BER Research Highlights

Search Date: October 19, 2017

27 Records match the search term(s):


August 01, 2017

Insights into an Eukaryotic Alga that Lives by the Sea

The genome of Porphyra umbilicalis reveals the mechanisms by which it thrives in the intertidal zone at the edge of the ocean.

The Science
Researchers have sequenced and analyzed the genome of Porphyra umbilicalis, a red alga that is thought to represent one of the oldest forms of marine life and the origin for diatoms and other photosynthetic microorganisms. The team found strong cytoskeletal limitations in Porphyra and most other red algae with sequenced genomes, offering a possible explanation for why red algae tend to be small compared to other multicellular eukaryotes.  A 50-member team led by University of Maine, Carnegie Institution for Science, and East Carolina University used the Community Science Program of the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, to carry out the study.

The Impact
Though red algae are one of the oldest multicellular lineages, only a few have had their genomes sequenced. Porphyra umbilicalis is found in the ocean’s intertidal zone, and is subject to constantly changing environmental conditions including temperature, light, and desiccation levels. Analyzing the alga’s genome lends insights into its stress-tolerance mechanisms and how that impacts its ability to fix carbon. Also, since diatoms and other photosynthesizing microorganisms evolved from red algae, red algae metabolism has a significant impact on the planet’s carbon cycle.

Summary
The intertidal zone is the area between land and sea that is sometimes concealed by high tide or revealed by low tide. As this ecosystem is in constant flux, the organisms that inhabit the area have adapted to thrive under a range of constantly changing environmental conditions. Porphyra and other genera of bangiophyte red algae thrive in the intertidal zones of the northern and southern hemispheres. Their lineage is ancient, and the oldest taxonomically resolved fossil of a multicellular eukaryote, 1.2 billion years old, was also a bangiophyte.

As reported in the Proceedings of the National Academy of Sciences, the DOE JGI sequenced, assembled and annotated the genome of the red alga Porphyra umbilicalis to better understand how it harvests light and nutrients, and how warming oceans might impact its ability to fix carbon. The team led by University of Maine researchers found that the red alga has previously unrecognized means of tolerating its physically stressful intertidal habitat. For example, Porphyra umbilicalis has multiple strategies to protect cells from being damaged by high light levels, including expanded families of proteins that protect the photosynthetic apparatus from high light and unusual genomic arrangements of the genes that synthesize the mycosporine-like amino acids that protect against ultraviolet light. They also found that the alga has a significantly reduced cytoskeleton and lacks many motors other organisms rely on for intracellular transport. This may explain why red algae, compared to many other multicellular eukaryotes, are smaller and less structurally complex and how they can survive, in the closing words of the publication, in “in the pounding waves, baking sun, and drying winds of the high intertidal zone”

The green algae and red algae are both groups of plants that carry out photosynthesis using light-harnessing organelles called chloroplasts, which evolved from cyanobacteria that were engulfed by the ancestral eukaryotic algae. Later, other environmentally important algae such as diatoms, dinoflagellates and haptophytes evolved when other non-photosynthetic eukaryotes captured red algae and integrated the red algal chloroplast and red algal nuclear genes into their genomes. These processes greatly diversified the organisms capable of conducting photosynthesis, and the red algal imprint on global productivity, aquatic food webs, and oxygen production is significant.

PM Contact
Daniel Drell, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
U.S. Department of Energy
daniel.drell@science.doe.gov

PI Contact
Jeremy Schmutz
Plant Program Head
DOE Joint Genome Institute
jschmutz@hudsonalpha.com

Susan Brawley
School of Marine Sciences
University of Maine
brawley@maine.edu

Funding
Work was conducted by the U.S. Department of Energy (DOE) Joint Genome Institute, a DOE Office of Science user facility (contract number DE-AC02-05CH11231). This work was also supported by the National Science Foundation, National Oceanic and Atmospheric Administration, German Research Foundation, French National Research Agency, US Department of Agriculture/National Institute of Food and Agriculture, Biotechnology and Biological Sciences Research Council and European Union FP7 e Curie Photo. COMM, Connecticut Sea Grant College Program, NOAA National Marine Aquaculture Initiative, National Institutes of Health, UK Natural Environment Research Council IOF Pump-priming + scheme, The Great Barrier Reef Foundation, Australian Research Council, and a University of Queensland Early Career Researcher grant.

Publications
S. Brawley, N. Blouin, E. Ficko-Blean, G. Wheeler, M. Lohr, H. Goodson, J. Jenkins, C. Blaby-Haas, K. Helliwell, C. Chan, T. Marriage, D. Bhattacharya, A. Klein, Y. Badis, J. Brodie, Y. Cao, J. Collén, S. Dittami, C. Gachon, B. Green, S. Karpowicz, J. Kim, U. Kudahl, S. Lin, G. Michel, M. Mittag, B. Olson, J. Pangilinan, Y. Peng, H. Qiu, S. Shu, J. Singer, A. Smith, B. Sprecher, V. Wagner, W. Wang, Z.Y. Wang, J. Yan, C. Yarish, S. Zäuner-Riek, Y. Zhuang, Y. Zou, E. Lindquist, J. Grimwood, K. Barry, D. Rokhsar, J. Schmutz, J. Stiller, A. Grossman, and S. Prochnik “Insights into the red algae from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta).” Proc Natl Acad. Sci. 2017. [DOI: 10.1073/pnas.1703088114] (Reference link)

Related Links
University of Maine News Release: “Sequencing reveals how Porphyra thrives in a tough environment
Carnegie Institution of Science News Release: “What makes red algae so different and why should we care?
Scottish Association for Marine Science News Release: “Scientists unlock secrets of red alga immunity
DOE JGI CSP 2008: Why Sequence Porphyra umbilicalis?
Porphyra umbilicalis on DOE JGI Genome Portal
2012 DOE JGI Science Highlight: “Algal Lipid Pathways Linked to Those in Plants and Fungi
Brawley Lab at the University of Maine
2012 DOE JGI News Release: “Tiny Algae Shed Light on Photosynthesis as a Dynamic Property

Topic Areas:



Porphyra umbilicalis (laver) attains high biomass despite the high levels of stress in its habitat in the upper intertidal zone of the North Atlantic, as shown here at low tide at Sand Beach, Acadia National Park, Maine. [Image courtesy of Susan Brawley]



July 21, 2017

Scaling Microbial Genomics Discoveries for Ecosystem Modeling

Nutrient availability in model wetlands helps regulate microbial metabolism and soil carbon cycling rates.

The Science
Researchers linked microbial metabolism and nutrient availability to soil carbon cycling rates by studying microbial communities in San Joaquin Delta rice fields.

The Impact
Establishing the inter-relationships among microbial metabolism, nutrient availability and soil carbon cycling rates is critical to applying genomic information to understand the global carbon cycle. In showing how microbial metabolism is regulated by coupled nutrient cycling and soil carbon availability, researchers demonstrate how genomics studies of microbial communities can be scaled up to the ecosystems level. This will contribute to a deeper understanding of ecological processes and will aid the development of better global carbon cycling models.

Summary
To better understand the relationship between carbon cycling, nutrient availability, and microbial communities in soil, it is necessary to conduct studies across a nutrient gradient. Rice fields are model wetland systems that allow researchers to focus on chosen biogeochemical variables, while factors such as water and vegetation are controlled. Adjacent to the Twitchell Island restored wetlands are rice fields with soil carbon contents that can vary between 2.5 percent and 25 percent, covering much of the global range of carbon found in soils.

Wetlands are of interest to the U.S. Department of Energy to understand the roles of microbial communities in long-term impacts on carbon emissions and carbon sequestration. These ecosystems can trap as much as 30 percent of global soil carbon but contribute nearly 40 percent of global methane emissions. Thus, studying these ecosystems provides an opportunity to understand their roles as both carbon sinks and carbon sources. Researchers at the Joint Genome Institute, a DOE Office of Science User Facility, studied the ecosystems of Twitchell Island in the Sacramento-San Joaquin Delta, where the U.S. Geological Survey had a pilot study on restored wetlands.

A combination of metagenomic sequencing of soil samples, biogeochemical characterization and weekly greenhouse gas emission measurements led to the team’s results, published in The ISME Journal. The findings suggest that the microbial metabolic rates align with Biological Stoichiometry Theory, a metabolic theory of ecology that suggests organisms with faster growth rates require more phosphorus to increase nitrogen-rich protein synthesis. Until now, this theory had not been applied to soil microbes in situ due to methodological limitations, which the scientists addressed using a novel genomic approach.

Studying the microbial communities in these soils, the researchers found that the rate at which microbes break down organic matter is coupled to the availability of carbon, nitrogen and phosphorus in the soils. Specifically, the availability of phosphorus is a key factor in determining these soil carbon cycling rates. An abundance of phosphorus increases microbial activity and metabolic rates, which in turn means higher carbon turnover. Lower phosphorus in high carbon soils may help stabilize accumulated carbon, while high phosphorus soils may more rapidly lose carbon stores. These associations at the ecosystem scale were also reflected in genomic data from the soil microbes which drive soil element cycling. Soil metagenome sequence data were assessed for microbial potential to metabolize carbon, nitrogen and phosphorus, while predictive functional profiling software allowed the researchers to compare tradeoffs in these functions among microbial lineages. This approach revealed clusters of genome sequences that could be grouped into “guilds” based on genomic profiles of metabolic genes, which the researchers used to develop novel predictive models of microbial community composition and soil carbon cycling.  This work is an important advance toward understanding the relationship between microbial communities and soil nutrients and the effects of those interactions on ecosystem activity and health.

PM Contact
Daniel Drell, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
daniel.drell@science.doe.gov

Pablo Rabinowicz, Ph.D.
Program Manager
Biological systems Science Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
pablo.rabinowicz@science.doe.gov

PI Contact
Susannah Tringe
Deputy, User Programs
DOE Joint Genome Institute
sgtringe@lbl.gov

Funding
Work was funded by the DOE Early Career Research Program and conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, supported under contract no. DE-AC02-05CH11231. This material is also based on work supported by the National Institute of Food and Agriculture, US Department of Agriculture.

Publications
Hartman WH et al. A genomic perspective on stoichiometric regulation of soil carbon cycling. ISME J. 2017 Jul 21. [doi: 10.1038/ismej.2017.115] Epub ahead of print. (Reference link)

Related Links
DOE JGI Science Highlight: “Charting Short-Term Results of Wetlands Restoration”

DOE JGI News Release: “JGI’s Susannah Tringe Receives Prestigious $2.5M DOE Early Career Research Award”

Susannah Tringe 2012 video: “Wetlands, Microbes, and the Carbon Cycle: Behind the Scenes at Berkeley Lab”

Susannah Tringe 2015 video: “JGI's Carbon Cycling Studies on Restored Remnant Marshes”

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Study co-author Rhonzhong Ye and graduate student Jennifer Morris collecting greenhouse gas fluxes from the rice fields studied on Twitchell Island, CA. [Image courtesy of Wyatt Hartman]



July 05, 2017

New Technology Illuminates Microbial Dark Matter

Demonstrating the microfluidic-based, mini-metagenomics approach on samples from hot springs shows how scientists can delve into microbes that can’t be cultivated in a laboratory.

The Science
At Stanford University, researchers have used a new microfluidic analysis system to extract 29 novel microbial genomes (the complete set of genetic material) from samples from two Yellowstone National Park hot springs. They extracted the genomes while still preserving single-cell resolution, meaning they knew which cells the genetic material came from. This work was made possible by a new technology that divides the sample to enable accurate analysis of a microbe’s genetic material. Specifically, it offers details on genome function and abundance. The work was enabled by the Emerging Technology Opportunity Program, a part of the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science user facility.

The Impact
This new technology illuminates microbial “dark matter,” genetic information from the majority of the planet’s microbial diversity that has not been grown in a lab. These microbes live in locations as diverse as hot springs and deserts, underneath Antarctic ice and in acid mine drainage from Superfund sites. Tools that can determine microbes’ genetics and metabolism will have applications in fields ranging from bioenergy to biotechnology to environmental research.

Summary
There are more than 50,000 microbial genome sequences in the DOE JGI’s Integrated Microbial Genomes publicly accessible database, and many of them have been uncovered through the use of metagenomic sequencing and single-cell genomics. Despite their utility, these sequencing and genomics techniques have limits: single-cell genome amplifications are time-consuming, often incomplete, and metagenomic sequencing generally works best if the environmental sample is not too complex. In eLife, a team of researchers from Stanford University reports the development of a microfluidics-based, mini-metagenomics approach to mitigate these challenges. The technique starts with reducing the environmental sample’s complexity by separating it, using microfluidics, into 96 subsamples each with 5 to 10 cells. Then, the genomes in the cells in each subsample are amplified and libraries are created for sequencing these mini-metagenomes. The smaller subsamples can be held to single-cell resolution for statistical analyses. Co-occurrence patterns from many subsamples can also be used to perform sequence-independent genome binning. The technology was developed through resources provided by the DOE JGI’s Emerging Technologies Opportunity Program, which was launched in 2013. The aim of this program is to use these new technologies to tackle energy and environment applications, adding value to the high-throughput sequencing and analysis being done for DOE JGI users. The team validated the technique using a synthetic microbial community, and then applied it to samples from the Bijah and Mound hot springs at Yellowstone National Park. Among their findings was that the microbes at Mound Spring had higher potential to produce methane than the microbes from Bijah Spring. They also identified a microbial genome from Bijah Spring that could reduce nitrite to nitrogen. Applying this new technology to additional sample sites will add to the range of hitherto uncharacterized microbial capabilities with potential DOE mission applicability.

PM Contact
Daniel Drell, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
U.S. Department of Energy
daniel.drell@science.doe.gov

PI Contact
Tanja Woyke
Microbial Program Head
DOE Joint Genome Institute
twoyke@lbl.gov

Stephen Quake
Department of Bioengineering
Stanford University
quake@stanford.edu

Funding
Work was conducted by the U.S. Department of Energy (DOE) Joint Genome Institute, a DOE Office of Science user facility (contract DE-AC02-05CH11231). This work was also supported by the John Templeton Foundation, Stanford University, National Science Foundation, and the Burroughs Wellcome Fund.

Publications
F.B. Yu, P.C. Blainey, F. Schulz, T. Woyke, M.A. Horowitz, and S.R. Quake, “Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples.” eLife 2017, e26580 (2017). [DOI: 10.7554/eLife.26580] (Reference link)

Related Links
DOE Joint Genome Institute (JGI) news release: The DOE Joint Genome Institute Expands Capabilities via New Partnerships (JGI Emerging Technologies Opportunity Program)
DOE JGI webpage: Phylogenetic Diversity (a mission of the microbial program)
DOE JGI news release: Boldly Illuminating Biology’s “Dark Matter”
DOE JGI science highlight: Confirming Microbial Lineages Through Cultivation-Independent Means
DOE JGI science highlight: Elucidating Extremophilic “Microbial Dark Matter”
DOE JGI science highlight: Solving Microbial “Dark Matter” With Single-Cell Genomics
DOE JGI video: Why Mine Microbial Dark Matter?
DOE JGI video: Slava Epstein, Northeastern University, on the importance of studying microbial dark matter 
DOE JGI video: Steve Quake at the 2014 DOE JGI Genomics of Energy & Environment Meeting

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Scientists used this integrated microfluidic circuit to perform mini-metagenomic microbial cell partitioning and genomic DNA amplification. [Image courtesy of Brian Yu]



July 05, 2017

Tiny Green Algae Reveal Large Genomic Variation

First complete picture of genetic variations in a natural algal population could help explain how environmental changes affect global carbon cycles.

The Science
Although they are invisible to the unaided eye, tiny green algae called Ostreococcus play a big role in how carbon, including carbon dioxide, cycle through our world. Researchers have sequenced and analyzed the complete set of genes (the genome) of 13 members of a natural Ostreococcus population. The analysis revealed that the O. tauri population is larger than anticipated. It’s also diverse in terms of its genetics and appearance. The algae’s natural resistance to ocean viruses influenced it’s diversity.

The Impact
Ostreococcus is a microscopic model species for algal studies in marine environments. These picoplankton use sunlight together with carbon dioxide (CO2) to create organic matter. The algae are significant primary producers (i.e., they convert CO2 into biomass) and thus contribute to the global carbon cycle. This study offers insights into the genetic variability of various Ostreococcus strains. The results will help scientists see how environmental changes affect algae’s ability to survive and thrive.

Summary
Picophytoplankton such as Ostreococcus are invisible to the naked eye. Despite their size, their global abundance means they are a widespread primary producer and form the bases of several marine food webs. In coastal areas, they account for as much as 80 percent of the available biomass. A decade ago, the Joint Genome Institute (JGI), a U.S. Department of Energy (DOE) Office of Science user facility, sequenced one of the Ostreococcus strains. That genome, along with other genome sequences from three groups of Ostreococcus, revealed the tiny algae’s diversity and adaptation to different ecological niches around the world.

Now, a team led by researchers at the Oceanological Observatory of Banyuls, France, and including scientists at the DOE JGI, has resequenced and analyzed 13 members of a natural population of Ostreococcus tauri from the northwest Mediterranean Sea. The analysis offers a complete picture on the surprisingly large population and correspondingly high genetic and phenotypic diversity within O. tauri species. The team identified two large candidate mating type loci, consistent with the pervasive evidence of recombination and thus sexual reproduction within the population. The work reported in Science Advances was enabled in part by the DOE JGI’s Community Science Program. A deeper understanding of algal genomic diversity and potential will help scientists track carbon (and nitrogen) traffic through marine ecosystems as well as provide insights into the structure and operation of algal plant communities.

PM Contact
Daniel Drell, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
U.S. Department of Energy
daniel.drell@science.doe.gov   

PI Contact
Igor Grigoriev
Fungal Genomics Program Head
DOE Joint Genome Institute
ivgrigoriev@lbl.gov

Gwenael Piganeau
Integrative Biology of Marine Organisms Lab
Oceanological Observatory of Banyuls, France
gwenael.piganeau@obs-banyuls.fr

Funding
Work was conducted by the U.S. Department of Energy (DOE) Joint Genome Institute, a DOE Office of Science user facility (contract DE-AC02-05CH11231). This work was also supported by the European Community’s 7th Framework program FP7 and the Agence Nationale de la Recherche (contract ANR-13-JSV6-0005).

Publication
R. Blanc-Mathieu, M. Krasovec, M. Hebrard, S. Yau, E. Desgranges, J. Martin, W. Schackwitz, A. Kuo, G. Salin, C. Donnadieu, Y. Desdevises, S. Sanchez-Ferandin, H. Moreau, E. Rivals, I. Grigoriev, N. Grimsle, A. Eyre-Walker, and G. Piganeau, “Population genomics of picophytoplankton unveils novel chromosome hypervariability.” Science Advances 3(7), e1700239 (2017). [DOI: 10.1126/sciadv.1700239] (Reference link)

Related Links
Joint Genome Institute Genome Portal: Algae
Joint Genome Institute news release: Puzzling Plankton Yield Secrets to Role in Evolution/Global Photosynthesis 
Joint Genome Institute: Community Science Program
Joint Genome Institute project description: Why sequence Ostreococcus tauri?
Joint Genome Institute Genome Portal: Ostreococcus tauri RCC4221
Joint Genome Institute project description: Why sequence the low-light strain of Ostreococcus?
Joint Genome Institute Genome Portal: Ostreococcus RCC809

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Transmission electron microscopy image of O. tauri strain RCC4221. [Image courtesy of Martin Hohmann-Marriott.]



June 23, 2017

First Snapshot of a Bacterial Microcompartment’s Protein Shell

Reveals construction principles for nanobioreactor. 

The Science
Bacteria, unicellular organisms, are often defined by what they lack: membrane-bound organelles. However, many bacteria express highly organized primitive organelles, known as bacterial microcompartments (BMCs), composed of an outer protein shell and an internal core of enzymes. BMCs can be thought of as individual bioreactors; they segregate, within a bacterial cell, enzyme-catalyzed chemical reactions important for metabolism. A team of scientists has now provided for the first time a clear picture at atomic level resolution of the structure and assembly of a BMC’s protein shell.

The Impact
The most commonly known type of BMC is the carboxysome, which converts CO2 into carbon-containing compounds important for cellular metabolism. Carboxysomes and BMCs involved with other metabolic processes, also relevant to DOE's mission areas of bioenergy and the environment, exist in a wide variety of bacteria. The clear picture of how a BMC protein shell is assembled furthers the potential for scientists to design and engineer microcompartments, thereby harnessing bacteria's biosynthetic processing power for advanced biofuels production.

Summary
Researchers at the Department of Energy (DOE) Lawrence Berkley National Laboratory (LBNL) and Michigan State University (MSU) demonstrated how a combination of five different proteins assemble in a variety of shapes (hexagons, pentagons, and a pair of stacked hexagons) to form a 20-sided protein shell. Under controlled laboratory conditions, scientists genetically altered a bacterium to produce a BMC shell using the five different protein types. The BMC was 40 nanometers across—to put this size in perspective, an average E. coli bacterium is about 2000 nm in length. In order to visualize the protein mega-complex the researchers isolated the BMCs from the bacteria and gathered X-ray diffraction data at the Stanford Synchrotron Radiation Lightsource (SSRL). Also, they collected X-ray diffraction data for two of the protein components that were previously uncharacterized at the Berkley Lab Advance Light Source (ALS). Using a low-resolution map, generated by cryo-electron microscopy, of the BMC to locate the positions of the five individual protein components and help interpret the higher resolution X-ray data, the complete BMC atomic level structure was determined. Although BMCs have been observed within their hosts in a wide variety of sizes, 55 to 600 nm, the structure of the constructed BMC in this study suggests the general assembly principles remain the same regardless of BMC size. Understanding how a BMC shell assembles can be used to inform the design of shells with novel functionalities such as bioproduct synthesis or otherwise-optimized metabolism for advanced biofuels production.

PM Contacts
Amy Swain Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
U.S. Department of Energy
Amy.Swain@science.doe.gov

Peter Lee Ph.D.
X-ray and Neutron Scattering Facilities Division
Office of Basic Energy Science
Office of Science
U.S. Department of Energy
Peter.Lee@science.doe.gov

PI Contact
Cheryl A. Kerfeld
Michigan State University
Lawrence Berkley National Laboratory
Ckerfeld@lbl.gov

Funding
This work was supported by the National Institutes of Health-National Institute of Allergy and Infectious Diseases grant 1R01AI114975-01 and the U.S. DOE, Office of Science, Office of Basic Energy Sciences under contract no. DE-FG02-91ER20021. The Advanced Light Source is supported by the U.S. DOE, Director, Office of Science, Office of Basic Energy Sciences under contract no. DE-AC02-05CH11231. B.G. was supported by an advanced postdoctoral mobility fellowship from the Swiss National Science Foundation (project P300PA_160983). The Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory, is supported by the U.S. DOE, Office of Science, Office of Basic Energy Sciences under contract no. DE-AC02-76SF00515.  The SSRL resources used are supported, in part, by the DOE, Office of Science, Office of Biological and Environmental Research.

Publications
M. Sutter, B. Greber, C. Aussignargues, C.A. Kerfeld “Assembly principles and structure of a 6.5-MDa bacterial microcomponent shell” Science (2017) 356 (6344). [DOI: 10.1126/science.aan3289] (Reference link)

Related Links
MSU coverage with video
LBNL press release: Study sheds light on how bacterial organelles assemble
News MSU-DOE Plant Research Laboratory: Our first ever look at a bacterial organelle shells
Stanford Synchrotron Radiation Lightsource: Structural Molecular Biology

Topic Areas:



Representation of a BMC’s surface structure.  [Image courtesy of Markus Sutter/Berkeley Lab and MSU.]



June 20, 2017

Discovering the Genetic Timekeepers in Bioenergy Crops

A new class of plant-specific genes required for flowering control in temperate grasses is found.

The Science
To get more feedstock from grass crops, scientists sought to identify the genetic “timekeeper” that stops plant growth and starts plant flowering. They studied the genes that keep a grass growing, or prevent it from flowering, until it has undergone prolonged cold exposure. After screening for and identifying model grasses, the team identified a mutant that flowers rapidly without cold exposure. They then described and characterized the mutant’s missing gene. They named their newly discovered gene REPRESSOR OF VERNALIZATION1.

The Impact
Increasing plant growth could improve the economics of biomass as an energy source. However, once a plant starts flowering, it stops growing. This study furthers the molecular-level knowledge of the flowering regulatory network in the model grass Brachypodium distachyon. The results advance the potential to manipulate flowering time in bioenergy grass crops. Such control would increase biomass yield and subsequently U.S. energy independence.

Summary
The timing of flowering is a key trait for biomass yield. A requirement for vernalization, the process by which prolonged cold exposure provides the ability for grass to flower when given the correct signal (known as competence), is an important adaptation to temperate climates that ensures flowering does not occur before the onset of winter. In temperate grasses, vernalization results in the up-regulation of the gene VERNALIZATION1 (VRN1) to establish competence to flower; however, little is known about the mechanism underlying repression of VRN1 in the fall season, which is necessary to establish a vernalization requirement. Scientists at the Great Lakes Bioenergy Research Center reported that a plant-specific gene containing a bromo adjacent homology and transcriptional elongation factor S-II domain, named RVR1, represses VRN1 before vernalization in the model grass specie Brachypodium distachyon. Thus, RVR1 plays a role in establishing a vernalization requirement in B. distachyon and is likely to play the same role in other vernalization-requiring grasses. Interestingly, RVR1 is a plant-specific gene that is conserved across the plant kingdom, and this study provides the first example of a role for this class of plant-specific genes.

PM Contact
N. Kent Peters, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
U.S. Department of Energy
kent.peters@science.doe.gov

PI Contact
Richard M. Amasino
University of Wisconsin-Madison
amasino@biochem.wisc.edu

Funding
This work was funded in part by the National Science Foundation (grant IOS-1258126), the U.S. Department of Energy (DOE) Great Lakes Bioenergy Research Center (DOE Office of Science, Biological and Environmental Research, DE-FC0-07ER64494), a National Institutes of Health-sponsored predoctoral training fellowship to the University of Wisconsin Genetics Training program, and the Gordon and Betty Moore Foundation and the Life Sciences Research Foundation for their postdoctoral fellowship, and Wallonie-Bruxelles International for their postdoctoral fellowships.

Publication
D.P. Woods, T.S. Ream, F. Bouche, J. Lee, N. Thrower, C. Wilkerson, and R.M. Amasino, “Establishment of a vernalization requirement in Brachypodium distachyon requires REPRESSOR OF VERNALIZATION1.” Proceedings of the National Academy of Sciences USA 114, 6623-6628(2017) [DOI: 10.1073/pnas.1700536114] (Reference link)

Related Links
Great Lakes Bioenergy Research Center
University of Wisconsin-Madison press release: Newly identified gene helps time spring flowering in vital grass crops
Wisconsin State Farmer article: Newly id'd gene helps grass crops
Earth.com article: Newly discovered gene could increase plant yield

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Waiting through a cold season to flower weighs heavily on the amount of biomass a plant accumulates. The Brachypodium grass on the right holds out through winter before beginning the promotion of a flower response (vernalization) and flower production. The plant on the left flowers without vernalization, and it does less work to establish roots and leaves. [Image courtesy of Daniel Woods]



June 19, 2017

Isotope Delivery in Lignin: Not an Easy Path

Scientists attempt to overcome challenge of limited deuterium uptake by lignin for studies of biomass breakdown pathways.

The Science
Isotopic labeling of biological molecules has long been used to investigate complex chemical and structural interactions. In a previous study, deuterium (D) was successfully incorporated into a 50% solution of deuterated water (D2O) in three grass species and Lemna duckweed. However, while isotopic labeling with deuterium using 50% D2O in higher plants is promising for understanding plant cell wall structure, it has exhibited low deuterium uptake in lignin while higher D2O concentrations inhibit growth. In this study, the objective was to determine if deuterium isotopic labeling can be targeted to lignin through the absorption of deuterated phenylalanine by roots of growing whole plants.
The Impact
Lignin plays key roles in biomass recalcitrance, pyrolysis, biochar, manufacture of carbon fiber and other products, therefore imaging of lignin in biomass is an important research tool. By enabling deuteration of natural lignocellulosic plant biomass, unique insights can be found using nuclear magnetic resonance (NMR) and small-angle neutron scattering (SANS) and a host of other bioimaging techniques.

Summary
Researchers at Oak Ridge National Laboratory (ORNL) examined the effects of phenylalanine and deuterated phenylalanine in four species of monocotyledonous plants: two annual grasses, one perennial grass, and duckweed. Switchgrass, a dedicated bioenergy perennial crop, was observed to grow at a similar rate to the control plants when in a 2mM deuterated phenylalanine concentration well. Similarly, winter rye grain, a forage and winter cover crop, was able to tolerate deuterated phenylalanine at the same concentration. Annual ryegrass, a forage and amenity grass also used for phytoremediation and toxicity studies, had significantly reduced growth rates with phenylalanine—less inhibition was observed with deuterated phenylalanine. Duckweed, a small aquatic plant commonly used for toxicity tests, exhibited toxic effects with both phenylalanine and deuterated phenylalanine. Overall, deuterium was not incorporated at a high enough level (30-40%) for lignocellulosic neutron scattering studies. However, the observed 0.5-3% levels of deuterium incorporation may be high enough for discovery of metabolic pathways through mass spectroscopy or other imaging techniques. This research aligns with DOE’s bioenergy and environmental missions.

PM Contact
Roland Hirsch Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
U.S. Department of Energy
Roland.Hirsch@science.energy.gov

PI Contact
Barbara Evans
Chemical Sciences Division
Oak Ridge National Laboratory
evansb@ornl.gov

Funding
This research was supported by the U. S. Department of Energy, Office of Science, through the Genomic Science Program, Office of Biological and Environmental Research, under Contract FWP ERKP752. The research at Oak Ridge National Laboratory’s Center for Structural Molecular Biology (CSMB) was supported by the U. S. Department of Energy, Office of Science, through the Office of Biological and Environmental Research under Contract FWP ERKP291, using facilities supported by the Office of Basic Energy Sciences, U. S. Department of Energy. R. Shah was partly supported by the graduate fellowship program of the Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville. C. Howard, F. Lavenhouse, and D. Ramirez, with K. Ramey as teacher-mentor, were supported by the Siemens Foundation through the Siemens Teachers As Research Scientists (STARS) summer 2014 program administered by Oak Ridge Institute of Science and Education, Oak Ridge Associated Universities. V. Cangemi, B. Kinney, C. Partee, and T. Ware were participants in the Appalachian Regional Commission/Oak Ridge National Laboratory Summer Math Science Technology Institute 2015 summer program. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the U. S. Department of Energy under Contract DE-AC05-00OR22725.

Publications
B.R. Evans, G. Bali, A. Ragauskas, R. Shah, H. O’Neill, C. Howard, F. Lavenhouse, D. Ramirez, K. Weston, K. Ramey, V. Cangemi, B. Kinney, C. Partee, T. Ware, and B. Davidson, “Allelopathic effects of exogenous phenylalanine: A comparison of four monocot species” Planta (2017). [DOI:10.1007/s00425-017-2720-x] (Reference link)

Related Links
Science Focus Area: Oak Ridge National Laboratory (ORNL) Biofuels Program  

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Switchgrass was grown hydroponically in perdeuteration chambers on deuterated phenylalanine to label lignin and on 50% D2O to label the entire biomass. [Image courtesy of Barbara Evans, Oak Ridge National Laboratory (ORNL)]



June 01, 2017

Mutant Rice Database for Bioenergy Research

Genome-wide rice studies yield first major, large-scale collection of mutations for grass model crops, vital to boosting renewable fuel production.

The Science
Researchers produced a database of mutations in an important grass crop: rice. They used fast-neutron irradiation, a process that efficiently induces a wide variety of genetic mutations through exposure to high-energy neutrons. After irradiating the plants, they resequenced 1,504 mutants and identified structural variants and mutations. The results provide an invaluable resource for grass models being used to improve candidate bioenergy feedstock crops such as switchgrass.

The Impact
Boosting yields of bioenergy feedstock crops such as grasses requires a better understanding of how enzymes and proteins synthesize plant cell walls in order to modify the processes and the composition. The team’s goal is to have a functional genomics resource for grass models involved in plant cell wall biosynthesis studies. Until now, mutant collections for grass models have lagged behind those available for the Arabidopsis model system.

Summary
For more than half of the world’s population, rice is the primary staple crop. As a grass, it is a close relative of the candidate bioenergy feedstock switchgrass. A team led by University of California, Davis, and including researchers at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility and the Joint Bioenergy Institute (JBEI), a DOE Bioenergy Research Center, have assembled the first major large-scale collection of mutations for grass models. They used the model rice cultivar Kitaake (Oryza sativa L. ssp. japonica), and compared the genes against the reference rice genome of another japonica subspecies called Nipponbare available on the DOE JGI Plant Portal Phytozome.

Through fast-neutron irradiation, the time-consuming procedures involving plant transformation or tissue culture were bypassed, allowing for faster development of rice mutant collections. The DOE JGI resequenced 1,504 rice mutants and identified structural variants and mutations. The work follows a pilot, genome-wide study begun two years ago, in which 41 rice mutants were sequenced and analyzed to identify mutations and structural variants. This new, large-scale collection of more than 90,000 mutations affecting nearly 60 percent of all rice genes is now available on a publicly accessible database called KitBase, is a comprehensive resource that will allow researchers to quickly identify rice lines with mutations in specific genes and to characterize gene function. Among other uses, the collection will allow bioenergy researchers to quickly identify mutations involved in cell wall biosynthesis, critical for increasing plant yields.

PM Contact
Daniel Drell, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
daniel.drell@science.doe.gov

Kent Peters, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of
kent.peters@science.doe.gov

PI Contact
Jeremy Schmutz
Plant Program Head
DOE Joint Genome Institute
jschmutz@hudsonalpha.com

Pamela Ronald
University of California, Davis
pcronald@ucdavis.edu

Funding
Work was conducted by the U.S. Department of Energy (DOE) Joint Genome Institute, a DOE Office of Science user facility and the DOE Joint BioEnergy Institute (contract number DE-AC02-05CH11231). This work was also supported by the National Institutes of Health (NIH) and the National Science Foundation (NSF).

Publications
G. Li, R. Jain, M. Chern, N.T. Pham, J.A. Martin, T. Wei, W.S. Schackwitz, A.M. Lipzen, P.Q. Duong, K.C. Jones, L. Jiang, D. Ruan, D. Bauer, Y. Peng,  K.W. Barry, J. Schmutz, and P.C. Ronald. “The Sequences of 1,504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies.” The Plant Cell(2017) [DOI: 10.1105/tpc.17.00154]  (Epub ahead of print) (Reference link)

Related Links
Berkeley Lab News Release: A Whole-Genome Sequenced Rice Mutant Resource for the Study of Biofuel Feedstocks
Berkeley Lab News Release:  Plant Cell Highlight: “Technology Turbocharges Functional Genomics”
KitBase (Kitaake Rice Mutant Database)
Crop Genetics Innovation
Pilot Study: Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation
Nipponbare/japonica subspecies of Oryza sativa on Phytozome
JBEI Feedstocks Division
Grasses: The Secrets Behind Their Stomatal Success

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Genome-wide distribution of fast neutron-induced mutations in the Kitaake rice mutant population. [Image courtesy of Guotian Li and Rashmi Jain]



May 30, 2017

Unlocking the Potential of Fungal Enzymes to Break Down Plant Cell Walls

Biomass-degrading enzyme complexes could improve biofuel production.

The Science
A major bottleneck in biofuel production is the difficulty of breaking down lignocellulose—the primary building block of plant cell walls. A recent study suggests that unlike bacterial enzyme complexes for breaking down lignocellulose, fungal enzyme complexes have a more diverse functionality.

The Impact
The findings highlight the powerful degradation activity of fungal lignocellulose-degrading enzymes, which could be harnessed to develop novel strategies for efficient biofuel production.

Summary
Gut microbes play a major role in helping ruminants such as cows, goats and sheep break down lignocellulose-rich plant matter in their diet. Anaerobic bacteria and fungi inhabiting the ruminant gut have evolved a suite of lignocellulose-degrading enzymes, whose activity supports microbial metabolism while supplying nutrients to ruminants. These enzymes often assemble together in large, multi-protein complexes called cellulosomes, which enhance the ability of gut microbes to degrade lignocellulose by confining all the enzymes in one place. Although bacterial cellulosomes now serve as a standard model for biomass conversion and synthetic biology applications, fungal cellulosomes have not been well characterized due to the lack of genomic and proteomic data, despite their potential value for biofuel and bio-based chemical production. To address this knowledge gap, a collaborative effort by researchers from the University of California, Santa Barbara, the Environmental Molecular Sciences Laboratory ( EMSL); the Department of Energy Joint Genome Institute (DOE JGI); Pacific Northwest National Laboratory; Centre National de la Recherche Scientifique; French National Institute for Agricultural Research; Radboud University; King Abdulaziz University; and the University of California, Berkeley combined next-generation sequencing with functional proteomics to describe the comprehensive set of proteins that play a role in fungal cellulosome assembly. This research was performed under the Facilities Integrating Collaborations for User Science (FICUS) initiative and used resources at DOE JGI and EMSL, which are DOE Office of Science User Facilities. This analysis revealed a new family of genes that likely serves as scaffolding proteins critical for cellulosome assemblies across diverse species of anaerobic gut fungi. Unlike bacterial cellulosomes, which have high species specificity, fungal cellulosomes are likely a composite of enzymes from several species of gut fungi. Although many bacterial and fungal plant biomass-degrading enzymes have shared similarities, the fungal cellulosomes were found to contain additional lignocellulose-degrading enzymes not found in bacterial cellulosomes. These features may not only confer a selective advantage of fungi over bacteria in the ruminant gut, but also impart fungal cellulosomes with great potential for biomass conversion. Taken together, the findings highlight key differences in bacterial and fungal cellulosomes and suggest enzyme connections (known as tethering) play such an important role in plant cell wall degradation.

BER PM Contact
Paul Bayer, SC-23.1, 301-903-5324

PI Contact
Michelle A. O’Malley
University of California, Santa Barbara
momalley@engineering.ucsb.edu

EMSL Contact
Sam Purvine
EMSL
samuel.purvine@pnnl.gov

Funding
This work was supported by the U.S. Department of Energy’s Office of Science (Office of Biological and Environmental Research), including support of the Environmental Molecular Sciences Laboratory (EMSL) and the DOE Joint Genome Institute (DOE JGI), DOE Office of Science User Facilities; U.S. Department of Agriculture; National Science Foundation; U.S. Army; University of California, Santa Barbra and Berkeley; and California NanoSystems Institute.

Publication
C.H. Haitjema, S.P. Gilmore, J.K. Henske, K.V. Solomon, R. de Groot, A. Kuo, S.J. Mondo, A.A. Salamov, K. LaButti, Z. Zhao, J. Chiniquy, K. Barry, H.M. Brewer, S.O. Purvine, A.T. Wright, M. Hainaut, B. Boxma, T. van Alen, J.H.P. Hackstein, B. Henrissat, S.E. Baker, I.V. Grigoriev, and M.A. O’Malley, “A Parts List for Fungal Cellulosomes Revealed by Comparative Genomics.” Nature Microbiology (2017). DOI 10.1038/nmicrobiol.2017.87 (Reference link)

Related Links
Unlocking the Potential of Fungal Enzymes to Break Down Plant Cell Walls EMSL science highlight
Fungal Enzymes Team Up to More Efficiently Break Down Cellulose DOE JGI news release
Biofuel breakdown science highlight

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Lignocellulose-degrading enzymes in fungal cellulosomes have great potential for biomass conversion. [Image courtesy of EMSL]



May 23, 2017

First Look at a Living Cell Membrane

Neutrons provide the solution to nanoscale examination of living cell membrane and confirm the existence of lipid rafts.

The Science
The cell membrane, a thin bilayer of lipid molecules with embedded proteins, provides the essential function of protecting the cell from its outside environment and controlling the movement of substances in and out of the cell. However, much about this thin bilayer of lipid molecules has remained a mystery despite being extensively studied. This has been due to the difficulty of viewing a living cell membrane; previous methods employed to investigate membrane structure, such as X-rays and electron beams, were not well suited for studying living cells due to their high-energy nature (>5,000 eV) that damage membranes. Using cold neutrons with a low kinetic energy (<0.025 eV), for the first time, researchers performed direct nanoscale examination of a living cell membrane.

The Impact
Using isotopes to create internal contrast within living cells the membrane structure and thickness of the bacterium, B. subtilis, was determined. In addition, the researchers were able to confirm the existence of the long hypothesized presence of lipid rafts, tightly packed free-floating membrane lipids and proteins thought to be important to cell signaling and facilitating movement of essential biomolecules in and out of the cell, along with a variety of other functions. The methods developed may prove valuable in areas of interest to DOE such as biomass feedstock and biofuel production, in which bacteria have an important role.

Summary
Examining a living cellular membrane has remained an unsolved challenge up to this point due to the dynamic, chemically diverse, and fragile nature of living cells. Too small to be seen by a traditional optical microscope, neutrons emerged as the solution to studying a living lipid bilayer at nanoscale without damaging the cell. Neutrons can be used as a probe for characterizing biological materials because a neutron beam scattered by a biological sample creates a pattern that is dependent on the material’s isotopic composition and reflects the material’s structural arrangement. Deuterium is an isotope of a highly abundant atom in biological matter, hydrogen. It contains a neutron and a proton, in contrast to hydrogen, which contains a single proton but no neutron. This seemingly small difference makes substituting deuterium for hydrogen an ideal approach to studying membranes and other nanoscale biological systems.  Cells perceive little difference between hydrogen and its isotope, deuterium, while the isotopes appear very differently using the neutron scattering technique. A team of researchers at Oak Ridge National Laboratory (ORNL) was able to introduce enough deuterium into the membrane of the bacterium B. subtilis to differentiate it from other cell components. Further, the team was able to tune the specific proportions of deuterium and hydrogen by introducing into the cell two fatty acid (the molecules that comprise the membrane lipids) types, with unique isotope ratios. The cell incorporated the specific mix of isotope-labeled fatty acids into its membrane and a non-uniform distribution of lipids was observed, confirming the lipid raft hypothesis. These experiments answer some of biology’s longest-standing questions, aligning with the DOE Office of Science mission of providing fundamental science research to address some of the most pressing challenges of our time.

PM Contact
Amy Swain, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
U.S. Department of Energy
Amy.Swain@science.doe.gov

PI Contact
John Katsaras
katsarasj@ornl.gov

Funding
This research was sponsored by the Laboratory Directed Research and Development Program (grant number 6988) of Oak Ridge National Laboratory (ORNL), managed by UT-Battelle, LLC, for the U. S. Department of Energy (DOE) under Contract No. DE-AC05-00OR22725. Support for J.K. provided by the DOE Office of Basic Energy Sciences, Scientific User Facilities Division and for R.F.S by the DOE Office of Biological and Environmental Research (grant number ERKP-851). This research used resources of the Oak Ridge Leadership Computing Facility at ORNL, supported by the DOE Office of Advanced Scientific Computing Research, Facilities Division. Small-angle neutron scattering was performed at ORNL using the Bio-SANS instrument at the High Flux Isotope Reactor, supported by the DOE Office of Biological and Environmental Research, Biological Systems Science Division, through the ORNL Center for Structural Molecular Biology, and the EQ-SANS instrument at the Spallation Neutron Source, supported by the DOE Office of Basic Energy Sciences, Scientific User Facilities Division (grant number ERKP-SNX). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Publications
J.D. Nickels, S. Chatterjee, C.B. Stanley, S. Qian, X. Cheng, D.A.A. Myles, R.F. Standaert, J.G. Elkins, and J. Katsaras, “The in vivo structure of biological membranes and evidence for lipid domains,” PLoS Biology 5, 15. DOI:10.1371/journal.pbio.2002214. (Reference link)

Related Links
ORNL Press Release: Neutrons provide the first nanoscale look at a living cell membrane

Topic Areas:



Neutron scattering is a valuable technique for studying cell membranes, but signals from the cell’s other components such as proteins, RNA, DNA and carbohydrates can get in the way (left). An ORNL team made these other components practically invisible to neutrons by combining specific levels of heavy hydrogen (deuterium) with normal hydrogen within the cell (right). [Image courtesy of ORNL/Xiaolin Cheng and Mike Matheson]



May 23, 2017

Modifications to the Bacterial Cell Envelope Increase Lipid Production

A new strategy significantly increases the production and secretion of microbial lipids in bacteria that can be grown at industrial scale.

The Science
High-yield microbial production of lipids presents a significant challenge, often falling short of what can be theoretically obtained. This study characterized high-lipid (HL) mutant variants of Rhodobacter sphaeroides and showed that alterations to the bacterial cell envelope can result in increased accumulation of lipids relative to the parent strain.

The Impact
Knowledge of the mechanisms that limit microbial lipid production can reveal new strategies to increase lipid yield and the economic viability of alternatives to fuels or chemicals currently derived from petroleum.

Summary
Microbial lipids are potential replacements for petroleum-based fuels and chemicals; however, their production often falls short of theoretical yield, and improvement strategies are needed. Researchers from the Department of Energy’s (DOE) Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, and Environmental Molecular Sciences Laboratory (EMSL; a DOE Office of Science user facility) advanced their research on microbial lipid production by examining a new class of Rhodobacter sphaeroides mutants that exhibited enhanced lipid accumulation relative to the parent strain. The researchers used EMSL’s FEI Tecnai T-12 cryo-transmission electron microscope and structured illumination super resolution fluorescence microscope, in which chemical sensitivity profiles indicated HL mutants were sensitive to drugs that target the cell envelope. Changes in cell shape were also observed, suggesting that previously undescribed alterations in the bacterial cell envelope could be used to increase bacterial lipid production. Importantly, a subset of the HL mutants were able to secrete lipids, two of which accumulated approximately 60 percent of their total lipids extracellularly, potentially enabling easy product recovery from a bioreactor. When one of the highest lipid-secreting strains was grown in a fed-batch bioreactor, its lipid content was comparable to oleaginous microbes, defined as those accumulating 20 percent or more of their dry cell weight as lipid. Knowledge of the biological mechanisms that limit lipid production can inform new genetic engineering and growth strategies and enable this important class of molecules to be adopted as fuels or chemicals on a larger scale.

BER PM Contacts
Paul Bayer, SC-23.1, 301-903-5324
Kent Peters, SC-23.2, 301-903-5549

PI Contact
Timothy J. Donohue
University of Wisconsin-Madison
tdonohue@bact.wisc.edu

EMSL Contacts
Alice Dohnalkova
EMSL
Alice.Dohnalkova@pnnl.gov

Dehong Hu
EMSL
Dehong.Hu@pnnl.gov

Galya Orr
EMSL
Galya.Orr@pnnl.gov

Funding
This work was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, including support of the Environmental Molecular Sciences Laboratory and Great Lakes Bioenergy Research Center.

Publication
Lemmer, K. C., W. Zhang, S. J. Langer, A. C. Dohnalkova, D. Hu, R. A. Lemke, J. S. Piotrowski, G. Orr, D. R. Noguera, and T. J. Donohue. 2017. “Mutations That Alter the Bacterial Cell Envelope Increase Lipid Production,” mBio 8(3), e00513-17. DOI: 10.1128/mbio.00513-17. (Reference link)

Related Links
Modifications to the Bacterial Cell Envelope Increase Lipid Production, EMSL science highlight
Modifying Cell Wall Can Increase Bacterial Lipids, Great Lakes Bioenergy Research Center highlight
Lipid Biofuels EMSL science highlight
Enhancing Microbial Lipid Production, Great Lakes Bioenergy Research Center highlight

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


May 19, 2017

High Yield Biomass Conversion Strategy Ready For Commercialization

Researchers demonstrate 80% of biomass is converted into high-value products.

The Science
Researchers show that the three main components of plant biomass can be converted to high value products in economically favorable yields. Using the concept of an integrated biorefinery multiple products streams are produced, comparable to the process of a petroleum refinery, making lignocellulosic (nonedible) biomass a promising alternative source of carbon. The products produced--dissolving pulp, furfural, carbon foam, and battery anodes--have established markets, minimizing market risk for the first commercial plant.

The Impact
This technology can be expanded upon to produce fermentable sugars, advanced biofuels, or specialty chemicals, and could enable the concept of an integrated renewable biorefinery that is cost-competitive with petroleum. The techno-economic analysis estimates an overall revenue of $500 per dry megaton; this results in an internal rate of return over 30%, thereby making the technology attractive for investment.

Summary
The production of renewable chemicals and biofuels must be cost-competitive with petroleum-derived equivalents to be accepted by markets. At the Great Lakes Bioenergy Research Center (GLBRC), one of three DOE Bioenergy Research Centers (BRCs), scientists propose a biomass conversion strategy that maximizes the conversion of lignocellulosic biomass. Using this method, up to 80% of the biomass can be converted into high value products that can be commercialized, providing the opportunity for successful translation to a viable commercial process. Their fractionation method preserves the value of all three primary biomass components: cellulose, which is converted into dissolving pulp for fibers and chemical production; hemicellulose, which is converted into furfural, a building block chemical; and lignin, which is converted into carbon products (carbon foam, fibers, or battery anodes). Since these products are all existing targets for pulp mills, they can be directly introduced into current markets, minimizing market risk for the first commercial plant. The overall revenue of the process is about $500 per dry megaton of biomass, which combined with low total cost, results in an internal rate of return of over 30%. Once de-risked, the technology can be extended to produce fermentable sugars, advanced biofuels, or other specialty chemicals. This research aligns closely with DOE’s environmental and energy independence missions.

Contact
N. Kent Peters
Program Manager, Office of Biological and Environmental Research
kent.peters@science.doe.gov, 301-903-5549

(PI Contacts)
James A. Dumesic
University of Wisconsin - Madison
dumesic@engr.wisc.edu

Christos T. Maravelias
University of Wisconsin - Madison
christos@engr.wisc.edu

Troy Runge
University of Wisconsin - Madison
trunge@wisc.edu

Funding
This work was funded in part by NSF SBIR 1602713 and 1632394 and by the DOE Great Lakes Bioenergy Research Center (DOE Office of Science BER DE-FC02-07ER64494). Additional funding provided by Glucan Biorenewables LLC.

Publications
Alonso, D.M. et al, “Increasing the revenue from lignocellulosic biomass: Maximizing feedstock utilization.” Science Advances (2017), DOI: 10.1126/sciadv.1603301 (Reference link)

Related Links
University of Wisconsin-Madison Press Release: Triple play boosting value of renewable fuel could tip market in favor of biomass
Great Lakes Bioenergy Research Center (GLBRC)

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



UW-Madison researchers and collaborators have developed a new “green” technology for converting non-edible biomass into three high-value chemicals that are the basis for products traditionally made from petroleum. [Image courtesy of Phil Biebl/UW-Madison College of Engineering]



May 08, 2017

Fungi: Gene Activator Role Discovered

High levels of DNA base modification reported in early-derived fungi.

The Science
DNA, the molecule carrying instructions for development, growth, function, and reproduction, is made up of four bases: cytosine (C), guanine (G), adenine (A), and thymine (T)–defining the genetic code. When the organism’s genetic code is modified by changing a single base this can cause changes in protein structure and function, impacting an organism’s traits. However, there are other subtler changes which can affect the activity of a DNA segment without changing the sequence. One of the most common examples involves the methylation (addition of a methyl group) of cytosine (C) on the 5th position of its carbon ring (5mC). This research explores one of the other less known modifications, adding a methyl group to base 6 of adenine (6mA) in early-diverging fungi.

The Impact
In comparison to other lineages, early-diverging fungi have not been well studied or understood. However, many of these fungi are powerful plant biomass degraders with potential bioenergy applications. In this study, the discovery of adenine methylation associated with effects on gene expression in early-diverging fungi may explain the historic difficulty in altering the DNA of these early-diverging fungi, and aid in the development of future tools for their genetic modification.

Summary
The Fungi kingdom is estimated to be ~1 billion years old; the first six phyla comprise the ‘early-diverging’ fungi and the last two phyla make-up the Dikarya, which evolved ~500 million years ago.   In this study, for the first time, 6mA base modification was identified as a widespread marker for transcriptionally active genes in early diverging fungi. The researchers examined long-read sequences from 16 diverse fungal genomes for the presence of adenine methylation. In the early-diverging fungi up to 2.8% of adenines were methylated, much higher than is seen in comparison to the eukaryotes and the more derived fungi (both less than 0.4%). Interestingly, despite fungi and animals’ closer phylogenetic relation, early-deriving fungi and algae-two distantly related kingdoms-are more similar in 6mA profiles than their more recently derived- (but more closely related)- fungi and animals. In early-derived fungi and algae, 6mA’s presence signals gene expression, while the role appears reversed in animals. This significant finding suggests 6mA’s association with gene expression is ancestral to the eukaryotic domain of life. This research also represents a previously uncharacterized difference between the role of 6mA in early-derived fungi and Dikarya of gene suppression and expression. More broadly this research highlights the variation in how 6mA is used to modify gene expression across eukaryotes, further defining the collective understanding of transcriptional regulation in this domain of life.

Contact
BER PM
Daniel Drell, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
daniel.drell@science.doe.gov

PI
Igor V Grigoriev, Ph.D.
Fungal Genomics Program Lead, DOE Joint Genome Institute
ivgrigoriev@lbl.gov

Funding
Work conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. This work was partially supported by funding from the National Science Foundation (DEB-1441715 to JES, DEB-1441604 to J.W.S. and DEB-1354625 to T.Y.J. and I.V.G.). This work was further supported by the Office of Science (BER), US Department of Energy (DE-SC0010352) and the Institute for Collaborative Biotechnologies through grant W911NF-09- 0001. R.J.S. is supported by funding from the Office of the Vice President of Research at UGA as well as the Pew Charitable Trusts.

Publications
S.J. Mondo, R.O. Dannebaum, R.C. Kuo, K.B. Louie, A.J. Bewick, K. LaButti, S. Haridas, A. Kuo, A. Salamov, S.R. Ahrendt, R. Lau, B.P. Powen, A. Lipzen, W. Sullivan, B.B. Andreopoulos, A. Clum, E. Lindquist, C. Daum, J. Magnuson, T.Y. James, M.A. O’Malley, J.E. Stajich, J.W. Spatafora, A. Visel, I.V. Grigoriev, “Widespread adenine N6-methylation of active genes in fungi” Nature Genetics (2017). [DOI: 10.1038/ng.3859] (Reference link)

Related Links
JGI Press Release: Finding a New Major Gene Expression Regulator in Fungi

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



The genome of the Linderina pennispora, a fungus belonging to the earliest branches of the fungal kingdom, was sequenced and annotated as part of the Nature Genetics study. [Image courtesy of (ZyGoLife Research Consortium, Flickr, CC BY-SA 2.0)]



April 18, 2017

A Gene that Influences Grain Yields in Grasses

Genetic screen identifies mutations that impact green foxtail panicle formation

The Science
Through deep sequencing of the model grass green foxtail (Setaria viridis), researchers pinpointed a gene critical for the development of flowers that give rise to the grain. Using this information, a homologous gene in maize was identified as playing a similar role highlighting the utility of S. virdis as a model crop.

The Impact
Maize, an important food and bioenergy crop, has been limited in the progress of gene discovery due to its large and complex genome. Recently, S. virdis has been proposed as a model crop for maize. In a new study, researchers screening for mutants of the model grass green foxtail identified several mutations that disrupt the regular pattern of panicle development, the panicle is the spear-shaped flowering cluster at the tip of each branch necessary for reproduction.

Summary
Setaria species, among them green foxtail (S. viridis) and foxtail millet (S. italica), are related to several candidate bioenergy grasses including switchgrass and Miscanthus and serve as grass model systems to study grasses that photosynthetically fix carbon from CO2 through a water-conserving (C4) pathway. The genomes of both green foxtail and foxtail millet have been sequenced and annotated through the DOE JGI’s Community Science Program. A team led by Tom Brutnell at the Donald Danforth Plant Science Center and including researchers at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, reported in Nature Plants, that they had identified genes that may play a role in flower development on the panicle of green foxtail.

The team identified four recessive mutants, tagged spp1 through spp4, that lead to panicles with reduced and uneven flower clusters. Focusing on the spp1 mutation, they performed deep sequencing to specifically locate the genes that cause the mutation, narrowing their search down to a 1-million base sequence. They ultimately identified the SvAUX1 gene in green foxtail as one critical for flower cluster development in green foxtail. Panicle development is critical for determining grain yield that is crucial to food crops as well as candidate crops for producing renewable and sustainable fuels.  A homologous gene in maize was identified as playing a similar role, illustrating the value of model systems in finding genes involved in important properties in potential bioenergy-relevant plants.

BER Contacts
Daniel Drell, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
daniel.drell@science.doe.gov

Pablo Rabinowicz, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
Pablo.Rabinowicz@science.doe.gov

PI Contacts
Jeremy Schmutz
Plant Program Head
DOE Joint Genome Institute
jschmutz@hudsonalpha.com

Thomas Brutnell
Donald Danforth Plant Science Center
tbrutnell@danforthcenter.org

Funding
This work was conducted by the U.S. Department of Energy’s (DOE) Joint Genome Institute, a DOE Office of Science user facility (contract number DE-AC02-05CH11231). This work was also supported by a Department of Energy grant to T. Brutnell (DE-SC0008769), and a National Science Foundation grant to E.A. Kellogg (IOS-1413824).

Publications
P. Huang, H. Jiang, C. Zhu, K. Barry, J. Jenkins, L. Sandor, J. Schmultz, M.S. Box, E.A. Kellogg, and T.P. Brutnell “Sparse panicle1 is required for inflorescence development in Setaria viridis and maize” Nat. Plants. (2017) DOIi: 10.1038/nplants.2017.54 (Reference link)

Related Links
Green foxtail Community Science Program proposal
Foxtail millet Community Science Program proposal
Foxtail millet genome publication
Community Science Program
Setaria italica on Phytozome

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Traits including its relatively small genome and short life cycle make green foxtail (Setaria viridis) a model grass system for finding genes involved in important properties in potential bioenergy-relevant plants. (Jose Sebastian, Wikimedia Commons, CC BY-SA 3.0)



April 17, 2017

Biosynthetic Pathway to Nylons

Biological production of cyclic precursors of nylon and related products avoids harsh chemicals and high heat.

The Science
Nylons are a class of widely used synthetic compounds known for their extreme toughness, strength, and elasticity. There are millions of tons produced annually for commercial applications as fibers (apparel, rubber reinforcement, flooring), shapes (electrical equipment, parts for cars, etc.) and films (mostly food packaging). Five- and six-member ring lactams are important commodity chemicals used as precursors in the manufacture of nylons. (Precursors are compounds that participate in a chemical reaction producing another compound). However, biological production of these highly-valued chemicals has been limited due to a lack of appropriate enzymes that form these lactam rings. An enzyme in the bacteria Streptomyces aizunensis has been enlisted to fulfill a crucial step in biological synthesis of these precursors.  

The Impact
Current commercial nylon production methods start with crude oil that requires energy intensive processes and harsh acidic reaction conditions. This is the first study to demonstrate a suitable enzyme for synthesis of lactams under microbial fermentation conditions for the manufacture of nylon. A Streptomyces enzyme enables five-membered, six-membered and even seven-membered ring formation at mild temperatures, resulting in the production of important industrial lactams via fermentation from biological molecules avoiding petroleum, harsh chemicals and heat.

Summary
Five- and six-member ring lactams are important commodity chemicals because they are used as precursors in the manufacture of nylons with millions of tons produced annually requiring harsh conditions. Biological production of these highly-valued precursors will reduce the need of petroleum and avoid toxic harsh conditions. However, biological production has been limited due to a lack of enzymes that carry out crucial steps at room temperature and pressure. DOE Joint BioEnergy Institute (JBEI) researchers demonstrated production of these precursors using an acyl-CoA ligase from Streptomyces aizunensis. This enzyme has a broad substrate spectrum and can cyclize linear amino acids into their corresponding cyclic lactam when expressed in Escherichia coli. Further metabolic engineering of the pathway lead to production of the lactams directly from the common amino acid lysine. This research advances DOE’s environmental and energy missions.

PM Contact
N. Kent Peters
Program Manager, Office of Biological and Environmental Research
kent.peters@science.doe.gov, 301-903-5549

PI Contact
Jay Keasling
CEO, Joint BioEnergy Institute, Emeryville, California 94608, United States
jdkeaslilng@lbl.gov

Funding
This work was funded by the Joint BioEnergy Institute (http:// www.jbei.org/), which is supported by the US Department of Energy, Office of Science, Office of Biological and Environmental Research, through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the US Department of Energy and The Synthetic Biology Engineering Research Center (SynBERC) through National Science Foundation grant NSF EEC 0540879

Publications
J. Zhang, J.F. Barajas, M. Burdu, G. Wang, E.E. Baidoo, and JD. Keasling (2017) “Application of an Acyl-CoA Ligase from Streptomyces aizunensis for Lactam Biosynthesis” ACS Synthetic Biology [DOI: 10.1021/acssynbio.6b00372] (Reference link)

Related Links
JBEI Website

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Biological production of lactams has been limited due to a lack of enzymes that cyclize ?-amino fatty acid precursors to corresponding lactams under ambient conditions.  In this study, we demonstrated production of these chemicals using ORF26, an acyl-CoA ligase involved in the biosynthesis of ECO-02301 in Streptomyces aizunensis. [Image courtesy of JBEI]



April 07, 2017

Tracking Genome Expansion in Giant Viruses

Piecemeal acquisition of genes from hosts may explain the rise of giant viruses.

The Science
The number of microbes in, on, and around the planet is said to outnumber the stars in the sky. The number of viruses found worldwide is at least an order of magnitude greater. As their name suggests, giant viruses are larger than many bacterial and eukaryotic cells. They were first discovered in 2003, and the true breadth of their diversity remains unknown. Researchers recently uncovered a new group of giant viruses after sifting through metagenomic datasets. Dubbed Klosneuviruses, these giant viruses contain a more complete set of translation machinery genes than any other virus known to date.  

The Impact
Contrary to popular belief, most viruses do not affect humans. They do, however, impact microbes, which regulate biogeochemical cycles. Protists such as algae, for example, sequester large fractions of carbon in the atmosphere and are key components of the global carbon cycle. Viruses can significantly impact the productivity of the protist population, reducing their capabilities in regulating global cycles. As protists are thought to be the host of these Klosneuviruses, a better understanding of how viruses impact microbial survival and community interactions is relevant to Department of Energy (DOE) missions in bioenergy and environment.

Summary
While sifting through metagenomic sequence datasets for a DOE Joint Genome Institute (JGI) Community Science Program project, DOE JGI researchers identified genome sequences typically found in giant viruses. A group of giant viruses called Mimiviruses was first discovered in 2003, and a handful of such groups have been reported since. DOE JGI researchers assembled a 1.57-million base (Megabase) genome of a putative virus they called Klosneuvirus, and further searching through the metagenomic datasets uncovered three more related giant virus genomes. Three of the four Klosneuviruses were found with representatives of the protist phylum Cercozoa. This is unusual because until now, all giant viruses had been recovered with Acanthamoeba (amoebas found in soils and fresh waters), which was not seen with the Klosneuviruses. The team also found that the Klosneuviruses encoded components for a far more expansive translation system than had been seen with other giant viruses. Aside from increasing the known gene pool of giant viruses by nearly 2,500 additional gene families, comparing the genes to previously discovered giant viruses revealed that the Klosneuviruses are a subfamily of Mimiviruses. Starting then from their last shared ancestor with the Mimiviruses, the researchers suggest that over time, the Klosneuviruses picked up genes from various different hosts. Overall, the team’s findings lend credence to the theory that giant viruses evolved from much smaller viruses, rather than aligning with theories that they may instead be descended from a cellular ancestor. The consequences of Klosneuvirus infection of protist hosts remains to be explored.

Contacts (BER PM)
Daniel Drell, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
U.S. Department of Energy
daniel.drell@science.doe.gov 

(PI Contact)

Tanja Woyke
Microbial Genomics Program Lead
DOE Joint Genome Institute
twoyke@lbl.gov

Funding
This work was conducted by the U.S. Department of Energy’s (DOE) Joint Genome Institute, a DOE Office of Science user facility (contract number DE-AC02-05CH11231). Additional support was provided by the U.S. Department of Health and Human Services, European Research Council, Austrian Science Fund, and John Templeton Foundation.

Publication
Schulz, F., N. Yutin, N. N. Ivanova, D. R. Ortega, T. K. Lee, J. Vierheilig, H. Daims, M. Horn, M. Wagner, G. J. Jensen, N. C. Kyrpides, E. V. Koonin, and T. Woyke. 2017. “Giant Viruses with an Expanded Complement of Translation System Components,” Science 356(6333), 82-85. DOI: 10.1126/science.aal4657. (Reference link)

Related Links
JGI Earth’s viral diversity
JGI IMG/VR database
JGI Surveying viral populations
JGI Community Science Program

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Giant virus acquiring genes from different eukaryotic host cells. [Image courtesy Ella Maru Studio]



March 23, 2017

Small Proteins Secreted by Poplar Roots Form Communication Route with Associated Fungal Communities

The Science  
Small proteins that are secreted from the plant roots were found to act as communication signals between the plant and associated beneficial fungus. These molecular cues have the potential to alter development of both beneficial and pathogenic fungi.

The Impact
This work elucidates the complex communications that occur between mutualistic plant-microbe interactions and the influence of such associations on both partners, opening new avenues for development of high-yielding, sustainable bioenergy field crops.

Summary
Microbial communities surrounding plant roots can form symbiotic associations with the plant, an interaction that requires complex communications between both organisms. Mutualistic associations offer several benefits to the plant such as enhanced growth and tolerance to drought. Mutualistic fungi have evolved elaborate protein-based signals (effectors) that communicate their metabolic requirements to their plant hosts; in turn, root exudates contain small secreted proteins (SSPs) that influence mutualism with the microbes and could function as effector proteins during symbiotic interactions. While many new SSPs have been discovered through annotation of plant genome sequences, their roles as secreted effector proteins during mutualistic symbiosis was uncertain. Researchers at the Oak Ridge National Laboratory, supported by the DOE BER Plant-Microbe Interfaces Scientific Focus Area, used computational prediction and experimentation to identify SSPs in the bioenergy tree Populus trichocarpa and elucidate their effect during mutualistic symbiosis with the ectomycorrhizal fungus, Laccaria bicolor. Of the 2,819 Populus protein-encoding genes that were identified as differentially expressed across all stages of mycorrhizal root tip development during symbiosis between P. trichocarpa and L. bicolor, 417 were predicted to be SSPs (=250 aa in length). Experimentation verified that a subset of these SSPs were able to enter and accumulate in L. bicolor, then alter the development of multiple ectomycorrhizal and pathogenic fungi. This study demonstrates that SSPs in Populus can function as effector proteins during symbiotic interactions, highlighting a novel avenue by which plants communicate with and possibly influence their mutualistic microbial partners.

Contacts (BER PM)
Cathy Ronning 
SC 23.2
catherine.ronning@science.doe.gov

(PI Contact)
Xiaohan Yang
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
yangx@ornl.gov

Funding
Genomic Science Program, US Department of Energy, Office of Science, Biological and Environmental Research, as part of the Plant-Microbe Interfaces Scientific Focus Area (http://pmi. ornl.gov)

Publications
J.M. Plett, H. Yin, R. Mewalal, R. Hu, T. Li, P. Ranjan, S. Jawdy, H.C. DePaoli, G. Butler, T.M. Burch-Smith, H-B Guo, C.J. Chen, A Kohler, I.C. Anderson, J.L. Labbé, F. Martin, G.A. Tuskan, and X. Yang, “Populus trichocarpa encodes small, effector-like secreted proteins that are highly induced during mutualistic symbiosis.” Scientific Reports 7:382 (2017). [DOI:10.1038/s41598-017-00400-8]. (Reference link)

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



The Populus-Laccaria association established in vitro. Photo credits: Anne Jambois, INRA.



March 17, 2017

Grasses: The Secrets Behind Their Stomatal Success

Finding a grass gene impacting stomatal morphology underscores the importance of developing a mutant gene index.

The Science
The evolution of adjustable pores, or stomata, enables plants to modify their stomatal pore size to control the amount of CO2 that enters and water that escapes. Plants have evolved two kidney shaped guard cells that swell to create the stomate. In grasses, however, they have further evolved with the addition of two subsidiary cells flanking the guard cells, which may be linked to improved stomatal physiology. In a recent study, researchers identified a transcription factor needed for subsidiary cell formation using a genetic screen.

The Impact
Subsidiary cells, unique to grasses, have been linked to improved physiological performance. These cells enable a greater range of pore size and quicker stomatal responsiveness. The ability to better control water loss and increase carbon assimilation in plants could affect its ability to handle stressors such as drought and play a role in the health and yields of candidate bioenergy feedstocks. Understanding the water management mechanism could aid the identification and selection of individuals better suited for growing in otherwise marginal soils.

Summary
Brachypodium distachyon is a small, rapidly growing grass that serves as a model for candidate bioenergy grasses such as Miscanthus and switchgrass. For this reason, in 2010, the B. distachyon genome was sequenced and annotated as part of the Community Science Program of the U.S. Department of Energy’s (DOE) Joint Genome Institute (JGI), a DOE Office of Science user facility. To further accelerate research in the development of biofuel feedstocks, a project to sequence thousands of B. distachyon mutants was selected for the 2015 CSP portfolio. This library of sequenced mutants will aid researchers in studying and rapidly identifying and ordering plants with mutations in any gene in their genomes.

Using a forward genetic screen, a Stanford University team identified a B. distachyon subsidiary cell identify defective (sid) mutant; as a result, the mutant is unable to produce subsidiary cells. In comparing the whole genome sequence of B. distachyon with the sid mutant, a 5-base pair deletion that encodes for the transcription factor BdMUTE was discovered. Further, BdMUTE was identified as a mobile transcription factor responsible for coordinating the development of subsidiary and guard cell complexes. The unique subsidiary cells in grasses may enable enhanced performance when stressors such as increased temperature or drought are placed on the plant. Though his contribution to the work predates his time at DOE JGI, JGI’s Plant Functional Genomics lead and study co-author John Vogel provided the team with the mutant population and showed them how to manipulate the plant for their studies.

Contacts
Daniel Drell, Ph.D.
Program Manager
Biological Systems Science Division
Office of Biological and Environmental Research
Office of Science
U.S. Department of Energy
daniel.drell@science.doe.gov

John Vogel
Plant Functional Genomics Lead
DOE Joint Genome Institute
jpvogel@lbl.gov

Funding
U.S. Department of Energy Office of Science
Swiss National Science Foundation
The Gordon and Betty Moore Foundation
National Science Foundation
Howard Hughes Medical Institute

Publication
Raissig, M. T., J. L. Matos, M. X. A. Gil, A. Kornfeld, A. Bettadpur, E. Abrash, H. Allison, G. Badgley, J. P. Vogel, J. A. Berry, and D. C. Bergmann. 2017. “Mobile MUTE Specifies Subsidiary Cells to Build Physiologically Improved Grass Stomata,” Science 35(6330), 1215â€"18. DOI: 10.1126/science.aal3254. (Reference link)

Related Links
Stanford Press Release: Scientists reveal how grass developed a better way to breathe
JGI Brachypodium Resources
JGI Plant Flagship Genomes
JGI News Release: First Wild Grass Species and Model System for Energy Crops Sequenced
Brachypodium distachyon on Phytozome portal
JGI: Indexed Collection of Brachy Mutants

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Researcher John Vogel with Brachypodium plants at the Department of Energy’s Joint Genome Institute. [Image courtesy Lawrence Berkeley National Laboratory]



March 15, 2017

Phosphate Stress and Immunity Systems in Plants are Orchestrated by the Root Microbial Community

Better understanding of these plant-microbe interactions could lead to improved bioenergy feedstocks.

The Science 
The microbial community associated with plant roots coordinates the simultaneous response of plants to both nutrient stress and disease. In a recent study, researchers established that a genetic network controlling the phosphate stress response influences how the root microbiome community is structured, even under nonstress phosphate conditions.

The Impact
Understanding how plants interact with beneficial soil microbial communities may lead to novel approaches for breeding high-yielding bioenergy feedstocks on marginal lands with few inputs. This study, for the first time, provides evidence that genes controlling phosphate starvation response (PSR) and plant defense regulation are coordinated.

Summary
To become a sustainable and viable source of biofuels, biomass feedstock crops must be capable of high productivity on marginal lands not fit for food crop production. Nutrients such as phosphorus are critical to plant productivity but are scarce in low-fertility soils, so breeding biomass plants that efficiently utilize nutrients even in nutrient-depleted soils is critical to their use as a sustainable and cost-effective bioenergy resource. Plants form intimate associations with the soil microbial communities that surround their root systems. These communities are diverse and can contain both pathogenic microbes that compete with the plant for nutrients as well as beneficial microbes that increase plant health, vigor, and productivity. Soil nutrient content can influence the composition of the microbial community, but the mechanisms are unknown. Researchers at the University of North Carolina at Chapel Hill, with partial funding from the U.S. Department of Energy-U.S.Department of Agriculture Plant Feedstocks Genomics for Bioenergy program, used mutants of the model plant Arabidopsis thaliana with altered PSR to show that genes controlling PSR contribute to normal root microbiome assembly. They discovered that the regulatory gene PHR1 can fine-tune this response. They further showed that PSR regulation and pathogen defense are coordinated, providing insight into the coordinated interchange of plant response to nutritional stress, the plant immune system, and the root microbiome, as well as a foundational basis for using the soil microbiome to enhance phosphate use efficiency in plants.

Contacts (BER PM)
Cathy Ronning
SC-23.2
catherine.ronning@science.doe.gov

(PI Contact)
Jeffery L. Dangl
University of North Carolina at Chapel Hill
dangl@email.unc.edu

Funding
Partial support for this work was provided by the U.S. Department of Energy-U.S. Department of Agriculture Plant Feedstock Genomics for Bioenergy (award DE-SC001043) and National Science Foundation INSPIRE grant IOS-1343020.

Publication
Castrillo, G., P. J. P. L. Teixeira, S. H. Paredes, T. F. Law, L. de Lorenzo, M. E. Feltcher, O. M. Finkel, N. W. Breakfield, P. Mieczkowski, C. D. Jones, J. Paz-Ares, and J. L. Dangl. 2017. “Root Microbiota Drive Direct Integration of Phosphate Stress and Immunity,” Nature 543, 513-18. DOI: 10.1038/nature21417. (Reference link)

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Synthetic Bacterial Community Induces Typical Phosphate Starvation Phenotypes in Arabidopsis. Phenotypes of plants lacking phosphate in the presence of a 35-member synthetic community (+ Synthetic Community) or in matching axenic conditions (No Bacteria). Typical responses to phosphate starvation, including shorter primary roots and stunted shoots, are exacerbated in the presence of the bacterial community. [Image courtesy Castrillo et al. 2017. “Root Microbiota Drive Direct Integration of Phosphate Stress and Immunity,” Nature 543, 513-518. DOI: 10.1038/nature21417.]



March 14, 2017

Unplugging the Cellulose Bottleneck

Molecular-level understanding of cellulose structure reveals why it resists degradation and could lead to cost-effective biofuels.

The Science
A major bottleneck hindering cost-effective production of biofuels and many valuable chemicals is the difficulty of breaking down cellulose—an important structural component of plant cell walls. A recent study addressed this problem by characterizing molecular features that make cellulose resistant to degradation.

The Impact
The findings reveal for the first time structural differences between surface layers and the crystalline core of the two types of cellulose found in plant cell walls. These insights could help researchers develop efficient, cost-effective strategies for breaking down cellulose for renewable energy production and other industrial applications.

Summary
A molecular-level understanding of the resistance of cellulose to degradation is a key step toward overcoming the fundamental barrier to making biofuels cost-competitive. However, significant questions remain with respect to cellulose’s structure, particularly its surface layers and crystalline core. To address this knowledge gap, researchers from Washington State University; the Environmental Molecular Sciences Laboratory (EMSL), a DOE Office of Science user facility ; and Pacific Northwest National Laboratory developed a novel high-resolution technique called Total Internal Reflection Sum Frequency Generation Vibrational Spectroscopy (TIR-SFG-VS) and combined it with conventional non-TIR SFG-VS to characterize molecular structures of cellulose’s surface layers and crystalline bulk, respectively. The researchers used Sum Frequency Generation for Surface Vibrational Spectroscopy at EMSL. The findings revealed for the first time the structural differences between the surface layers and the crystalline core of cellulose. By revealing cellulose’s conformation and non-uniformity, the results challenge the traditional understanding of cellulose materials and showcase the strong value of powerful spectroscopic tools in advancing knowledge about the structure of cellulose.

BER PM Contact
Paul Bayer, SC-23.1, 301-903-5324

PI Contact
Bin Yang
Washington State University
bin.yang@wsu.edu

Funding
This work was supported by the U.S. Department of Energy’s Office of Science (Office of Biological and Environmental Research), including support of the Environmental Molecular Sciences Laboratory (EMSL), a DOE Office of Science User Facility; a DARPA Young Faculty Award; and the U.S. National Science Foundation.

Publication
L. Zhang, L. Fu, H.-F. Wang, and B. Yang, “Discovery of Cellulose Surface Layer Conformation by Nonlinear Vibrational Spectroscopy.” Scientific Reports 7:44319 (2017). DOI: 10.1038/srep44319 (Reference link)

Related Links
Unplugging the Cellulose Bottleneck EMSL science highlight
New way to characterize cellulose, advance bioproducts WSU News Post

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



A research collaboration between WSU Tri-Cities, EMSL and PNNL substantially increased understanding of cellulosic biomass recalcitrance, which not only challenges traditional understanding but provides further insight into the molecular structure of cellulose that will advance bioproducts. [Image courtesy of EMSL]



February 23, 2017

Microbes Drive Methane Release from Wetlands

Study reveals how shallow wetlands act as hotspots for greenhouse gas generation.

The Science
Inland waters and wetlands are increasingly recognized as critical sites of methane emissions to the atmosphere, but little is known about the biological and geochemical processes driving the release of this powerful greenhouse gas from these ecosystems. A new study of microbial and geochemical processes in shallow wetlands known as “potholes” reveals that these wetlands are biogeochemical hot spots for some of the highest methane fluxes to the atmosphere ever reported.

The Impact
The study's findings reveal high concentrations of carbon and sulfur compounds in the Prairie Pothole Region wetlands of North America and that these wetlands support microorganisms that generate high levels of methane. Moreover, the results show that this region is a hot spot of geochemical and microbial activity and plays an important role in regional elemental cycling—the flow of chemical elements and compounds between living organisms and the physical environment.

Summary
Small ponds and lakes recently have been found to play an oversized role in degrading carbon and catalyzing fluxes of greenhouse gases such as methane and carbon dioxide to the atmosphere. The Prairie Pothole Region is a huge wetland ecosystem containing thousands of shallow wetlands that span five states in the United States and two provinces in Canada. This region's wetland sediments contain some of the highest concentrations of dissolved organic carbon and sulfur compounds ever recorded in terrestrial aquatic environments. The observations suggest that these wetlands likely support high levels of microbial activity, which, in turn, could account for substantial greenhouse gas emissions from this ecosystem. To explore this possibility, researchers from The Ohio State University; Environmental Molecular Sciences Laboratory (EMSL), a Department of Energy Office of Science user facility; and the U.S. Geological Survey conducted one of the first studies of coupled geochemical and microbial processes driving methane emissions from Prairie Pothole Region wetlands. They collected sediment and pore water samples from these wetlands; used chemical analysis techniques to measure the concentrations of carbon, sulfur and methane; and conducted gene sequencing to identify members of the microbial community. They also performed in-depth chemical analysis of the dissolved carbon pools using 600-MHz nuclear magnetic resonance (NMR) spectrometers and the 12 Tesla Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer at EMSL. The findings suggest that conversion of abundant carbon pools into methane in the Prairie Pothole Region results in some of the highest fluxes of this greenhouse gas to the atmosphere ever reported. Moreover, high levels of carbon and sulfur compounds support some of the highest sulfate reduction rates ever measured in terrestrial aquatic environments. Taken together, the findings reveal a significant and previously underappreciated role for this ecosystem in supporting extremely high levels of microbial activity that directly impact terrestrial elemental cycling. As such, the results offer novel insights into how Prairie Pothole Region wetlands and other small inland waters act as hot spots for greenhouse gas generation.

BER PM Contact
Paul Bayer, SC-23.1, 301-903-5324

PI Contact
Michael J. Wilkins
Ohio State University
wilkins.231@osu.edu

EMSL Contacts
Malak Tfaily
malak.tfaily@pnnl.gov
David Hoyt
david.hoyt@pnnl.gov

Funding
This work was supported by the U.S. Department of Energy’s Office of Science (Office of Biological and Environmental Research), including support of the Environmental Molecular Sciences Laboratory (EMSL) and the DOE Joint Genome Institute, both DOE Office of Science User Facilities; U.S. Geological Survey Climate and Land Use Change R&D Program; and National Science Foundation.

Publication
P. Dalcin Martins, D.W. Hoyt, S. Bansal, C.T. Mills, M. Tfaily, B.A. Tangen, R.G. Finocchiaro, M.D. Johnston, B.C. McAdams, M.J. Solensky, G.J. Smith, Y-P Chin, and M.J. Wilkins, “Abundant carbon substrates drive extremely high sulfate reduction rates and methane fluxes in Prairie Pothole Wetlands.” Global Change Biology (2017). [DOI: 10.1111/gcb.13633] (Reference link)

Related Links
EMSL Science Highlight: Microbes Drive Methane Release from Wetlands

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


February 10, 2017

Poplar Gene Enhances Lateral Root Formation and Biomass Growth Under Drought Stress

The Science 
A newly characterized poplar gene expressed primarily in roots influences the plant’s root development and drought resistance.

The Impact
This discovery will facilitate the development of bioenergy poplar trees with enhanced drought resistance, a key trait for the sustainable growth of bioenergy feedstocks on marginal lands.

Summary
Developing crops with improved drought resistance and water use efficiency is important for sustainable agriculture. These traits are particularly critical for plants to be grown as dedicated biomass feedstocks on marginal lands with little or no inputs such as irrigation. Since water is taken up by the roots, root architecture is directly related to the plant’s ability to tolerate drought conditions, and researchers have found several genomic regions (quantitative trait loci, or QTL) for root traits associated with drought resistance. However, the multigenic nature of many of these traits make using these QTL in a breeding program difficult, and few specific genes have been identified. Recently, scientists at Michigan Technological University and Oak Ridge National Laboratory used a powerful forward genetics approach known as activation tagging in the bioenergy crop poplar to identify a specific transcription factor gene (PtabZIP1-like), predominately expressed in poplar roots, that moderates the development of lateral roots and drought resistance through multiple metabolic pathways. The discovery of this gene provides a path to further knowledge of the functional mechanism of drought resistance, which could, in turn, offer potential new approaches to breeding more sustainable bioenergy feedstocks.

Contacts (BER PM)
Cathy Ronning
Biological Systems Science Division
Office of Biological and Environmental Research
Office of Science
U.S. Department of Energy
catherine.ronning@science.doe.gov

(PI Contact)
Victor Busov
Michigan Technological University, Houghton MI
vbusov@mtu.edu

Funding
This work was supported by the U.S. Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research, Genomic Science program, Plant Feedstock Genomics (DE-SC0008462); and U.S. Department of Agriculture (USDA), National Institute of Food Agriculture, Institute  of Bioenergy, Climate and Environment (grant number 2009-65504-05767). This work was also sponsored in part by DOE’s Genomic Science program (Science Focus Area ‘Plant-Microbe Interfaces’ at Oak Ridge National Laboratory) under contract DE-AC05-00OR22725  and USDA National Institute of Food Agriculture (MICW-2011-04378).

Publication
Dash, M., Y. S. Yordanov, T. Georgieva, T. J. Tschaplinski, E. Yordanova, and V. Busov. 2017. “Poplar PtabZIP1-Like Enhances Lateral Root Formation and Biomass Growth Under Drought Stress,” The Plant Journal 89(4), 692-705. DOI: 10.1111/tpj.134. (Reference link)

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


January 30, 2017

Vitamin B12 Plays Broad Role in Cellular Metabolism

Scarce compound is key for microbial growth and may help shape microbial communities.

The Science
Vitamin B12 regulates the production of deoxyribonucleic acid (DNA) and many proteins required for normal cellular function. A recent study revealed that this compound plays an even greater role in cellular metabolism and growth than previously thought, and may even coordinate the behavior of complex microbial communities.

The Impact
The findings suggest that vitamin B12 helps shape microbial communities, which affect wide-ranging processes including energy and food production, the environment, and human health.

Summary
Vitamin B12 is used by all domains of life to control the production of DNA and a variety of proteins that support cellular function, but this vitamin is only produced by certain bacterial and archaeal species. A recent study showed that this compound has an unexpectedly broad influence on metabolic processes important for synthesis of DNA, ribonucleic acid (RNA), and proteins. To explore vitamin B12’s role in a variety of cellular processes, researchers from Pacific Northwest National Laboratory, Sanford-Burnham-Prebys Medical Discovery Institute, and Polytech Nice-Sophia set out to identify which proteins bind to vitamin B12. To do so, they first developed a chemical probe that mimics vitamin B12 and then directly applied the probe to live Halomonas bacterial cells. The researchers next analyzed the probe-labeled proteins using an Orbitrap mass spectrometer at the Environmental Molecular Sciences Laboratory, a Department of Energy Office of Science user facility. They found that the vitamin B12-mimicking probe interacted with 41 different proteins, including enzymes involved in the synthesis and metabolism of another B vitamin called folate, an amino acid called methionine, and a compound called ubiquinone. These metabolic processes, in turn, increase the production of DNA, RNA, and proteins. The findings reveal vitamin B12 plays a more pivotal role in cellular growth and metabolism than previously thought. As a result, this scarce compound may facilitate the coordination of cell behavior in complex microbial communities, shaping their structure, stability, and overall function.

BER PM Contact
Paul Bayer, SC-23.1, 301-903-5324

PI Contact
Lee Ann McCue
Environmental Molecular Sciences Laboratory
leeann.mccue@pnnl.gov

Funding
This work was supported by the U.S. Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research, including support of the Environmental Molecular Sciences Laboratory, a DOE Office of Science user facility; Genome Science Program Foundational Scientific Focus Area at Pacific Northwest National Laboratory; Russian Foundation for Basic Research; and Russian Academy of Sciences.

Publication
M. Romine, D. Rodionov, Y. Maezato, L. Anderson, P. Nandhikonda, I. Rodionova, A. Carre, X. Li, C. Xu, T. Clauss, Y.-M. Kim, T. Metz, and A. T. Wright, “Elucidation of roles for vitamin B12 in regulation of folate, ubiquinone, and methionine metabolism.” Proceedings of the National Academy of Sciences (USA) 114(7), E1205-E1214 (2017). DOI: 10.1073/pnas.1612360114. (Reference link)

Related Links
EMSL Article
PNNL News Release

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER



Researchers explore functions controlled by vitamin B12 and the importance for microbial communities. [Image courtesy Department of Energy’s Environmental Molecular Sciences Laboratory]



January 25, 2017

Using Microbial Community Gene Expression to Highlight Key Biogeochemical Processes

A study of gene expression in an aquifer reveals unexpectedly diverse microbial metabolism in biogeochemical hot spots.

The Science
Researchers conducted a study of naturally reduced zones (NRZs)—biogeochemical hot spots—in the Rifle, Colo., aquifer, a legacy Department of Energy uranium mill site. They performed a state-of-the-art analysis of gene expression in the aquifer’s microbial communities, elucidating metabolic pathways and organisms underlying observed biogeochemical phases as well as revealing unexpected metabolic activities.

The Impact
NRZs, organic-rich deposits heterogeneously distributed in alluvial aquifers, modulate aquifer redox status and influence the speciation and mobility of metals. Overall, NRZs have an outsized effect on groundwater geochemistry. This study’s results highlight the complex nature of organic matter transformation in NRZs and the microbial metabolic pathways that interact to mediate redox status and elemental cycling.

Summary
Organic matter deposits in alluvial aquifers have been shown to result in the formation of NRZs, which can modulate aquifer redox status and influence the speciation and mobility of metals, significantly affecting groundwater geochemistry. In this study, researchers sought to better understand how natural organic matter fuels microbial communities within anoxic biogeochemical hot spots (or NRZs) in a shallow alluvial aquifer at the Rifle site. The researchers conducted an anaerobic microcosm experiment in which NRZ sediments served as the sole source of electron donors and microorganisms. Biogeochemical data indicated that native organic matter decomposition occurred in different phases, beginning with the mineralization of dissolved organic matter (DOM) to carbon dioxide (CO2) during the first week of incubation. This was followed by a pulse of acetogenesis that dominated carbon flux after two weeks. DOM depletion over time was strongly correlated with increases in the expression of many genes associated with heterotrophy (e.g., amino acid, fatty acid, and carbohydrate metabolism) belonging to a Hydrogenophaga strain that accounted for a relatively large percentage (roughly 8%) of the metatranscriptome. This Hydrogenophaga strain also expressed genes indicative of chemolithoautotrophy, including CO2 fixation, dihydrogen (H2) oxidation, sulfur compound oxidation, and denitrification. The acetogenesis pulse appeared to have been collectively catalyzed by a number of different organisms and metabolisms, most prominently pyruvate:ferredoxin oxidoreductase.  Unexpected genes were identified among the most highly expressed (more than 98th percentile) transcripts, including acetone carboxylase and cell-wall-associated hydrolases with unknown substrates.  Many of the most highly expressed hydrolases belonged to a Ca. Bathyarchaeota strain and may have been associated with recycling of bacterial biomass. Overall, these results highlight the complex nature of organic matter transformation in NRZs and the microbial metabolic pathways that interact to mediate redox status and elemental cycling.

Contacts (BER PM)
David Lesmes
SC-23
david.lesmes@science.doe.gov

(PI Contact)
Harry R. Beller
Senior Scientist, Lawrence Berkeley National Laboratory
HRBeller@lbl.gov

Funding
This work was supported as part of the Subsurface Biogeochemical Research Scientific Focus Area funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under award number DE-AC02-05CH11231. This work used the Vincent J. Coates Genomics Sequencing Laboratory at the University of California, Berkeley, supported by the National Institutes of Health S10 instrumentation grants S10RR029668 and S10RR027303.  

Publication
Jewell, T. N. M., U. Karaoz, M. Bill, R. Chakraborty, E. L. Brodie, K. H. Williams, and H. R. Beller. 2017. “Metatranscriptomic Analysis Reveals Unexpectedly Diverse Microbial Metabolism in a Biogeochemical Hot Spot in an Alluvial Aquifer,” Frontiers in Microbiology, DOI: 10.3389/fmicb.2017.00040. (Reference link)

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


January 16, 2017

Scientists Program Yeast to Turn Plant Sugars into Biodiesel

Redox metabolism was engineered in Yarrowia lipolytica to increase the availability of reducing molecules needed for lipid production.

The Science  
With the depletion of fossil fuels, biodiesel precursors produced by oleaginous (oil-producing) yeast from renewable carbohydrates are a promising alternative to fossil- and food-crops-derived fuels. However, production yields are still too low to be commercially competitive. In a new study, researchers achieved a 25% improvement in lipid production, relative to existing oil-producing yeast strains, by rewiring the metabolism in a naturally high lipid producing yeast.

The Impact
Diesel is used to power large vehicles (e.g., trucks) and is a sought after fuel source due to its high fuel efficiency and energy density. Until now, advances in microbial production of biodiesel were not significant enough to make it close to a commercially viable option. The titer, yield, and productivity of oil achieved in an engineered strain of Y. lipolytica using sugar as substrate are now close to those required to make microbial carbohydrate conversion into fuels commercially viable.

Summary
Researchers at the Massachusetts Institute of Technology used a mathematical model to identify the oil production bottlenecks in the industrial yeast Y. lipolytica. With information provided by the model, they designed several metabolic engineering strategies to increase conversion of surplus NADH (a product of glucose degradation) to NADPH, which is needed for lipid biosynthesis. Of the strategies tested, a combination of two were the most effective in lipid yield improvement. By introducing heterologous yeast and bacterial glyceraldhyde-3-phosphate dehydrogenase (GDP) genes that utilize NADP+ instead of NAD+ w into Y. lipolytica and overexpressing a bacterial malic enzyme (MCE2) in the GDP-expressing strain, an improvement of 25% over previously engineered yeasts was observed. In addition, as the engineered Y. lipolytica required less oxygen, it could be grown at higher density in the bioreactor, further increasing biomass and lipid yields. The redox engineering approach reported in this work could be optimized for converting plant biomass into biofuel precursors and other Department of Energy-relevant bioproducts.

(BER Contact)
Pablo Rabinowicz
Biological Systems Science Division
Office Biological and Environmental Research
U.S. Department of Energy
pablo.rabinowicz@science.doe.gov

(PI Contact)
Gregory Stephanopoulos
Department of Chemical Engineering
Massachusetts Institute of Technology
Cambridge, Massachusetts
gregstep@mit.edu

Funding
This work was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under award DE-SC0008744.  

Publication
K. Qiao, T. M. Wasylenko, K. Zhou, P. Xu, and G. Stephanopoulos, “Lipid production in Yarrowia lipolytica is maximized by engineering cytosolic redox metabolism.” Nature Biotechnology 35, 173 (2017). [DOI: 10.1038/nbt.3763] (Reference link)

Related Links
MIT Press Release: A step towards renewable diesel

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Yarrowia cells, at the initiation of lipogenesis, metabolically engineered to overproduce oil. [Image courtesy Stephanopoulos Lab, Massachussetts Institute of Technology]



January 09, 2017

Microbial Communities Thrive by Transferring Electrons

A newly discovered microbial metabolic process linking different microbes in a community could enhance bioenergy production.

The Science
Photosynthetic bacteria are major primary producers on Earth, using sunlight to convert inorganic compounds in the environment into more complex organic compounds that fuel all living systems on the planet. A team of researchers recently discovered a new microbial metabolic process called syntrophic anaerobic photosynthesis, which could represent an important, widespread form of carbon metabolism in oxygen-depleted zones of poorly mixed freshwater lakes.

The Impact
The discovery of syntrophic anaerobic photosynthesis reveals new possibilities for bioengineering microbial communities for use in waste treatment and bioenergy production.

Summary
Almost all life on Earth relies directly or indirectly on primary production—the conversion of inorganic compounds in the environment into organic compounds that store chemical energy and fuel the activity of organisms. Nearly half of global primary productivity occurs through photosynthetic carbon dioxide (CO2) fixation by sulfur bacteria and cyanobacteria. In oxygen-depleted environments, photosynthetic bacteria use inorganic compounds such as water, hydrogen gas, and hydrogen sulfide to provide electrons needed to convert CO2 into organic compounds. These organic compounds also make their way into the food web, where they support the growth of heterotrophs—organisms that cannot manufacture their own food. A recent study revealed a new metabolic process, called syntrophic anaerobic photosynthesis, in which photosynthetic and heterotrophic bacteria cooperate to support one another’s growth in oxygen-depleted environments. Researchers from Washington State University, Pacific Northwest National Laboratory (PNNL), China University of Geoscience, and Southern Illinois University made this discovery using the Quanta scanning electron microscope and the FEI Tecnai T-12 cryo-transmission electron microscope at the Environmental Molecular Sciences Laboratory (EMSL), a Department of Energy Office of Science user facility. Their analysis revealed that a heterotrophic bacterial species, Geobacter sulfurreducens, directly transfers electrons to a photosynthetic bacterial species, Prosthecochloris aestuarii, which uses electrons to fix CO2 into cell material. At the same time, donating electrons allows G. sulfurreducens to support its own metabolic needs by converting acetate into CO2 and water. This potentially widespread, symbiotic form of metabolism, which links anaerobic photosynthesis directly to anaerobic respiration, could be harnessed to develop new strategies for waste treatment and bioenergy production.

BER PM Contacts
Roland Hirsch (FSFA), SC-23.2, 301-903-9009
Paul Bayer (EMSL), SC-23.1, 301-903-5324

PI Contacts
Haluk Beyenal
Washington State University
beyenal@wsu.edu

Alice Dohnalkova
EMSL
Alice.Dohnalkova@pnnl.gov

Funding
This work was supported by the U.S. Department of Energy (DOE), Office of Biological and Environmental Research, Genomic Science program and is a contribution of the PNNL Foundational Scientific Focus Area (FSFA). A portion of this work was conducted at EMSL, a DOE Office of Science user facility.

Publication
P. T. Ha, S. R. Lindemann, L. Shi, A. C. Dohnalkova, J. K. Fredrickson, M. T. Madigan, and H. Beyenal, “Syntrophic anaerobic photosynthesis via direct interspecies electron transfer.” Nature Communications 8 (2017). DOI:10.1038/ncomms13924. (Reference link)

Related Links
EMSL Article
WSU Article

Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER,SC-23.2 Biological Systems Science Division, BER



Electron microscopy image of two distinct microbes that can, when in close association, produce electric current. Researchers studied metabolic processes in microbes for potential applications to waste treatment and bioenergy production. [Image courtesy Ha et al. 2017. DOI: 10.1038/ncomms13924. (CC-BY 4.0)]



January 03, 2017

Modified Switchgrass: Success in Biofuel-relevant Characteristics

Introduced traits remain stable for improved biofuel production in a field setting.

The Science  
The development of near-term fossil fuel alternatives is needed to reduce carbon emissions and to ensure U.S. energy security. Switchgrass, a biofuel feedstock (biological material that can be converted into a fuel), is a perennial grass that is able to grow on marginal lands and has served as an adaptable lignocellulosic bioresource. Due to its complex composition, the plant cell wall is resistant to deconstruction to its component sugars, known as recalcitrance. Overcoming this recalcitrance is necessary to enable the economic feasibility of biofuel production. In this study, researchers evaluated the physiological and chemical effects of genetically modified switchgrass lignin in a three year field study.

The Impact
Using a genetically modified line of switchgrass a team of scientists was able to demonstrate that biofuel-relevant characteristics remained stable while recalcitrance was reduced after three generations in the field. This is a vital step towards understanding how to overcome the recalcitrance problem and thus has the potential to reduce economic barriers to cost-effective biofuel production.
 
Summary
The plant cell wall is primarily made up of three biopolymers: lignin, hemicellulose, and cellulose. Lignin’s complex architecture provides structural support and pathogen defense, but it is due to these functions lignin is considered a major contributor to recalcitrance. Researchers at the Department of Energy’s (DOE) BioEnergy Science Research Center (BESC) silenced the caffeic acid O-methyltransferase (COMT) gene in the lignin biosynthesis pathway and demonstrated over three growing seasons that the genetically modified plants retained both reduced cell wall recalcitrance and lignin content in comparison to the non-transgenic controls. A 35-84% higher sugar release was reported in the lignin modified plants after a 72-h enzymatic hydrolysis without pretreatment and a 25-32% increase in enzymatic sugar release (after hydrothermal pretreatment). For years 2 and 3 in the field, lignin modified plants had 12% and 14% reduced lignin content, respectively. This study demonstrated the important traits associated with the COMT-silenced field-grown switchgrass are an increase in cell wall accessibility for sugar release and a reduction in lignin content. These traits were able to remain durable in the field for 3 years in field trials. This research helps to provide a mechanistic understanding of lignin modified switchgrass relevant to DOE’s energy and environmental missions.

Contact
Kent Peters, Ph.D.
Program Manager Biological Systems Sciences
Division Office of Biological and Environmental Research
Office of Science 
U.S. Department of Energy
kent.peters@science.energy.doe.gov

(PI Contact)
Arthur Ragauskas
aragausk@utk.edu

Funding
This work was supported by the BioEnergy Science Center, a U.S. Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science under Contract No. DE-AC05-00OR22725.

Publications
M. Li, Y. Pu, C. Yoo, E. Gjersing, S.R. Decker, C. Doeppke, T. Shollenberger, T.J. Tschaplinski, N.L. Engle, R.W. Sykes, M.F. Davis, H.L. Baxter, M. Mazarei, C. Fu, R.A. Dixon, Z. Wang, C.N. Stewart, and A.J. Ragauskas, “Study of traits and recalcitrance reduction of field-grown COMT down-regulated switchgrass.” Biotechnology for Biofuels 10, 12 (2017) [DOI: 10.1186/s13068-016-0695-7] (Reference link)

Related Links
BESC: Biomass formation and modification

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Field site for studying switchgrass species with enhanced biofuel-relevant characteristics [Image courtesy of BESC]