Doe Science news source
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.
  • 2018-01-04 15:20:48
  • Article ID: 687511

Real World Native Biocrusts: Microbial Metabolism

Functionally linking microbial community structure with environmental chemistry

  • Credit: Tami Swenson

    Biocrust amongst one of its many natural habitats, taken about 20 miles from the sampling site (near the Corona Arch, Moab, UT).

Arid lands, which cover some 40 percent of the Earth’s terrestrial surface, are too dry to sustain much in the way of vegetation. But far from being barren, they are home to diverse communities of microorganisms—including fungi, bacteria, and archaea—that dwell together within the uppermost millimeters of soil. These biological soil crusts, or biocrusts, can exist for extended periods in a desiccated, dormant state. When it does rain, the microbes become metabolically active, setting in motion a cascade of activity that dramatically alters both the community structure and the soil chemistry.

“These biocrusts and other soil microbiomes contain a tremendous diversity of both microbes and small molecules (‘metabolites’). However, the connection between the chemical diversity of soil and microbial diversity is poorly understood,” said Trent Northen, a senior scientist at Lawrence Berkeley National Laboratory (Berkeley Lab).

In a paper published January 2, 2018, in Nature Communications, Berkeley Lab researchers led by the Northen lab report that specific compounds are transformed by and strongly associated with specific bacteria in native biological soil crust (biocrust) using a suite of tools Northen calls “exometabolomics.” Understanding how microbial communities in the biocrusts adapt to their harsh environments could provide important clues to help shed light on the roles of soil microbes in the global carbon cycle.

 The work follows a 2015 study that examined how specific small molecule compounds called “metabolites” were transformed in a mixture of bacterial isolates from biocrust samples cultured in a milieu of metabolites from the same soil. “We found that the microbes we investigated were ‘picky’ eaters,” Northen said. “We thought we could use this information to link what’s being consumed to the abundance of the microbes in the intact community, thereby linking the biology to the chemistry.”

In the new study, the investigators set out to determine whether the microbe-metabolite relationships observed in the simplified test-tube system could be reproduced in a more complex soil environment.

Biocrusts from the same source – representing four successive stages of maturation – were wet, and the soil water was sampled at five time points. The samples were analyzed by liquid chromatography-mass spectrometry (LC-MS) to characterize the metabolite composition (“metabolomics”), and biocrust DNA was extracted for shotgun sequencing to measure single copy gene markers for the dominant microbe species (“metagenomics”).

“When we compare the patterns of metabolite uptake and production for isolated bacteria that are related to the most abundant microbes found in the biocrusts, we find that, excitingly, these patterns are maintained,” said Northen. That is, increased abundance of a given microbe is negatively correlated with the metabolites that they consume and positively correlated with metabolites that they release.

When active, biocrusts take up atmospheric carbon dioxide and fix nitrogen, contributing to the ecosystem’s primary productivity. They also process organic matter in soil, modifying key properties related to soil fertility and water availability.

“This study suggests that laboratory studies of microbial metabolite processing can help understand the role of these microbes in carbon cycling in the environment. This study gets us closer to understanding the complex food webs that are vital in nutrient dynamics and overall soil fertility,” said study first author Tami Swenson, a scientific engineering associate in Northen’s group within the Berkeley Lab Biosciences Area’s Environmental Genomics and Systems Biology (EGSB) Division.

Northen’s group is currently working on expanding these studies to capture a greater fraction of microbial diversity. Ultimately, this may enable the prediction of nutrient cycling in terrestrial microbial ecosystems, and perhaps even manipulation by adding specific metabolites.

The following Berkeley Lab researchers also contributed to the study: Benjamin Bowen, a member of Northen’s lab in EGSB and at the Joint Genome Institute, a DOE Office of Science User Facility, helped analyze metabolomics data; Ulas Karaoz in the Earth and Environmental Sciences Area (EESA) analyzed metagenomics data; and Joel Swenson, a former postdoctoral researcher in Biosciences’ Biological Systems and Engineering Division, helped conduct correlation and statistical analyses.

This work was supported under a DOE Office of Science Early Career Research Program award. DNA was sequenced using the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by a National Institutes of Health Instrumentation Grant.

 # # #

Lawrence Berkeley National Laboratory addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel Prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. For more, visit

DOE’s 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 the Office of Science website at

  • Filters

  • × Clear Filters

Remotely Predicting Leaf Age in Tropical Forests

New approach offers data across species, sites, and canopies, providing insights into carbon uptake by forests.

Conservation Mind Game

A new study led by Kathryn Caldwell, an assistant professor of psychology at Ithaca College, demonstrates that homeowners can be encouraged to make changes to their energy use with a simple education plan and some helpful tricks from the world of social psychology.

X-Rays Reveal 'Handedness' in Swirling Electric Vortices

Scientists used spiraling X-rays at Berkeley Lab to observe, for the first time, a property that gives left- or right-handedness to swirling electric patterns - dubbed polar vortices - in a layered material called a superlattice.

Breaking Bad Metals with Neutrons

By combining the latest developments in neutron scattering and theory, researchers are close to predicting phenomena like superconductivity and magnetism in strongly correlated electron systems. It is likely that the next advances in superconductivity and magnetism will come from such systems, but they might also be used in completely new ways such as quantum computing.

ORNL Researchers Use Titan to Accelerate Design, Training of Deep Learning Networks

For deep learning to be effective, existing neural networks to be modified, or novel networks designed and then "trained" so that they know precisely what to look for and can produce valid results. This is a time-consuming and difficult task, but one that a team of ORNL researchers recently demonstrated can be dramatically expedited with a capable computing system.

Dark Energy Survey Publicly Releases First Three Years of Data

At a special session held during the American Astronomical Society meeting in Washington, D.C., scientists on the Dark Energy Survey (DES) announced today the public release of their first three years of data. This first major release of data from the Survey includes information on about 400 million astronomical objects, including distant galaxies billions of light-years away as well as stars in our own galaxy.

Ingredients for Life Revealed in Meteorites That Fell to Earth

A detailed study of blue salt crystals found in two meteorites that crashed to Earth - which included X-ray experiments at Berkeley Lab - found that they contain both liquid water and a mix of complex organic compounds including hydrocarbons and amino acids.

Rewritable Wires Could Mean No More Obsolete Circuitry

An electric field switches the conductivity on and off in atomic-scale channels, which could allow for upgrades at will.

Research Outlines the Interconnected Benefits of Urban Agriculture

a team of researchers led by Arizona State University and Google has assessed the value of urban agriculture and quantified its benefits at global scale. They report their findings in "A Global Geospatial Ecosystems Services Estimate of Urban Agriculture," in the current issue of Earth's Future.

Filtering Water Better than Nature

Water passes through human-made straws faster than the "gold standard" protein, allowing us to filter seawater.

  • Filters

  • × Clear Filters

North Dakota State University Joins Two National Distributed Computing Groups

The NDSU Center for Computationally Assisted Science and Technology (CCAST) joins OSG (Open Science Grid) and XSEDE (Extreme Science and Engineering Discovery Environment).

DOE Announces Funding for New HPC4Manufacturing Industry Projects

The Department of Energy's Advanced Manufacturing Office (AMO) today announced the funding of $1.87 million for seven new industry projects under an ongoing initiative designed to utilize DOE's high-performance computing (HPC) resources and expertise to advance U.S. manufacturing and clean energy technologies.

DOE Announces First Awardees for New HPC4Materials for Severe Environments Program

The Department of Energy's Office of Fossil Energy (FE) today announced the funding of $450,000 for the first two private-public partnerships under a brand-new initiative aimed at discovering, designing and scaling up production of novel materials for severe environments.

Two Argonne Scientists Recognized for a Decade of Breakthroughs

Two scientists with the U.S. Department of Energy's (DOE) Argonne National Laboratory have been named to the Web of Science's Highly Cited List of 2017, ranking in the top 1 percent of their peers by citations and subject area. Materials Scientist Khalil Amine and Energy and Environmental Policy Scientist David Streets say they are thrilled to see their work -- and the laboratory -- recognized in such a way.

Argonne Welcomes Department of Energy Secretary Perry

U.S. Department of Energy Secretary Rick Perry visited Argonne National Laboratory yesterday, getting a first-hand view of the multifaceted and interdisciplinary research program laboratory of the Department.

Argonne names John Quintana Deputy Laboratory Director for Operations and COO

John Quintana has been named Deputy Laboratory Director for Operations and Chief Operations Officer (COO) of the U.S. Department of Energy's (DOE) Argonne National Laboratory.

Developing Next-Generation Sensing Technologies

Recently, the Advanced Research Projects Agency-Energy (ARPA-E) announced $20 million in funding for 15 projects that will develop a new class of sensor systems to enable significant energy savings via reduced demand for heating and cooling in residential and commercial buildings.

Supporting the Development of Offshore Wind Power Plants

Offshore wind is becoming a reality in the United States, especially in the northeast states. To support this development, the Center for Future Energy System (CFES) at Rensselaer Polytechnic Institute will present a webinar titled "Turbine and Transmission System Technologies for Offshore Wind (OSW) Power Plants." The program will be held on Wednesday, Dec. 20, from 2 to 4 p.m. Advance registration is required.

LLNL Releases Newly Declassified Nuclear Test Videos

Researchers at Lawrence Livermore National Laboratory (LLNL) released 62 newly declassified videos today of atmospheric nuclear tests films that have never before been seen by the public.

NAU Researchers Join DOE Project to Study the Soil Microbiome and Its Effect on Carbon Persistence

NAU Regents' Professor Bruce Hungate, director of the Center for Ecosystem Science and Society (Ecoss), recently joined a new initiative lead by LLNL to study how the soil microbiome controls the mechanisms that regulate the stabilization of the organic matter in soil.

  • Filters

  • × Clear Filters

Remotely Predicting Leaf Age in Tropical Forests

New approach offers data across species, sites, and canopies, providing insights into carbon uptake by forests.

What's the Noise Eating Quantum Bits?

The magnetic noise caused by adsorbed oxygen molecules is "eating at" the phase stability of quantum bits, mitigating the noise is vital for future quantum computers.

Rewritable Wires Could Mean No More Obsolete Circuitry

An electric field switches the conductivity on and off in atomic-scale channels, which could allow for upgrades at will.

Filtering Water Better than Nature

Water passes through human-made straws faster than the "gold standard" protein, allowing us to filter seawater.

Machine Learning Provides a Bridge to the Texture of the Quantum World

Machine learning and neural networks are the foundation of artificial intelligence and image recognition, but now they offer a bridge to see and recognize exotic insulating phases in quantum materials.

A Rare Quantum State Realized in a New Material

A revolutionary material harbors magnetism and massless electrons that travel near the speed of light--for future ultrasensitive, high-efficiency electronics and sensors.

Discovering Secrets of Superfluids

Observed atomic dynamics helps explain bizarre flow without friction that has been puzzling scientists for decades.

An Exotic State of Matter Discovered in 2-D Material

Electrons are forced to the edge of the road on a thin sheet of tungsten ditelluride.

Studying Crowd Behavior at MINERvA

Detector measures the energy a neutrino imparts to protons and neutrons to help explain the nature of matter and the universe.

Tweaking Quantum Dots Powers-Up Double-Pane Solar Windows

Using two types of "designer" quantum dots, researchers are creating double-pane solar windows that generate electricity with greater efficiency and create shading and insulation for good measure. It's all made possible by a new window architecture which utilizes two different layers of low-cost quantum dots tuned to absorb different parts of the solar spectrum.


Wednesday January 17, 2018, 12:05 PM

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

Fermi National Accelerator Laboratory (Fermilab)

Wednesday January 17, 2018, 12:05 PM

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

Fermi National Accelerator Laboratory (Fermilab)

Wednesday December 20, 2017, 01:05 PM

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

SLAC National Accelerator Laboratory

Monday December 18, 2017, 01:05 PM

The Future of Today's Electric Power Systems

Rensselaer Polytechnic Institute (RPI)

Monday December 18, 2017, 12:05 PM

Supporting the Development of Offshore Wind Power Plants

Rensselaer Polytechnic Institute (RPI)

Tuesday October 03, 2017, 01:05 PM

Stairway to Science

Argonne National Laboratory

Thursday September 28, 2017, 12:05 PM

After-School Energy Rush

Argonne National Laboratory

Thursday September 28, 2017, 10:05 AM

Bringing Diversity Into Computational Science Through Student Outreach

Brookhaven National Laboratory

Thursday September 21, 2017, 03:05 PM

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

SLAC National Accelerator Laboratory

Thursday September 07, 2017, 02:05 PM

Students Discuss 'Cosmic Opportunities' at 45th Annual SLAC Summer Institute

SLAC National Accelerator Laboratory

Thursday August 31, 2017, 05:05 PM

Binghamton University Opens $70 Million Smart Energy Building

Binghamton University, State University of New York

Wednesday August 23, 2017, 05:05 PM

Widening Horizons for High Schoolers with Code

Argonne National Laboratory

Saturday May 20, 2017, 12:05 PM

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

Rensselaer Polytechnic Institute (RPI)

Monday May 15, 2017, 01:05 PM

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

Oak Ridge National Laboratory

Friday April 07, 2017, 11:05 AM

Champions in Science: Profile of Jonathan Kirzner

Department of Energy, Office of Science

Wednesday April 05, 2017, 12:05 PM

High-Schooler Solves College-Level Security Puzzle From Argonne, Sparks Interest in Career

Argonne National Laboratory

Tuesday March 28, 2017, 12:05 PM

Champions in Science: Profile of Jenica Jacobi

Department of Energy, Office of Science

Friday March 24, 2017, 10:40 AM

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

Brookhaven National Laboratory

Wednesday February 15, 2017, 04:05 PM

Middle Schoolers Test Their Knowledge at Science Bowl Competition

Argonne National Laboratory

Friday January 27, 2017, 04:00 PM

Haslam Visits ORNL to Highlight State's Role in Discovering Tennessine

Oak Ridge National Laboratory

Tuesday November 08, 2016, 12:05 PM

Internship Program Helps Foster Development of Future Nuclear Scientists

Oak Ridge National Laboratory

Friday May 13, 2016, 04:05 PM

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

Thomas Jefferson National Accelerator Facility

Monday April 25, 2016, 05:05 PM

Giving Back to National Science Bowl

Ames Laboratory

Friday March 25, 2016, 12:05 PM

NMSU Undergrad Tackles 3D Particle Scattering Animations After Receiving JSA Research Assistantship

Thomas Jefferson National Accelerator Facility

Tuesday February 02, 2016, 10:05 AM

Shannon Greco: A Self-Described "STEM Education Zealot"

Princeton Plasma Physics Laboratory

Monday November 16, 2015, 04:05 PM

Rare Earths for Life: An 85th Birthday Visit with Mr. Rare Earth

Ames Laboratory

Tuesday October 20, 2015, 01:05 PM

Meet Robert Palomino: 'Give Everything a Shot!'

Brookhaven National Laboratory

Tuesday April 22, 2014, 11:30 AM

University of Utah Makes Solar Accessible

University of Utah

Wednesday March 06, 2013, 03:40 PM

Student Innovator at Rensselaer Polytechnic Institute Seeks Brighter, Smarter, and More Efficient LEDs

Rensselaer Polytechnic Institute (RPI)

Friday November 16, 2012, 10:00 AM

Texas Tech Energy Commerce Students, Community Light up Tent City

Texas Tech University

Wednesday November 23, 2011, 10:45 AM

Don't Get 'Frosted' Over Heating Your Home This Winter

Temple University

Wednesday July 06, 2011, 06:00 PM

New Research Center To Tackle Critical Challenges Related to Aircraft Design, Wind Energy, Smart Buildings

Rensselaer Polytechnic Institute (RPI)

Friday April 22, 2011, 09:00 AM

First Polymer Solar-Thermal Device Heats Home, Saves Money

Wake Forest University

Friday April 15, 2011, 12:25 PM

Like Superman, American University Will Get Its Energy from the Sun

American University

Thursday February 10, 2011, 05:00 PM

ARRA Grant to Help Fund Seminary Building Green Roof

University of Chicago

Tuesday December 07, 2010, 05:00 PM

UC San Diego Installing 2.8 Megawatt Fuel Cell to Anchor Energy Innovation Park

University of California San Diego

Monday November 01, 2010, 12:50 PM

Rensselaer Smart Lighting Engineering Research Center Announces First Deployment of New Technology on Campus

Rensselaer Polytechnic Institute (RPI)

Friday September 10, 2010, 12:40 PM

Ithaca College Will Host Regional Clean Energy Summit

Ithaca College

Tuesday July 27, 2010, 10:30 AM

Texas Governor Announces $8.4 Million Award to Create Renewable Energy Institute

Texas Tech University

Friday May 07, 2010, 04:20 PM

Creighton University to Offer New Alternative Energy Program

Creighton University

Wednesday May 05, 2010, 09:30 AM

National Engineering Program Seeks Subject Matter Experts in Energy

JETS Junior Engineering Technical Society

Wednesday April 21, 2010, 12:30 PM

Students Using Solar Power To Create Sustainable Solutions for Haiti, Peru

Rensselaer Polytechnic Institute (RPI)

Wednesday March 03, 2010, 07:00 PM

Helping Hydrogen: Student Inventor Tackles Challenge of Hydrogen Storage

Rensselaer Polytechnic Institute (RPI)

Thursday February 04, 2010, 02:00 PM

Turning Exercise into Electricity

Furman University

Thursday November 12, 2009, 12:45 PM

Campus Leaders Showing the Way to a Sustainable, Clean Energy Future

National Wildlife Federation (NWF)

Tuesday November 03, 2009, 04:20 PM

Furman University Receives $2.5 Million DOE Grant for Geothermal Project

Furman University

Thursday September 17, 2009, 02:45 PM

Could Sorghum Become a Significant Alternative Fuel Source?

Salisbury University

Wednesday September 16, 2009, 11:15 AM

Students Navigating the Hudson River With Hydrogen Fuel Cells

Rensselaer Polytechnic Institute (RPI)

Showing results

0-4 Of 2215