DOE User Facilities Partner for Greater Scientific Impact

EMSL and DOE JGI announce FY 2018 FICUS projects

Two Department of Energy user facilities, the Environmental Molecular Sciences Laboratory (EMSL) and the Joint Genome Institute (JGI), have selected 14 proposals from a joint call for 2018 research under the Facilities Integrating Collaborations for User Science (FICUS) initiative. This was the fifth FICUS call between EMSL and the DOE JGI since the collaborative science initiative was formed in 2014 by the Office of Biological and Environmental Research (BER) to harness the combined expertise and resources of two of the national user facilities stewarded by the DOE Office of Science in support of DOE’s energy, environment, and basic research missions.

“We are making considerable headway on achieving the goal of FICUS by enabling scientists to conduct fundamental science experiments in ways not possible with projects undertaken separately at either user facility,” said DOE JGI User Programs Deputy Susannah Tringe. “It is gratifying to already see the fruit of these collaborative endeavors in high-profile publications.”

Through the EMSL-JGI FICUS calls, users can combine EMSL’s unique imaging, omics and computational resources with cutting-edge genomics, DNA synthesis and complementary capabilities at DOE JGI. Because the facilities offer a breadth of characterization and analytical power, researchers are not expected to be expert users on all of the scientific instruments. Instead, members of the scientific staff from both user facilities work with the researchers to assess their needs and help them with their methodologies, experiments and visualizations.

“The FICUS program has been such a success at many levels,” said Nancy Hess, EMSL’s Science Lead for Terrestrial and Subsurface Ecosystems, “from the scientific accomplishments of the researchers using our capabilities to the greater degree of strategic integration between our two facilities to the growing scientific community that has taken advantage of this opportunity.”

The accepted proposals are:

• Scott Saleska of the University of Arizona is investigating the biogeochemical implications of changing microbial leaf litter decomposition across a permafrost thaw gradient. The Saleska team intends to examine the ways in which fresh plant litter deposition influences microbial activity across three stages of permafrost thaw and the overall impact of these changes on greenhouse gas emissions. They seek to increase understanding of the importance of species-specific interactions on biogeochemical cycling and the complex factors that control arctic greenhouse gas emissions.
• Tullis Onstott and co-PI Maggie Lau, of Princeton University, seek to document the microbial ecosystem of an active fault zone in South Africa and determine how these microbial communities respond to pulses of hydrogen gas released during seismic activity. They anticipate that the change in local gas composition will trigger bacterial activity to rapidly generate methane and other reduced compounds. Analyses of deep subsurface syntrophic consortia could provide ecologists with the first images of subsurface trophic associations and identify the mechanisms of electron transfer to better understand the transformation of methane in the environment.

• Victoria Orphan of the California Institute of Technology will characterize the ecophysiologies of uncultured syntrophic associations – the phenomenon in which one species lives off the products of another species – that are driving anaerobic methane oxidation using meta’omics and multi-modal analytical imaging of diverse archaeal-bacterial consortia. The project will greatly improve understanding of the diverse syntrophic associations involved in the anaerobic oxidation of methane, a process which consumes ~80% of methane in anaerobic sediments preventing its release into the water column, and ultimately the atmosphere.
• Krishna Niyogi, University of California, Berkeley, and co-PI Sabeeha Merchant, University of California, Los Angeles will conduct an integrated systems analysis of trophic transitions (transitions in nutrient sources, e.g. from inorganic to organic) in Chromochloris zofingiensis, an emerging model green alga that is one of the highest producers of the preferred lipid precursor for biofuel products, triacylglycerol (TAG), making it a promising biofuel feedstock. Using transcriptomic, proteomic and metabolomic analyses, together with fluorescence, electron and mass spectrometry based imaging, this effort will gain new understanding of how genomic information is translated into functional capabilities to enable alteration of the genes in this green alga for sustainable biofuel production.
• David Walsh of Concordia University and co-PI Celine Gueguen of Trent University are leading a study to obtain a molecular-level understanding of terrestrial organic matter transformations by microbes in the rapidly changing Arctic Ocean. The goal is to provide fundamental knowledge on pathways and mechanisms that influence biogeochemical processes and the impact of permafrost thaw on Arctic marine ecosystems.
• Michael Betenbaugh of Johns Hopkins University and Co-PI Karsten Zengler of the University of California, San Diego are developing an in silico model, in combination with transcriptomics, metabolomics and fluxomics characterization, that will reveal the molecular interactions in phototroph-heterotroph co-cultures. Understanding interactions in these types of populations will be critical to the wider use of co-culture systems for a range of applications including biofuels and bioproducts production.

• Roland Hatzenpichler, Montana State University, will conduct a large- scale characterization, by combining activity-based cell sorting, super resolution fluorescence and isotopic imaging, and genomic sequencing to study “microbial dark matter” using a model system comprised of a group of microbes found in Yellowstone National Park hot springs. By developing a highly parallelizable and adaptable workflow, he hopes to address two long-standing problems in microbial ecology: identifying the factors driving metabolic activity of microbes in their natural environment, and determining the substrates that are fueling that activity.
• Jay Keasling of Lawrence Berkeley National Laboratory (Berkeley Lab) and co-PI Michael Jewett from Northwestern University will exploit JGI’s DNA synthesis capabilities and EMSL’s molecular characterization expertise to explore the range of potential activities of diverse polyketide synthases, or PKSs. They plan to identify and apply underlying principles via machine learning to improve recombinant PKSs with high efficiency so they can be readily targeted for producing many different biofuels and high-value bioproducts. They also hope to inform the scientific community about the rational design of PKSs to enable more rapid use of these incredibly flexible and important enzymes.
• Lisa Tiemann from Michigan State University and co-PI Maren Friesen of Washington State University want to develop new tools to characterize root exudate chemistry of the bioenergy crop switchgrass, growing in marginal land soils, to increase understanding of plant-microbe interactions, especially regarding nitrogen cycling. They plan to couple DNA stable isotope probing and metagenomic sequencing with compound specific analysis of isotopically labelled root exudates to better explore the connections between plant root exudate chemistry and the dynamics of the rhizosphere microbiome. Their goal is to improve existing knowledge of bioenergy cropping systems to better inform management decisions regarding productivity, efficiency and sustainability of these systems.

• Jennifer Bowen of Northeastern University and co-PI Jonathan Sanderman of Woods Hole Research Center will combine high resolution organic matter characterization and microbial meta-omics to assess the effects of nutrient loading on salt marsh carbon sequestration. They will analyze sediment samples from three-meter-deep cores, where the deepest sediments are approximately 3000 years old, that have been collected as part of a multi-investigator project studying the long-term nutrient enrichment of salt marshes at the NSF initiated Plum Island Ecosystem Long Term Ecological Research site. Their goal is to obtain new insights into the forces that control carbon storage in salt marsh sediments and how exposure of those sediments to a critical global change driver, nitrate enrichment, alters carbon storage capacity, a critical ecosystem service.
• Jennifer Talbot of Boston University with co-PI Hui-ling Liao of University of Florida plan to use metagenomic and metatranscriptomic sequencing from JGI, as well as metabolomic, metaproteomic and soil organic matter chemistry (i.e. “humeomic”) analyses from EMSL, to obtain mechanistic understandings of microbial interactions that can alter the emergent carbon cycling properties of an ecosystem. Specifically, they hope to understand how ectomycorrhizal fungi –critical members of the forest microbiome – link the cycling of carbon and nitrogen at the molecular scale and the consequences for these element cycles at the ecosystem scale.
• Eoin Brodie and co-PI Nicholas Bouskill, both of Berkeley Lab, will study the synchronization of microbial and plant phenology in a mountainous watershed to understand its importance for nutrient retention under changing hydrologic regimes. This study will provide new and extensive field and laboratory observations of the activation of microbial metabolic potential beneath the snowpack during winter and during the snowmelt period, as well as advanced characterization of the chemistry of carbon and nutrient transformations and assimilation by microorganisms and vegetation in response to earlier snowmelt timing.

• Melanie Mayes and co-PI Chongle Pan, both of Oak Ridge National Laboratory, will use the omics capabilities at DOE JGI and EMSL to link microbial function for decomposition of soil organic matter (SOM) to substrate organic chemistry to improve process representation in a soil organic carbon and phosphorus (P) cycling model. The project will apply the Microbial Enzyme Decomposition (MEND) model to utilize specific enzymes and microbes to generate SOM decomposition pools. Their results will enable improved predictions of the proportion of carbon dioxide and methane gas fluxes from tropical wetlands.
• Steven Hallam of Canada’s University of British Columbia plans to use ‘omic studies spanning multiple levels of biological information (DNA, RNA and metabolites) to monitor and recapitulate bacterial biomass deconstruction processes in synthetic microbial communities constructed from environmental genomic libraries. The results will help determine the functional capacities of bacterial networks driving lignin transformation in the environment; harnessing this information will result in the design of whole cell biocatalysts that improve biorefining process streams.

 

A full list of accepted projects under the DOE JGI-EMSL FICUS initiative is available at: https://www.emsl.pnl.gov/emslweb/ficus-projects-doe-jgi-and-emsl. Questions regarding the FICUS initiative may be directed to the EMSL User Support Office, 509-371-6003, or the DOE JGI Program Office.

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EMSL, the Environmental Molecular Sciences Laboratory, is a DOE Office of Science User Facility that leads molecular-level discoveries that translate to predictive understanding and accelerated solutions for national energy and environmental challenges. Research enabled by EMSL’s capabilities supports research in atmospheric aerosols, biofuels and bioproducts, biogeochemical processes, subsurface science, catalysis, and energy materials. EMSL helps users address challenges in a wide range of research including synthesis, characterization, theory and modeling, dynamic properties, and environmental analysis.