The Joint Genome Institute (JGI) and the Environmental Molecular Sciences Laboratory (EMSL) are seeking collaborative research applications through the Facilities Integrating Collaborations for User Science (FICUS) program. The FICUS program was established in 2014 to encourage and enable ambitious research projects integrating the expertise and capabilities of multiple user facilities.

For FY2022 proposals, additional capabilities are available to users through the National Ecological Observatory Network (NEON) and access to the Bio-SANS beamline at the High Flux Isotope Reactor (HFIR) through the Center for Structural Molecular Biology (CSMB).

Successful applications will address high risk/high payoff projects in the focus topic areas that can be completed in a 24-30 month timeline, use a range of the capabilities of each facility, and generate datasets beyond what users of each of these facilities could generate through separate projects. Because this program offers a diverse but integrated set of capabilities, applicants are strongly encouraged to talk to facility staff in advance to design a set of analyses that is directed at their research goals. For more details regarding the FICUS application process, sample limits or the capabilities available at the user facilities, please check the frequently asked questions (FAQ) or the contacts listed below.

How to submit a proposal

• Submit a Letter of Intent by March 17, 2021. Letters may be created and submitted starting March 1.
• Submit a Full Proposal by May 3, if invited following Letter of Intent review
• Letters of Intent and Full Proposals must be submitted through EMSL’s User Portal.

EMSL is upgrading its User Portal on March 1, 2021, and Letters of Intent and full proposals for this call will be submitted through the upgraded portal. Any prior user and project information will be transferred to the new system, but the appearance and some functionality will change.

FICUS applications follow a proposal package guidance, schedule, and review process that is tailored to meet the requirements of the facilities involved. Returning users are advised to carefully review the unique elements of this joint program as some of the procedures and requirements change each year.

Focused Topic Areas

• Biofuels, biomaterials and bioproducts – Projects should be aimed at characterizing biological processes (including those novel pathways generated by synthetic biology approaches) that are relevant to biofuels, biomaterials, and bioproducts production, and connecting these processes to omics-based analyses in DOE-relevant plants, microbes, and viruses. Relevant biological processes include biosynthesis and deconstruction of plant polymers, especially lignocellulose, and production of metabolites that are precursors of biofuels, biomaterials, and/or non-pharmaceutical bioproducts. Proposals focused on discovery and characterization of enzymes and metabolic pathways for polymer breakdown and/or conversion to novel products are also of interest. Proposals to investigate organisms and/or biological products involved in plant-microbial interactions that impact biofuel and bioproduct feedstock productivity are also encouraged.
• Hydro-biogeochemistry – Projects should focus on the cycling and transport of elements, nutrients and other compounds in soils, the atmosphere, river and coastal sediments, and the subsurface, or on their involvement in regulatory/metabolic processes of plants, microbes, and viruses. Proposals should seek to illuminate key hydro-biogeochemical processes through which these organisms and their communities/ecosystems influence the cycling of biogeochemically critical elements and compounds, as well as the transformation and transport of contaminants and colloids. Such projects should seek to link microbial populations, genes, and traits to molecular biochemistry and geochemistry.
• Inter-organismal interactions – Projects should explore the exchange of carbon, nitrogen, and other elements among plants, microbes, and viruses in above- and below-ground ecosystems and their interfaces (e.g., terrestrial-aquatic interfaces), as well as investigate signaling, cooperation, or competition via physical or chemical means. Proposals about the impact of genetic diversity within plant populations, on plant-associated microbial communities, and plant-microbial interactions are also encouraged, as are those structurally or functionally characterizing transporters, surface proteins, and secondary metabolites potentially involved in multiorganismal and organism-environment interactions.
• Novel applications of molecular techniques – Projects should be aimed at stretching the boundaries of scientific integration of capabilities across the User Facilities. Outcomes should have long-term benefits to DOE/BER missions involving biofuels, biomaterials, and bioproducts production, plant-microbe interactions and nutrient exchange, ecosystem resilience or plasticity in response to environmental stress, and land-atmosphere exchanges and feedbacks. Structural and functional characterization of novel proteins (e.g., enzymes), compounds (e.g., secondary metabolites), or biomaterials produced by genes found in (meta)genomic data, as well as functional analysis of uncultivated organisms, are of particular interest. For high-risk, exploratory studies aimed at assessing the general feasibility or establishing proof of principle, the scope should be limited to a scale required to demonstrate novel results, with the possibility of expanded support after successful completion.
• Ecosystem-scale research using samples from the NEON Biorepository – NEON, the National Ecological Observatory Network, is a national network of terrestrial and aquatic sites located across the US, including Alaska, Hawaii, and Puerto Rico that captures more than 180 data products collected either continuously or with vast seasonal standardized sampling campaigns, including soils. Projects should investigate the biogeochemistry and microbial communities across NEON sites along climate/vegetation gradients or seasonal variation at specific sites. A diversity of genomic sequencing data products, capturing the composition of soil microbiomes, is available from the NEON data portal for a subset of the seasonal soil sampling. The FICUS Letter of Intent must include a letter of support from NEON for the specific samples that are required. Additional information is listed below about NEON, the NEON Biorepository and data products, such as metagenomic sequences.

Partnering Facilities

EMSL provides a wide range of unique and state-of-the-art omics, imaging, and computational capabilities that can be applied to proposals under this call. Applicants should especially consider emerging cutting-edge capabilities that are available to users who coordinate their proposals with the EMSL scientists leading their development. The capabilities include but are not limited to the following:

• Stable isotope probing and analysis platform that includes labeled CO2 plant growth facilities, NMR, IRMS, and NanoSIMS (Contact: Jim Moran, Mary Lipton, or Pubudu Handakumbura)
• Transcriptomics and proteomics from single or a small number of cells detected and isolated by flow cytometry, fluorescence microscopy and/or laser capture micro-dissection and enabled by microfluidics and nanoPOTS (Contact: Galya Orr or Ying Zhu)
• Krios cryoTEM in combination with native mass spectrometry and cell-free expression capabilities for characterization of protein complexes or in combination with new Aquilos cryoFIB/SEM for subcellular tomography studies. (Contact: Irina Novikova or Mowei Zhou)
• Soft X-ray nanotomography system for 3D nanoscale imaging of cells and biological materials (Contact: James Evans or Scott Lea)
• High-resolution micro-X-ray computed tomography system for characterization of biogeochemical samples such as soil, rhizosphere, and sediment samples to investigate porous microstructure, plant root architecture, hydrology, etc. Two resolution options are available; 0.8 µm resolution and 0.2 µm (Contact: Tamas Varga or Mark Bowden)
• Noninvasive root imaging platform for monitoring and characterizing plant root systems in transparent growth medium (Contact: Amir Ahkami or Thomas Wietsma)
• Optical Coherence Tomography offers a non-invasive approach for in situ, 3D imaging of living tissues. The approach can be applied to static samples or deployed in various growth chambers to provide timeseries imaging of plant or other systems. (Contact: Jim Moran or Amir Ahkami)
• Interactive data visualization tools that support exploration of complex natural organic matter or proteomics data and comparison of data across treatment groups (Contact: Allison Thompson)
• Tahoma, BER’s new heterogeneous computing system, has 184 Intel Cascade Lake nodes, each of which has 2 18-core CPUs running at 3.1 GHz.  Of these 184 nodes, 160 have 384 GB of RAM per node, and 24 have 1536 GB of RAM per node as well as 2 NVIDIA Tesla V100 32GB GPUs.  The system has a theoretical peak performance of 1015 teraflops.  Tahoma features a 10 PB global storage system, 536 TB local disk (solid state), and HDR-100 Infiniband networking. This system will support computational research requiring significant memory as well as processing speed to enable data mining, image processing, and multiscale modeling. (Contact: Jaydeep Bardhan).

Other capabilities that offer opportunities for novel and exciting experimental data include a variety of in-situ probes for NMR, advanced electron microscopy in a specialized “quiet” facility, high-resolution mass spectrometry including a 21 Tesla FTICR, and Atom Probe Tomography. Applications may request any combination of these or other EMSL capabilities, but they must provide adequate information to demonstrate the plan for integration and justify the amount of time or other resources requested. Applicants are strongly urged to discuss their resource needs with the EMSL Science Area Leads prior to responding to the Call. Applicants may also contact the EMSL User Services Office for assistance.

JGI employs both next-generation short-read sequencing platforms and 3rd generation single-molecule/long-read capabilities as well as DNA synthesis and mass spectrometry-based metabolomics. The capabilities available for this call are listed below. FICUS proposals should request no more than 1 Tb of sequencing, 500 kb of synthesis, and up to 200 samples for metabolomics polar analysis and 500 samples for nonpolar analysis. Researchers are encouraged to review JGI’s sample submission guidelines to obtain additional information about the amounts of material that are required for various product types. Individual proposals may draw from one or more of these capabilities as needed to fulfill project goals. Successful projects frequently exploit a combination of capabilities.

• De novo sequencing and annotation of plant, algal, fungal, bacterial, archaeal, and viral genomes
• Resequencing for variation detection
• Fluorescence activated cell sorting for targeted metagenomics and single-cell genomics
• Microbial community DNA/RNA sequencing and annotation
• Stable isotope probing enabled metagenomics
• Comprehensive transcriptome analysis
• Whole genome DNA methylation analysis
• Chromatin analysis including ATAC-seq and ChIP-seq library preparation from User immunoprecipitated DNA
• Gene and pathway DNA synthesis
• Whole genome gRNA library construction and QC
• Organism engineering
• LC-MS/MS based metabolomic analysis of polar and non-polar metabolites for functional genomics
• Integrated metabolomic and genomic analyses

Center for Structural Molecular Biology – CSMB supports the user access and science program of the Biological Small-Angle Neutron Scattering (Bio-SANS) instrument at the High-Flux Isotope Reactor located at Oak Ridge National Laboratory. Through this FICUS partnership, CSMB is providing access to resources for studies of hierarchical and complex biological systems. Bio-SANS is dedicated to the analysis of the structure, function, and dynamics of complex biological systems. The CSMB also operates a Bio-Deuteration Laboratory for deuterium labeling of biological macromolecules. These tools help researchers understand how macromolecular systems are formed and how they interact with other systems in living cells. For further information about the CSMB and Bio-SANS please visit https://www.ornl.gov/facility/csmb.

National Ecological Observatory Network – NEON, a large facility project funded by the National Science Foundation (NSF), is a continental-scale platform for ecological research. It comprises terrestrial, aquatic, atmospheric, and remote sensing measurement infrastructure and cyberinfrastructure that deliver standardized, calibrated data to the scientific community through a single, openly accessible data portal. NEON infrastructure is geographically distributed across the United States and will generate data for ecological research over a 30-year period. The network is designed to enable the research community to ask and address their own questions on a regional to continental scale around a variety of environmental challenges. Additional information about the network is available below:

• NEON field sites
• NEON Letters of support
• Biorepository website
• NEON Megapit Archive
• NEON Metagenomic sequencing

Contacts:

General Inquiries

• EMSL: Alison Hatt, ajhatt@pnnl.gov, 509-371-7579
• JGI: Christa Pennacchio, jgi-jira+pmosupport@lbl.gov
• CSMB/HFIR: Janell Thomson, thomsonji@ornl.gov, 865-576-2281
• NEON: Letters of Support information

Detailed Research Questions

• EMSL: Mary Lipton, mary.lipton@pnnl.gov, 509-371-6589
• JGI: Tanja Woyke, TWoyke@lbl.gov, 510-495-8506
• CSMB/HFIR: Hugh O’Neill, oneillhm@ornl.gov, 865-574-5283
• NEON: Michael SanClements msanclements@battelleecology.org, 720-836-2499

Review Criteria

FICUS proposals are reviewed for technical feasibility by scientific staff at each facility. Proposals also undergo external peer review against four scientific criteria. For each criterion, the reviewer rates the proposal Extraordinary, Excellent, Good, Fair, or Poor and provides detailed comments on the quality of the proposal to support each rating, noting specifically the proposal’s strengths and weaknesses. The reviewer also provides overall comments and recommendations to support the ratings given. These scores and comments serve as the starting point for Proposal Review Panel (PRP) discussions. The PRP is responsible for the final score and recommendation to the facilities’ managements.

Criterion 1: Scientific merit and quality of the proposed research (25%)

Potential Considerations: How important is the proposed activity to advancing knowledge and understanding within its own field or across different fields? To what extent does the proposed activity suggest and explore creative and original concepts? How well conceived and organized is the proposed activity? What is the likelihood that the proposed activity will answer the proposed questions?

Criterion 2: Qualifications of the proposed research team to achieve proposal goals and contribute to high-impact science (25%)

Potential Considerations: Does the proposal team, combined with relevant EMSL and JGI staff expertise, possess the appropriate breadth of skill/knowledge to successfully perform the proposed research and drive progress in this science area? Proposals will be evaluated on whether scientists with expertise and the necessary skills will be ready to perform follow-up research and publications. If successful, would the proposed research deliver high-impact products (for example, be publishable in high-impact journals)? The size and productivity of the user community will also be considered.

Note: Impact factors are a measure of the average number of citations per published articles. Journals with higher impact factors reflect a higher average of citations per article and are considered more influential within their scientific field.

Criterion 3: Relevance of the proposed research to DOE missions (25%)

EMSL and JGI are managed by the Department of Energy’s Office of Biological and Environmental Research, and both play critical roles in supporting DOE’s energy, environment and basic research missions. They provide integrated experimental and computational data and analysis, as well as high-throughput DNA sequencing, synthesis and analysis in support of BER’s missions in plant/fungal/microbial bioenergy feedstocks, carbon and nutrient cycling, and biogeochemistry.

Potential Considerations: What is the relationship of the proposed research to DOE missions? Does the research project significantly advance the mission goals? Proof of concept proposals for the demonstration of a technology that would be applicable to a DOE mission are acceptable. How well does the project plan represent a unique or innovative demonstration and to what extent does it advance the mission area?

Criterion 4: Appropriateness and reasonableness of the request for resources for the proposed research (25%)

Potential Considerations: Are EMSL and JGI capabilities and resources essential to performing this research? Does the project generate a dataset unique to these facilities and beyond what each could generate by itself?  Are the proposed methods/approaches optimal for achieving the scientific objectives of the proposal? Are the requested resources reasonable and appropriate for the proposed research? Does the complexity and/or scope of effort justify the duration of the proposed project? Is the specified work plan practical and achievable within the shortened project timeframe (less than JGI’s CSP projects)?

Proposal Schedule

The full FY22 schedule is below:

Calls for proposals issued	January 11, 2021
Letters of intent received	March 17, 2021
Invitation of proposals	April 5, 2021
Proposals received	May 3, 2021
Technical and scientific review	mid-June 2021
Approval and rejection notices sent	by July 31, 2021
Prepare user agreements	August – September 2021
Projects start	October 1, 2021 or as soon as user agreement is finalized