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    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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    Algae growing in a bioreactor. (Dennis Schroeder, NREL)
    Refining the Process of Identifying Algae Biotechnology Candidates
    Researchers combined expertise at the National Labs to screen, characterize, sequence and then analyze the genomes and multi-omics datasets for algae that can be used for large-scale production of biofuels and bioproducts.

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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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    Ian Rambo, graduate student at UT-Austin, was a DOE Graduate Student Research Fellow at the JGI
    Virus-Microbe Interactions of Mud Island Mangroves
    Through the DOE Office of Science Graduate Student Research (SCGSR) program, Ian Rambo worked on part of his dissertation at the JGI. The chapter focuses on how viruses influence carbon cycling in coastal mangroves.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

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    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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    Integrating JGI Capabilities for Exploring Earth’s Secondary Metabolome
    Natural Prodcast podcast: Nigel Mouncey
    JGI Director Nigel Mouncey has a vision to build out an integrative genomics approach to looking at the interactions of organisms and environments. He also sees secondary metabolism analysis and research as a driver for novel technologies that can serve all JGI users.

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Home › Our Projects › Approved User Proposals › Approved Proposals FY22

Approved Proposals FY22

Following are the approved user proposals for CSP and FICUS JGI-EMSL calls.

Community Science Program

Proposer Affiliation Proposal Title Proposal Description
Bowen, Jennifer Northeastern University Microbial controls on carbon cycling and storage resulting from salt water intrusion in tidal fresh, brackish, and saline marshes The push of saltwater into fresher reaches from sea level rise results in the replacement of plant communities with salt tolerant species. This global-scale disturbance disrupts established plant-microbe interactions, alters the structure of soil microbial communities, and fundamentally changes controls on soil carbon cycling and storage. The goal of this research is to characterize changes in the genetic potential of microbes that control soil carbon cycling and storage along salinity and elevation gradients in a river-estuary system with documented shifts in salt-tolerant wetland vegetation.
Colwell, Frederick Oregon State University Defining microbial functional capabilities across high-latitude, glacially impacted, wetland landscapes Globally, wetlands provide crucial ecosystem services but are stressed by a changing climate. We propose to study microbial communities, and their genes, that live on Alaska’s glacially dominated Copper River Delta. Home to iconic fish and waterfowl, the Delta hosts microorganisms dependent on glaciers and the nearby ocean, and that cycle carbon and iron in the wetland sediments. We will study how these microbes cycle carbon, the factors that control their presence, and the relationship of microbes to glacier proximity yielding data broadly useful for studying high latitude wetlands.
de Vries, Ronald Westerdijk Fungal Biodiversity Institute (Netherlands) Mining the unknown part of fungal genomes by combining machine learning with multi-omics and functional characterization Developing efficient processes for plant biomass utilization (e.g., for production of food and feed, pulp and paper or biofuels) remains challenging due to the structural complexity and variability of this biomass. This project aims to identify a large number of these missing genes in five well-studied reference fungi to get a more complete picture of the overall process of plant biomass conversion and the diversity in approaches fungi use to achieve this. The results will provide a more complete picture of the genes involve in plant biomass conversion and will enable more efficient strain engineering to obtain the next generation of fungal cell factories for biotechnology.
DeAngelis, Kristen University of Massachusetts Amherst Using genomics to understand microbial adaptation to soil warming Healthy soils require a diverse and abundant microbial community. The earth’s climate is warming, and long-term warming has many ecosystem effects including increased greenhouse gas emissions and accelerated soil carbon loss. Our recent research shows that chronic warming is irreversibly altering how microbes interact with their environment, potentially accelerating soil carbon loss. These irreversible effects should have genetic or genomic signatures, and our proposal is to combine genome sequencing with metabolomics of bacteria and fungi to describe these changes.
Dick, Gregory University of Michigan Metagenomic and metatranscriptomic insights into the role of microbial interactions in the cycling of carbon and nutrients during toxic cyanobacterial bloomse The proposed project strongly aligns with DOE’s interests and mission to study inter-organism interactions and microbes and communities involved in elemental cycling and secondary metabolites. Although microbial processing of biogeochemistry in lakes plays a substantial role in water quality, which is threatened under continued eutrophication and climate change, the microbial communities underpinning these processes have been understudied and thus controls on the fate of carbon and the production of greenhouse gases are not well understood.
Gawryluk, Ryan University of Victoria (Canada) Adapting ultra-low input long read sequencing methods to predatory algae in a complex culture system Recently, a completely new group of species were discovered that belong to the same eukaryotic supergroup as plants, along with green and red algae. Surprisingly, these organisms – known as Rhodelphis – are the opposite of what one would expect of a plant relative: they do not harness energy through photosynthesis, but actively hunt other microbial cells. Elucidating the gene content and structure of Rhodelphis will have wide-ranging implications for the origin and evolution of plants, including the genomic consequences of losing photosynthesis.
Jesus, Edeson EMBRAPA (Brazil) Unveiling the functional potential of microbial communities of the Amazon forest floor through metagenomics The soil organic layers play an essential role in the tropical forest’s nutrient cycling. In this project, we will use metagenomics to understand how the microbial interactions in these layers contribute to diversity estimation and element nutrient cycles in a scenario still little explored. A forest in the Eastern Amazon and an adjacent pasture will be our model systems. We aim to promote awareness about the importance of preserving the Amazon forest and point to alternative ways of taking advantage of its biodiversity in a context in which it has been threatened by increasing deforestation.
Krukenberg, Viola Montana State University Exploring the microbial methane cycle in terrestrial geothermal environments Microbially mediated methanogenesis and methane oxidation are key processes in the global carbon cycle and control the atmospheric levels of the potent greenhouse gas methane. This project will explore the microbial methane cycle in terrestrial geothermal environments. We will use metagenome, metatranscriptome and single cell genome sequencing to identify novel methanogens and characterize their taxonomic and functional diversity, metabolic activity and impact on biogeochemical element cycles.
Mengiste, Tesfaye Purdue University Whole genome resequencing of 400 sorghum core subset germplasm collection Availability of whole genome sequences are critical for crop improvement. Identification of genets that control critical traits is facilitated by knowledge on the variations in DNA sequences of diverse plant resources. Sorghum bicolor is a plant with high potential for biofuel production. This proposal is to sequence diverse set of sorghum germplasm that may carry important traits including high biomass, high sugar, tolerance to stress such as drought and cold. This work will expedite the discovery of genes regulating processes in stress tolerance and biomass production.
Myburg, Alexander University of Pretoria (South Africa) Eucalypt genomic resources for woody biomass production and carbon drawdown We will perform large-scale genome sequencing of a group of fast-growing tree species (eucalypts) that are a sustainable source of carbon and energy rich biomass globally, with high relevance to the DOE mission in sustainable biofuels and bioproducts. Eucalypts are widely grown as feedstocks for lignocellulosic and other biorefinery products. Their prevalence in the vast, carbon dense woodlands of Australia and their high potential for landscape restoration and new afforestation for carbon drawdown make eucalypts relevant to the DOE mission on global carbon cycling.
Nelson, Andrew Boyce Thompson Institute (Cornell University) Molecular basis of natural rubber biosynthesis in Parthenium argentatum (Guayule) This proposal represents a joint effort by private and public research interests to understand and enhance the rubber biosynthesis pathway (RBP) in Parthenium argentatum (guayule), a drought-tolerant shrub cultivated in the American Southwest. Guayule is truly a multi-use commodity crop; guayule also accumulates high levels of resins with commercial application and is an ideal feedstock for biofuel generation. By developing genomic resources and understanding how the environment influences the RBP, we hope to unlock guayule’s full potential as a renewable source of plant-based products.
Preston, Jill University of Vermont Development of the grass subfamily Pooideae as a powerful comparative genomics model for temperate crop and biofuel development The use of warm-season grasses for the harvest of renewable biofuels is greatly contributing to local demand for renewable energy sources. However, effort is still required to diversify these crops in order to (1) deal with increasingly variable environments globally, and (2) develop perennial biofuel species that are carbon neutral. Here, we develop genomic resources in cool-season grasses to decipher key differences between annual and perennial species. This will allow for the discovery of genes that will enhance sustainable biomass, and add to burgeoning knowledge on plant diversification.
Purcell, Alicia Northern Arizona University Quantifying the ecophysiology of growing microbes responding to warming along a productivity gradient of the Marr Ice Piedmont Glacier, West Antarctic Peninsula The Antarctic Peninsula is warming, expanding terrestrial environments. Glacier forefield ecosystems are home to diverse microbial communities that are responsible for carbon and nutrient cycling and plant development. Using metagenomics enabled qSIP, metatranscriptomics, and metabolomics, we aim to understand how warming impacts in situ microbial growth rates and activity. Our project will quantify and elucidate the metabolism of individual microbes that facilitate carbon and nutrient processes in a climate sensitive ecosystem.
Read, Betsy Cal State University San Marcos The Haptophyte Genome Project Haptophyte microalgae contribute a major portion of the world’s photosynthetic activity with more than 400 species. They inhabit freshwater and marine ecosystems and exhibit remarkable morphologic and metabolic flexibility. They are able to produce spectacular calcium carbonate cell coverings, delicate organic scales, powerful toxins, unusual lipids; and can also elicit predatory tendencies, form massive blooms, be widely distributed, and thrive in harsh environments. To unravel the genomic underpinnings of these incredible algae we will sequence the genomes of 35 diverse species.
Roth, Melissa UC Berkeley Deciphering the role of master regulators in carbon flow for enhanced lipid production Photosynthetic organisms are promising sources for sustainable solutions to help meet the growing global needs for energy and products, but there are currently practical limitations. Our research focuses on master regulators in algae that naturally produce high amounts of the preferred biofuel precursor triacylglycerols (TAG), and seeks to understand how carbon is converted into TAG production. Through identifying essential factors that are critical for high TAG, this research will enable redesign and engineering of algae and other organisms for improved biofuel and bioproduct production.
Vallon, Olivier Centre National de la Recherche Scientifique (France) A Chlamydomonas pan-genome The land plants that make up our forests and produce most of our food have tiny relatives, called green algae. Their study allows us to learn more on how plants carry out photosynthesis, the only way nature can withdraw CO2 from the atmosphere, to build living matter. Among these inconspicuous organism, the unicellular Chlamydomonas reinhardtii is a key model organism, because of its ease of manipulation. It has been used in laboratories since 1945 and has allowed many discoveries. Our project will explore the natural biodiversity of this species and discover new functions for its many genes.
Wilkins, Michael Colorado State University Impacts of changing wildfire regimes on soil microbiome succession and function This work aims to understand how soil microbiomes in fire-adapted ecosystems (montane coniferous forest, chaparral shrubland) respond to low and high severity wildfire. While studies have reported changes in the composition of soil microbiomes following wildfire, here we will determine how these shifts affect carbon and nitrogen cycling in burned soils. We will access recently burned soils in California and Colorado, and use novel “pyrocosm” apparatus. Combined metagenomic, metatranscriptomic, and metabolomic analyses will offer unique insights into soil microbiomes in burned ecosystems.

FY 2022 Facilities Integrating Collaboration for User Science (FICUS) JGI-EMSL Proposals

Proposer Affiliation Proposal Title Proposal Description
Baldrian, Petr Institute of Microbiology of the Czech Academy of Sciences (Czech Republic) Effects of plant functional diversity on the ecosystem responses to forest harvesting Forests maintain the global carbon balance and play an important ecological role in raw materials. This project will analyze and compare the functioning of forest soil microbiomes following various tree harvesting schemes. Understanding these effects is critical because harvested forest stands may become temporary carbon sources through greenhouse gas emissions.
Blenner, Mark University of Delaware Plastic Degrading Microbial Communities from Insect Larvae Guts Insect microbial consortia degrade plastics more rapidly than microbial isolates. While several bacterial members of these communities have been isolated, the full set of microbes and their specific pathways responsible for biodegradation have not been elucidated. This research will examine the role for microbial interactions in plastic degradation.
Kroeger, Marie Los Alamos National Laboratory Temporal Dynamics of Microbial Traits – Driving Divergent Patterns of Carbon Flow During Surface Litter Decomposition Climate change projections show that microbially driven surface litter decomposition rates will increase with rising temperatures as more carbon is released into the atmosphere and less is stored in soils. This project will build a foundation of research to identify microbial effect traits that create substantial variations in carbon cycling.
Master, Emma University of Toronto (Canada) Functional and structural analysis of microbial expansin-related proteins that transform lignocellulosic biomass Bringing together functional genomics, structural biology, and materials science techniques, this project will evaluate the untapped potential of microbial expansin-related proteins on lignocellulose organization for production of bio-based chemicals and materials.
Merchant, Sabeeha University of California Berkeley Systems analysis of a microbial phototroph-heterotroph symbiosis Phytoplankton rely on the sun for energy but change their metabolic strategy at night. This project will exploit a system with reduced complexity, established reference organisms with well-described physiologies, and a suite of methodologies to improve understanding of trophic interactions and diel patterns.
Meredith, Laura University of Arizona Belowground genotype-phenotype controls on nitrogen use efficiency of a sorghum bioenergy crop Plant-microbe interactions drive nitrogen transformations in soil. This research will address critical barriers to observing rhizosphere nitrogen transformations in real-time by using below-ground measurements of volatile metabolites. The project will provide a detailed understanding of inter-organismal interactions that drive nitrogen transformations and loss in soils.
Miesel, Jessica Michigan State University Investigating interactions between soil microbial communities and soil organic matter dynamics along climate and vegetation gradient Organic matter in soils is critical to nutrient cycling and climate change. As the primary agents of decomposition, soil microbes are key to soil organic-matter. turnover. The project uses NEON soil samples, utilizing EMSL and JGI facilities to better understand the mechanisms controlling soil organic matter persistence within and across ecosystems.
Nuccio, Erin Lawrence Livermore National Laboratory Beneficial Partners: Context Dependent Mycorrhizal Resource Exchange in Bioenergy Cropping Systems The plant microbiome critically impacts plant health and productivity. This project will examine the resource exchange between Panicum hallii, a model grass species related to the bioenergy flagship plant switchgrass, and two mycorrhizal fungi, demonstrating how drought alters the benefit of fungi to the plant host.
Roden, Eric University of Wisconsin-Madison Tracking the degradation of fresh particulate organic matter in permeable riverbed sediments using FT-ICR-MS and metagenomic/ metatranscriptomic sequencing This project combines Fourier-transform ion cyclotron resonance mass spectrometry with metagenomic/transcriptomic sequencing and metabolomics to track the transformation and degradation of fresh, photosynthetically derived particulate organic matter in permeable riverbed sediments influenced by hydrologically-driven transport of solutes and colloidal particulate organic matter.
Ruff, Emil Marine Biological Laboratory Assessing the contribution of sediment bioirrigation to the oxidative removal of methane from a fluvial wetland Wetlands are the largest natural source of the greenhouse gas methane. This project investigates the microbiome of the insect burrows in freshwater sediments and studies aerobic methanotrophy in the burrow walls. The project will assess the path of methane carbon through the food web and the contribution of bioirrigation to methane removal.
Zheng, Jianqiu PNNL Leveraging a reciprocal soil transplant experiment to illuminate soil biogeochemical responses to moisture and salinity disturbance Coastal ecosystems are highly dynamic systems undergoing high rates of natural variability and anthropogenic changes. Researchers will use EMSL and JGI resources to attain molecular-level understandings of biogeochemical transformations that underpin emergent ecosystem functions, which can then be captured in process models to advance the predictability of the Earth system.
Zimmerman, Amy Pacific Northwest National Lab Resolving taxon-specific contributions to nutrient cycling in soil microbial communities through stable isotope enabled multi-omics Combining multiple omics approaches, this project will quantify taxonomically. resolved growth, substrate use, and functional allocation phenotypes, within diverse soil communities, in response to nitrogen source and temperature. This research will contribute to a framework for predicting how shifts in microbial community composition and physiology regulate nutrient cycling in soils.

 

 

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