Following are the approved user proposals for fiscal year 2016 including CSP, CSP Small-Scale, Synthesis, and FICUS projects.
FY 2016 Community Science Program (CSP) Plans
| PI | Affiliation | Project Description |
| Catcheside, David | Flinders University (Australia) | Acquisition of the sequestrate (truffle like) habit by basidiomycete macrofungi |
| Cooper, Elizabeth | Clemson University | Comparative transcriptomics of sweet and grain sorghum to understand the mechanism and timing of sugar accumulation in an important bioenergy crop |
| de Vries, Ronald | CBS-KNAW Fungal Biodiversity Centre (Netherlands) | Dissecting the different approaches of ascomycete fungi to degrade plant biomass |
| DeLong, Ed | University of Hawaii at Manoa | Going long and going deep: Comprehensive open ocean community single cell genome sequencing at the model open ocean time series study site, station ALOHA |
| Dollhofer, Veronika | Bavarian State Research Center for Agriculture (Germany) | Anaerobic fungi and assessment of their potential for biogas production |
| Duplessis, Sebastien | INRA (France) | Sequencing a reference genome for Phakopsora pachyrhizi, the fungal pathogen responsible for the Asian Soybean Rust |
| Francis, Christopher | Stanford University | Metagenomic characterization of nitrogen-cycling microbial communities impacting uranium release in the Upper Colorado River Basin |
| Hamelin, Richard | University of British Columbia (Canada) | Pathobiome of bioenergy trees |
| Hibbett, David | Clark University | Comparative and functional genomics of shiitake mushrooms: an international collaboration to resolve evolutionary relationships, substrate specificity, growth profiles, and routes to domestication in the amphi-Pacific genus Lentinula |
| Juenger, Tom | University of Texas at Austin | Exploring natural genetic diversity in switchgrass (Panicum virgatum) and its microbiome |
| Kalyuzhnaya, Marina | University of Washington | Systems level insights into methane cycling in arid and semi-arid ecosystems via community metagenomics and metatranscriptomics |
| Lorito, Matteo | University of Naples (Italy) | Supporting the development of microbial probiotics for grasses useful in sustainable bioenergy production |
| Martin, Francis | INRA (France) | 1KFG: Deep sequencing of ecologically-relevant Dikarya |
| Mayali, Xavier | Lawrence Livermore National Laboratory | Influence of phycosphere-associated bacteria on microalgal biofuel production |
| McMahon, Katherine | University of Wisconsin-Madison | Diel cycles of gene expression in oligotrophic, dystrophic, and eutrophic lakes to identify new gene functions and dissect carbon cycling metabolisms |
| Merchant, Sabeeha | University of California, Los Angeles | Comparative genomics and expression profiling of snow algae Chlamydomonas cribrum and Chloromonas nivalis |
| Niyogi, Kris | University of California, Berkeley | Functional genomics of photosynthesis in Chlamydomonas, JGI’s flagship alga |
| O’Malley, Michelle | University of California, Santa Barbara | Genomic basis for syntrophic interactions between anaerobic gut fungi and methanogenic archaea |
| Pires, J. Chris | University of Missouri-Columbia | Investigating the diversity of mycorrhizal fungi to understand the evolution and function of symbiosis with orchids |
| Plett, Jonathan | University of Western Sydney (Australia) | Exploring the genomic basis for the global diversification by the ectomycorrhizal genus Pisolithus |
| Poland, Jesse | Kansas State University | The Intermediate Wheatgrass Genome: A resource for understanding mechanisms of perenniality and accelerating the development of perennial crops |
| Rappe, Michael | University of Hawaii at Manoa | Metagenomics of viral and microbial communities inhabiting warm, anoxic fluids of the sediment-buried deep ocean crust |
| Schachtman, Daniel | University of Nebraska | Systems analysis of the physiological and molecular mechanisms of Sorghum nitrogen use efficiency, water use efficiency and interactions with the soil microbiome |
| Spatafora, Joey | Oregon State University | Genomics of the early diverging lineages of fungi and their transition to terrestrial, plant-based ecologies |
| Umen, James | Donald Danforth Plant Science Center | Single cell and population dynamics of chromatin across the diurnal cycle in the model alga Chlamydomonas |
| Walsh, David | Concordia University (Canada) | Microbial metagenomics of carbon cycling communities in northern aquatic ecosystems |
| Wrighton, Kelly | Ohio State University | Life in the extreme deep terrestrial subsurface: microbial metabolism before and after shale gas extraction |
Small-Scale Proposals |
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| Proposer | Affiliation | Project Description |
| Beman, J Michael | University of California, Merced | Metagenomics of methane production and oxidation in high altitude lakes of Yosemite National Park |
| Chistoserdova, Ludmila | University of Washington | Understanding methane cycling through manipulation of synthetic methane-oxidizing communities |
| Cullings, Ken | NASA Ames | Extreme endosymbiosis: An investigation into a unique fungal microbiome found in geothermal ecosystems in Yellowstone National Park and New Zealand |
| DeAngelis, Kristen | University of Massachusetts, Amherst | Expanding genomic diversity of terrestrial bacteria: linking genes to metabolism in the slower-growing members of forest soil bacterial communities |
| Kostka, Joel | Georgia Institute of Technology | The role of the Sphagnum microbiome in carbon and nutrient cycling in peatlands |
| McMahon, Katherine | University of Wisconsin-Madison | Reference genomes for abundant freshwater taxa – Actinobacteria and Verrucomicrobia phase 2 |
| Meredith, Laura | Stanford University | Microbial, chemical, and physical drivers of COS fluxes and 18O-CO2 exchange rates in soils |
| Miller, Christopher | University of Colorado, Denver | Developing a systems-level understanding of biotic and abiotic controls on microbial methane cycling in freshwater wetlands |
| Redmond, Molly | University of North Carolina, Charlotte | Metagenomic sequencing of methane-oxidizing mesocosms from the Gulf of Mexico and Hudson Canyon |
| Rich, Jeremy | Brown University | Metagenomic sequencing of an uncultivated bacterial phylum in marine sediments amended with organic carbon and nitrate |
| Saito, Mak | Woods Hole Oceanographic Institution | Characterizing Synechococcus dominated populations from the Costa Rica dome and surrounding waters |
| Shade, Ashley | Michigan State University | Response and recovery of surface soil microbial communities to an ongoing underground coalmine fire |
| Simister, Rachel | University of British Columbia | Linking microbial genomic capacity to geochemical process in the deep terrestrial biosphere |
| Slonczewski, Joan | Kenyon College | Cyanobacterial communities of Antarctic Lake Fryxell liftoff mats and glacier meltwater |
| Tolar, Bradley | Stanford University | Monitoring the transcriptional response of a representative low-salinity ammonia-oxidizing thaumarchaeote to shifts in environmental conditions |
| Walsh, Davi | Concordia University | Metagenomics of western Arctic Ocean microbial communities |
| Wilkins, Michael | Ohio State University | Seasonal sulfur cycling as a control on methane flux in carbon-rich prairie pothole sediment ecosystems |
| Wrighton, Kelly | Ohio State University | Identifying key genomes and metabolisms responsible for near-surface methane cycling in freshwater wetlands |
Synthesis Proposals |
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| Proposer | Affiliation | Project Description |
| Chang, Jui-Jen | Biodiversity Research Center,Academia Sinica | Designer Operons-A biomimic approach to the regulation of an enzyme cocktail for an artificial enzyme complex |
| Chen, Brandon | Genomatica, Inc. | Engineering efficient methanol utilization for renewable chemicals |
| McCourt, Peter | University of Toronto | Exploring the perception landscape of the strigolactone receptor |
| Prather, Kristala | Massachusetts Institute of Technology | Combinatorial assembly, screening and functional characterization of a recombinant glucaric acid pathway in S. cerevisiae |
| Shen, Ben | The Scripps Research institute | Construction of bacterial artificial chromosome (BAC) vector libraries for comparative genomics, elucidation of gene functions and heterologous expression of targeted genes |
| Smanski, Mike | University of Minnesota | Towards a mechanistic understanding of disease suppressive soils: Refactoring natural product gene clusters |
| Wang, Clay | University of Southern California | Identification of fungal secondary metabolites with novel structures |
| Zimmer, Jochen | University of Virginia | Synthesis of cellulose synthase genes implicated in primary and secondary plant cell wall formation for structural and functional analyses of plant cellulose biosynthesis |
FY 2016 Facilities Integrating Collaboration for User Science (FICUS) JGI-EMSL Plans
| Proposer | Affiliation | Project Description |
| Bell-Pedersen, Deborah | Texas A&M University | Specialized Ribosomes: A New Frontier in Gene Regulation |
| Cardon, Zoe | Marine Biological Laboratory | 3D Reality Check: Developing Structural Support for Predicting Microbial Function and Interpreting Microbial “Omics” Data |
| Doty, Sharon | University of Washington | Nitrogen fixation in Populus: Identification and localization of the key diazotrophs in planta |
| Duhaime, Melissa | University of Michigan | Building the phage-host-environment interaction data to scale from genes-to-ecosystems: Towards predictive modeling of wild microbial and viral community dynamics |
| Eastwood, Dan | Swansea University (UK) | Genomes to dynamic decay communities: Understanding fungal interactions during early decomposition events in natural lignocellulosic substrate |
| Neumann, Rebecca | University of Washington | A Rhizosphere-Scale Investigation of the Relationship Between Plant Productivity and Methane Emissions from Wetlands |
| Orphan, Victoria | California Institute of Technology | Fluorescence-based cell sorting and targeted proteomic analysis of active methane-oxidizing syntrophic consortia from environmental samples |
| Pan, Chongle | Oak Ridge National Laboratory | Integrated Omics Analyses of a Populus Pedigree for Crop Improvement |