BER Research Highlights

Search Date: December 11, 2019

23 Records match the search term(s):


December 18, 2018

Drought Stress Changes Microbes Living at Sorghum’s Roots

Scientists explore how drought-tolerant plants communicate to nearby microorganisms, suggesting ways to engineer more resilient bioenergy crops.

The Science
Droughts stress crops, but what if that wasn’t the case? Answering that question involves looking at the bacteria and other microbes living on and around the plants’ roots. Researchers examined microbes on sorghum roots, as the plant resists drought damage. They found that during a drought, sorghum shifts the balance of microbes in their root systems. The team’s work suggests that drought plays a role in changing the development of the microbial communities around the roots. Further, the findings reveal evidence for a communication system between plants and nearby microbes.  

The Impact
While it’s well known that soil moisture and other factors affect the composition of the microbes associated with plants, little is known about how the changes occur. This study offers insights into how plants trigger those changes. Specifically, it sheds new light on how plants communicate. Understanding the molecular mechanisms involved during drought stress may provide novel approaches to increase plant tolerance and, hence, productivity.

Summary
Drought stress can greatly reduce the health and productivity of plants, including candidate bioenergy feedstocks such as sorghum. Microbial communities associated with plant roots (root “microbiome”) can have a significant influence on plant fitness, and the negative effects of drought stress on plant growth can be mitigated by the association of roots with certain bacteria. Host and environmental factors such as soil moisture affect the composition of the plant-associated microbiome, but little is known about the mechanisms by which this happens. Knowledge of this process could lead to the development of strategies to manipulate the root microbiome for enhanced plant resilience and productivity during drought stress. To gain a better understanding of the drought stress-plant development-plant microbiome interaction, researchers at the University of California, Berkeley and collaborating institutions investigated the root microbiome of a candidate bioenergy crop, sorghum. They found that root microbiome development was significantly delayed under drought conditions, while abundance and activity of a particular group of bacteria containing thick cell walls and lacking an outer cell membrane increased. Additionally, they observed enhanced expression of many bacterial genes associated with transport of specific amino acids and carbohydrates. They correlated this expression with increased production of the same compounds within the plant root. These results suggest the existence of a “communication” system between the root microbiome and host plant, whereby drought stress-induced metabolites are exuded by roots and may signal increased activity of bacterial transporters. This study highlights the importance of temporal sampling of plant-associated microbiomes. Also, the work suggests that strategies for manipulating the plant microbiome to develop crop plants with increased adaptation and higher productivity under conditions of stress could be feasible.

Contact
Program Manager
Cathy Ronning
Department of Energy, Office of Science, Biological and Environmental Research
catherine.ronning@science.doe.gov  

Principal Investigator
Peggy Lemaux
University of California, Berkeley
lemauxpg@berkeley.edu

Funding
The Department of Energy (DOE), Office of Science, Biological and Environmental Research (BER), Genomic Science Program, U.S. Department of Agriculture, and the DOE Office of Science BER Joint BioEnergy Institute funded this work. Research was performed using Environmental Molecular Sciences Laboratory, a DOE Office of Science user facility sponsored by BER.

Publications
L. Xu, D. Naylor, Z. Dong, T. Simmons, G. Pierroz, K.K. Hixson, Y.M. Kim, E.M. Zink, K.M. Engbrecht, Y. Wang, C. Gao, S. DeGraaf, M.A. Madera, J.A. Sievert, J. Hollingsworth, D. Birdseye, H.V. Scheller, R. Hutmacher, J. Dahlberg, C. Jansson, J.W. Taylor, P.G. Lemaux, and D. Coleman-Derr, “Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria.” Proceedings of the National Academy of Sciences USA 115, E4284(2018). [DOI: 10.1073/pnas.1717308115]

Related Links
University of California, Berkeley press release: Drought treatment restructures plants’ microbiomes

Topic Areas:

Division: SC-23 BER


November 09, 2018

Diverse Biofeedstocks Have High Ethanol Yields and Offer Biorefineries Flexibility

Evidence suggests that biorefineries can accept various feedstocks without negatively impacting the amount of ethanol produced per acre.

The Science
Biorefineries are picky eaters. They only consume one or two types of plant matter. Researchers processed and experimentally measured ethanol production from five different herbaceous feedstocks. They examined two annuals (corn stover and energy sorghum) along with three perennials (switchgrass, miscanthus, and restored prairie). They determined that a lignocellulosic ethanol refinery could use a range of plant types without having a major impact on the amount of ethanol produced per acre, or per land area.

The Impact
Many biorefineries consume one, or sometimes two, feedstocks grown and harvested nearby. The feedstock contains lignocellulose. That chemical is processed and fermented into biofuels or bioproducts. Accepting a variety of feedstocks could improve the refinery’s environmental footprint, economics, and logistics. The team’s study showed that a lignocellulosic refinery could be relatively agnostic in terms of the feedstocks used.

Summary
Refineries to convert biomass into fuels often rely on just one feedstock. If the refineries could accept more than one feedstock, it would greatly benefit refinery operation. Scientists at the Great Lakes Bioenergy Research Center investigated how five different feedstocks affected process and field-scale ethanol yields. Two annual crops (corn stover and energy sorghum) and three perennial crops (switchgrass, miscanthus, and restored prairie) were pretreated using ammonia fiber expansion, hydrolyzed, and fermented separately using yeast or bacteria. They found that both biomass quality (chemical composition, moisture content, etc.) and biomass yield affected how much ethanol each acre (or land area) produces. However, the effect differed. Biomass quality was the main driver for the ethanol yields for high-yielding crops, such as switchgrass. Biomass yield was the main driver for the ethanol yields for low-productivity crops, such as corn stover. Therefore, to increase ethanol yield for high-yielding crops, focusing efforts on improving biomass quality or conversion efficiency may be prudent. For low-yielding crops, focusing on increasing biomass yield may be the best strategy. When measuring the amount of ethanol produced during fermentation, most feedstocks fell within a similar range, especially when scientists used bacteria to ferment the biomass. In total, the results of this study suggest that a lignocellulosic refinery may use a variety of feedstocks with a range of quality without a major negative impact on field-scale ethanol yields.

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
Rebecca G. Ong
Michigan Technological University
rgong1@mtu.edu, (906) 487-2662

Funding
The Department of Energy, Office of Science, Office of Biological and Environmental Research Great Lakes Bioenergy Research Center funded this research

Publications
Y. Zhang, L.G. Oates, J. Serate, et al., “Diverse lignocellulosic feedstocks can achieve high field-scale ethanol yields while providing flexibility for the biorefinery and landscape-level environmental benefits.” GCB Bioenergy (2018). [DOI: 10.1111/gcbb.12533]

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


November 09, 2018

Microbes Eat the Same in Labs and the Desert

Analyses of natural communities forming soil crusts agree with laboratory studies of isolated microbe-metabolite relationships.

The Science
Far from barren, arid lands host diverse communities of bacteria and other microbes. The biocrust these communities form affects local and global resources. The residents of these communities are dormant through long, dry spells, but are active when it rains. While it’s obvious that the community consumes more when it’s active, scientists need more details. Previous research used simplified tests to identify which community members thrived and which didn’t during wet and dry seasons. Now, a team examined microbes in their more complex native setting. They found the same patterns.

The Impact
This study sheds new light on the microbial communities that make up the biocrust. While that might seem like a small detail, 40 percent of the world’s land is arid. These communities affect the soil chemistry. That chemistry affects water availability, soil fertility, and the movement of nutrients and energy. This study gets us closer to understanding the complex microbial food webs and their impact on the global carbon cycle.

Summary
Scientists can determine the structure and metabolic potential of microbial communities by established metagenomic approaches. However, linking microbial species data to exogenous metabolites that microbes process and produce (the exometabolome) is still a challenge. A group of scientists at Lawrence Berkeley National Laboratory examined microbe-metabolite relationships in native biological arid soil crusts (biocrusts) upon changes in water availability. The water levels are a critical factor affecting metabolic activity in these ecosystems. The researchers discovered that those relationships are consistent with previous laboratory tests using bacterial isolates from the same ecosystems. Overall, most soil metabolites displayed the expected correlation with four dominant bacteria over time, after it rained. The results show that scientists can successfully combine metabolite profiling, shotgun sequencing, and exometabolomics to link microbial community structure with environmental chemistry. Such research techniques can shed light on biological carbon cycling processes in arid environments.

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

Principal Investigator
Trent Northen
Lawrence Berkeley National Laboratory
TRNorthen@lbl.gov  

Funding
The Office of Science Early Career Research Program, Office of Biological and Environmental Research, Office of Science, Department of Energy funded this research. DNA was sequenced using the Vincent J. Coates Genomics Sequencing Laboratory at the University of California, Berkeley, supported by a grant from the National Institutes of Health.

Publications
T.L. Swenson, U. Karaoz, J.M. Swenson, B.P. Bowen, and T.R. Northen, “Linking soil biology and chemistry in biological soil crust using isolate exometabolomics.” Nature Communications 9, 19 (2018). [DOI: 10.1038/s41467-017-02356-9]

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


November 06, 2018

Novel Soil Bacteria with Unusual Genes Synthesize Unique Antibiotic Precursors

A large-scale soil project uncovered genetic information from bacteria with the capacity to make specialized molecules that could lead to new pharmaceuticals.

The Science
Many commonly used antibiotics were isolated from soil-dwelling bacteria. These bacteria grow in the lab, letting researchers more easily analyze the antibiotics and other products they produce. However, many other soil bacteria don’t grow in the lab, making it difficult to determine what, if anything, they produce and if the products might be useful. Now, that may be changing. By directly sequencing DNA from microbial communities in soil, researchers reconstructed the genetic details of hundreds of individual bacterial organisms in the community. And they found a surprise. They found novel lineages of bacteria. These bacteria encode genes to produce potentially unique compounds. From these compounds, it may be possible to derive new antibiotics drugs.

The Impact
Previously, most naturally derived antibiotics were isolated from families of soil bacteria that grow easily in the lab. This work opens up a new frontier of antibiotic discovery. How? It allows researchers to analyze the genetic data of microbes that don’t grow in the lab. Also, the team identified specific species in highly understudied groups of soil bacteria that are likely productive sources for antibiotic discovery.

Summary
As part of a study on carbon cycling in soils, researchers deeply sequenced 60 soil metagenomes across a single grassland meadow at the Angelo Coast Range Reserve in northern California. A metagenome is all the genetic material present in an environmental sample, which includes many different individual organisms. By assembling these metagenomes and extracting the genomes of individual organisms at an unprecedented scale, they gained a picture of the genomic potential of hundreds of the most common bacteria in this complex soil ecosystem. The team then computationally searched the genomes for homologs (similar DNA sequences that share a common ancestry) of the genes required for the biosynthesis of antibiotics, siderophores, and other bioactive molecules. Unexpectedly, the team found that the bacteria commonly known and studied for the production of these complex compounds possess a minority of genes in the community for biosynthesis. Instead, researcher identified novel members of bacterial groups that scientists rarely study due to their slow growth and poor ability to grow in the laboratory. These novel groups possessed a majority of the biosynthetic genes in this soil environment. By characterizing these organisms and their biosynthetic genes, researchers plan to enable targeted study of these organisms and specific interrogation for their biosynthetic capabilities.

Contact
Jillian Banfield
University of California, Berkeley
jbanfield@berkeley.edu

Funding
Sequencing was carried out under a Community Sequencing Project at the Joint Genome Institute. The Department of Energy, Office of Science, Office of Biological and Environmental Research; the Paul G. Allen Family Foundation; and the Innovative Genomics Institute of the University of California, Berkeley provided funding.

Publications
A. Crits-Christoph, S. Diamond, C.N. Butterfield, B.C. Thomas, and J.F. Banfield, "Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis." Nature 558, 440 (2018). [DOI: 10.1038/s41586-018-0207-y]

Related Links
Discover magazine blog: Dirt could help fight superbugs

University of California Berkeley press release: Soil prospecting yields wealth of potential antibiotics

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


October 24, 2018

Sampling Guts of Live Moose to Understand how they Break Down Biomass

First-of-a-kind study advances understanding of microbial and viral communities involved in biomass breakdown.

The Science
Microbes in the gastrointestinal tract of ruminants such as moose help break down recalcitrant plant biomass into carbon nutrients, but how do they do this over the course of seasons when the moose diet changes, and what microbes are involved? Now, an international research team has studied microbial communities in the rumen of live moose and gained a more holistic view of a complex microbial food web that is responsible for carbon processing in that ecosystem.

The Impact
Microbes breaking down biomass play a vital role in a surprising number of processes, including which chemicals are released into the air and whether a useful biofuel or bioproduct can be formed. By understanding how microbes process woody material like twigs and bark in the guts of moose, scientists can better predict how changes in the seasonal diet of these animals affects their ability to break down these woody materials. They can then extend this understanding to help biofuel, bioproduct, and chemical processing in industry.

Summary
While previous studies used hunter-killed animals, this study sampled live free-ranging Alaska moose grazing in the wild. By equipping these moose with rumen fistula, a port to their gut, the team could sample the animals as they digested a natural diet. The effort provided first-of-its-kind access to the microbial communities residing in the rumen of these animals as communities actively degraded woody plant biomass during spring, summer, and winter foraging months. A team of researchers from The Ohio State University, University of Alaska Anchorage, Norwegian University of Life Sciences, Denmark’s University of Copenhagen, the UK’s Newcastle University, Pacific Northwest National Laboratory, and the Alaska Department of Fish and Game took a deep look into microbial functioning in rumen. The work made use of protein and metabolite data gathered using 600-MHz nuclear magnetic resonance spectroscopy at EMSL, the Environmental Molecular Sciences Laboratory, and genomic data obtained from JGI, the Joint Genome Institute through a Facilities Integrating Collaborations for User Science (FICUS) initiative, which allowed the team access to the expertise of the two Department of Energy Office of Science user facilities, both sponsored by the Office of Biological and Environmental Research. Studying such rich data in combination with state-of-the-art enzymology gave researchers a glimpse into how microbes are specialized and how they coordinate their tasks to mediate the overall “flow” of carbon within the rumen. The analysis enabled metabolic insights into 180 genomes, most of which were previously unknown, and addressed the underappreciated influence that viruses exert in ruminant digestion. Their efforts deciphered community structure and metabolic handoffs underpinning this animal hosted-microbial ecosystem, with findings relevant to agriculture, human health, and biofuel production.

BER EMSL Contact
Paul Bayer, SC-23.1

BER JGI Contact
Ramana Madupu, SC-23.2,

PI Contacts
Kelly C. Wrighton
Colorado State University, formerly The Ohio State University
kwrighton@gmail.com

Phillip B. Pope
Norwegian University of Life Sciences
phillip.b.pope@gmail.com

Funding and User Facility Access
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 Joint Genome Institute (JGI), both DOE Office of Science User Facilities. A portion of the work was performed under the Facilities Integrating Collaborations for User Science (FICUS) initiative, using resources at both EMSL and JGI. The European Research Council provided additional support, as did an Early Career Award in Biological Science for Wrighton from the National Science Foundation.

Publication
Solden, L.M., A.E. Naas, S. Roux, R.A. Daly, W.B. Collins, C.D. Nicora, S.O. Purvine, D.W. Hoyt, J. Schückel, B. Jorgensen, W. Willats, D.E. Spalinger, J.L. Firkins, M.S. Lipton, M.B. Sullivan, P.B. Pope, and K.C. Wrighton. “Interspecies cross-feedings orchestrate carbon degradation in the rumen ecosystem.” Nature Microbiology 3(11), 1274-1284 (2018). [DOI:10.1038/s41564-018-0225-4]

Related Links
Sampling Guts of Live Moose to Understand how they Break Down Biomass science highlight

Topic Areas:

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


August 22, 2018

KBase: The Department of Energy Systems Biology Knowledgebase

Collaborative, open-source software and data platform accelerates systems biology research.

The Science
Advance biofuel and bioproduct production. This is a key goal of Department of Energy (DOE) research. We need to further our understanding of plants and microbial systems as a basis for developing innovative processes for bioenergy and bioproducts production from inedible cellulosic biomass. To accelerate research, scientists need to perform collaborative, complicated analyses. They must have access to very large and disparate datasets. The DOE Systems Biology Knowledgebase (KBase) is a free, open-source software and data platform that meets these needs. It lets researchers collaboratively generate, test, compare, and share hypotheses about biological functions. It makes research accessible, shareable, and reproducible.

The Impact
KBase empowers scientists across a broad range of systems biology domains that involve big data and require high-performance computing. These domains include environmental analysis, biosystems design, and bioenergy. Science done so far within KBase appears in over 40 peer-reviewed articles. Scientists have used KBase to analyze large microbial communities, predict plant-microbe interactions, and model the metabolism of microbes. The KBase Narratives associated with these experiments are available. They can be copied, re-run, and extended by others.

Summary
KBase is an open-source, extensible community resource that enables data sharing, integration, and analysis of genomic information of microbes, plants, and their communities. KBase’s growing suite of scientific tools and reference data offers “one-stop shopping” for users who want to build and share sophisticated bioinformatics workflows. For example, a user can predict species interactions from metagenomic data by assembling raw DNA sequencing reads, binning assembled contigs (sets of overlapping DNA segments that together represent a consensus region of DNA) by species, annotating genomes from these bins, and reconstructing and analyzing individual and community-level metabolic models based on these genomes. External developers can add open-source analysis tools to KBase to make them available to all and allow users to choose among different tools that may have different strengths for particular datasets or workflows. KBase’s Narrative Interface, built on the Jupyter platform, lets users do the following:

- Upload their data
- Search and retrieve extensive public reference data
- Access data shared by others
- Share their data with others
- Select and run applications on their data
- View and analyze the results from those applications
- Record their thoughts and interpretations along with the analysis steps.

All of this work is saved in the Narratives, which are private by default but users can choose to make their Narrative public or share it with other individual users. Recording a user’s KBase activities in a sharable Narrative is a central pillar of KBase’s support for reproducible, transparent research.

Contact
Adam P. Arkin
Principal Investigator
Lawrence Berkeley National Laboratory
aparkin@lbl.gov

Robert Cottingham
Co-Principal Investigator
Oak Ridge National Laboratory
cottingham@ornl.gov

Christopher Henry
Co-Principal Investigator
Argonne National Laboratory
chenry@anl.gov

Funding
This work is supported by the Department of Energy, Office of Science, Office of Biological and Environmental Research Genomic Science Program.

Publications
A.P. Arkin, R.W. Cottingham, C.S. Henry, et al., “KBase: The United States Department of Energy Systems Biology Knowledgebase.” Nature Biotechnology 36, 566 (2018). [DOI: 10.1038/nbt.4163]

Related Links
KBase website: http://kbase.us

KBase publications list: http://kbase.us/publications

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


August 22, 2018

Locating the Production Site of Glucan in Grass Cell Walls

Research offers new insights for maximizing sugar production in biofuel crops.

The Science
Where an item is manufactured tells you a lot about it. Is it made by an assembly line or handcrafted one at a time? To learn more about glucose, the sugary feedstock of biofuel refineries, scientists want to know where a polymer of glucose, mixed-linkage glucan (MLG), resides in grasses as grass species are a major potential renewable biomass feedstock. Scientists from the center demonstrated that MLG is present primarily in the Golgi apparatus (flattened, stacked pouches near the cell’s nucleus). These findings offer new insight and new targets to maximize MLG production.

The Impact
Increasing the content of easily digestible, six-carbon sugars can increase the fuel yield from bioenergy crops. This study adds to the understanding of the synthesis of glucose polymers, including where it is synthesized in cells and where it accumulates in plants. These findings could help guide engineered increases of MLG levels in plants.

Summary
Mixed-linkage glucan (MLG), a (1,3;1,4)-ß-linked glucose polymer, is important for the structural integrity of the plant and a source of glucose that can be converted to biofuels and bioproducts within a biorefinery. MLG is present predominantly in the cell wall of grasses. It is synthesized by cellulose synthase-like enzymes, with CSLF6 being the best-characterized MLG synthase. Although the function of this enzyme in MLG production has been established, the site of MLG synthesis in the cell is debated. In this study, Great Lakes Bioenergy Research Center researchers tested the various possibilities to establish a better understanding of the fundamentally important mechanisms of plant cell wall biosynthesis. Using immuno-localization analyses with MLG-specific antibody in Brachypodium and in barley, MLG was identified in the Golgi, in post-Golgi structures, and in the cell wall. Analyses of a functional fluorescent protein fusion of CSLF6 stably expressed in Brachypodiumdemonstrated that the enzyme is localized in the Golgi. Further, the team demonstrated that the overproduction of MLG caused developmental and growth defects in Brachypodium and barley. Together, these results indicate that MLG production occurs in the Golgi similar to other cell wall matrix polysaccharides and supports the broadly applicable model that MLG accumulation is under tight control in the cell wall during development and growth. Future studies that build on this work will enable scientists to develop strategies that increase MLG levels in bioenergy crops.

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

Principal Investigator 
Federica Brandizzi
Michigan State University
fb@msu.edu

Funding
This work was funded primarily by the Department of Energy Great Lakes Bioenergy Research Center. Partial infrastructure support was also provided from the Chemical Sciences, Geosciences, and Biosciences Division, Office of Basic Energy Sciences, Office of Science, Department of Energy and AgBioResearch.

Publications
S.J. Kim, S. Zemelis-Durfee, J.K. Jensen, C.G. Wilkerson, K. Keegstra, and F. Brandizzi, “In the grass species Brachypodium distachyon, the production of mixed-linkage (1,3;1,4)-ß-glucan (MLG) occurs in the Golgi apparatus.” The Plant Journal 93, 1062(2018). [DOI: 10.1111/tpj.13830]

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


August 09, 2018

Complex Networks Identify Genes for Biofuel Crops

Systems biology leads the way to exascale computing on Summit supercomputer.

The Science
To improve biofuel production, scientists must understand the fundamental interactions that lead to the expression of key traits in plants and microbes. To understand these interactions, scientists are using different layers of information (about the relationships between genes, and between genes and phenotypes) combined with new computational approaches to integrate vast amounts of data in a modeling framework. Researchers can now identify genes controlling important traits to target biofuel and bioproduct production. The algorithm used in this work has been used to break the supercomputing exascale barrier for the first time anywhere in the world.

The Impact
This approach lets scientists analyze massive data sets. They can do so using exascale computing, where computers perform 1018 calculations per second. With this approach, scientists can understand how cells work. They can use the insights to bioengineer beneficial traits into plants and microbes. The ability to use exascale computing opens up possibilities to study highly complex and interrelated molecular processes in cells at a level of detail not previously possible. Such computing also heralds a new era for systems biology.

Summary
Biological organisms are complex systems composed of functional networks of interacting molecules and macromolecules. Complex traits (phenotypes) within organisms are the result of orchestrated, hierarchical, heterogeneous collections of expressed genes. However, the effects of these genes and gene variants are the result of historic selective pressure and current environmental and epigenetic signals, and, as such, their co-occurrence can be seen as genome-wide correlations in different ways. Biomass recalcitrance (that is, the resistance of plants to degradation or deconstruction, which ultimately enables access to a plant’s sugars for bioenergy purposes) is a complex multigene trait of high importance to biofuels initiatives.

To better understand the molecular interactions involved in recalcitrance and identify target genes involved in lignin biosynthesis/degradation, this study makes use of data derived from the re-sequenced genomes from over 800 different Populus trichocarpa genotypes in combination with metabolomics data (the concentrations of the metabolites) and pyrolysis-molecular beam mass spectrometry data. In addition, the scientists used other forms of gene regulation including co-expression, co-methylation, and co-evolution networks.

In analyzing this data, a team developed a “lines of evidence” (LOEs) scoring system to integrate the information in the different layers and quantify the number of LOEs linking genes to target functions. They applied this new scoring system to quantify the LOEs linking genes to lignin-related genes and phenotypes across the network layers. Applying the scoring system allowed for the generation of new hypotheses for new candidate genes involved in lignin biosynthesis in P. trichocarpa, including various AGAMOUS-LIKE genes (a type of transcription factor that controls the expression of other genes). The resulting Genome Wide Association Study networks are proving to be a powerful approach to determine the pleiotropic (genes that affect multiple phenotypes) and epistatic (multiple genes that work together to affect a single phenotype) relationships underlying cellular functions and, as such, the molecular basis for complex phenotypes, such as recalcitrance.

The algorithm in the CoMet software, which creates the co-evolution network used in this study, has since been ported to the new Summit supercomputer, currently world’s fastest and smartest supercomputer at the Oak Ridge Leadership Computing facility. The research team used the CoMet software to break the exascale barrier, achieving a peak throughput of 1.88 exaops—faster than any previously reported science application—while analyzing genomic data on the Summit supercomputer. The research team achieved the feat, the equivalent to carrying out nearly 2 billion billion calculations per second, by using a mixture of numerical precisions on a new NVIDIA graphic processing unit computer chip technology called tensor cores. In this case, researchers implemented a new approach that used the tensor cores to obtain a dramatic increase in performance.

Contact
Daniel Jacobson
Chief Scientist for Computational Systems Biology
Oak Ridge National Laboratory
jacobsonda@ornl.gov

Funding
Funding provided by the BioEnergy Science Center and the Center for Bioenergy Innovation, Department of Energy (DOE) Bioenergy Research Centers supported by the Office of Biological and Environmental Research in the Office of Science. This research was also supported by Laboratory Directed Research and Development funding at the Oak Ridge National Laboratory (ORNL), which is supported by the DOE Office of Science. This research used resources of the Oak Ridge Leadership Computing Facility and the Compute and Data Environment for Science at ORNL, which is supported by the DOE Office of Science. In addition, the DOE Office of Science ESNet was also used. Support for the Poplar Genome Wide Association Study (GWAS) dataset was provided by the BioEnergy Science and the Center for Bioenergy Innovation. The Poplar GWAS used resources of the Oak Ridge Leadership Computing Facility and the Compute and Data Environment for Science at ORNL. The Joint Genome Institute (JGI) Plant Gene Atlas project was supported by the DOE Office of Science. Full Gene Atlas data sets are available at http://phytozome.jgi.doe.gov.

Publications
D. Weighill, P. Jones, M. Shah, P. Ranjan, W. Muchero, J. Schmutz, A. Sreedasyam, D. Macaya-Sanz, R. Sykes, N. Zhao, M. Martin, S. DiFazio, T. Tschaplinski, G. Tuskan, and D. Jacobson, “Pleiotropic and epistatic network-based discovery: Integrated networks for target gene discovery.” Frontiers in Energy Research 6, 30 (2018). [DOI: 10.3389/fenrg.2018.00030]

Related Links
Oak Ridge National Laboratory: Genomics Code Exceeds Exaops on Summit Supercomputer
Summit supercomputer: https://www.olcf.ornl.gov/olcf-resources/compute-systems/summit/

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


July 18, 2018

Community Matters When Using Algae to Produce Energy

Algae that turn carbon dioxide into fuel feedstock are enhanced by surrounding bacteria.

The Science
Algae fix carbon. That is, they convert carbon dioxide in the air into other compounds, thus fixing atmospheric carbon in water or soil. Researchers showed that bacteria growing on certain algae increase carbon fixation. Further, the team found this increase in two species of microalgae via two different and species-dependent mechanisms.

The Impact
By fixing carbon, tiny algae can potentially produce renewable fuels reliably and affordably. But first they need to work better. This study shows that to improve algae’s performance in producing energy, scientists need to consider the ubiquitous microbes, including bacteria, that intimately associate with algal cells on the microscopic scale.

Summary
The researchers observed mutualistic interactions between heterotrophic bacteria and two species of biofuels-relevant microalgae, Nannochloropsis salina and Phaeodactylum tricornutum, mediated by physical association between individual cells. At the bulk scale, microalgae in these co-cultures exhibited enhanced growth and yield. At the microscale, the researchers used the Lawrence Livermore National Laboratory nanoscale secondary ion mass spectrometry to observe that both species exhibited enhanced carbon fixation in response to the presence of the microbiomes, but there were divergent responses by each species to bacterial attachment. The research illustrates how P. tricornutum may be predisposed to interact mutualistically with bacteria via attachment, but N. salina does not share these traits. Attached bacteria benefit from these relationships by receiving more reduced carbon from their algal host compared to free living cells. Through the selection of bacteria that positively impact algal physiology, this work highlights one approach to ecologically engineer microbiomes conferring growth benefits to the algal host, potentially paving the way to cheaper, reliably produced, and renewable algae-based fuels and products.

Contact
Program Manager
Dawn Adin
DOE Office of Biological and Environmental Research, Biological Systems Science Division
Dawn.Adin@science.doe.gov

Xavier Mayali
Lawrence Livermore National Laboratory
mayali1@llnl.gov  

Rhona Stuart
Lawrence Livermore National Laboratory
stuart25@llnl.gov

Funding
The Department of Energy, Office of Science, Office of Biological and Environmental Research, Biological Systems Science Division, Genomic Sciences Program funded this research.

Publications
T.J. Samo, J.A. Kimbrel, D.J. Nilson, J. Pett-Ridge, P.K. Weber, and X. Mayali, “Attachment between heterotrophic bacteria and microalgae influences symbiotic microscale interactions.” Environmental Microbiology (2018). [DOI: 10.1111/1462-2920.14357]

Related Links
Lawrence Livermore National Laboratory: Biofuels Scientific Focus Area

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


July 16, 2018

Getting To Know the Microbes that Drive Climate Change

The genetics of viruses living along a permafrost thaw gradient may help scientists better predict the pace of climate change.

The Science
Ocean viruses impact carbon and nutrient cycling and the climate. What impact to do viruses that inhabit the soil have? To answer key questions about soil viruses, a team recovered the genomic sequences from ~2,000 soil viral populations. They also retrieved multiple lines of evidence for viral impacts on carbon cycling in climate-impacted thawing permafrost ecosystems.

The Impact
Soil viruses have been studied less than their ocean counterparts because of the difficulty in examining them in a complex environment. Some people suggested these viruses were the “least important” factor for structuring soil microbial communities. On the contrary, this work suggests that viruses impact terrestrial ecosystems by directly and indirectly modifying soil microbial food webs. These webs degrade complex carbon to the greenhouse gases carbon dioxide and methane.

Summary
Over the last two decades, scientists have learned a great deal about the impacts of ocean viruses on microbial mortality, carbon and nutrient cycling, and climate, yet they know next to nothing about soil viruses. A team led by an ecologist from The Ohio State University sampled and assessed soils for the microbial and viral populations present. They focused on soils from a portion of Sweden in the Arctic Circle where the permafrost is rapidly changing. The approximately 2,000 soil viruses they recovered were so novel that they have doubled the total number of known microbe-infecting viral groups worldwide. More than half of these viruses were active, which was unexpected given soil’s propensity for preservation, and approximately a third were linked to microbial hosts that included key carbon cycling microbes predominant in thawing permafrost soils. This implies viral controls on soil carbon cycling and provides first looks, in any ecosystem, at lineage-specific virus:host ratios and how viral pressures change along a thaw gradient. These observations suggest that viral infection dynamics and impacts on host-driven biogeochemistry will change as permafrost thaws. In addition, the recovery of virus-encoded glycoside hydrolase genes suggests that viruses may directly enable degradation of plant-derived polymers to monomeric and small oligomeric sugars during infection to supply bioavailable carbon sources to greenhouse gas-emitting microbial food webs. These findings suggest that soil viruses, just like their ocean counterparts, impact ecosystem function and in these climate-critical, terrestrial habitats will alter the trajectory of soil carbon cycling under a thaw regime.

Contact

Program Manager
Dawn Adin
DOE Office of Biological and Environmental Research, Biological Systems Science Division
Dawn.Adin@science.doe.gov

Matthew B. Sullivan 
The Ohio State University
sullivan.948@osu.edu

Virginia Rich 
The Ohio State University
rich.270@osu.edu

Funding
This research was supported by the Department of Energy, Office of Science, Office of Biological and Environmental Research under the Genomic Science program, with partial support from the Gordon and Betty Moore Foundation and National Science Foundation awards (M.B.S.). Further, A.E.N. and P.B.P. were supported by the European Research Council.

Publications
J.B. Emerson, S. Roux, J.R. Brum, et al., “Host-linked soil viral ecology along a permafrost thaw gradient.” Nature Microbiology 3, 870 (2018). [DOI: 10.1038/s41564-018-0190-y]

Related Links
The Ohio State University press release: Getting to know the microbes that drive climate change
Broader IsoGenie project page: https://isogenie.osu.edu/  
Sullivan Lab Viral Ecology webpage: http://u.osu.edu/viruslab/
Emerson Lab Viral Ecology webpage: https://emersonlab.faculty.ucdavis.edu/

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


July 12, 2018

Microbial Types May Prove Key to Gas Releases from Thawing Permafrost

Scientists discover key types of microbes that degrade organic matter and release carbon dioxide and methane into the atmosphere.

The Science
Rising temperatures mean permafrost—ground at or below freezing for two or more years— begins thawing, releasing carbon in the form of organic matter. This carbon is gobbled up by microbes in the soil. Microbial activity in turn gives off carbon dioxide and methane. How can we predict how much carbon dioxide and methane is released without understanding more about the microbes involved? An international team of scientists has identified the genomes of more than 1,500 of these microbes and discovered their potential for eating soil carbon.

The Impact
About 24 percent of the land in the Northern Hemisphere is covered in permafrost. As frozen ground thaws, it may collapse to form bogs or fens whose resident microbes can degrade the formerly frozen soil carbon, as well as new carbon from plant growth. Understanding how the activities of these microbes contribute to carbon dioxide and methane in the atmosphere has been challenging because of the complexity and diversity of the microbial communities. By studying these communities at the genomic level, scientists can not only identify the species present but shed light on how they use and release carbon.

Summary
An international team tracked the genomic composition of microbes in thawing permafrost to determine which had the most impact on releases of carbon dioxide and methane to the atmosphere. The research team included scientists from the University of Queensland (Australia), Stockholm University (Sweden), the University of New Hampshire, Rochester Institute of Technology (New York), Florida State University, The Ohio State University, the University of Arizona, and Pacific Northwest National Laboratory. Scientists collected soil samples from Stordalen Mire in northern Sweden, an Arctic peatland ecosystem that is undergoing permafrost thaw, to identify the types of microbes living there. Through the Facilities Integrating Collaborations for User Science (FICUS) initiative, researchers leveraged the advanced scientific instrumentation and extensive expertise of EMSL (the Environmental Molecular Sciences Laboratory) and JGI (the Joint Genome Institute), both Office of Science user facilities that are sponsored by the Department of Energy’s Office of Biological and Environmental Research. Looking deep into the genomic composition of these microbes, the team determined which types of microbes degraded organic matter into carbon dioxide and methane. The results link changing biogeochemistry to specific microbial types involved in carbon processing, providing key information for predicting the impact of change on permafrost ecosystems. The work expands the number of genomes recovered from microbes in permafrost-associated soils by two orders of magnitude, laying a powerful foundation for future research at this and other rapidly changing sites across the Arctic.

BER PM Contact EMSL
Paul Bayer, SC-23.1

BER PM Contact JGI
Dan Drell, SC-23.2

PI Contact
Virginia Rich
The Ohio State University

Funding
This work was supported by the U.S. Department of Energy’s Office of Science (Office of Biological and Environmental Research) through the Genomic Science Program, including support of the Environmental Molecular Sciences Laboratory (EMSL) and the Joint Genome Institute (JGI), both DOE Office of Science User Facilities. A portion of the work was performed under the Facilities Integrating Collaborations for User Science (FICUS) initiative, using resources at both JGI and EMSL.

Publication
Woodcroft, B.J., C.M. Singleton, J.A. Boyd, P.N. Evans, J.B. Emerson, A.AF. Zayed, R.D. Hoelzle, T.O. Lamberton, C. K. McCalley, S.B. Hodgkins, R.M. Wilson, S.O. Purvine, C.D. Nicora, C. Li, S. Frolking, J.P. Chanton, P.M. Crill, S.R. Saleska, V.I. Rich, and G.W. Tyson. “Genome-centric view of carbon processing in thawing permafrost.” Nature 560, 49-54 (2018). [DOI:10.1038/s41586-018-0338-1]

Related Links
IsoGenie

Topic Areas:

Division: SC-23 BER


June 13, 2018

Unexpected Complexity: A 3D Look into Plant Root Relationships with Nitrogen-Fixing Bacteria

Scientists develop a molecular map of metabolic products of bacteria in root nodules to aid sustainable agriculture.

The Science
By taking nitrogen out of the air and turning it into plant nutrients, some bacteria help plants like beans, peas, and clovers thrive. However, a recent study shows that the traditional view of this symbiotic relationship doesn't capture the entire picture. Scientists resolved a 3D map of the metabolic products of bacteria found in plant root nodules. This spatial perspective could help unravel the overall complexity of these highly interdependent organisms.

The Impact
As bacteria found in plant root nodules interact with legumes like soybeans, the nodules grow on the plants’ roots. In these nodules, bacteria convert atmospheric nitrogen into molecules that the plants need to grow. Understanding the metabolic processes occurring within these nodules is essential for developing more sustainable agricultural practices for food crops used all over the world.

Summary
Previous studies led scientists to believe the distribution of bacterially derived metabolic byproducts within the nodules was uniform. Scientists from the Environmental Molecular Sciences Laboratory (EMSL), a U.S. Department of Energy Office of Science user facility, joined with colleagues at the University of Missouri and George Washington University to dig deep into the metabolic structure of soybean root nodules. They used one of EMSL's high-field Fourier transform ion cyclotron resonance mass spectrometers to visualize the array of metabolites within the nodules. Of the approximately 140 regulating substances identified, some were located together in distinct anatomical compartments. A few, however, were more unevenly distributed throughout the middle of the nodule, where the bacteria reside. This discovery points to a previously unrecognized biochemical complexity in the nodules that is key for symbiotic plant-microbe interactions. Armed with this understanding, scientists can suggest ways to optimize crop production and sustainability.

Biological and Environmental Research Program Manager
Paul Bayer
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Climate and Environmental Sciences Division (SC-23.1)
DOE Environmental Molecular Sciences Laboratory
paul.bayer@science.doe.gov

Principal Investigator
Christopher Anderton
Environmental Molecular Sciences Laboratory
Christopher.Anderton@pnnl.gov  

Funding
This work was supported by the U.S. Department of Energy's (DOE's) Office of Science, Office of Biological and Environmental Research, including support of the Environmental Molecular Sciences Laboratory (EMSL), a DOE Office of Science user facility; the DOE Mickey Leland Energy Fellowship; University of Missouri's Gus. T. Ridgel Fellowship; George Washington Carver Fellowship; and the National Science Foundation Plant Genome Program.

Publications
Velickovic, D., B. J. Agtuca, S. A. Stopka, A. Vertes, D. W. Koppenaal, L. Paša-Tolic, G. Stacey, and C. R. Anderton. "Observed metabolic asymmetry within soybean root nodules reflects unexpected complexity in rhizobacteria-legume metabolite exchange." The ISME Journal 12, 2335 (2018). [DOI:10.1038/s41396-018-0188-8]

Related Links
Environmental Molecular Sciences Laboratory science highlight: Unexpected Complexity: A Three-dimensional Look into Plant Root Relationships with Nitrogen-fixing Bacteria

Environmental Molecular Sciences Laboratory website: 6-Tesla high-field Fourier transform ion cyclotron resonance mass spectrometer

Topic Areas:

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


June 01, 2018

Renewable Solvents Derived From Lignin Lower Waste in Biofuel Production

New class of solvents breaks down plant biomass into sugars for biofuels and bioproducts in a closed-loop biorefinery concept.

The Science
A closed-loop biorefinery could dramatically lower the cost of biofuels and related products. In this approach, the refinery produces the solvents it needs, rather than “importing” them. Scientists at the Joint BioEnergy Institute are developing a closed-loop biorefinery concept that uses waste lignin as a potential process solvent. How? They synthesized a new and renewable class of deep eutectic solvents. These solvents work well. When mixed with other liquids and used for biomass pretreatment, these solvents released sugar from grassy feedstocks for fuel and chemical production.

The Impact
The deep eutectic solvents offer a wide range of advantages over other available biomass pretreatment options, such as ionic liquids. The solvents are easy to synthesize due to the wide availability of inexpensive waste lignin. Further, there’s a good potential for significant scale-up of the solvent production process. Lignin is a major component of plant biomass. It is also a major waste stream during biomass processing. Turning waste into an asset makes these renewable solvents an attractive new approach for biomass conversion into biofuels and products that are less expensive. Further, the deep eutectic solvents offer a sustainable alternative to conventional solvents and ionic liquids.

Summary
Deep eutectic solvents (DESs) represent a new class of renewable solvents derived from the conversion of lignin-derived compounds. Naturally found in lignocellulosic biomass, lignin accounts for 20 to 30 percent of the dry weight of biomass. With the development of commercial production of biofuels and bioproducts, it is anticipated that a significant amount of lignin will be generated annually that needs to be converted into desired bioproducts. Thus, lignin valorization is a very important topic for researchers to address to enable the growth of a U.S. bioeconomy. Ten lignin-derived phenolic compounds were tested as hydrogen bond donors in varying mixtures with choline chloride to synthesize deep DESs—solvents that when mixed have a lower melting temperature than the individual solvents. After initial screening, the team selected and used four DESs for biomass pretreatment of switchgrass. The researchers washed the pretreated biomass to remove potential inhibitory effects on enzymatic hydrolysis and fermentation. A fresh batch of the DES and choline chloride mixture resulted in approximately 87 percent glucose yield, while recycled DES resulted in decreased yields of 78 percent and 70 percent for second and third rounds, respectively. Biomass processes utilizing these renewable DESs could reduce operating costs by achieving a closed-loop biorefinery that generates the solvents needed for biomass pretreatment from the process of biomass conversion itself.

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

Funding
This work was conducted at the Department of Energy (DOE) Joint BioEnergy Institute and supported by the DOE, Office of Science, Office of Biological and Environmental Research, through a contract between Lawrence Berkeley National Laboratory and DOE. 

Publications
K.H. Kim, T. Dutta, J. Sun, B. Simmons, and S. Singh, “Biomass pretreatment using deep eutectic solvents from lignin derived phenols.” Green Chemistry 20, 809 (2018). [DOI: 10.1039/C7GC03029K]

Related Links
Joint BioEnergy Institute: http://www.jbei.org

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


May 28, 2018

New Method Helps Predict Metabolite Concentrations, Rate Constants, and Enzyme Regulation Within Cells

Researchers use Neurospora crassa, a reliable model organism, to demonstrate new method.

The Science
Researchers at PNNL are now able to predict cellular metabolite concentrations, rate constants, and regulation of enzymes using the same physical principles as those applied to thermodynamics.

The Impact
Biologists’ understanding of cells has been hampered by the inability to measure critical parameters that control dynamics within each cell. Now, with new physics-based data analysis and simulations, researchers are able to predict these parameters and use them to estimate the concentrations of metabolites within cells, as well as identify which enzymes require regulation.
In this study, researchers used Neurospora crassa to demonstrate that a key regulatory point in glycolysis is critical to preventing the cell’s interior from becoming thick like molasses, thus slowing metabolism, energy production, and growth. Armed with this information, researchers are a step closer to designing pathways for synthetic biology.

Summary
The research combined a new approach for modeling and data inference using a discarded, 110 year-old physics equation.  It helped scientists determine estimates of the concentrations of chemicals and their reaction rates inside a cell by selecting the set of reactions and metabolite concentrations that would produce the most thermodynamically efficient set of pathways to use. In other words, the chosen pathways waste the least amount of energy in the form of heat. The resulting metabolite concentrations are then used to determine the reaction rates and rate constants. Comparison of the measured metabolite concentrations with  predicted estimates of metabolite concentrations allows researchers to determine which reactions are regulated in central metabolism. The rate parameters and enzyme activities are then used in a simulation to predict the energetics, power requirements, resistance, and flux of individual reactions and pathways. The next step is to scale-up the method to model all of metabolism and the interactions of metabolites with the proteins that control the circadian clock within the cell.

Contacts (BER PM)
Ramana Madupu
Biological and Environmental Research, U.S. Department of Energy
Ramana.Madupu@Science.doe.gov

(PI Contact)
William Cannon
Pacific Northwest National Laboratory
William.cannon@pnnl.gov

Funding
The work was jointly funded by the National Institute of Biomedical Imaging and Bioengineering and the U.S. Department of Energy, Office of Biological and Environmental Research.

Publications
Cannon, W.R., J. D. Zucker, D. J. Baxter, N. Kumar, J. M. Hurley, and J. C. Dunlap. "Prediction of metabolite concentrations, rate constants and post-translational regulation using maximum entropy-based simulations with application to central metabolism of Neurospora crassa." Processes 6, 63 (2018). [DOI:10.3390/pr6060063]

Related Links
Cannon, W.R., and S. E. Baker. "Non-steady state mass action dynamics without rate constants: dynamics of coupled reactions using chemical potentials." Phys Biol. 14(5) 055003 (2017). DOI:10.1088/1478-3975/aa7d80]

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


April 24, 2018

A Functional Genomics Database for Plant Microbiome Studies

Catalog of candidate genes involved in plant-microbe relationships.

The Science
Could marginal lands be bountiful fields for biofuel crops? To answer that question, scientists are investigating soil microbes, which can aid plant growth. Here, researchers isolated bacteria from around the roots of poplar trees, maize, and a type of mustard plant. They developed a catalog of the genetic material (genome) of the soil bacteria they found. In mining the data, they found genes involved in bacterial root colonization.

The Impact
Knowing how beneficial microbes and microbial communities colonize plants, along with subsequent plant-microbe interactions, could assist in growing food and energy crops with fewer chemical inputs. These inputs include fertilizer, pesticides, and fungicides.

Summary
To facilitate crop-breeding strategies for making plants more productive on marginal lands and more tolerant of stresses such as drought and low nutrient availability, researchers are focusing on understanding and promoting beneficial plant-microbe relationships. To date, most plant microbiome studies in the field have focused on community structure rather than function, but there is a need to understand microbial community functions to engineer the microbiome to support plant growth. In this study, researchers isolated bacteria from the root environments of Brassicaceae, poplar trees, and maize, and sequenced, assembled, and compared the genomes with thousands of publicly available genomes including bacteria from both plant and non-plant environments. This broad analysis allowed the researchers to identify genes enriched in the genomes of plant-associated and root-associated organisms. They found that plant- and soil-associated genomes were enriched in genes involved in sugar metabolism and transport, likely an adaptation to the production of photosynthesis-derived plant carbon compounds. Further, they found that numerous genes seem to mimic plant functions in a strategy similar to that employed by plant pathogens. The identification of two new, rapidly evolving protein families containing genes often used in offense or defense against another organism provides evidence for a “molecular arms race” between competing bacteria within the same environment. This research provides a valuable resource for researchers studying plant-microbe interactions to identify novel and potentially interesting genes and gain a better functional understanding of the plant microbiome that can be exploited for enhancing crop production.

Contact
BER Program Managers
Cathy Ronning 
Biological Systems Science Division
Office of Biological and Environmental Research
Office of Science
Department of Energy
catherine.ronning@science.doe.gov

Dan Drell
Biological Systems Science Division
Office of Biological and Environmental Research
Office of Science
Department of Energy
daniel.drell@science.doe.gov

Principal Investigator 
Jeff Dangl
University of North Carolina at Chapel Hill and Howard Hughes Medical Institute
dangl@email.unc.edu  

Funding
The Department of Energy (DOE) Joint Genome Institute, Integrated National Science Foundation Support Promoting Interdisciplinary Research and Education, National Institutes of Health, Howard Hughes Medical Institute (HHMI), Gordon and Betty Moore Foundation, SystemsX.ch, European Research Council, DOE Office of Science Biological and Environmental Research (BER and U.S. Department of Agriculture National Institute of Food and Agriculture Plant Feedstocks Genomics for Bioenergy, and the DOE BER Genomic Science Program and Science Focus Area: Plant Microbe Interfaces (Oak Ridge National Laboratory) funded the research.

Publications
A. Levy, I.S. Gonzalez, M. Millelviefhaus, et al., “Genomic features of bacterial adaptation to plants.” Nature Genetics 50,138 (2018). [DOI: 10.1038/s41588-017-0012-9]

Related Links
Joint Genome Institute press release: A Functional Genomic Database for Plant Microbiome Studies

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


April 24, 2018

A Novel Method for Comparing Plant Genes

Researchers develop a method of identifying gene expression patterns in drought-resistant plants.

The Science
During normal photosynthesis, plants open their stomata (microscopic pores in the plant epidermis that permit the flow of gases and water vapor) during the day to take in carbon dioxide needed for carbohydrate production. But a small percentage of plants open their stomata to capture carbon dioxide only at night, thereby conserving water. This form of photosynthesis is called crassulacean acid metabolism (CAM). In this study, scientists created a new method to analyze this conservation by comparing genes of CAM plants with each other and with the genes of plants possessing a more common type of photosynthesis called C3. They found a collection of gene “triangles”—and a new method of studying time-related patterns of gene expression across species.

The Impact
The study provides insights into CAM mechanisms. The research will serve scientists across the biological and chemical science domains who have a long-term goal of engineering CAM into bioenergy and food crops, so they will be more tolerant to drought. The team said this newly developed Fisher triangle enrichment method could be applied to study any mechanism across species. The team believes the method may even have potential applications in human clinical genomics studies, such as those related to diseased versus nondiseased populations.

Summary
The water-saving characteristics developed by CAM plants allow for survival in arid climates. Plant species such as orchid, pineapple, and Kalanchoë use CAM photosynthesis to conserve water by keeping their stomata, or pores, shut during the day and open at night to collect carbon dioxide. In studying the building blocks of CAM, scientists open doors to bioengineering the metabolic processes of water-intensive crops such as rice, wheat, and soybeans to accelerate their adaptation to more arid environments.

In this study, a team developed a new method of comparing genes of CAM plants with genes of C3 plants that will provide scientists with a detailed understanding of the mechanisms behind CAM. The team compared plant data that described the abundance of expressed (activated) genes throughout the day based on sequenced RNA molecules in each plant’s tissue. The team searched for gene families in which an Arabidopsis gene (1) had an opposite expression pattern to genes of pineapple and Kalanchoë, both CAM plants, and (2) shared the same expression patterns with pineapple and KalanchoëArabidopsis belongs to the cress family of plants—it was the first plant to have its genome sequenced and is the domain standard for studying gene expression in plants. The scientists ended up with a collection of gene triangles that detailed the similarities among CAM genes and a method of comparing genes of CAM versus non-CAM plants. The team’s results also enabled scientists at Oak Ridge National Laboratory to identify 54 genes that showed convergent regulatory patterns in CAM species, providing insight into CAM mechanisms that may prove useful for bioengineering plants that use water more efficiently.

Contact
Daniel Jacobson
Oak Ridge National Laboratory
jacobsonda@ornl.gov

Xiaohan Yang
Oak Ridge National Laboratory
yangx@ornl.gov

Funding
This research was supported by the Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research Genomic Science Program; the United Kingdom Biotechnology and Biological Sciences Research Council; the Laboratory Directed Research and Development Program of Oak Ridge National Laboratory (ORNL); and the DOE Joint Genome Institute. This research used resources of the Oak Ridge Leadership Computing Facility and the Compute and Data Environment for Science at ORNL.

Publications
X. Yang, R. Hu, H. Yin, et al., “The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism.” Nature Communications 8,1899 (2017). [DOI: 10.1038/s41467-017-01491-7]

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


April 23, 2018

A Game Changer: Protein Clustering Powered by Supercomputers

New algorithm lets biologists harness massively parallel supercomputers to make sense of a “data deluge.”

The Science
In the world of big data, biologists create data sets containing hundreds of millions of proteins and other cellular components. They apply clustering algorithms to the datasets to identify key patterns. Many of the techniques have been widely used for more than a decade. But they can’t keep up with the torrent of biological data. In fact, few clustering algorithms can handle a biological network with millions of nodes (proteins) and edges (connections). Researchers from Lawrence Berkeley National Laboratory and the Joint Genome Institute took on one of the most popular clustering approaches in modern biology—the Markov Clustering (MCL) algorithm. They modified it to run quickly, efficiently, and at scale on distributed memory supercomputers.

The Impact
The team’s high-performance algorithm—called HipMCL—handles massive biological networks. These networks were impossible to cluster with MCL. With HipMCL, biologists can identify and characterize novel aspects of microbial communities. It works without sacrificing the sensitivity or accuracy of MCL. Using HipMCL, scientists processed a network with about 70 million nodes and 68 billion edges in a few hours. To do this, HipMCL used about 140,000 processor cores at the National Energy Research Scientific Computing Center. As an added benefit, HipMCL runs seamlessly on any computing system.

Summary
Given an arbitrary graph or network, it is difficult to know the most efficient way to visit all of the nodes and links. A random walk gets a sense of the footprint by exploring the entire graph randomly; it starts at a node and moves arbitrarily along an edge to a neighboring node. Because there are many different ways of traveling between nodes in a network, this step repeats numerous times. Algorithms such as MCL will continue running this random walk process until there is no longer a significant difference between the iterations. Performing random walks is by far the most computationally and memory intensive step in a cluster analysis. The best way to execute a random walk simultaneously from many nodes of the graph is with sparse matrix-matrix multiplication.

The unprecedented scalability of HipMCL comes from its use of state-of-the-art algorithms for sparse matrix manipulation. Berkeley Lab computer scientists developed some of the most scalable parallel algorithms for GraphBLAS’s sparse matrix-matrix multiplication and modified one of their state-of-the-art algorithms for HipMCL.  

Contact
Ariful Azad 
Lawrence Berkeley National Laboratory 
azad@lbl.gov  

Aydin Buluç 
Lawrence Berkeley National Laboratory 
abuluc@lbl.gov  

Nikos Kyrpides 
DOE’s Joint Genome Institute and Lawrence Berkeley National Laboratory 
nckyrpides@lbl.gov  

Funding
Development of HipMCL was primarily supported by the Department of Energy’s (DOE’s) Office of Science via the Exascale Solutions for Microbiome Analysis (ExaBiome) project, which is developing exascale algorithms and software to address current limitations in metagenomics research. The development of the fundamental ideas behind this research was also supported by DOE’s Office of Advanced Scientific Computing Research’s Applied Math Early Career program. The team used resources at the Joint Genome Institute and the National Energy Research Scientific Computing Center, both DOE Office of Science user facilities.

Publications
A. Azad, G.A. Pavlopoulos, C.A. Ouzounis, N.C. Kyrpides, and A. Buluç, “HipMCL: A high-performance parallel implementation of the Markov clustering algorithm for large-scale networks.” Nucleic Acids Research gkx1313 (2018). [DOI: 10.1093/nar/gkx1313]

Related Links
Lawrence Berkeley National Laboratory press release: A Game Changer: Metagenomic Clustering Powered by HPC

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


March 26, 2018

Rewriting Resistance: Genetic Changes Increase Crops’ Biomass and Sugar Release

Using genetic engineering, scientists improve biomass growth and conversion in woody and grassy feedstocks.

The Science
A major barrier to using switchgrass, poplars, and other plants to make fuels is the natural resistance of plant cell walls to deconstruction. To overcome this resistance to deconstruction, a detailed understanding of the structure and genetics of plant cell walls is essential. In this study, scientists targeted a specific gene associated with plant cell wall formation (GAUT4) in switchgrass and poplar. Thus, they could examine the impact of this gene on biomass yield and resistance to deconstruction. They found that plants with a downregulated GAUT4 exhibited greater biomass yield and greater sugar release upon deconstruction even after a 3-year field trail. The study demonstrates a potentially vital tool for developing dedicated bioenergy crops.

The Impact
This is the first example of a specific plant cell wall structural modification that resulted in increased biomass yield and sugar release in both woodyand grassy biofuel feedstocks. This research also illustrates the impact of pectin cross linkages within cell wall polymers. Further, the research highlights the impact of engineering reduced pectin linkages in cell walls on sugar release from the deconstructed biomass.

Summary
Scientists at the BioEnergy Science Center used targeted engineering of plant cell wall polymers to genetically modify switchgrass and poplar, promising bioenergy grassy and woody crops, to improve the biomass yield and ethanol production. Scientists accomplished this modification by downregulating the gene, GAUT4, which reduced the activity and production of two cell wall pectin polymers, homogalacturonan and rhamnogalacturonan II. These changes lead to loosened plant cell walls with increased cell expansion, plant growth, and polymer accessibility during the sugar release process. All downregulated GAUT4-KD grasses and trees showed enhanced growth in the greenhouse and improved enzymatic sugar release and fermentation into ethanol, an important biofuel. GAUT4-KD switchgrass lines grown 3 years in the field provide up to 7-fold increased extractability of cell wall sugars and ethanol production, and 6-fold more biomass yield over field-grown controls. This study shows that GAUT4 is an effective gene target for improved biomass production with improved properties for fuel production.

Contact
BER Program Manager
Kent Peters Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
Department of Energy
Kent.Peters@science.doe.gov

Principal Investigators 
Debra Mohnen
Complex Carbohydrate Research Center
University of Georgia
dmohnen@ccrc.uga.edu

Gerald A. Tuskan
Director, The Center for Bioenergy Innovation
Oak Ridge National Laboratory
tuskanga@ornl.gov

Funding
The research was primarily funded by the BioEnergy Science Center and partially by the Center for Bioenergy Innovation, which are Department of Energy (DOE) Bioenergy Research Centers supported by the Office of Biological and Environmental Research in the DOE Office of Science.

Publications
A.K. Biswal, M.A. Atmodjo, M. Li, et al., “Sugar release and growth of biofuel crops are improved by downregulation of pectin biosynthesis.” Nature Biotechnology 36, 249 (2018). [DOI: 10.1038/nbt.4067]

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


March 14, 2018

The Secret Lives of Cells

Supercomputer simulations predict how E. coli adapts to environmental stresses.

The Science
Warmer temperatures can alter a cell’s protein structure. Researchers developed a systems-level computational model, FoldME, that can accurately predict how E. coli responds to temperature changes and genetic mutations. The model can also predict how the bacterium then reallocates its resources to stabilize proteins. This study, led by the University of California, San Diego, used supercomputers to run large-scale simulations. The computing services let the team run calculations in parallel for hundreds of proteins. The computer sped up what would otherwise have been weeklong simulations.

The Impact
To have full control over living cells, scientists need to understand the fundamental mechanisms by which they survive and quickly adapt to changing environments. FoldME could aid in designing engineered organisms. These organisms could have use in biofuel production and patient-specific treatments for bacterial infections.

Summary
This work and the FoldME model provide a comprehensive, genome-scale understanding of how cells adapt under environmental stress, with statistical descriptions of multiscale cellular responses consistent with numerous datasets. Using first principles calculations and computational resources at the National Energy Research Scientific Computing Center allowed the researchers to gain a deep understanding of how multiple protein folding events and other intracellular reactions all work together to enable the cell to respond to environmental and genetic stresses. These findings have implications for precision medicine, where adaptive cell modeling could provide patient-specific treatments for bacterial infections, and for biofuel production.

Contact

BER Program Managers
Pablo Rabinowicz
Biological Systems Science Division
Office of Science
Department of Energy
pablo.rabinowicz@science.doe.gov

Ramana Madupu
Biological Systems Science Division
Office of Science
Department of Energy
ramana.madupu@science.doe.gov

Principal Investigator
Bernhard Palsson
University of California, San Diego
palsson@ucsd.edu  

Funding
This work was funded by National Institutes of Health grants and the Novo Nordisk Foundation. This research used resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy (DOE) Office of Science user facility. Allocation of computer time at NERSC was awarded by the DOE Office of Science, Office of Biological and Environmental Research, Biological Sciences Division.

Publications
K. Chen, Y. Gao, N. Mih, E.J. O’Brien, L. Yang, and B.O. Palsson, “Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation.” Proceedings of the National Academy of Sciences USA 114 (43), 11548 (2017). [DOI: 10.1073/pnas.1705524114]

Related Links
University of California at San Diego Systems Biology Research Group

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


February 28, 2018

Discovery of a New Microbe that Produces Methane in Oxygenated Soils

Global models may be underestimating net wetland methane emissions.

The Science
In a Lake Erie wetland, scientists showed that microbes produce methane in an oxygen-rich environment. This finding disproves the long-accepted idea that oxygen limits microbe’s ability to produce methane. The team performed DNA sequence analyses of samples across the wetland. They uncovered a dominant new species of methane-producing Archaea. This Archaea was also present in samples from many different oxygen-rich ecosystems.

The Impact
Existing global climate models do not take into account microbes producing methane, a greenhouse gas, in oxygenated surface soils. This study indicates current global climate models could be greatly underestimating where these microbes live. The study also sheds light on a new Archaea species. This species is probably responsible for a large fraction of methane emissions in oxygen-containing soils.

Summary
A group of scientists set out to sample microbes living in Old Woman Creek National Estuarine Research Reserve, a wetland of Lake Erie, in an effort to start to piece together the broad picture of methane production. However, they made an unexpectedly important discovery when they found oxygen-rich soils containing up to 10 times more methane than non-oxygenated soils. Moreover, up to 80 percent of the net methane emissions was a result of microbial methane production in oxygenated soils. Through DNA sequencing of microbes from these soils, the research team discovered a previously uncatalogued methane-producing (methanogen) organism that belongs to the Archaea group of microbes and they named it Candidatus Methanothrix paradoxum. This microorganism not only thrives in the oxygen-rich wetland, but the researchers also found evidence of its presence at more than 100 diverse environments across the world (rice paddies, wetlands, and peatlands), suggesting that this microbe significantly contributes to methanogenesis in a wide variety of oxygen-containing habitats. The results from this study indicate global climate models have greatly underestimated the role methanogens play in global methane emissions and their effects on the climate.

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

Paul Bayer
SC-23.1
Office of Biological and Environmental Research
Office of Science
Department of Energy
Paul.Bayer@science.doe.gov

Principal Investigator
Kelly C. Wrighton
The Ohio State University
wrighton.1@osu.edu

Funding
This work was supported by the Office of Biological and Environmental Research (BER) within the Department of Energy’s Office of Science (SC) Early Career Research Program award to Kelly Wrighton, including contributions from BER’s Ameriflux and Regional and Global Climate Modeling programs supported under BER, the SC Graduate Student Research Program, and the SC user facilities Environmental Molecular Sciences Laboratory and the Joint Genome Institute. The authors also acknowledge support from the Ohio Water Development Authority and the National Science Foundation.

Publications
J. Angle, T. Morin, L. Solden, A. Narrowe, G. Smith, M. Borton, C. Rey-Sanchez, R. Daly, G. Mirfenderesgi, D. Hoyt, W. Riley, C. Miller, G. Bohrer, and K. Wrighton, “Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions.” Nature Communications 8, 1567 (2017). [DOI: 10.1038/s41467-017-01753-4]

Topic Areas:

Division: SC-23 BER


February 28, 2018

Modified Switchgrass Has No Negative Effect on Soils

Genetically engineered switchgrass does not change soil chemistry, microbiology, or carbon storage potential.

The Science
Overcoming the natural resistance of plant cell walls to deconstruction, known as recalcitrance, is a major bottleneck to cost-effective biofuel production. In response, scientists modified lignin. Lignin is one of the polymers responsible for recalcitrance and crucial for structural support within plant tissues. Modifying lignin improved the conversion of plant biomass to fuel. Yet a question remained. Will specifically modified bioenergy crops negatively impact the local soil? In field studies, researchers confirmed that growing genetically manipulated switchgrass as no negative effects on soils over the short terms studied.

The Impact
Cultivating genetically modified bioenergy crops over large areas could greatly improve biofuel production. However, little is known about the impact such crops could have on soil health relative to native plants. This study sought to characterize these impacts. The team evaluated physical, chemical and biological parameters of soil health over several years during field trials of engineered switchgrass. The study found no significant effects.

Summary
Scientists at the BioEnergy Science Center (BESC) genetically modified switchgrass, a promising bioenergy crop, to produce less lignin resulting in an improved ethanol conversion process. However, the longer-term impact of lignin-reduced switchgrass on soils in terms of its physical, chemical, microbiological attributes was unknown. An analysis comparing lignin-altered lines of switchgrass against non-altered switchgrass (controls) showed no detectable effect on soil chemistry, with no significant changes to soil pH or 19 other major measured elements. The soil microbiome, important to the fate of nutrients and carbon, exhibited seasonal differences between the altered and control crops, but overall there was no significant difference. Furthermore, the rate of carbon sequestration, the production and storage of carbon in the soil, occurred at rates similar to the positive rates in control plots with unaltered switchgrass.

Contacts
BER Program Manager
Kent Peters, Ph.D.
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
U.S. Department of Energy
Kent.Peters@scienc.energy.gov

Principal Investigator
Jennifer DeBruyn
University of Tennessee Knoxville
jdebruyn@utk.edu  

Funding
This work was funded by the Southeastern Region Sun Grant Program at the University of Tennessee. The research was enabled by the BioEnergy Science Center, which is a U.S. Department of Energy (DOE) Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science.

Publications
DeBruyn, J., D. Bevard, M. Essington, J. McKnight, S. Schaeffer, H. Baxter, M. Mazarei, D. Mann, R. Dixon, F. Chen, C. Zhuo, Z. Wang, and C. Stewart Jr., “Field-grown transgenic switchgrass (Panicum virgatum L.) with altered lignin does not affect soil chemistry, microbiology, and carbon storage potential.” Global Change Biology Bioenergy 9(6), 1100-1109 (2017). [DOI: 10.1111/gcbb.12407]
(Reference link)

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Test field plot of modified switchgrass (with altered lignin) and unaltered (control) switchgrass (Panicum virgatum L) after three years of growth. Cultivation of perennial switchgrass increases soil organic carbon. [Image courtesy of BioEnergy Science Center]



January 22, 2018

Optimal Foraging: How Soil Microbes Adapt to Nutrient Constraints

Understanding how microbial communities adjust to nutrient-poor soils at the genomic and proteomic level gives scientists insights into land use and terrestrial biosphere modeling.

The Science
The vital growth nutrient, phosphorus, is scarce in many tropical ecosystems, yet microbes in tropical soils thrive. New research from a team of scientists has now revealed at the genomic and proteomic level how these microbes acquire rare nutrients.

The Impact
This study provides insights into soil microbial communities and how they adapt to different levels of nutrients available in a tropical rainforest. Significant changes in metabolic capabilities, shifts in community structure, and regulation of enzyme abundances revealed how soil microbes adapt to limited nutrients in tropical soils. These findings could have important implications for enhancing agricultural crops and for modeling terrestrial processes and elemental cycles.

Summary
A team of scientists set out to determine whether the theory of optimal foraging, which suggests any ecological community will adjust its consumption strategy to balance the distribution of the life-sustaining elements, applied to microorganisms in soils. While the theory had been applied to plants and animals, which can be easily observed, it is more difficult to apply to tiny, unseen microbes. Scientists from Oak Ridge National Laboratory and The University of Tennessee, Knoxville gathered samples from a 17-year fertilization experiment of the Smithsonian Tropical Research Institute in Panama. Samples included phosphorus-rich and phosphorus-deficient soil. The advanced Fourier-Transform Ion Cyclotron Resonance Mass Spectrometer at the Environmental Molecular Sciences Laboratory (EMSL), a U.S. Department of Energy (DOE) Office of Science User Facility, provided the team with spectra that enabled the scientists to look at samples containing soil organic matter in ways that enabled them to understand what organic compounds were available to the microbes. The Joint Genome Institute (JGI), also a DOE Office of Science User Facility, helped team members probe microbial genes in the samples, and the scientists used mass spectrometers at Oak Ridge National Laboratory to identify more than 7,000 proteins in each soil sample. What the researchers found closely matched their theories. The microbes in the two types of soils used different foraging strategies and adjusted their allocation of different genes and proteins to make the most of the scarce phosphorus resources in their environment. Scientists also identified differences in genes associated with the use of carbon, nitrogen, and sulfur. These results could help scientists understand how to better model microbial communities, plan for optimal land use, and predict changes in the earth system.

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

PI Contact
Chongle Pan
Oak Ridge National Laboratory
panc@ornl.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 Joint Genome Institute (JGI), both DOE Office of Science user facilities, and Laboratory Directed Research and Development funding from Oak Ridge National Laboratory.

Publication
Qiuming, Y., L. Zhou, Y. Song, S.J. Wright, X. Guo, S.G. Tringe, M.M. Tfaily, L. Pasa-Tolic, T.C. Hazen, B.L. Turner, M.A. Mayes, and C. Pan, “Community Proteogenomics Reveals the Systemic Impact of Phosphorus Availability on Microbial Functions in Tropical Soil.”  Nature Ecology and Evolution 2,499-509 (2018). [DOI:10.1038/s41559-017-0463-5]

Related Links
Optimal Foraging:  How Soil Microbes Adapt to Nutrient Constraints on EMSL’s website.
Researchers reveal how microbes cope in phosphorus-deficient tropical soil Oak Ridge National Laboratory news release

Topic Areas:

Division: SC-23 BER



Scientists are studying how microbes in soil use nutrients like phosphorus at the molecular level, helping better model efficient land use and terrestrial processes.



January 18, 2018

Engineering Yeast Tolerance to a Promising Biomass Deconstruction Solvent

Chemical genomic-guided engineering of gamma-valerolactone-tolerant yeast.

The Science
To convert plant matter to fuel and other sustainable bioproducts, it must first be broken into digestible sugars for microbes. Gamma-valerolactone (GVL) is a promising chemical solvent for biomass degradation. However, it is toxic to fermentative microbes. Scientists discovered the mechanisms of GVL toxicity to fermentative microbes. They identified gene deletions that created sensitivity or tolerance to the solvent. They used this knowledge to engineer a fermenting yeast strain with improved tolerance to GVL and enhanced conversion of sugars to biofuel.

The Impact
The team modified the yeast using chemical genomic-guided engineering. It offered a rapid method for tailoring existing yeast strains to specific chemical stressors. The work suggests a way to create a GVL-tolerant yeast strain with increased conversion to biofuel efficiency.

Summary
Biomass deconstruction using the solvent GVL has several advantages over more traditional deconstruction methods; however, biological conversion to biofuels can be challenging, as fermentation microbes are sensitive to any residual GVL. Researchers at the Great Lakes Bioenergy Research Center sought to identify the mechanisms of GVL toxicity using chemical genomics, which measures the impact of small molecules on microbes by deleting nonessential genes. Chemical genomics profiling of GVL predicted that this chemical affects the membranes and membrane-bound processes of the fermenting yeast strain Saccharomyces cerevisiae. Their research showed that GVL has a toxic effect on S. cerevisiae cell membrane integrity, which is magnified by ethanol produced during fermentation. Their analysis also revealed that deletion of enzymes Pad1p andFdc1p mediated toxicity to GVL in an engineered fermenting yeast strain. Moreover, deletion of PAD1 and FDC1 in a fermenting yeast strain, led to improved growth, sugar utilization, and ethanol production in synthetic hydrolysate-containing GVL relative to the non-engineered strain. Chemical protein analysis of the engineered strain revealed that enzymes involved in cell membrane biosynthesis were more abundant in the presence of GVL and cellular levels of this sterol were elevated compared to the non-engineered strain. These results suggest that one route to GVL tolerance in yeast is through alteration of membrane fluidity. Future studies are needed to address the role of PAD1 and FDC1 in cell membrane biosynthesis. This study also illustrates the utility of chemical genomics approaches to rapidly identify cellular targets of small molecules and strategies to engineer microbial strains for improved biofuel and bioproduct production.

Contact
Principal Investigators
Jeff Piotrowski
Yumanity Therapeutics
jpiotrowski@yumanity.com

Robert Landick
University of Wisconsin-Madison
landick@bact.wisc.edu

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

Funding
This work was funded by the Department of Energy Great Lakes Bioenergy Research Center (Office of Science, Biological and Environmental Research). Additional funding (C.M.) was provided by grants from the National Institutes of Health and the National Science Foundation.

Publications
Bottoms, S., Q. Dickinson, M. McGee, L. Hinchman, A. Higbee, A. Hebert, J. Serate, D. Xie, Y. Zhang, J.J. Coon, C.L. Myers, R. Landick, and J.S. Piotrowski, “Chemical genomic guided engineering of gamma-valerolactone tolerant yeast.” Microbial Cell Factories 17, 5 (2018). [DOI: 10.1186/s12934-017-0848-9]

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Flow-through reaction setup dissolved biomass to sugars using gamma-valerolactone fractionation. [Image courtesy of Matthew Wisniewski, Great Lakes Bioenergy Research Center]