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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.
  • 2018-04-26 09:05:57
  • Article ID: 693388

A Functional Genomics Database for Plant Microbiome Studies

Catalog of candidate genes involved in plant-microbe relationships.

  • Credit: Image courtesy of Asaf Levy, Joint Genome Institute, and Isai Salas Gonzalez, University of North Carolina

    Phylogenetic tree of over 3,800 high quality and non-redundant bacterial genomes. The outer ring denotes the taxonomic group, central ring denotes the isolation source, and inner ring denotes the root-associated genomes within plant-associated genomes. Taxon names are color-coded based on phylum: green = Proteobacteria, red = Firmicutes, blue = Bacteroidetes, and purple = Actinobacteria.

The Science

Could marginal lands be bountiful fields for biofuel crops? To answer that question, scientists are investigating soil microbes, which can aid plant growth. Here, researchers isolated bacteria from around the roots of poplar trees, maize, and a type of mustard plant. They developed a catalog of the genetic material (genome) of the soil bacteria they found. In mining the data, they found genes involved in bacterial root colonization.

The Impact

Knowing how beneficial microbes and microbial communities colonize plants, along with subsequent plant-microbe interactions, could assist in growing food and energy crops with fewer chemical inputs. These inputs include fertilizer, pesticides, and fungicides.

Summary

To facilitate crop-breeding strategies for making plants more productive on marginal lands and more tolerant of stresses such as drought and low nutrient availability, researchers are focusing on understanding and promoting beneficial plant-microbe relationships. To date, most plant microbiome studies in the field have focused on community structure rather than function, but there is a need to understand microbial community functions to engineer the microbiome to support plant growth. In this study, researchers isolated bacteria from the root environments of Brassicaceae, poplar trees, and maize, and sequenced, assembled, and compared the genomes with thousands of publicly available genomes including bacteria from both plant and non-plant environments. This broad analysis allowed the researchers to identify genes enriched in the genomes of plant-associated and root-associated organisms. They found that plant- and soil-associated genomes were enriched in genes involved in sugar metabolism and transport, likely an adaptation to the production of photosynthesis-derived plant carbon compounds. Further, they found that numerous genes seem to mimic plant functions in a strategy similar to that employed by plant pathogens. The identification of two new, rapidly evolving protein families containing genes often used in offense or defense against another organism provides evidence for a “molecular arms race” between competing bacteria within the same environment. This research provides a valuable resource for researchers studying plant-microbe interactions to identify novel and potentially interesting genes and gain a better functional understanding of the plant microbiome that can be exploited for enhancing crop production.

Funding

The Department of Energy (DOE) Joint Genome Institute, Integrated National Science Foundation Support Promoting Interdisciplinary Research and Education, National Institutes of Health, Howard Hughes Medical Institute (HHMI), Gordon and Betty Moore Foundation, SystemsX.ch, European Research Council, DOE Office of Science Biological and Environmental Research (BER and U.S. Department of Agriculture National Institute of Food and Agriculture Plant Feedstocks Genomics for Bioenergy, and the DOE BER Genomic Science Program and Science Focus Area: Plant Microbe Interfaces (Oak Ridge National Laboratory) funded the research.

Publication

A. Levy, I.S. Gonzalez, M. Millelviefhaus, et al., “Genomic features of bacterial adaptation to plants.” Nature Genetics 50,138 (2018). [DOI: 10.1038/s41588-017-0012-9]

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No Longer Whistling in the Dark: Scientists Uncover a Little-Understood Source of Waves Generated Throughout the Universe

Scientists at the U.S. Department of Energy's Princeton Plasma Physics Laboratory (PPPL) and other laboratories, using data from a NASA four-satellite mission that is studying reconnection, have developed a method for identifying the source of waves that help satellites determine their location in space.

New biofuel production system powered by a community of algae and fungi

MSU scientists have a new proof of concept for a biofuel production platform that uses two species of marine algae and soil fungi. It lowers cultivation and harvesting costs and increases productivity, factors that currently hold back biofuels from being widely adopted.

Multimodal Imaging Shows Strain Can Drive Chemistry in a Photovoltaic Material

A unique combination of imaging tools and atomic-level simulations has allowed a team led by the Department of Energy's Oak Ridge National Laboratory to solve a longstanding debate about the properties of a promising material that can harvest energy from light.

Study of tiny vortices could lead to new self-healing materials, other advances

Argonne scientists hope that tiny vortices, driven by various magnetic fields, will be able to move microscopic particles.

How a Molecular Signal Helps Plant Cells Decide When to Make Oil

Scientists identify new details of how a sugar-signaling molecule helps regulate oil production in plant cells. The work could point to new ways to engineer plants to produce substantial amounts of oil for use as biofuels or in the production of other oil-based products.

Neutrons Produce First Direct 3D Maps of Water During Cell Membrane Fusion

New 3D maps of water distribution during cellular membrane fusion could lead to new treatments for diseases associated with cell fusion. Using neutron diffraction at Oak Ridge National Laboratory, scientists made the first direct observations of water in lipid bilayers modeling cell membrane fusion.

Chemists Demonstrate Sustainable Approach to Carbon Dioxide Capture From Air

Chemists at Oak Ridge National Laboratory have demonstrated a practical, energy-efficient method of capturing carbon dioxide directly from air. If deployed at large scale and coupled to geologic storage, the technique may bolster the portfolio of responses to global climate change.

Nucleation a boon to sustainable nanomanufacturing

Young-Shin Jun, professor of energy, environmental & chemical engineering in the School of Engineering & Applied Science, and Quingun Li, a former doctoral student in her lab, are the first to measure the activation energy and kinetic factors of calcium carbonate's nucleation, both key to predicting and controlling the process.

Breaking the Symmetry Between Fundamental Forces

Scientists improve our understanding of the relationship between fundamental forces by re-creating the earliest moments of the universe.

Greater Than the Sum of Its Parts

Argonne scientists and their collaborators have developed a new model that merges basic electrochemical theory with theories used in different contexts, such as the study of photoelectrochemistry and semiconductor physics, to describe phenomena that occur in any electrode.


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Department of Energy Announces $218 Million for Quantum Information Science

The U.S. Department of Energy (DOE) announced $218 million in funding for 85 research awards in the important emerging field of Quantum Information Science (QIS).

Energy Secretary awards researchers for global threat reduction

Seven employees from the U.S. Department of Energy's (DOE) Argonne National Laboratory were among those presented with a Secretary of Energy Achievement Award at the Secretary's Honors Awards ceremony in Washington, D.C., on August 29.

University of Minnesota to lead $5.3 million federal grant to improve electronic circuit design

The University of Minnesota announced today that it has received a four-year, $5.3 million grant from the Defense Advanced Research Projects Agency (DARPA), an agency of the U.S. Department of Defense, to lead an effort that could spark the next wave of U.S. semiconductor innovation and broaden the competitive field for circuit design.

Berkeley Lab to Build an Advanced Quantum Computing Testbed

Lawrence Berkeley National Laboratory (Berkeley Lab) will receive $30 million over five years from the U.S. Department of Energy to build and operate an Advanced Quantum Testbed (AQT) allowing researchers to explore superconducting quantum processors to advance scientific research

Cheng wins Midwest Energy News' 40 Under 40 Award

Lei Cheng, an assistant chemist in the Materials Science division at the U.S. Department of Energy's (DOE) Argonne National Laboratory, has received a Midwest Energy News 40 Under 40 Award.

JCESR renewed for another five years

The U.S. Department of Energy (DOE) today announced its decision to renew the Joint Center for Energy Storage Research (JCESR), a DOE Energy Innovation Hub led by Argonne National Laboratory and focused on advancing battery science and technology.

Binghamton designated as NextFlex New York Node for flexible hybrid electronics initiative

NextFlex has designated Binghamton University to be the New York "Node" for its flexible hybrid electronics (FHE) initiative. As the NextFlex New York Node, Binghamton will design, develop and manufacture tools; process materials and products for flexible hybrid electronics; and attract, train and employ an advanced manufacturing workforce, building on the region's existing electronics manufacturing base.

First Particle Tracks Seen in Prototype for International Neutrino Experiment

The largest liquid-argon neutrino detector in the world has just recorded its first particle tracks, signaling the start of a new chapter in the story of the international Deep Underground Neutrino Experiment (DUNE). DUNE's scientific mission is dedicated to unlocking the mysteries of neutrinos, the most abundant (and most mysterious) matter particles in the universe.

Tais Gorkhover Wins LCLS Young Investigator Award for Pioneering Novel X-ray Imaging Methods

Tais Gorkhover, a principal investigator with the Stanford PULSE Institute, will receive the 2018 LCLS Young Investigator Award, granted to early-career scientists in recognition of exceptional research using the Linac Coherent Light Source (LCLS) X-ray free-electron laser at the Department of Energy's SLAC National Accelerator Laboratory.

ORNL, United Kingdom Lab Partner on Nuclear Energy Research

The United Kingdom's National Nuclear Laboratory and the U.S. Department of Energy's Oak Ridge National Laboratory have agreed to cooperate on a wide range of nuclear energy research and development efforts that leverage both organizations' unique expertise and capabilities.


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Breaking the Symmetry Between Fundamental Forces

Scientists improve our understanding of the relationship between fundamental forces by re-creating the earliest moments of the universe.

Water Plays Unexpected Role in Forming Minerals

Water molecules line up tiny particles to attach and form minerals; understanding how this happens impacts energy extraction and storage along with waste disposal.

Heavy Particles Get Caught Up in the Flow

First direct measurement show how heavy particles containing a charm quark get caught up in the flow of early universe particle soup.

Seeing Between the Atoms

New detector enables electron microscope imaging at record-breaking resolution.

Scaling Up Single-Crystal Graphene

New method can make films of atomically thin carbon that are over a foot long.

Discovered: Optimal Magnetic Fields Suppress Instabilities in Tokamak Plasmas

U.S. and Korean scientists show how to find and use beneficial 3-D field perturbations to stabilize dangerous edge-localized modes in plasma.

New Electron Glasses Sharpen Our View of Atomic-Scale Features

A new approach to atom probe tomography promises more precise and accurate measurements vital to semiconductors used in computers, lasers, detectors, and more.

Getting an Up-Close, 3-D View of Gold Nanostars

Scientists can now measure 3-D structures of tiny particles with properties that hold promise for advanced sensors and diagnostics.

Small, Short-Lived Drops of Early Universe Matter

Particle flow patterns suggest even small-scale collisions create drops of early universe quark-gluon plasma.

Tuning Terahertz Beams with Nanoparticles

Scientists uncover a way to control terahertz radiation using tiny engineered particles in a magnetic field, potentially opening the doors for better medical and environmental sensors.


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New graduate student summer school launches at Princeton Plasma Physics Laboratory

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Argonne hosts Modeling, Experimentation and Validation Summer School

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Students affected by Hurricane Maria bring their research to SLAC

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Brookhaven Lab Pays Tribute to 2018 Summer Interns

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CSUMB Selected to Host Architecture at Zero Competition in 2019

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Department of Energy Invests $64 Million in Advanced Nuclear Technology

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Professor Miao Yu Named the Priti and Mukesh Chatter '82 Career Development Professor

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2018 RHIC & AGS Annual Users' Meeting: 'Illuminating the QCD Landscape'

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Argonne welcomes The Martian author Andy Weir

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Professor Emily Liu Receives $1.8 Million DoE Award for Solar Power Systems Research

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Celebrating 40 years of empowerment in science

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Introducing Graduate Students Across the Globe to Photon Science

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Students from Massachusetts and Washington Win DOE's 28th National Science Bowl(r)

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Q&A: Al Ashley Reflects on His Efforts to Diversify SLAC and Beyond

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Insights on Innovation in Energy, Humanitarian Aid Highlight UVA Darden's Net Impact Week

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Ivy League Graduate, Writer and Activist with Dyslexia Visits CSUCI to Reframe the Concept of Learning Disabilities

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Photographer Adam Nadel Selected as Fermilab's New Artist-in-Residence for 2018

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Fermilab Computing Partners with Argonne, Local Schools for Hour of Code

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Q&A: Sam Webb Teaches X-Ray Science from a Remote Classroom

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From Science to Finance: SLAC Summer Interns Forge New Paths in STEM

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Binghamton University Opens $70 Million Smart Energy Building

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Rensselaer Polytechnic Institute Graduates Urged to Embrace Change at 211th Commencement

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ORNL, University of Tennessee Launch New Doctoral Program in Data Science

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Great Neck South High School Wins Regional Science Bowl at Brookhaven Lab

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Middle Schoolers Test Their Knowledge at Science Bowl Competition

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More Than 12,000 Explore Jefferson Lab During April 30 Open House

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