FICUS JGI-EMSL

The Joint Genome Institute (JGI), a Department of Energy (DOE) Office of Science user facility at Lawrence Berkeley National Laboratory (Berkeley Lab), and the Environmental Molecular Sciences Laboratory (EMSL), a DOE Office of Science user facility at Pacific Northwest National Laboratory, are seeking collaborative research applications through the Facilities Integrating Collaborations for User Science (FICUS) program. The FICUS program, originally established in 2014 to encourage and enable ambitious multidisciplinary research projects, integrates expertise and experimental capabilities of multiple DOE-supported user facilities.

The FY 2024 FICUS proposal call will include access to expanded capabilities available through DOE-supported user facilities, including the Bio-SANS beamline through the Center for Structural Molecular Biology (CSMB) at Oak Ridge National Laboratory, and the Advanced Photon Source at Argonne National Laboratory. Applicants can also request access to archived biological, genomic, and geological samples and specimens from terrestrial and aquatic sites through the National Science Foundation’s (NSF’s) National Ecological Observatory Network (NEON).

Successful applications will address high-risk/high-payoff projects in the focus topic areas that can be completed over a 24–30 month timeline, use a variety of available capabilities at two or more user facilities, and generate datasets beyond what users of each of these facilities can generate through separate projects. Applicants are strongly encouraged to contact facility staff (see contact information below) in advance of submitting a Letter of Intent for help designing a set of analyses that are directed at their research goals.

Focused Topic Areas

Proposals submitted to this call should be responsive to one or more of the following focus area topics aligned to the Biological and Environmental Research (BER) program.

• 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 at connecting these processes to omics-based analyses for DOE-relevant plants, microbes, and microbial communities including viruses. Relevant biological processes include biosynthesis and deconstruction of plant biomass, especially lignocellulose, and the production of metabolites that are precursors of biofuels, biomaterials, and/or non-pharmaceutical bioproducts. Topics of interest include the discovery and characterization of enzymes and metabolic pathways for synthetic polymer breakdown and/or conversion to novel products, the microbially mediated construction and deconstruction of plastics, secure synthetic biology and biocontainment, genome-enabled organic and inorganic material synthesis, and investigations into organisms and/or biological products involved in plant–microbial interactions that affect biofuel and bioproduct feedstock productivity.
• Hydro-biogeochemistry: Projects should focus on the cycling and transport of key elements, nutrients, and other compounds within ecosystems. Study systems can include soils, vegetation, microbial communities, the atmosphere, the subsurface, and land/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, nutrients, colloids, and other compounds under baseline or disturbance conditions. Understanding the regulatory/metabolic processes of plants, microbes, and microbial communities, including viruses, is of particular interest. Proposals that focus on aerosol particle formation, microbe–particle interactions and processes, and/or mineral–organic matter interactions are also encouraged. Projects should seek to link microbial populations, genes, and traits to molecular biogeochemistry and to the surrounding environment.
• Inter-organismal interactions: Projects should explore the exchange of metabolites, signals, and/or nutrients (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 under abiotic environmental stresses (e.g., drought, salinity). Proposals focused on the impacts of biological diversity and root structure within plant populations, on plant-associated microbial communities, and plant–microbial interactions are also encouraged. These investigations can include metabolite exchange, structural or functional characterization of transporters, surface proteins, exudates, and the enzymes, pathways, proteins, and metabolites involved in secondary metabolism that affect multi-organismal and organism–environment interactions.
• Novel applications of molecular techniques: Projects should be aimed at redefining the boundaries of scientific integration of experimental and data capabilities across DOE user facilities. Outcomes should have long-term benefits to the DOE/BER mission involving biofuels, biomaterials, and bioproducts production, plastic bioprocessing and degradation; plant–microbe interactions and nutrient exchange; ecosystem resilience or plasticity in response to environmental stress or disturbance; and land–atmosphere exchanges and feedbacks. Structural and functional characterization of novel proteins (e.g., enzymes), compounds (e.g., primary and 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 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 is a national network of terrestrial and aquatic sites located across the United States, including Alaska, Hawaii, and Puerto Rico. NEON 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 use capabilities from two or more of the participating user facilities, where at least one of the facilities must be EMSL and/or JGI.

Environmental Molecular Sciences Laboratory

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 who lead their development. The capabilities include but are not limited to the following:

• New single-cell transcriptomic workflows for elucidating the intercellular signaling, communication, and ensuing heterogeneity that underpin the behavior of complex multicellular/multispecies assemblages, including microbial communities and host–microbe systems. (Contact: Alex Beliaev)
• Developing capabilities in chemical biology to probe enzyme function and characterize biochemical pathways. For example, users are sought for a recently developed probe library to broadly profile amidase activity, which targets both canonical (peptide-like) and non-canonical amide hydrolase activity, and for developing probes for other activities. (Contact: Sankar Krishnamoorthy)
• A stable isotope probing and analysis platform that includes labeled CO₂ plant growth facilities, nuclear magnetic resonance (NMR), isotope ratio mass spectrometry  and nanoscale secondary ion mass spectrometry. (Contact: Mary Lipton, or Pubudu Handakumbura)
• Small sample omics analysis from a single cell 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: Sarai Williams or Ljiljana Pasa-Tolic)
• Spatial metabolomics, used to investigate the spatial distribution of molecules within biological samples. (Contact: Chris Anderton, Dusan Velickovic, and Kristin Burnum-Johnson)
• Structural biology approaches utilizing cell-free expression, native mass spectrometry, and NMR capabilities for characterization of protein complexes. (Contact: Irina Novikova or Mowei Zhou)
• Krios transmission electron cryomicroscopy (cryoTEM) for atomic-resolution structural analysis of proteins, protein complexes, and/or small molecule crystals or for high-resolution tomographic analysis of whole cells and tissues. (Contact: James Evans, Irina Novikova or Amar Parvate)
• Aquilos cryo-focused ion beam/scanning electron microscope for site-selective sample preparation for cryo-EM/tomography or serial section slice-and-view 3D imaging of large tissue or plant/microbe interactions. (Contact James Evans or Trevor Moser)
• Tender 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 characterizing 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 and 0.2 µm. (Contact: Tamas Varga)
• Noninvasive root imaging platform for monitoring and characterizing plant root systems in a transparent growth medium. (Contact: Amir Ahkami or Thomas Wietsma)
• Optical coherence tomography for a noninvasive 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: Amir Ahkami)
• Liquid and solid-state NMR-based metabolomics to define the metabolite profile in a biological system, including primary and secondary metabolites and plant cell wall components. (Contact: David Hoyt and Andrew Lipton)
• Interactive data visualization tools that support the exploration of complex natural organic matter or proteomics data and comparison of data across treatment groups. (Contact: Satish Karra)
• Tahoma, BER’s heterogeneous (CPU/GPU) computing system for highly parallel modeling/simulation and data processing needs (Contact: Satish Karra)
• Investigations using plant- and soil-based EcoFAB devices supplied by EMSL to conduct experiments to uncover the molecular mechanisms in microbial communities in soils and rhizosphere (root–microbe interactions). (Contact: Arunima Bhattacharjee or Amir Ahkami)
• A suite of synthetic soil habitats to measure the impact of targeted soil parameters on ecological interactions, including pore-scale micromodels, mineral-amended microfluidic habitats, RhizoChip, and Bioprinted Synthetic Soil Aggregates. These synthetic habitats are ideal for multiomics characterization and multimodal imaging of the spatial organization of soil and rhizosphere communities (plant, bacteria, and fungi) and mapping molecular exchanges between organisms. (Contact: Arunima Bhattacharjee, Jayde Aufrecht)

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 Fourier transform ion cyclotron resonance mass spectrometer, and atom probe tomography. Learn more about these and other EMSL capabilities.

Joint Genome Institute

JGI employs both next-generation short-read sequencing platforms and third-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. Read more about JGI. FICUS proposals should request no more than 3 Tb of sequencing, 500 kb of synthesis, and up to 200 samples for metabolomics polar analysis and 500 samples for nonpolar analysis. Requests for Pacific Biosciences long-read sequencing are capped at 1 Tb, while requests for DAP-seq should include a minimum of 70 transcription factors. For EcoFAB experiments, up to 50 EcoFABs are available. 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 and/or viral community DNA/RNA sequencing and annotation (i.e., metagenomes and metatranscriptomes)
• Stable isotope probing enabled metagenomics
• Transcriptome analysis including coding transcript annotation and expression profiling
• Prokaryotic whole-genome DNA methylation analysis
• Transcription factor binding site discovery with DAP-seq
• Gene and pathway DNA synthesis
• Whole-genome gRNA library and quality control
• Organism engineering
• LC-MS/MS based metabolomic analysis of polar (e.g., amino acids, organic acids, sugars, nucleobases, etc.) and nonpolar metabolites (e.g., secondary metabolites, lipids, etc.)
• Integrated metabolomic and genomic analyses
• Investigations using EcoFAB devices and, if desired, a defined microbiome supplied by JGI to conduct experiments to uncover the mechanisms underlying the interactions between plants and their root microbiomes.

For general questions, please contact Christa Pennacchio, Project Management Office. For questions about the appropriateness of projects or experimental design, please contact Tanja Woyke, Deputy for User Programs. Technical and scientific leads will also be available to answer any questions before proposal submission.

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 (Contact: Hugh O’Neill).

Advanced Photon Source 

Advanced Photon Source (APS) at Argonne National Laboratory (ANL) is being upgraded with new transformative accelerator technology. The new design of the storage ring, the beamline improvement program and new feature beamlines will offer a wide range of x-ray – based tools that will provide novel opportunities for research pertinent to the BER mission, including biological, geological, geochemical and environmental sciences, to address existing and new scientific challenges. eBERlight program is currently being developed as a virtual Collaborative Access Team (CAT) at APS. It will serve as a liaison between user community and the APS after the upgrade, offering an integrated platform enhancing user science through focused communication with users and coordinated activities among the relevant APS beamlines.

In addition to APS x-ray beamlines and techniques, eBERlight will offer expertise and additional infrastructure available at ANL (i) Advanced Protein Characterization Facility (APCF, sector 84 of APS, sample preparation), (ii) Advanced Leadership Computing Facility (ALCF, exascale computing for data processing using supercomputers), (iii) APS cryolab (sample preparation), and (iv) Molecular Environmental Science and Biogeochemical Process Group (MESBPG) laboratories (sample preparation).

In the first year of the FICUS proposal, eBERlight will work with the users on sample preparations, handling and environment. The x-ray measurements will be generally planned for the second year, when APS-U and eBERlight-available beamlines are expected to be able to accept novice users. Exceptions can be made if the capabilities are available sooner.

Specific capabilities/resources include:

• Protein production and structural characterization recourses/services in the Advanced Protein Characterization Facility for gene cloning, recombinant protein expression, purification, characterization, crystallization (access to the lab to perform the work or mail-in service for gene-to-structure pipeline). (Contact Karolina Michalska)
• APS capabilities (Contact Zou Finfrock)
• Macromolecular crystallography is for determination of 3D structures of macromolecules: proteins, nucleic acids and their complexes
• Full-field x-ray imaging is for micro- and nano-computed x-ray tomography (CT) to enable visualization of soil cores or aggregates, plant structures etc., Sample size ranges from microns to centimeters.
• Scanning x-ray microscopy enables the visualization of elemental distribution in 2D/3D (X-Ray Fluorescence (XRF)) and structural information in 3D (ptychography). XRF approaches are applicable for mapping of elements with an atomic number of 13 (Aluminum) and higher; ptychography is a computational scanning microscopy technique for acquiring structural information with resolutions beyond the limits of x-ray optics. Both techniques can be applied to a variety of samples in both, biological and environmental research, such as soils, plants, rhizosphere, aerosol particles, and microorganisms. Sample size ranges for XRF are from microns to centimeter with spatial resolution ranges from 5 nm to 30 microns. The highest achievable spatial resolution for ptychography is 5 nm.

For general questions, please contact Karolina Michalska.

National Ecological Observatory Network 

NEON, a large facility project funded by the NSF, is a continental-scale platform for ecological research. It comprises terrestrial, aquatic, atmospheric, and remote-sensing measurements and cyberinfrastructure that deliver standardized, calibrated data to the scientific community through a single, openly accessible data portal. In addition to its openly available data products, NEON provides access to hundreds of thousands of archived biological, genomics, and geological samples and specimens from terrestrial and aquatic sites. 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

National Microbiome Data Collaborative (NMDC) and DOE Systems Biology Knowledgebase (KBase )

Applicants are encouraged to interface with NMDC and KBase, as appropriate, for the registration and processing of their data (NMDC) and advanced analysis and data integration (KBase).

NMDC is an integrated microbiome data ecosystem hosting high-quality, consistently processed multi-omics microbiome data to enable data sharing, management, and cross-comparison across studies in accordance with the FAIR (Findable, Accessible, Interoperable, Reusable) data principles. Applicants interested in collaborating with the NMDC team and having their data hosted within the NMDC Data Portal should indicate so in their proposal.

KBase is a free, open-source data analysis platform for system biology research that supports the FAIR data principles, reproducible analysis workflows, and sharing and publishing of datasets and knowledge generated from your analysis. Please explore the analyses supported by KBase, available at www.kbase.us/learn, and reach out to the KBase staff to discuss how they can support your project.

Data Policies:

EMSL:  https://www.emsl.pnnl.gov/basic/data-management-policy/1243

JGI: https://jgi.doe.gov/user-programs/pmo-overview/policies/

NEON: https://www.neonscience.org/data-samples/data-policies-citation

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:

• User Agreement Requirements
• EMSL’s Data Management Policy
• Terms and Conditions of EMSL Use

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

2) 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 and DOE BER missions and feedback may be provided regarding the feasibility of the proposed research.

3) Submit a Full Proposal – If invited, describe your project in detail in a ten-page proposal, following guidance. Upload your project description to the User Portal and provide other project details through an online form.

If your Letter of Intent meets the stated criteria for responsiveness and mission alignment, you will be invited to submit a full proposal. Full proposals for this call may only be submitted by invitation.

Initiate a full proposal by logging into the EMSL User Portal. The form will be pre-populated with the details entered into your Letter of Intent but all content can be modified if needed.

The research project description is uploaded into the form as a PDF. See the Proposal Guidance for EMSL-JGI Program for formatting and content requirements. Note that several required appendices must be included with the project description as a single PDF document.

Your proposal should incorporate or respond to any feedback provided following your Letter of Intent. You are strongly encouraged to contact facility staff to discuss your project prior to submitting the full proposal. Any discussions with staff should be initiated at least two weeks prior to the submission deadline.

Review Criteria

User proposals are peer reviewed against the five criteria listed below. For each criterion, the reviewer rates the proposal Outstanding, Excellent, Good, Fundamentally Sound, or Questionable Impact as well as 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 EMSL management.

Criterion 1: Scientific merit and quality of the proposed research (50%)

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?

Criterion 2: Qualifications of the proposed research team to achieve proposal goals and contribute to high-impact science (10%)

Potential Considerations: Does the proposal team, combined with relevant EMSL staff expertise, possess the breadth of skill/knowledge to successfully perform the proposed research and drive progress in this science area? If successful, would the proposed research deliver high-impact products (for example, be publishable in high-impact journals)?

Note: Impact factors are a measure of the average number of citations per published article. 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 EMSL’s mission (10%)

EMSL’s mission is to accelerate scientific discovery and pioneer new capabilities to understand biological and environmental processes across temporal and spatial scales. EMSL leads the scientific community toward a predictive understanding of complex biological and environmental systems to enable sustainable solutions to the nation’s energy and environmental challenges.

EMSL supports the DOE BER program in achieving a predictive understanding of complex biological, Earth, and environmental systems for energy and infrastructure security, independence, and prosperity. BER seeks to understand the biological, biogeochemical, and physical processes that span from molecular and genomics-controlled scales to the regional and global scales that govern changes in watershed dynamics, climate, and the Earth system.

Starting with the genetic information encoded in organisms’ genomes, BER research seeks to discover the principles that guide the translation of the genetic code into the functional proteins and the metabolic and regulatory networks underlying the systems biology of plants and microbes as they respond to and modify their environments. This predictive understanding will enable the design and reengineering of microbes and plants underpinning energy independence and a broad clean energy portfolio, including improved biofuels and bioproducts, improved carbon storage capabilities, and controlled biological transformation of materials such as nutrients and contaminants in the environment.

BER research further advances the fundamental understanding of dynamic, physical, and biogeochemical processes required to systematically develop Earth System models that integrate across the atmosphere, land masses, oceans, sea ice, and subsurface. These predictive tools and approaches are needed to inform policies and plans for ensuring the security and resilience of the Nation’s critical infrastructure and natural resources.

Note: Projects with direct relevance in these areas will have the best chance for selection. Other projects of scientific significance also are welcomed, but the applicant should clearly outline how the project will further a DOE mission or other areas with economic or societal impact.

Potential Considerations: What is the relationship of the proposed research to EMSL’s mission? Does the research project significantly advance the mission goals? How well does the project plan represent a unique or innovative application or development of EMSL capabilities?

Criterion 4: Impact of the proposed research on one or more EMSL Science Areas (20%)

Potential considerations: Will the proposed research advance scientific or technological understanding of issues pertaining to one or more EMSL science areas? To what extent does the proposed research suggest and explore creative and original concepts related to one or more EMSL science areas? How strongly does it relate to the science area’s focused topics as outlined in the most recent Call for Proposals? How well will it advance EMSL along the directions specifically outlined in the focused topics?

Criterion 5: Appropriateness and reasonableness of the request for EMSL resources for the proposed research (10%)

Potential considerations: Are EMSL capabilities and resources essential to performing this research? 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 or scope of effort justify the duration of the proposed project–including any modifications to EMSL equipment to carry out research? Is the specified work plan practical and achievable for the proposed research project? Is the amount of time requested for each piece of equipment clearly justified and appropriate?

Proposal Schedule

The full FY24 schedule is below:

Calls for proposals issued	January 10, 2023
Letters of intent received	March 15, 2023
Invitation of proposals	April 4, 2023
Proposals received	May 4, 2023
Technical and scientific review	June 15-16 2023
Approval and rejection notices sent	by July 31, 2023
Prepare user agreements	August – September 2023
Projects start	October 1, 2023 or as soon as user agreement is finalized