploring this world-class research facility. The biennial open house features tours of the lab's unique particle accelerator facilities, as well as hands-on activities and interactive displays and demonstrations.


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Getting Magnesium Ions to Pick Up the Pace

Magnesium ions move very fast to enable a new class of battery materials.

Seeing How Next-Generation Batteries Power-Up

Scientists directly see how the atoms in a magnesium-based battery fit into the structure of electrodes.

Worm-Inspired Tough Materials

Scientists mimic a worm's lethal jaw to design and form resilient materials.

How to Turn Light Into Atomic Vibrations

Converting laser light into nuclear vibrations is key to switching a material's properties on and off for future electronics.

Superacids Are Good Medicine for Super Thin Semiconductors

Scientists demonstrated that powerful acids heal certain structural defects in synthetic films.

Tubular Science Improves Polymer Solar Cells

Novel engineered polymers assemble buckyballs into columns using a conventional coating process.

Fast! Hard X-Ray Flash Breaks Speed Record

Lasting just a few hundred billionths of a billionth of a second, these bursts offer new tool to study chemistry and magnetism.

Scientists Have Overestimated Meteor Sizes

First demonstration of high-pressure metastability mapping with ultrafast X-ray diffraction shows objects aren't as large as previously thought.

Rewriting Resistance: Genetic Changes Increase Crops' Biomass and Sugar Release

Using genetic engineering, scientists improve biomass growth and conversion in woody and grassy feedstocks.

Measuring the Glow of Plants From Below

Novel observations suggest a great potential of measuring global gross primary production via solar-induced fluorescence.


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