BER Research Highlights

Search Date: June 27, 2017

14 Records match the search term(s):


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 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.]



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]