FICUS JGI-EMSL FY23

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 FY2023 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 available capabilities, and generate datasets beyond what users of each of these facilities could generate through separate projects. Applicants are strongly encouraged to talk to facility staff in advance of submitting a letter of intent, for help designing a set of analyses that is directed at their research goals.

Focused Topic Areas

Proposals submitted to this call should be responsive to one or more of the following focus topics. These topics are aligned with EMSL and JGI missions.

• 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 biomass, especially lignocellulose, and production of metabolites that are precursors of biofuels, biomaterials, and/or non-pharmaceutical bioproducts. Specific topics include the discovery and characterization of enzymes and metabolic pathways for polymer breakdown and/or conversion to novel products, the microbially-mediated construction and deconstruction of plastics, secure synthetic biology, genome-enabled material synthesis, and investigations into organisms and/or biological products involved in plant-microbial interactions that impact biofuel and bioproduct feedstock productivity.
• Hydro-biogeochemistry: Projects should focus on the cycling and transport of elements, nutrients, and other compounds.  Study systems can include soils, the atmosphere, the subsurface, and aquatic interfaces, including but not limited to river/stream systems, coastal zones, and/or urban ecosystems. Proposals should seek to illuminate key hydro-biogeochemical processes through which microorganisms influence the biogeochemical cycling of critical elements, metals and/or colloids under baseline or disturbance conditions. Understanding the regulatory/metabolic processes of plants, microbes, and viruses is of particular interest. Proposals that focus on aerosol production and/or mineral-organic matter interactions are also encouraged. 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 the enzymes, pathways and metabolites for secondary metabolites potentially involved in multi-organismal 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 or disturbances, 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, but could also include sites that have experienced disturbance. Several genomic sequencing data products, capturing the composition of soil microbiomes, are 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 (e.g., megapit samples) and/or the NEON Biorepository (all other samples) for the specific samples that are required. Additional information is listed below about NEON, as well as the NEON Biorepository and data products, such as metagenomic sequences.

Highlighted Capabilities

Proposals should make use of capabilities from two or more of the participating user facilities, including EMSL and/or JGI. Note that competitive proposals will typically require use of both EMSL and JGI.

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)
• Spatial metabolomics, used to investigate the spatial distribution of molecules within biological samples (Contact: Dusan Velosovik and Kristin Burnum Johnson)
• Structural biology approaches utilizing cell-free expression and native mass spectrometry capabilities for characterization of protein complexes (Contact: Irina Novikova or Mowei Zhou)
• Krios cryoTEM for atomic resolution structural analysis of protein complexes, organelles, whole cells, and small molecule crystals. [More…]
• 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)
• 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 time-series imaging of plants 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. [More…]
• Tahoma, BER’s new heterogeneous (CPU/GPU) computing system for highly parallel modeling/simulation and data processing needs. [More…]
• Investigations using soil-based EcoFAB devices (https://eco-fab.org/) supplied by the EMSL to conduct experiments to uncover the molecular mechanisms in microbial communities in soils.

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. Learn more about these and other EMSL capabilities.

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; more details can be found about JGI products here. 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
• Transcription factor binding site discovery with DAP-seq
• Gene and pathway DNA synthesis
• Whole genome gRNA library construction and QC
• Organism engineering
• LC-MS/MS based metabolomic analysis of polar (e.g. amino acids, organic acids, sugars, nucleobases, etc.) and non-polar metabolites (e.g. secondary metabolites, lipids, etc.)
• Integrated metabolomic and genomic analyses
• Investigations using EcoFAB devices (https://eco-fab.org/) and, if desired, a defined microbiome supplied by the JGI to conduct experiments to uncover the mechanisms underlying the interactions between plants and their root microbiomes

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. Neutrons provide unique structural information due to their sensitivity to hydrogen and deuterium that is unattainable by other means. Through this FICUS partnership, CSMB is providing access to resources for studies of hierarchical and complex biological systems.

• Small-angle neutron scattering at Bio-SANS provides structural information about a range of biological systems across length scales from 1 – 100 nm. Examples include biomacromolecules and their complexes in solution, biomembranes, and hierarchical and complex systems such as plant cell walls and soils.
• Deuterium labeling of biological macromolecules including, proteins, lipids, nucleic acids, biopolymers.

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. Requests for large numbers of samples or that require additional sample processing may incur a service fee.

Additional information about the network is available below:

• NEON field sites
• NEON Research Support and Assignable Assets
• NEON Letters of support
• Biorepository website
• NEON Megapit Archive
• NEON Metagenomic sequencing

How to Apply

Get started – create an account on the EMSL User Portal and familiarize yourself with user program requirements and data policies.

In order to submit a proposal, you will need to create a user account in the EMSL User Portal. As part of the registration process, you will either need to register for an ORCID iD or enter your existing ORCID iD on your “User Info” page.At this stage, you should familiarize yourself with the requirements and policies for users:

EMSL’s Data Policy

JGI’s Data Policy

NEON Data Policy

Terms and Conditions of EMSL Use

JGI User Agreement Process

For administrative help at any point in the proposal submission process, please contact EMSL User Services.

2) Develop a research plan

Learn about EMSL’s Science Areas and Integrated Research Platforms; successful user projects must be aligned with EMSL’s scientific mission and capabilities as described in these pages.

Browse the list of EMSL Instruments and Resources to inform your research plan. Explore JGI’s science programs and learn more about their capabilities.

Contact EMSL staff and JGI staff to discuss your research needs. Staff can help you develop and refine your research plan to best suit EMSL and JGI capabilities. For help identifying the most appropriate contacts at JGI, email [email protected].

3) Submit a Letter of Intent  – briefly describe your project in a two-page letter of intent (LOI), following guidance. Upload your project description to the User Portal and provide other project details through an online form.

Initiate a new Letter of Intent (LOI) by logging into the EMSL User Portal and clicking “Submit a Proposal/LOI” in the left-hand navigation of the home screen. The form will guide you to enter details about the proposal, the participants, funding, resources, and samples. Review the entire form well in advance of the submission deadline to make sure you have enough time to compile the required information.The Proposed Research Project Description is uploaded into the form as a PDF. See the Letter of Intent Guidance for formatting and content requirements. Note that several required appendices must be included with the project description as a single PDF document.Your LOI will be reviewed for responsiveness to the call and alignment to EMSL, JGI, and DOE BER missions and feedback may be provided regarding the feasibility of the proposed research.

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 FY23 schedule is below:

Calls for proposals issued	January 10, 2022
Letters of intent received	March 16, 2022
Invitation of proposals	April 4, 2022
Proposals received	May 4, 2022
Technical and scientific review	mid-June 2022
Approval and rejection notices sent	by July 31, 2022
Prepare user agreements	August – September 2022
Projects start	October 1, 2022 or as soon as user agreement is finalized