BER Research Highlights

Search Date: April 29, 2017

7 Records match the search term(s):


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 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 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 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)]