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. |