Following are the approved user proposals for fiscal year 2017, including CSP, CSP Small-Scale, Synthesis, JGI-EMSL FICUS, and JGI-NERSC FICUS.
Community Science Program (CSP)
Small-Scale Microbial/Metagenome
| PI | Affiliation | Project Description |
| Alvarez-Cohen, Lisa | University of California, Berkeley | Unraveling functional dynamics and regulation crucial for the stability of an anaerobic ammonium oxidizing (anammox) community via community metatranscriptomics and 16S rRNA sequencing |
| Andras, Jason | Mount Holyoke College | The effect of ecological restoration on the structure and function of soil microbial communities in coastal wetlands |
| Averill, Colin | Boston University | Molecular mechanisms of ectomycorrhizal interactions that stabilize soil carbon |
| Bell, Terrence | Pennsylvania State University | How interactions with soil microbiomes impact the survival and activity of a nitrogen-fixing soil surface consortium |
| Bowen, Jennifer | Northeastern University | Building a foundation for understanding carbon and nitrogen cycling in microbially diverse salt marsh sediments |
| Chistoserdova, Ludmila | University of Washington | Probing the role of electron transfer redox mediators in methane-oxidizing communities |
| Coleman, Maureen | University of Chicago | Teasing apart coexisting picocyanobacteria and their contributions to biogeochemistry |
| Cotner, James | University of Minnesota-Duluth | Translating stoichiometric diversity into genomic diversity: What elements are responsible for variability in bacterial biomass stoichiometry? |
| Craft, Chris | Indiana University | Microbial activity and community composition in a tidal freshwater marsh in response to sea level rise and saltwater intrusion: A field manipulation |
| D’Agostino, Paul | Technische Universität München (Germany) | Genome mining and synthetic biology of underrepresented organisms in the search for novel (bio-)chemistry |
| Dove, Nicholas | University of California, Merced | Immediate effects of prescribed fire on microbial communities, decomposition, and nitrification |
| Dynarski, Katherine | University of California, Davis | Microbial community composition and function throughout decomposition in temperate forests across a bedrock nitrogen gradient |
| Freedman, Zachary | West Virginia University | Assessing the recovery of microbial traits in bioenergy crop agroecosystems on reclaimed surface mines |
| Gutierrez, Tony | Heriot-Watt University (UK) | Genomic reconstruction to resolve the functional potential of oil-degrading bacteria in deep and surface waters of the Faroe-Shetland Channel |
| Hatzenpichler, Roland | Montana State University | Genomic characterization of cosmopolitan sediment-dwelling archaea hypothesized to be involved in anaerobic carbon cycling |
| Hatzinikolaou, Dimitris | University of Athens (Greece) | Genome sequencing of lignin and cellulose degrading isolates from Greek habitats |
| Hunt, Dana | Duke University | Seasonal and disturbance-related alterations in the biogeochemical cycling of estuarine carbon |
| Jensen, Paul | University of California, San Diego | Extracellular electron shuttles: A mechanism for obligate aerobes to survive anaerobic conditions |
| Kelly, Charlene | West Virginia University | Quantifying ecosystem changes following American chestnut restoration: From microbes to ecosystem function |
| Konstantinidis, Konstantinos | Georgia Institute of Technology | Real-time identification of horizontal gene transfer events using series metagenomes |
| Lebeis, Sarah | University of Tennessee | Characterizing functional chemotaxis receptors in different root zones |
| Lindemann, Steve | Purdue University | Identifying genome properties and environmental conditions governing the assembly of stable cyanobacterial-heterotroph consorta |
| Lindow, Steven | University of California, Berkeley | Trait-driven assembly of the leaf surface microbiome in an agricultural context |
| Maresca, Julia | University of Delaware | Light-induced gene expression in cosmopolitan freshwater Actinobacteria |
| Martens-Habbena, Willm | Fort Lauderdale Research and Education Center | Biogeochemistry of carbon and nitrogen cycling in subsiding subtropical soils |
| Mavrodi, Dmitri | University of Southern Mississippi | Transcriptomic responses of beneficial Pseudomonas rhizobacteria to Brachypodium root exudates |
| McMahon, Katherine | University of Wisconsin-Madison | Reference Genomes for Freshwater Bacteria – Alpha- and Beta-Proteobacteria |
| Müller, Henry | Graz University of Technology (Austria) | Elucidating the relevance of DNA methylation of strain-specific plant-microbe interactions |
| Myroid, David | Oregon State University | The metagenome of DIRT: How 20 years of altered carbon inputs have altered the functional potential of soil microbial communities |
| Oliveira, Rafael | State University of Campinas (Brazil) | Unravelling microbial communities associated with native plant species from P-impoverished soils of a global biodiversity hotspot |
| Ottesen, Elizabeth | University of Georgia | The genetic drivers and metabolic consequences of pelagic stream microbial community assembly |
| Pan, Chongle | Oak Ridge National Laboratory | Multi-cycle Selection of Sorghum Microbiomes for Biological Nitrogen Fixation |
| Richardson, Ruth | Cornell University | Metatranscriptomic responses of a butyrate-to-methane enrichment culture to sulfate and iron availability: elucidating the identities and strategies of metabolically versatile sulfate and iron reducing populations |
| Samuel, Buck | Baylor College of Medicine | Genomic analyses of the natural microbiome of Caenorhabditis elegans |
| Schmer, Marty | USDA-ARS | Nitrogen effects on soil microbial communities and soil organic carbon in a resilient bioenergy cropping system |
| Seyfferth, Angelia | University of Delaware | Impacts of rice cultivation practices on carbon and iron cycling: Unraveling functional microbial diversity in rice paddy rhizocompartments subject to silica-rich rice residue amendment |
| Valentine, David | University of California, Santa Barbara | Metagenomic reconstruction of novel archaeal genomes from energy-limited hypersaline sediments. |
| Veley, Kira | Donald Danforth Plant Science Center | Epigenetic and transcriptional changes that occur in populations of bacteria colonizing plant hosts. |
| Venturi, Vittorio | International Centre of Genetic Engineering and Biotechnology (ICGEB) (Italy) | Sequencing of a set of identified and characterized rice bacterial endophytes |
Synthesis
| PI | Affiliation | Project Description |
| Baker, David | University of Washington | Large scale de novo enzyme design for next generation metabolic engineering |
| Beisel, Chase | North Carolina State University | Profiling the functional diversity of CRISPR-Cas systems using cell-free transcription-translation systems |
| Bokinsky, Gregory | Delft University of Technology (Netherlands) | Plug adapters for biology: Activating heterologous iron-sulfur enzymes to fully exploit Nature’s catalytic potential |
| Chistoserdova, Ludmila | University of Washington | Establishing lanthanides as new life metals and understanding redox properties of lanthanide enzymes in metabolism of methane |
| Dueber, John | University of California, Berkeley | Identification of novel D-altronate dehydratases in the enolase superfamily enabling pectin utilization in S. cerevisiae |
| Huang, Possu | Stanford University | New protein platform for secondary metabolite detection |
| Jewett, Michael | Northwestern University | Reframing combinatorial assembly and rapid prototyping of biosynthetic pathways with cell-free systems |
| Juminaga, Alex | LanzaTech, Inc. | Advancing understanding of acetogenic CO2 fixation by generating a gene knock-out library to accelerate design of commercial strains for autotrophic production of fuels and bioproducts |
| Mead, David | Varigen Biosciences | Metagenomic mining for next generation DNA polymerases |
| Philmus, Benjamin | Oregon State University | Linking cyanobacterial orphan biosynthetic gene clusters to secondary metabolites |
| Redding, Kevin | Arizona State University | Chloroplastic CO2 reduction to formate supporting synthetic carbon xation |
| Schmeing, Thomas | McGill University | Synthetic DNA to facilitate structural and functional understanding of nonribosomal peptide synthetase production of secondary metabolites |
| Scott, Kathleen | University of South Florida | Creation of constructs for functional expression of recently described inorganic carbon transporters widespread among sulfur- and iron-oxidizing chemolithoautotrophic microorganisms |
| Subramanian, Venkatamaranan | National Renewable Energy Laboratory | Molecular engineering of Trichoderma reesei for improved cellulase production |
| Welander, Paula | Stanford University | Expression of novel triterpenoid biosynthesis proteins from environmental metagenomes |
FY 2017 Facilities Integrating Collaboration for User Science (FICUS) JGI-EMSL Plans
FY 2017 Facilities Integrating Collaboration for User Science (FICUS) JGI-NERSC Plans
| Proposer | Affiliation | Project Description |
| Babbitt, Patricia | University of California, San Francisco | Environmental Profiling of Enzyme Superfamilies for Function Prediction |
| Baker, David | University of Washington | Eukaryotic Protein Structure Determination Using Metagenome and Metatranscriptome Sequence Data |
| Brooks, Phillip | University of California, Davis | Advancing Metagenome Classification and Comparison by MinHash Fingerprinting of IMG/M Data Sets |
| DeLong, Edward | University of Hawaii at Manoa | Quantitative Analyses of Naturally Occurring Small RNAs in Global Metagenomic and Metatranscriptomic Datasets |
| Hallam, Steven | University of British Columbia (Canada) | Charting Global Biogeochemical Cycles using Fast Phylogenetic Mapping of Functional Anchor Genes |
| Konstantinidis, Konstantinos | Georgia Institute of Technology | Assessing Microbiomes at the Individual Population Level: Tool Development and Applications to Soil Carbon Cycling |