BER Research Highlights

Search Date: December 11, 2019

6 Records match the search term(s):


May 15, 2019

Trees Consider the Climate When Choosing Their Partners

Forest trees establish symbiotic relationships with microbes depending on how the climate determines the rate of soil organic matter decomposition.

The Science
Bacteria and fungi living inside plant roots help plants capture mineral nutrients from the soil while benefiting from the food that the plant produces using energy from the sun. Trees can establish several types of symbiotic relationships with fungi and bacteria. Researchers constructed a global map of the types of tree symbioses across the world. With the map, they determined that the type of fungal symbiosis found in trees depends on how quickly the organic matter in the soil decomposes. The team also found that bacteria that convert nitrogen gas from the atmosphere into plant-usable products form tree symbioses in arid environments.

The Impact
The health of the world’s forest is of critical importance for the well-being of the planet. Symbiotic microbes that associate with trees affect their capacity to acquire essential nutrients from the soil and air around them. Our knowledge of the effects of geographic and climatic factors on these symbioses has so far come from analyses of a limited number of environments. The study provides a global map of tree symbioses across large numbers of species and ecosystems. This comprehensive analysis not only sheds light on the important role of microbes in shaping the landscape of the world’s forests, but it will also help improve global biogeochemical models.

Summary
To understand how tree-microbial symbioses affect the state of forests at the global scale, an international consortium of researchers surveyed tree-microorganism symbioses in 1.1 million locations around the world. These ecosystems included over 28,000 tree species and a vast climatic and geographic diversity. This comprehensive study demonstrated that the majority of tree symbioses are ectomycorrhizal, although they represent a small percentage of all tree species. This type of tree symbiosis is predominant in seasonally cold and dry climates as well as at high latitude and elevation. In these conditions, decomposition of soil organic matter is slow. In warm tropical forests, where decomposition is faster, trees prefer to establish arbuscular mycorrhizal associations, and the researchers observed a fairly sudden geographical transition between the two types of symbioses. On the other hand, the research showed that symbioses with nitrogen-fixing rhizobia and actinobacteria occur in arid and hot ecosystems. The global microbial biogeographical map of forest symbioses constructed in this study shows that forests transition from low-latitude arbuscular mycorrhizal through nitrogen-fixer to high-latitude ectomycorrhizal ecosystems, confirming predicted rules of mycorrhizal distribution.

Contact
Kabir Gabriel Peay
Stanford University
kpeay@stanford.edu  

Program Manager
Pablo Rabinowicz
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
Foundational Genomics Research and Biosystems Design
pablo.rabinowicz@science.doe.gov

Funding
This work was supported in part by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Early Career Research Program. The authors also acknowledge support from other sources listed in https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-019-1128-0/MediaObjects/41586_2019_1128_MOESM3_ESM.pdf.

Publication
Steidinger, B. S., T. W. Crowther, J. Liang, et al. “Climatic controls of decomposition drive the global biogeography of forest-tree symbioses.” Nature 569, 404 (2019). [DOI:10.1038/s41586-019-1128-0]

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


April 16, 2019

Feeding Sugars to Algae Makes Them Fat

Adding glucose to a green microalga culture induces accumulation of fatty acids and other valuable bioproducts.

The Science
Algae can make dramatic shifts in their metabolism in response to changes in their environment. Some microscopic green algae stop photosynthesizing and start accumulating fats and other valuable molecules when certain changes happen. However, scientists don’t know the details of those swift metabolic changes. A team examined a green microalga to better understand this process. After a few days of feeding this microbe sugar, it completely dismantled its photosynthetic apparatus while accumulating fat. In contrast, after the team stopped feeding it sugar, the microbe returned to its normal metabolism.

The Impact
Algae could be a sustainable source of biofuels and other valuable chemicals. As they trap carbon dioxide from the air by photosynthesis, they convert greenhouse gases into oils and other useful industrial products. Scientists need to know how algae control their metabolism to engineer strains that can make desirable products. This study showed that feeding glucose (sugar) to this alga affects one-third of its genes. This extensive catalog of affected genes opens the door to identify and manipulate critical genes that will dramatically increase oil production along with other tailored bioproducts.

Summary
Microalgae can produce large quantities of valuable oils and other chemicals, but their tight metabolic regulation poses a challenge for engineering these organisms for industrial-level production of biofuels and bioproducts. Using a variety of imaging and genomics technologies, a team from the University of California and national laboratories determined that only a few days after adding glucose to a culture of the green alga Chromochloris zofingiensis growing in the light, algal cells accumulate large amounts of the biofuel precursors triacylglycerols, as well as economically important products such as carotenoids. Further, they observed that photosynthesis shut off and the photosynthetic apparatus disappeared, while the overall culture biomass increased. At the same time, nearly one-third of the genes in the genome changed their expression during these growth and metabolic alterations. The researchers also discovered that these changes were readily reversed when they removed the glucose from the culture. Elucidation of the pathways that lead to high accumulation of those biofuels and bioproducts will allow scientists to engineer algae as sustainable biofactories.

Program Manager
Pablo Rabinowicz
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
Foundational Genomics Research and Biosystems Design
pablo.rabinowicz@science.doe.gov

Principal Investigators
Melissa Roth
University of California, Berkeley
melissa.s.roth@gmail.com

Krishna K. Niyogi
University of California, Berkeley
niyogi@berkeley.edu

Funding
This research was supported by the U.S. Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research. The authors acknowledge work performed by the DOE Joint Genome Institute (a DOE Office of Science user facility), the DOE Joint BioEnergy Institute, and the National Center for X-ray Tomography. The cryo-soft X-ray tomography was supported by the Photosynthetic Systems program in the DOE, Office of Science, Office of Basic Energy Sciences. The authors also acknowledge funding and support from the U.S. Department of Agriculture National Institute of Food and Agriculture, the National Institutes of Health, the National Science Foundation, and the Howard Hughes Medical Institute. 

Publications
Roth, M. S., S. D. Gallaher, D. J. Westcott, et al. “Regulation of oxygenic photosynthesis during trophic transitions in the green alga Chromochloris zofingiensis.” The Plant Cell 31, 579–601 (2019). [DOI:10.1105/tpc.18.00742]

Related Links
University of California, Los Angeles news release: Discovery of an alga’s ‘dictionary of genes’ could lead to advances in biofuels, medicine

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


February 26, 2019

Microbes Retain Toxicity Tolerance After They Escape Toxic Elements

Groundwater microbes living outside a contaminated area contain mobile genetic elements that give them resistance to heavy metals.

The Science
Bacteria and other microbes contain mobile genetic elements called plasmids that are circular DNA molecules. Plasmids often encode traits that confer some advantage to the harboring microbe such as antibiotic resistance. A team of researchers has developed a method to purify and study plasmids from groundwater microbial communities. Using this method, they discovered several hundred different plasmids in samples from a U.S. Department of Energy site in Tennessee. The most common trait encoded in those plasmids was resistance to toxic metals such as mercury. The team also found that the plasmids were diverse but not as much as the microbial community from which they came.

The Impact
Studying plasmids from microbial communities that live in groundwater is difficult because of the low concentration of cells in those habitats. Researchers knew that heavy metal resistance genes were present in groundwater microbes, but their new method allowed them to prove that these mobile elements harbor metal resistance genes. The method will also facilitate the discovery of new plasmids in other water environments.

Summary
Plasmids are mobile genetic elements that often contain genes that confer important functions to the microbial host. They are composed of circular DNA molecules and are easy to purify. However, plasmid purification methods do not work well if the concentration of cells is low, as is the case in samples of microbial communities from groundwater environments. To solve this problem, a team of researchers developed a method to purify and analyze plasmids from such environments. With this method, the team uncovered over 600 different plasmids that showed an enrichment in metal tolerance genes in addition to antibiotic- and virus-resistance genes. Given that the team did not detect heavy metals in the microbial habitat, they hypothesize that plasmids may represent a mechanism to maintain latent resistance within a microbial community. The discovery of new plasmid genes allowed by this research will provide new possibilities for engineering novel and useful microbial strains.

Contact
Aindrila Mukhopadhyay
Lawrence Berkeley National Laboratory
amukhopadhyay@lbl.gov  

Program Managers
Pablo Rabinowicz
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
Foundational Genomics Research and Biosystems Design
pablo.rabinowicz@science.doe.gov

Todd Anderson
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
todd.anderson@science.doe.gov

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

Publications
Kothari, A., Y. W. Wu, J. M. Chandonia, M. Charrier, L. Rajeev, A. M. Rocha, D. C. Joyner, T. C. Hazen, S. W. Singer, and A. Mukhopadhyay. “Large circular plasmids from groundwater plasmidomes span multiple incompatibility groups and are enriched in multimetal resistance genes.” mBio 10, e02899-18 (2019). [DOI:10.1128/mBio.02899-18]

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


January 11, 2019

New Method Knocks Out Yeast Genes with Single-Point Precision

Researchers can precisely study how different genes affect key properties in a yeast used industrially to produce fuel and chemicals.

The Science
How do you make yeast work harder? Not to make bread, but in processes that yield chemicals and pharmaceuticals. Industries currently use a yeast called Saccharomyces cerevisiae. They’d like it to work better. The answer is in manipulating the yeast’s genetic code. To get at that code, researchers developed a method that turns off targeted genes in the yeast, introducing mutations. The team’s approach deletes specific points in the DNA sequence. They study how each deletion affects the yeast. Does a deletion cause the yeast to stop working in certain chemicals? Does a deletion make the yeast grow more slowly? The team’s approach lets them study each gene, as well as in combination with other genes. With this approach, scientists can construct libraries of mutants for use in discovering how each gene works.

The Impact
Libraries of genetic mutations have so far only been achieved in simpler organisms, specifically prokaryotes. Now, scientists can build such libraries for more complex organisms. The new technique lets scientists rapidly engineer tens of thousands of genes. They can target the genes with 98 percent efficiency. The results ease identifying and isolating mutant strains that show desired traits, such as tolerance to toxic compounds necessary to produce industrial products.

Summary
Researchers developed a method called CRISPRCas9- and homology-directed-repair-assisted genome-scale engineering (CHAnGE) using libraries of synthetic oligonucleotides (cassettes) containing a CRISPR guide sequence, gene-specific sequences to target homologous recombination to those selected genes, and unique barcodes to track each mutant strain. The oligonucleotide library was cloned into a plasmid and introduced into Saccharomyces cerevisiae. Nearly 25,000 sequences representing almost every one of the 6,500 yeast open reading frames were synthesized. More than 98 percent of the CHAnGE cassettes resulted in mutations in the target genes at least 82 percent of the time, demonstrating a high editing efficiency. The technology proved to be effective for the introduction of both small deletions and single-base mutations, as well as for saturation mutagenesis of a single gene or domain. CHAnGE was successfully applied to engineer yeast strains that are tolerant to furfural, indicating that it could be used to engineer industrially relevant eukaryotes to advance toward renewable production of biofuels and valuable chemicals.

Contact
Program Manager
Pablo Rabinowicz
Department of Energy, Office of Science, Biological and Environmental Research
pablo.rabinowicz@science.doe.gov

Principal Investigator
Huimin Zhao
University of Illinois at Urbana-Champaign 
zhao5@illinois.edu  

Funding
This work was supported by the Office of Biological and Environmental Research within the Department of Energy’s Office of Science and the Carl R. Woese Institute for Genomic Biology at the University of Illinois at Urbana-Champaign.

Publications
Z. Bao, M. HamediRad, P. Xue, H. Xiao, I. Tasan, R. Chao, J. Liang, and H. Zhao, “Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision.” Nature Biotechnology 36, 505 (2018). [DOI: 10.1038/nbt.4132]

Related Links
University of Illinois press release: New CRISPR technology ‘knocks out’ yeast genes with single-point precision

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


January 09, 2019

How Plants Regulate Sugar Deposition in Cell Walls

Identified genes involved in plant cell wall polysaccharide production and restructuring could aid in engineering bioenergy crops.

The Science
Ultimately, researchers want to engineer bioenergy crops to accumulate large amounts of easy-to-use sugars. Researchers from the Great Lakes Bioenergy Research Center identified a major part of the sugar production process in a model leafy grass. They discovered a transcription factor, which turns a gene on and off. The gene triggers the synthesis of a sugar, called mixed-linkage glucan (MLG). Characterizing downstream genes regulated by this transcription factor provides insight into how plants make MLG. This information is vital to overcoming growth defects associated with engineering plants to produce large quantities of MLG.

The Impact
To make fuels from grasses or other plants, scientists often focus on certain sugars, such as mixed-linkage glucan. Understanding the genes that produce and restructure such sugars should lead to a better understanding of how the bioenergy grass sorghum stores sugar in cell walls. With such information, Great Lakes Bioenergy Research Center researchers aim to engineer bioenergy crops like sorghum to accumulate large amounts of the sugar in the stem. They aim to do it without disrupting plant growth.

Summary
Mixed-linkage glucan (MLG) is an energy-rich polysaccharide found at high levels in some grass endosperm cell walls and at lower amounts in other tissues. Cellulose synthase-like F and cellulose synthase-like H genes synthesize MLG, but it is unknown if other genes participate in the production and restructuring of MLG. Working with the model grass Brachypodium distachyon, GLBRC researchers identified a trihelix family transcription factor (BdTHX1) that is highly co-expressed with the BdCSLF6 gene and which appears to help regulate MLG biosynthesis. They showed that BdTHX1 protein can bind with high affinity to BdCSLF6 as well as BdXTH8, which encodes a grass-specific endotransglucosylase, an enzyme involved in cell wall structuring. The team found that BdXTH8 preferentially interacts with MLG and xyloglucans, suggesting it may mediate their binding in plant tissues. In addition, B. distachyon shoots grown from cells overexpressing BdTHX1 showed abnormal growth and early death. These results indicate that the transcription factor BdTHX1 likely plays an important role in MLG biosynthesis and restructuring by regulating the expression of BdCSLF6 and BdXTH8. This knowledge will be instrumental for engineering the bioenergy grass sorghum to accumulate large amounts of MLG in its stem tissue.

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

Principal Investigator
Curtis Gene Wilkerson
Michigan State University 
wilker13@msu.edu

Funding
This work was supported by the Department of Energy Great Lakes Bioenergy Research Center and the United Kingdom Biotechnology and Biological Sciences Research Council.

Publications
M. Fan, K. Herburger, J.K. Jensen, S. Zemelis-Durfee, F. Brandizzi, S.C. Fry, and C.G. Wilkerson, “A trihelix family transcription factor is associated with key genes in mixed-linkage glucan accumulation.” Plant Physiology 178, 1207 (2018). [DOI: 10.1104/pp.18.00978]

Related Links
Plant Physiology article: A Trihelix Family Transcription Factor Is Associated with Key Genes in Mixed-Linkage Glucan Accumulation

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


January 09, 2019

Scientists Identify Gene Cluster in Budding Yeasts with Major Implications for Renewable Energy

How yeast partition carbon into a metabolite may offer insights into boosting production for biofuels.

The Science
Yeasts are complex organisms that may become the workhorses of biofuel production. To move yeasts into this larger role, scientists need to understand the genetic machinery that leads to the production of complex molecules like the iron-binding molecule pulcherrimin in budding yeasts. Scientists revealed a four-gene cluster associated with pulcherrimin production. Further tests revealed likely functions for each of the genes: two biosynthetic enzymes, a transporter, and a transcription factor involved in both biosynthesis and transport.

The Impact
Yeasts use the same pathway to make pulcherrimin and an alcohol, isobutanol, of interest for biofuels. Some yeast strains direct a significant amount of carbon into pulcherrimin. Since both pulcherrimin and isobutanol are made from a common pathway, this suggests that the metabolic control of high pulcherrimin producers may be harnessed for increased isobutanol production in yeast. This could help engineer yeast to make larger quantities of isobutanol.

Summary
Despite the discovery of an iron-binding pigment known as pulcherrimin 65 years ago, the genes responsible for its biosynthesis remained uncharacterized. Using a comparative genomics approach among 90 genomes from the budding yeast subphylum Saccharomycotina, researchers from the Great Lakes Bioenergy Research Center identified the first yeast secondary metabolite gene cluster and showed that it’s responsible for pulcherrimin biosynthesis. Targeted gene disruptions in Kluyveromyces lactis identified putative functions for each of the four genes: two pulcherriminic acid biosynthesis enzymes, a pulcherrimin transporter, and a transcription factor involved in both biosynthesis and transport. The requirement of a functional putative transporter to utilize extracellular pulcherrimin-complexed iron demonstrates that pulcherriminic acid is a siderophore, an iron-chelating compound secreted by microorganisms. This research also characterized and named two genes that previously lacked assigned functions in the fuel-producing model yeast Saccharomyces cerevisiae. The evolution of this gene cluster in budding yeast suggests an ecological role for pulcherrimin akin to other microbial public goods systems. Because some yeasts species are particularly adept at funneling carbon into pulcherrimin, studying how high-level pulcherrimin producing strains are altered in their metabolic control may inform strategies for increased biofuel production in model organisms.

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

Principal Investigator
Chris Todd Hittinger
University of Wisconsin-Madison
cthittinger@wisc.edu

Funding
This material is based upon work supported by the Department of Energy, Office of Science, Office of Biological and Environmental Research, as well as the National Science Foundation. Additional funding was provided by the Pew Charitable Trusts and the Vilas Trust Estate.

Publications
D.J. Krause, J Kominek, D.A. Opulente, X. Shen, X. Zhou, Q.K. Langdon, J. DeVirgilio, A.B. Hulfachor, C.P. Kurtzman, A. Rokas and C.T. Hittinger, “Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts.” Proceedings of the National Academy of Sciences USA 115(43), 11030 (2018). [DOI: 10.1073/pnas.1806268115]

Related Links
Great Lakes Bioenergy Research Center news release: Red-hued yeasts hold clues to producing better biofuels

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER