Following are the approved user proposals for CSP, FICUS JGI-EMSL and CSP New Investigator calls.
| Proposer | Affiliation | Proposal Title | Proposal Description |
| Blonder, Benjamin | University of California at Berkeley | Identifying the genetic basis of complex phenotypes and climate adaptation in quaking aspen (Populus tremuloides) | Quaking aspen (Populus tremuloides) is the most widely-distributed tree species in North America, and is one of the iconic species of the West. The species has high economic, ecological, and bioenergy value. This project is a collaboration between scientists in the USA, Mexico, and Canada. It will generate a complete genome for the species, and will also generate sequencing data for thousands of individuals from across the species range, including relictual southern populations whose genetic information may be critical for climate adaptation and climate-smart management of this species. |
| Chen, Jay | Oak Ridge National Laboratory | Leveraging Natural Variations to Uncover Regulatory Mechanisms Governing Differential Biosynthesis of Terpenes in Populus | We propose to perform transcriptomics sequencing of leaf buds in 500 Populus trichocarpa natural variants to enable expression quantitative trait nucleotide mapping to identify genetic elements regulating terpene chemistry and bud phenology. The proposed research can provide new strategies for engineering terpene metabolism to produce terpenes as advanced biofuels and valuable bioproducts. The proposed research can also lead to new insights into the control of bud dormancy and enable new approaches for genetic engineering of dormancy-associated traits to enhance biomass production. |
| DeAngelis, Kristen | University of Massachusetts Amherst | Soil microbial stress-biogeochemistry metabolism adapts under climate change across seasons | Air temperatures are rising, winter snowpack is shrinking, and soil freeze/thaw events are increasing in high-latitude ecosystems. This research is designed to improve mechanistic understanding of how the combined stress of warming during the growing season and soil freeze/thaw cycles in winter impacts microbial biogeochemistry traits in northeastern forests. Our work integrates metagenomics, metatranscriptomics and metabolomics to study soil microbial communities at the Climate Change Across Seasons Experiment (CCASE) at the Hubbard Brook Experimental Forest (HBEF). |
| Dinneny, Jose | Stanford University | Understanding the mechanisms of metabolic exchange in the rhizosphere | The root system of plants represents a complex interface for microbial interactions. While much progress has been made in understanding specific symbiotic interactions between plants and microbes, much less is understood regarding the basic support functions that roots play in sustaining carbon delivery to the rhizosphere or in the functions that specific cell types in the root play in mediating such interactions. Here we utilize a genetic approach and a synthetic biology approach to manipulate the interfaces that root microbes interact with and the availability of key nutrients that likely determine the selective pressures that microbes experience within the rhizosphere. The use of JGI resources will allow us to better understand how these genetic manipulations ultimately affect the metabolic and transcriptional pathways that mediate such interactions. |
| Humphries, Jacqueline | Amyris, Inc. | A high-throughput, multi-omics approach to identifying new gene expression modules for industrial bioproduction in alternative fermentation hosts | Amyris is a company that engineers microbes for sustainable conversion of plant biomass into valuable molecules. We propose a high-throughput, sequencing-driven approach to designing new genetic tools for engineering less well-studied, yet industrially attractive microbial species. This work will, in alignment with the DOE mission, accelerate bioproduct development by expanding the tools we have to engineer a broader range of microbes and improve our understanding of physiology in these species of major interest to the scientific community. |
| Krasovec, Marc | National Center for Scientific Research (CNRS) | Phytoplankton spontaneous mutation rate | Mutations are the ultimate source of diversity and define the adaptive potential of species. The aim of this proposal is so to understand the evolution of the mutation rate and its variation with environmental changes in phytoplankton species. This will bring essential knowledge on phytolankton evolution and improve the genomic ressources by giving the map of genomes diversification. |
| Leewis, Mary-Cathrine | Agriculture and Agri-Food Canada | Life in Ancient Permafrost: using an isotope and ‘omics approach to determine how microorganisms survive and metabolize in subzero temperatures across geologic time | Permafrost is a layer of frozen soil that underlies about 25% of the Northern Hemisphere and contains almost half of the Earth’s soil carbon. Permafrost soils host a diverse microbial community however, we do not understand if and how those microorganisms survive and metabolize below freezing for millennia. We conducted a stable isotope probing experiment to track the activity of microorganisms that are metabolically active (18O-labeled) and/or involved in decomposition of labile carbon (13C-labeled) in permafrost from an age gradient of 5,000 to 33,000 years old. |
| Lofgren, Lotus | Duke University | Functional roles of secondary metabolism in ectomycorrhizal fungi | Despite the importance of Ectomycorrhizal fungi, we know little about how they interact with complex consortia to establish and maintain symbiosis. Using constructed communities of the Ectomycorrhizal genus Suillus, we are investigating the role of fungal secondary metabolites in 1) host-interfacing and mycorrhization, 2) competition via the production of antimicrobials and antifungals, and 3) the regulation of biotic and abiotic stress tolerance, using genome-informed transcriptomics and metabolomics. |
| Majumder, Erica | University of Wisconsin-Madison | Characterization of plastic deconstruction metabolic pathways in microbial communities derived from enrichments of plastic debris in soil and landfill samples | We propose the use of -omics to understand plastic-metabolizing microbial communities inhabiting soil and landfill debris samples. This project is related to the CSP FY2023 area of Biofuels, Biomaterials and Bioproducts because it implicates nutrient cycling in environmental microbiomes, i.e., plastic degradation in soil and landfill communities. This fits into the DOE mission for bioenergy by enabling sustainable processes for plastic degradation/upcycling and understanding plastic degradation in environmental microbiomes. |
| Nagy, Laszlo | Biological Research Centre of the Hungarian Academy of Sciences | A genome-wide view of the evolution of the most widely used lignocellulose-degrading Basidiomycota | Wood-decay fungi are primary contributors to the global carbon cycle by reintroducing organic carbon sequestered in plant biomass into the atmosphere. In this project we will analyse genomes and interrogate lignocellulose degradation of two of the most widely cultured groups of fungi worldwide, Agaricus spp. (button mushrooms) and Pleurotus spp. (oyster mushrooms). We anticipate that this project will contribute to a better understanding of plant biomass degradation by fungi and to harnessing this potential for transitioning to a greener and circular economy. |
| Nunn, Brook | University of Washington | Investigating the interactions of a phytoplankton community and its microbiome on a 4-hour timescale to reveal emerging and predictive properties across an algal bloom and bust cycle | Marine phytoplankton generate ~ 50% of the world’s oxygen. Understanding what initiates and terminates phytoplankton blooms is critical to generating accurate global carbon models for forecasting Earth’s future. Phytoplankton evolved in association with bacteria and their interactions potentially control and predict bloom dynamics. Here, we plan to leverage the first ever sample set of bacteria and phytoplankton collected every 4 hours across an entire phytoplankton bloom (from initiation to termination) to identify community interactions and molecular-level controls on algal bloom events. |
| Ohm, Robin | Utrecht University | Functional genomics of the lignocellulose-degrading fungus Schizophyllum commune: regulatory networks, sustainable fungal materials and fungal defense | Mushroom-forming fungi are among the most potent lignocellulose-degraders. In this project, we will study their regulatory network and the proteins they use to defend against competitors. Moreover, we use these fungi to make sustainable materials, such as leather-like and foam-like compounds. We will sequence several strains with properties that are beneficial to these fungal materials. |
| Pawlowska, Teresa | Cornell University | Unraveling the mechanisms behind the role of endosymbiotic bacteria in community structuring and evolution of Mucoromycota fungi | The goal of the project is to understand the mechanism allowing bacteria to live and persist inside cells of soil fungi over many generations. In addition, we propose to test several predictions concerning the roles of these symbiotic bacteria in: (1) diversification of their fungal host populations into new species and (2) structuring of ecological communities of their hosts. Our focal fungi include, among others, molds causing food spoilage and human diseases as well as beneficial associates of plant roots provisioning their hosts with mineral nutrients. |
| Saleska, Scott | University of Arizona | Primary succession of plant and microbial life: untangling inter-organismal interactions on a model early-successional landscape | We are investigating how biogeochemical cycles emerge from small-scale hydrological, geochemical, ecological and evolutionary processes interacting to create emergent landscape-scale terraformation. We focus on how microbial composition and function changes, in interaction with plants, as biological complexity increases: from simple microbial communities (including microbial crusts), to non-vascular plants (mosses without roots), to vascular plants with roots and sophisticated hydraulic architectures. This work thus illuminates pressing issues such as landscape restoration and carbon storage. |
| Wakao, Setsuko | Lawrence Berkeley National Laboratory | Evolutionary genomics of biomineralizing stramenopiles with impacts on global carbon cycling and biogeochemistry | Diatoms are an important group of oceanic algae that make intricately patterned silica cell walls and are responsible for 40% of the net photosynthesis that occur in the oceans making them a critical player not only in carbon cycling but also elemental cycling (Si) in the environment. In this work, we will sequence and compare the genomes and transcriptomes of algae from several related groups that produce silica biominerals to discover genes important for silica biomineralization. |
| Weimer, Bart | UC Davis | The role of carbohydrate and nitrogen fixation for sustainable plant microbiome interactions | The atmosphere is comprised of approximately 78% nitrogen, but crops cannot use this form of nitrogen directly. They require a microbial partner to convert atmospheric nitrogen into a biologically accessible form of nitrogen for use in growth. Legume crops, such as soybean and alfalfa, do this via an endo-symbiotic relationship with a bacterium. However, production of the major cereal crops relies on synthetic fertilizer. Identification of cereal crops with the ability to fix atmospheric N2 has been the “holy grail” of crop biologists for decades since this trait would potentially alleviate the need for synthetic fertilizers resulting in economic and environmental benefits. |
| Wilbanks, Elizabeth | University of California Santa Barbara | The role of population distributed immunity in the eco-evolutionary dynamics of bacteria and phage | In our proposal, we are looking how two different “bacterial immune systems” – known as CRISPR-Cas and diversity generating retroelements – evolve in natural populations of salt marsh bacteria. Our work will help us better understand how the battle between microbes and their phage unfolds, make better predictions about the future climate, and engineer new ways to produce renewable fuels and green chemicals. |
| Wilhelm, Steven | University of Tennessee, Knoxville | Direct resolution of virus-host interactions using bulk single-celled labeling and application to deep community metatranscriptomics | The project takes a recently developed approach that allows for single-cell resolution of hundreds to thousands of cells within a mixed community and uses it to ask which cells in nature are infected by viruses. Moreover, along with determining who is infected, the results will demonstrate which type of virus(es) are infecting which types of cells and provider insight into how the biochemistry and metabolism of all these different cell types change when infected. The end product of this research will provide new insight into how viruses shape the biogeochemistry of various ecosystems. |
| Wolfe, Marnin | Auburn University | Clover Genomics for Sustainable Bioenergy Mixtures | Adverse impacts of agriculture and climate change makes sustainable and economical bioenergy and food production urgently needed. Legumes offer a way to reduce fertilizer inputs because of their ability to biologically fix atmospheric nitrogen. In this project, we are developing genomic resources for clovers, genus Trifolium, one of the most important and broadly adapted legume genera. By bringing clover genomics up-to-par with bioenergy grasses, we seek a route forward for breeders and geneticists to develop bioenergy intercrops that produce more with less environmental input and expense. |
FY 2023 Facilities Integrating Collaboration for User Science (FICUS) JGI-EMSL Proposals
| Proposer | Affiliation | Proposal Title | Proposal Description |
| Bhatnagar, Jennifer | Boston University | Linking soil microbial stress metabolism to watershed biogeochemistry under climate change across seasons | With rising temperatures stemming from climate change, winter snowpack is shrinking and soil freeze and thaw events are increasing in high-latitude ecosystems. The project aims to improve understanding and model representation of the effects of warming during the growing season and soil freeze/thaw cycles in the winter for belowground biogeochemical cycles in northeastern forests. |
| Blazewicz, Steve | Lawrence Livermore National Laboratory | Parched: quantifying microbial ecophysiology and the fate of plant carbon during soil dry down | In seasonally dry grasslands, soil microbes bloom during the growing season, survive extremely dry periods, and rapidly mineralize soil carbon after the first rain in the wet season. This project will study the “dry-down” transition between seasons to determine how soil moisture shapes microbiome interactions, ecophysiological traits, and trait expression that affects the fate of cellular carbon. |
| Dalcin Martins, Paula | Radboud University (Netherlands) | Elucidating the impacts of viruses on soil organic carbon and greenhouse gas emissions from agricultural peat soils | Despite viruses being the most abundant biological entities on Earth, soil viruses are poorly characterized and their impacts on the biogeochemical cycles are vastly unquantified. The project aims to understand and quantify the impacts of viruses on soil organic carbon dynamics and carbon dioxide, methane, and nitrous oxide fluxes from agricultural peat soils. |
| Hug, Laura | University of Waterloo (Canada) | Microbial impacts on methane emission hot spots from municipal landfills | Landfills in Canada contribute 20% of methane emitted annually. Hot spots of methane emissions at landfills, associated with infrastructure that puncture cover soils, are unmonitored and not included in emissions models. This project aims to identify key factors and microbial populations that improve efficiency of methane oxidation to improve waste management protocols. |
| Hurley, Jennifer | Rensselaer Polytechnic Institute | Investigating the Effect of Negative Arm Protein Conformation on the Circadian Post-transcriptional Regulation of Cellulases | Fungal cellulases have the potential to be a major resource in biofuel production. Circadian timing over cellular metabolism could be tuned to maximize cellulase production. This project aims to map the clock “repressive complex” conformational shifts over the circadian day to analyze their effect on circadian regulation of biofuel production. |
| Kostka, Joel E | Georgia Institute of Technology | Metabolic exchange between Spartina alterniflora and sulfur chemosymbionts of the plant’s root microbiome | While root zones of coastal wetland plants are known hotspots for carbon and nutrient cycling, little is known about how plant–microbe interactions regulate coastal ecosystem function. The project aims to characterize the exchange of carbon and nitrogen that govern plant–microbe interactions in Spartina alterniflora—a dominant plant along the Gulf of Mexico and Atlantic coast. |
| Nelson, William C | Pacific Northwest National Laboratory | Environmental drivers of Inter-Kingdom metabolic interaction in marginal soil rhizosphere | Soils present a complex environment with numerous competing and cooperating populations that contribute to an overall ecosystem. The project aims to extend investigations into how soil moisture and seasonal changes affect carbon metabolism in marginal soils by quantifying and modeling the bacterial, archaeal, fungal, and viral community compositions and interactions in the rhizosphere. |
| O’Malley, Michelle | University of California, Santa Barbara | Deploying Advanced Molecular & Cell Free Expression Tools to Accelerate Characterization of Fungal Cellulosomes | Cellulosomes enable the breakdown of plant biomass into fermentable sugars. They are promising biotechnology tools to drive lignocellulosic conversion. While some sourced from fungi are known to host a wide diversity of enzymes, their diversity hampers structure determination via different methods. The project will pursue a two-pronged approach to enable structural characterization of fungal cellulosomes. |
| Umen, James | Donald Danforth Plant Science Center | Histone Methylomics and the Chromatin Landscape of Chlamydomonas reinhardtii | The genome for Chlamydromonas, a type of green algae, encodes 52 SET domain proteins, which are a family of lysine methyltransferases—enzymes that catalyze the transfer of methyl groups. Only two SET domain proteins have been biochemically characterized as Chlamydomonas. The project aims to identify and characterize methyltransferase domain enzymes in Chlamydomonas responsible for histone methylations. |
| van Munster, Jolanda | Scotland’s Rural College | Elucidating temporal-spatial patterns in lignocellulose degradation by morphologically distinct anaerobe gut fungi | Effective mechanisms to disassemble raw lignocellulose into simple sugars are required to advance biotechnology for biofuels and biomaterials. This project aims to understand how the powerful degradative mechanisms of anaerobic gut fungi affect the composition and structure of crude lignocellulose from wheat straw, a common biofuel feedstock. |