DE-FOA-0003453.000001.pdf

Department of Energy (DOE) Office of Science (SC)

Biological and Environmental Research (BER)

Systems Biology Research to Advance Bioenergy Crop Production

Notice of Funding Opportunity (NOFO) Number:

DE-FOA-0003453

NOFO Type: Amendment 000001 Catalog of Federal Domestic Assistance (CFDA) Number: 81.049

Amendment 000001 is issued to remove references to diversity, equity, and inclusion; to remove references to PIER plans; to update regulatory requirements from Title 2 CFR; and to update research, technology, and economic security provisions.

NOFO Issue Date: December 11, 2024 Submission Deadline for Pre-Applications:

January 17, 2025 at 5PM Eastern Time A Pre-Application is required.

Pre-Application Response Date: February 3, 2025 at 5PM Eastern Time Submission Deadline for Applications: March 26, 2025 at 11:59 PM Eastern Time

Table of Contents

I. BASIC INFORMATION

EXECUTIVE SUMMARY

FUNDING DETAILS

KEY FACTS

KEY DATES

AGENCY CONTACT INFORMATION

RECOMMENDATION

II. ELIGIBILITY

A. ELIGIBLE APPLICANTS

B. COST SHARING

C. ELIGIBLE INDIVIDUALS

D. LIMITATIONS ON SUBMISSIONS

III. PROGRAM DESCRIPTION

A. PURPOSE

B. PROGRAM GOALS, OBJECTIVES, AND PRIORITIES

C. AWARD CONTRIBUTION TO GOALS AND OBJECTIVES

D. PERFORMANCE GOALS

E. SUBSTANTIAL INVOLVEMENT

F. PROGRAM UNALLOWABLE COSTS

G. CITATIONS TO STATUTES AND REGULATIONS

H. PROGRAM HISTORY

I. OTHER INFORMATION

IV. APPLICATION CONTENTS AND FORMAT

A. PRELIMINARY SUBMISSIONS

B. APPLICATION

C. COMPONENT PIECES OF THE APPLICATION

D. INFORMATION THAT MUST BE SUBMITTED AFTER APPLICATION BUT

BEFORE AWARD

V. SUBMISSION REQUIREMENTS AND DEADLINES

A. ADDRESS TO REQUEST APPLICATION PACKAGE

B. UNIQUE ENTITY IDENTIFIER (UEI) AND SYSTEM FOR AWARD MANAGEMENT

(SAM.GOV)

C. SUBMISSION INSTRUCTIONS

D. SUBMISSION DATES AND TIMES

VI. APPLICATION REVIEW INFORMATION

A. RESPONSIVENESS REVIEW

B. REVIEW CRITERIA

C. REVIEW AND SELECTION PROCESS

D. RISK REVIEW ................................................. ERROR! BOOKMARK NOT DEFINED.

VII. AWARD NOTICES

A. TYPE OF AWARD INSTRUMENT

B. ANTICIPATED TIMELINE FOR NOTICE OF SELECTION FOR AWARD

NEGOTIATION

VIII. POST-AWARD REQUIREMENTS AND ADMINISTRATION

A. ADMINISTRATIVE AND NATIONAL POLICY REQUIREMENTS

B. REPORTING

C. REPORTING OF MATTERS RELATED TO RECIPIENT INTEGRITY AND

PERFORMANCE (DECEMBER 2015)

D. INTERIM CONFLICT OF INTEREST POLICY FOR FINANCIAL ASSISTANCE

IX. OTHER INFORMATION ................................... ERROR! BOOKMARK NOT DEFINED.

A. CHECKLIST FOR AVOIDING COMMON ERRORS ....... ERROR! BOOKMARK NOT

DEFINED.

B. HOW-TO GUIDES ........................................... ERROR! BOOKMARK NOT DEFINED.

C. ADMINISTRATIVE AND NATIONAL POLICY REQUIREMENTS .................. ERROR!

BOOKMARK NOT DEFINED.

D. REFERENCE MATERIAL .............................. ERROR! BOOKMARK NOT DEFINED.

I. Basic Information

Executive Summary The United States (U.S.) DOE SC program in Biological and Environmental Research (BER) announces it is receiving applications for research within the Biological Systems Science Division’s (BSSD) Genomic Science Program (GSP) (https://genomicscience.energy.gov). In this NOFO, applications are requested for:

i. Systems-level research to improve understanding of the molecular mechanisms underlying bioenergy feedstock productivity under varied and at times suboptimal environmental conditions.

ii. Systems biology-enabled investigations into the roles of microbes and microbial communities (including rhizosphere consortia, e.g. bacteria, fungi, diazotrophs, endophytes, viruses) in supporting plant productivity and vigor.

Funding Details Expected total available funding Up to $75 million Expected number of awards Approximately five (5) to fifteen (15) awards are expected Expected dollar amount of individual awards Approximately $1,000,000 - $3,000,000 per year. The maximum allowable budget per year is $3,000,000 independent of the proposed project period.

Expected award project period Up to five (5) years

Key Facts NOFO Title Systems Biology Research to Advance Bioenergy Crop Production NOFO Number DE-FOA-0003453 Announcement Type Amendment 0000091 Assistance Listing 81.049 Statutory Authority The programmatic authorizing statute is:

Section 646 of Public Law 95-91, U.S. Department of Energy Organization Act Section 901, et seq. of Public Law 109-58, Energy Policy Act of

Governing Regulations

Uniform Administrative Requirements, Cost Principles, and Audit Requirements for Federal Awards, codified at 2 CFR 200 U.S. Department of Energy Financial Assistance Rules, codified at 2

CFR 910

U.S. Department of Energy, Office of Science Financial Assistance Program Rule, codified at 10 CFR 605

Key Dates

Key dates are printed on the cover of this NOFO.

https://genomicscience.energy.gov/

Agency Contact Information

Grants.gov Customer Support

800-518-4726 (toll-free) support@Grants.gov

Portfolio Analysis and Management System (PAMS) Customer Support

855-818-1846 (toll-free) 301-903-9610 sc.pams-helpdesk@science.doe.gov

Technical/Scientific Program Contact

Kari Perez 240-931-9627 kari.perez@science.doe.gov

Administrative Contact (questions about budgets and eligibility)

Meredith Rutledge 202-329-6371 meredith.rutledge@science.doe.gov

Recommendation

SC encourages you to register in all systems as soon as possible. You are also encouraged to submit pre-applications and applications well before the deadline.

mailto:support@grants.gov mailto:sc.pams-helpdesk@science.doe.gov mailto:kari.perez@science.doe.gov mailto:Meredith.rutledge@science.doe.gov

II. Eligibility

A. Eligible Applicants

All types of domestic applicants are eligible to apply, except nonprofit organizations described in section 501(c)(4) of the Internal Revenue Code of 1986 that engaged in lobbying activities after December 31, 1995.

1. DOE/National Nuclear Security Administration (NNSA) National Laboratories

DOE/NNSA National Laboratories are not eligible to submit applications under this NOFO but may be proposed as subrecipients under another organization’s application. If recommended for funding as a proposed subrecipient, the value of the proposed subaward will be removed from the prime applicant’s award and will be provided to the laboratory through the DOE Field-Work Proposal System and work will be conducted under the laboratory’s contract with DOE. No administrative provisions of this NOFO will apply to the laboratory or any laboratory subcontractor. Additional instructions for securing authorization from the cognizant Contracting Officer are found in Section IX of this NOFO.

2. Non-DOE/NNSA Funded Research and Development Centers (FFRDC)

Non-DOE/NNSA FFRDCs are not eligible to submit applications under this NOFO but may be proposed as subrecipients under another organization’s application. If recommended for funding as a proposed subrecipient, the value of the proposed subaward may be removed from the prime applicant’s award and may be provided through an interagency agreement to the FFRDC’s sponsoring Federal Agency. Additional instructions for securing authorization from the cognizant Contracting Officer are found in Section IX of this NOFO.

3. Other Federal Agencies

Other Federal Agencies are not eligible to submit applications under this NOFO but may be proposed as subrecipients under another organization’s application. If recommended for funding as a proposed subrecipient, the value of the proposed subaward may be removed from the prime applicant’s award and may be provided through an interagency agreement. Additional instructions for providing statutory authorization are found in Section IX of this NOFO.

Notes for applicants of all types:

Applicants that are individual and/or not domestic organizations should be advised that:

• Individual applicants are unlikely to possess the skills, abilities, and resources to successfully accomplish the objectives of this NOFO. Individual applicants are encouraged to address this concern in their applications and to demonstrate how they will accomplish the objectives of this NOFO.

• Non-domestic applicants are advised that successful applications from non-domestic applicants include a detailed demonstration of how the applicant possesses skills, resources, and abilities that do not exist among potential domestic applicants.

This NOFO seeks to support basic research to advance understanding rather than to address commercial opportunities. Applications that propose research related to current commercial activity or current customer needs may be declined without merit review.

B. Cost Sharing

Cost sharing for basic and fundamental research is not required pursuant to an exclusion from the requirements of Section 988 of the Energy Policy Act of 2005.

Cost sharing is not required of DOE/NNSA National Laboratories, other Federal agencies, another Federal agency’s FFRDC, or their subcontractors at any tier. DOE/NNSA National Laboratories, other Federal agencies, and another Federal agency’s FFRDC may impose cost-sharing requirements on their contractors subject to their policies and procedures.

Cost sharing will not be considered as a factor during merit review or award selection.

C. Eligible Individuals

Individuals with the skills, knowledge, and resources necessary to carry out the proposed research as a Principal Investigator (PI) are invited to work with their organizations to develop an application. Individuals from underrepresented groups as well as individuals with disabilities are always encouraged to apply.

SC does not require that individuals be U.S. citizens or permanent residents to be proposed as a PI or in any other role under an award, but all personnel working or proposed to work under an award must have the legal right to perform such work in the jurisdiction where the work will be performed. Individuals at any stage of their career may be proposed as a PI if they have the skills, knowledge, and resources necessary to carry out the proposed research.

D. Limitations on Submissions

Applicant institutions are limited to one pre-application and/or applications for each PI at the applicant institution.

There is no limitation to the number of applications on which an institution appears as a subrecipient.

Should DOE receive submissions in excess of the applicable limits, DOE reserves the right, in its sole discretion, to request additional or clarifying information to ascertain the institution’s intended submissions. Otherwise, DOE will consider the latest received submissions to be the institution’s intended submissions.

• Pre-applications in excess of the limited number of submissions may be discouraged.

• Applications in excess of the limited number of submissions may be declined without review.

DOE/NNSA NATIONAL LABORATORY EFFORT

The scope of work to be performed by DOE/NNSA National Laboratories may not be more significant than the scope of work to be performed by the applicant.

The DOE/NNSA National Laboratory effort, in aggregate, shall not exceed 50 percent of the total estimated cost of the project, including the applicant’s and the DOE/NNSA National Laboratories’ portions of the effort.

LIMITATIONS ON PI

The PI on a pre-application or application may also be listed as a senior or key personnel including in any role on a proposed subaward, on an unlimited number of separate submissions.

III. Program Description

A. Purpose

The DOE SC program in Biological and Environmental Research (BER) announces it is receiving applications for research within the Biological Systems Science Division’s (BSSD) Genomic Science Program (GSP) (https://genomicscience.energy.gov) mission-space. In this NOFO, applications are requested for:

• Systems-level research to improve understanding of the molecular mechanisms underlying bioenergy feedstock productivity under changing and at times suboptimal environmental conditions,

• Systems biology-enabled investigations into the role(s) of microbes and microbial communities (including rhizosphere consortia, e.g. bacteria, fungi, diazotrophs, endophytes, viruses) in supporting plant productivity and vigor are also solicited.

SUPPLEMENTARY INFORMATION

Two areas vital to the Nation’s energy and environmental security motivate the BER research agenda: developing cost-effective biofuels and bioproducts and improving our ability to understand, predict, and mitigate the impacts of energy production in the face of a variable environment. BER has invested in plant and plant-microbe interactions research with the goal of advancing production of biofuels/bioproducts from domestic lignocellulosic and oilseed crop sources. These efforts have increased our understanding of the biological mechanisms underlying feedstock productivity and facilitated development of next- generation bioenergy crops that utilize novel, efficient bioenergy strategies that can be replicated on a mass scale. However, several knowledge gaps and challenges remain towards attaining the goal of developing vigorous crops with superior growth and yield under varying environmental conditions. A better understanding of the underlying genetic and physiological mechanisms influencing plant productivity, resource use efficiency, and adaptation and resilience to abiotic stress are needed.

Also of interest is how beneficial plant-microbe associations may enhance requisite plant processes to enable manipulation of these associations for improving plant traits. Furthermore, available computational technologies and infrastructure may provide opportunities to connect and integrate information across multiple spatial and temporal scales to better understand the behavior of complex biological systems and to develop a predictive understanding of sustainability outcomes over a range of future climate scenarios [U.S. DOE.2014. Research for Sustainable Bioenergy: Linking Genomic and Ecosystem Sciences, Workshop Report, DOE/SC- 0167. U.S. Department of Energy, Office of Science.

https://www.genomicscience.energy.gov/research-for-sustainable-bioenergy-linking-genomic-and-ecosystem-sciences/].

DOE-BER’s GSP (https://genomicscience.energy.gov/) supports fundamental research to identify the basic principles that drive biological systems. These principles govern translation of the genetic code into integrated networks of proteins, enzymes, regulatory elements, and metabolite pools underlying the functional processes of organisms. The Genomic Science program aims to support the DOE’s bioenergy development mission by leveraging omics-driven tools and systems biology approaches to address key challenges facing the sustainable https://genomicscience.energy.gov/ https://www.genomicscience.energy.gov/research-for-sustainable-bioenergy-linking-genomic-and-ecosystem-sciences/ https://www.genomicscience.energy.gov/research-for-sustainable-bioenergy-linking-genomic-and-ecosystem-sciences/ production of bioenergy crops as an economically and environmentally viable alternative resource for fuels, chemicals, and products currently produced from fossil fuel resources. This NOFO aims to build upon the advances made since previous BER investments in this area, seeking to apply systems biology and omics technologies to map the complex networks and molecular mechanisms of bioenergy crop growth, development, and metabolism for sustainable and resilient bioenergy crop production. Understanding the multi-organismal “biofuel crop+soil+microbe ecosystem” presents a unique challenge, which is further complicated by environmental impacts. The ability to predict plant and microbial species’ responses to a changing environment will be critical to understanding potential environmental impacts as well as for optimizing feedstock production.

Applications are solicited for systems biology-driven basic research on the fundamental principles of bioenergy crop production in relationship to the associated environmental context.

Species of interest include but are not limited to candidate bioenergy plants (e.g., sorghum, energy cane, Miscanthus, switchgrass, Populus) and non-food oilseed crops (e.g., Camelina).

Proposed projects should be hypothesis-driven and focus on understanding productivity and the effects of abiotic stresses and nutrient availability. Such deep understanding will enable the development of bioenergy crops that are tolerant to environmental stressors, require less agronomic inputs, and are resilient and/or adaptable to varying environmental conditions.

Acceptable topics include, but are not limited to, the following areas of interest. Applicants may address one or more subject areas within either or both main topics, but the overall application should be well integrated with all objectives and approaches designed to further understanding of the overarching, main goal:

i. Systems-level research to improve understanding of the molecular mechanisms underlying bioenergy feedstock productivity under varying and at times suboptimal environmental conditions. Proposed studies should provide better understanding of the molecular and physiological mechanisms that control bioenergy crop vigor, resource use efficiency, and resilience/adaptability to abiotic stress, as well as interactions with the surrounding environment. Topics can include but are not limited to:

a. Genetic manipulation of phenology to understand the traits and processes that affect the ability of a bioenergy crop to adapt to specific environmental conditions or stressors.

b. Processes that contribute to partitioning of photosynthates to various plant tissues to optimize biomass.

c. Investigations into the genetic and physiological mechanisms underlying processes that influence plant productivity such as resource use efficiency (e.g., water, nutrients, light); C and N metabolism and biomass allocation; vigor;

adaptability to specific environmental conditions; phenology; and

d. Utilization of genetic diversity and comparative genomics to identify key phenes/genes/alleles that confer key plant resilience traits, and to optimize plant species for various ecoregions of the U.S.

ii. Systems biology-enabled investigations into the role(s) of microbes and microbial communities (including rhizosphere consortia, e.g. bacteria, fungi, diazotrophs, endophytes, viruses) in supporting plant productivity and vigor. Proposed studies should contribute to a better understanding of bioenergy feedstock plant performance, adaptation, and resilience in varying environmental conditions and abiotic stressors.

Topics can include but are not limited to:

a. Influence of plant-associated microbiome composition and dynamics on fitness and productivity of bioenergy feedstock plants.

b. Microbial effects on soil as it pertains to overall plant productivity, particularly during crop establishment and growth.

c. Genomic basis by which plant genotypes cultivate specific interactions with rhizosphere communities and how microbes develop mutualistic relationship with plants over time and environments.

d. How plants differentiate between mutualists and pathogens, and how beneficial communities can be utilized to alleviate plant abiotic stress; and

e. Mechanisms controlling C inputs to and outputs from the belowground systems of bioenergy crops.

Additional Information:

This NOFO focuses on omics-driven basic research aimed at enabling the integrated development of sustainable bioenergy feedstock systems in terrestrial environments within the ecosystem context. Applications that include the development of integrative physiology-based models to attain a systems-level understanding of the plant and/or plant-microbiome ecosystem to identify key parameters of bioenergy plant sustainability are encouraged. Such applications should consider key variables such as genomic properties of biofuel crops and relevant biological processes (e.g. resource use efficiency, carbon and nitrogen metabolism, phenology, adaptation, rhizosphere community functions), enabling the quantitative, accurate prediction of plant performance and ecosystem processes under changing environments. In addition, applications that directly address bioenergy crops and their abiotic responses in a field setting are highly encouraged, as well as the use of computational technologies (e.g. machine learning) for integrative analyses and predictive modeling. Additionally, for applications focused on perennial crops, methods to reduce timelines such as the utilization of previously established perennial field sites are encouraged where applicable. Finally, applications focused on annual crops are encouraged to apply for an award duration of three years. Please see section ‘I. Basic Information’ of this NOFO for budgetary guidance for all project periods.

NOTE: BER encourages the submission of innovative “high-risk/high-reward” research applications that address critical knowledge gaps and have the potential for high impact. The probability of success and the risk- reward balance will be considered when making funding decisions. This NOFO encourages individual investigators as well as interdisciplinary teams that assemble a range of expertise into a coordinated approach. For the latter situation, applicants must include a clear plan describing the individual contributions of each participant, as well as an overall management scheme and the designation of a lead investigator and lead institution.

The following areas are not within the scope of this NOFO:

• Research on starch accumulation or nutritional qualities, digestion, and fermentation

• Studies of soybean, food-grade canola or other food-grade oilseed crops

• Crops targeted for food or human consumption, pharmaceutical production, or cosmetic use

• Applications targeting aquatic systems (e.g., algae)

• Applications focused on plant pathogen interactions

• Projects to develop life cycle analysis models

• Although the long-term vision of this research is to facilitate improvement of bioenergy feedstock crops, applications focused solely on applied breeding or breeding approaches will not be considered; and

• Applications primarily focused on plant or metagenomic sequencing are not encouraged for this NOFO and should instead be directed to the DOE Joint Genome Institute’s Community Science Program: https://jgi.doe.gov/user-programs/program-info/csp-overview/.

Other Supplementary Information:

The following programmatic areas within BER are at the interface with GSP’s sustainable bioenergy portfolio:

• Environmental Microbiology: The DOE-BER GSP within the BSSD includes research efforts in environmental microbiology focused on systems biology studies of regulatory, metabolic, and signaling networks of microbes, microbial consortia, and microbe-plant interactions involved in biogeochemical cycling of nutrients, and the development and application of –omics approaches to investigate microbial community processes involved in biogeochemical nutrient cycling in terrestrial ecosystems.

• Environmental System Science (ESS) research within Earth and Environmental Systems Sciences Division (EESSD) seeks to develop an integrated framework using a systems approach to elucidate the complex processes and controls on the structure, function, feedback, and dynamics of terrestrial ecosystems that span from the bedrock through the rhizosphere and vegetation to the atmospheric interface. The program scope advances foundational process knowledge from molecular to global scales and the interplay of key system components to enable an improved understanding of understudied ecosystems and environmental interfaces. This effort requires the linking of system components and their interfaces with ecological, watershed, and biogeochemical sciences to address key knowledge gaps across a range of spatial and temporal scales. Incorporation of process understanding into a range of scale appropriate models improves predictive understanding and future projections of the terrestrial system, which in turn enables the identification of new research questions and directions

Applications that focus on research that may be perceived to overlap with one of these programs need to provide details within the application that describes how the application is responsive to this specific NOFO.

Further information on DOE-BER objectives in this area of research can be found at:

https://www.genomicscience.energy.gov/sustainable-bioenergy/. Information on the research projects currently funded by the GSP and a description DOE-BER mission priorities and overall program organization can be found at: https://genomicscience.energy.gov/. Information on DOE- BER supported research efforts in ESS can be found at https://ess.science.energy.gov/program/.

https://jgi.doe.gov/user-programs/program-info/csp-%20overview/ https://jgi.doe.gov/user-programs/program-info/csp-%20overview/ https://www.genomicscience.energy.gov/sustainable-bioenergy/ https://ess.science.energy.gov/program/

Data Sharing and Promoting Inclusive and Equitable Research (PIER) Plan: Information about the DOE GSP data release policy, with which awardees will be expected to comply, is available at http://genomicscience.energy.gov/datasharing/. Any application submitted without a data sharing and digital data management plan will be returned without review. A PIER plan is also required. PIER development plans and resources can be found at https://science.osti.gov/grants/Applicant-and-Awardee-Resources/PIER-Plans. Applications submitted without a PIER plan will be declined without review.

Availability of User Facilities and Other Specialized Resources:

DOE has responsibility for programs and facilities that offer unique and complementary resources that support research in a wide variety of science areas. Applicants are encouraged to consider utilization or collaboration with DOE-funded facilities that have existing and dedicated financial support, thereby leveraging ongoing infrastructure investments, archived samples, User Facilities, and long-term data sets when developing their applications.

For Joint Genome Institute (JGI) and Environmental Molecular Sciences Laboratory (EMSL) capabilities (see table below), applicants should assess whether the project’s needs are within reasonable requests for the respective User Facility and reach out to the respective user program coordinator if the request might be considered large. Awarded projects will receive prioritized consideration for use of JGI capabilities, subject to an assessment of technical feasibility by the facility.

Examples of available user facilities and other specialized resources include:

Environmental Molecular Sciences Laboratory

(EMSL)

The EMSL (https://www.emsl.pnnl.gov/) located at the Pacific Northwest National Laboratory, is a DOE SC User Facility (https://science.osti.gov/User-Facilities). EMSL empowers scientific discovery of the mechanisms and dynamics that drive biological and environmental processes and interactions by providing users access to premier instruments for experimental research as well as igh Performance Computing (HPC). Experimental capabilities available include: advanced electron microscopy/imaging capabilities to study intra- and intercellular dynamics; nanoSIMS; computed x-ray tomography; high-resolution mass spectrometry and Nuclear Magnetic Resonance (NMR) spectroscopy for transcriptomics, metabolomics, and proteomics; controlled atmosphere plant growth chambers to study nutrient flux and interactions among plant roots, soil microbes and mineral surfaces; and software and associated hardware for data analytics and metabolic process modeling/simulation. These and other experimental and computational capabilities are available at no charge through a user proposal process (https://www.emsl.pnnl.gov/proposals ).

Applicants are also encouraged to explore the Facilities Integrating Collaborations for User Science (FICUS) initiative between JGI and EMSL (https://www.emsl.pnnl.gov/proposals/type/ficus-program ), through http://genomicscience.energy.gov/datasharing/ https://science.osti.gov/grants/Applicant-and-Awardee-Resources/PIER-Plans https://www.emsl.pnnl.gov/ https://science.osti.gov/User-Facilities https://www.emsl.pnnl.gov/proposals https://www.emsl.pnnl.gov/proposals/type/ficus-program which capabilities at both user facilities can be combined and accessed with one proposal.

High Performance Computing (HPC) Centers

The DOE Office of Science supports leadership and HPC User Facilities, which provide compute cycles and data storage through a proposal process to the scientific community. These resources include capabilities at EMSL (https://www.emsl.pnnl.gov/science/instruments-resources/mid-range-scientific-computing;

https://www.emsl.pnnl.gov/science/integrated-research-platforms/data-transformations), the National Energy Research Scientific Computing Center at the Lawrence Berkeley National Laboratory (LBNL) (https://www.nersc.gov), the Argonne Leadership Computing Facility at Argonne National Laboratory (ANL) (https://www.alcf.anl.gov/) and the Oak Ridge Leadership Computing Facility at Oak Ridge National Laboratory (ORNL) (https://www.olcf.ornl.gov/).

Joint Genome Institute (JGI)

The Joint Genome Institute (JGI) in Berkeley, California, is a DOE Office of Science User Facility that provides the scientific community access to state-of-the-art genomic sequencing and analysis capabilities, as well as modest amounts of deoxyribonucleic acid (DNA) synthesis and metabolomics capabilities, for microbial, plant, microbial community, and other (non- pathogen) targets. In all cases, the aim of the JGI is to provide to the national and international scientific community information on the genome-derived “parts lists” that support further discovery. These resources are available at no charge through a user proposal process (https://jgi.doe.gov/user-programs/).https://www.jgi.doe.gov). These resources are available at no charge through a user proposal process (https://jgi.doe.gov/user-programs/).

Applicants are also encouraged to explore the FICUS initiative between JGI and EMSL, through which capabilities at these (and potentially other) User Facilities can be combined and accessed with one proposal (https://jgi.doe.gov/user-program-info/community-science- program/how-to-propose-a-csp-project/emsl).

DOE Systems Biology Knowledgebase (KBase)

The U.S Department of Energy Systems KBase (https://www.kbase.us/) is an open-source software and data platform designed to meet the grand challenge of systems biology— predicting and designing biological function from the biomolecular (small scale) to the ecological (large scale). KBase is available for anyone to use, and enables researchers to collaboratively generate, test, compare, and share hypotheses about biological functions; perform large-scale analyses on scalable computing infrastructure; and combine experimental evidence and conclusions that lead to accurate models of plant and microbial physiology and community dynamics. The KBase platform has (1) extensible analytical capabilities (2) a web-browser-based user interface that supports building, sharing, and publishing reproducible and well-annotated analyses with integrated data; (3) access to extensive computational resources; and (4) a software https://www.emsl.pnnl.gov/science/instruments-resources/mid-range-scientific-computing https://www.emsl.pnnl.gov/science/instruments-resources/mid-range-scientific-computing https://www.emsl.pnnl.gov/science/integrated-research-platforms/data-transformations https://www.emsl.pnnl.gov/science/integrated-research-platforms/data-transformations https://www.nersc.gov/ https://www.alcf.anl.gov/ https://www.olcf.ornl.gov/ https://jgi.doe.gov/user-programs/ https://jgi.doe.gov/user-programs/ https://jgi.doe.gov/user-programs/ https://jgi.doe.gov/user-programs/ https://jgi.doe.gov/user-program-info/community-science-program/how-to-propose-a-csp-project/emsl https://jgi.doe.gov/user-program-info/community-science-program/how-to-propose-a-csp-project/emsl https://jgi.doe.gov/user-program-info/community-science-program/how-to-propose-a-csp-project/emsl https://www.kbase.us/ development kit allowing the community to add functionality to the system.

National Microbiome Data Collaborative

(NMDC)

The DOE NMDC supports microbiome data exploration through a sustainable data discovery platform that promotes open science and shared-ownership across a broad and diverse community of researchers (https://microbiomedata.org/). For more information on NMDC collaborations visit https://microbiomedata.org/community/.

Neutron Beam Facilities

DOE provides the scientific community access to high flux neutron sources that are capable of providing structural and chemical information often unavailable using other technologies. DOE has two such facilities at the ORNL, the Spallation Neutron Source ;(https://neutrons.ornl.gov/sns/) and the High Flux Isotope Reactor (https://neutrons.ornl.gov/hfir/). Use of the neutron sources is available at no charge through a user proposal process. For more information about the BER-supported structural biology resources at the synchrotron and neutron facilities, visit:

https://www.berstructuralbioportal.org/.

Synchrotron Light Sources

DOE provides the scientific community access to synchrotron light sources that are capable of providing structural and chemical information often unavailable with conventional sources of x-rays. Use of each synchrotron light source is available at no charge through its user proposal process. Information about each DOE synchrotron User Facility can be found at: ANL (https://www.aps.anl.gov/); Brookhaven National Laboratory (https://www.bnl.gov/ps/); LBNL (https://www.als.lbl.gov/); and Stanford Synchrotron Radiation Laboratory (https://www-ssrl.slac.stanford.edu/index.html). For more information about the BER-supported structural biology resources at the synchrotron and neutron facilities, visit:

https://www.berstructuralbioportal.org/.

Annual Meetings

If a project is funded, beginning in the first year of funding, one or more project participants will be required to attend an annual GSP PI meeting, generally held in the National Capital Region.

Reasonable travel expenses may be included as part of the project budget.

Teaming Arrangements

Multi-Institutional Teams

SC uses two different mechanisms to support teams of multiple institutions.

COLLABORATIVE APPLICATIONS

Collaborative applications (in which each team member submits its own application with a common project narrative) will not be accepted under this NOFO.

https://microbiomedata.org/ https://microbiomedata.org/community/ https://neutrons.ornl.gov/sns https://neutrons.ornl.gov/hfir https://www.berstructuralbioportal.org/ https://www.aps.anl.gov/ https://www.bnl.gov/ps/ https://www.als.lbl.gov/ https://www-ssrl.slac.stanford.edu/index.html https://www.berstructuralbioportal.org/

SUBAWARDS1

Multi-institutional teams must submit one application from a designated lead institution with all other team members proposed as subrecipients.

DOE/NNSA National Laboratories2, other Federal agencies, and another Federal agency’s FFRDCs3, if participating in a team led by another institution, must be proposed as subrecipients.

Note that the value of any such proposed subaward may be removed from any such prime award:

DOE may make separate awards to Federally affiliated institutions.

Open Science

SC is dedicated to promoting the values of openness in Federally supported scientific research, including, but not limited to, ensuring that research may be reproduced and that the results of Federally supported research are made available to other researchers. These objectives may be met through any number of mechanisms including, but not limited to, data access plans, data sharing agreements, the use of archives and repositories, and the use of various licensing schemes.

The use of the phrase “open-source” does not refer to any particular licensing arrangement, but is to be understood as encompassing any arrangement that furthers the objective of openness.

B. Program Goals, Objectives, and Priorities

The Office of Science’s (SC) mission is to deliver scientific discoveries and major scientific tools to transform our understanding of nature and advance the energy, economic, and national security of the United States (U.S.). SC is the Nation’s largest Federal sponsor of basic research in the physical sciences and the lead Federal agency supporting fundamental scientific research for our Nation’s energy future.

SC accomplishes its mission and advances national goals by supporting:

• The frontiers of science—exploring nature’s mysteries from the study of fundamental subatomic particles, atoms, and molecules that are the building blocks of the materials of our universe and everything in it to the DNA, proteins, and cells that are the building blocks of life. Each of the programs in SC supports research probing the most fundamental disciplinary questions.

• The 21st Century tools of science—providing the nation’s researchers with 28 state-of-the-art national scientific user facilities, the most advanced tools of modern science, propelling the

1 Subawards are made to subrecipients. Both terms are defined in 2 CFR 200.1 (https://www.ecfr.gov) 2 The phrase “National Laboratories” is used broadly to encompass DOE/NNSA laboratories and sites capable of performing the work described in this NOFO and capable of receiving funds through the DOE Field Work System.

3 An authoritative list of all Federally Funded Research and Development Centers (FFRDCs) may be found at https://www.nsf.gov/statistics/ffrdclist/ https://www.ecfr.gov/ https://www.nsf.gov/statistics/ffrdclist/

U.S. to the forefront of science, technology development, and deployment through innovation.

• Science for energy and the environment―paving the knowledge foundation to spur discoveries and innovations for advancing the Department’s mission in energy and environment. SC supports a wide range of funding modalities from single principal investigators to large team-based activities to engage in fundamental research on energy production, conversion, storage, transmission, and use, and on our understanding of the earth systems.

SC is an established leader of the U.S. scientific discovery and innovation enterprise. Over the decades, SC investments and accomplishments in basic research and enabling research capabilities have provided the foundations for new technologies, businesses, and industries, making significant contributions to our nation’s economy, national security, and quality of life.

C. Award Contribution to Goals and Objectives

Awards resulting from this NOFO are intended to increase our understanding of scientific phenomena.

D. Performance Goals

You will be expected to demonstrate progress toward increasing knowledge in annual progress reports and presentations at annual PI meetings.

E. Substantial Involvement

Not applicable.

F. Program Unallowable Costs

You must apply the cost principles of 2 CFR 200, as modified by 2 CFR 910 and 10 CFR 605, to your application and any resulting award.

G. Citations to Statutes and Regulations

The programmatic authorizing statutes are:

Section 646 of Public Law 95-91, U.S. Department of Energy Organization Act Section 901, et seq. of Public Law 109-58, Energy Policy Act of 2005 The governing regulations are:

Uniform Administrative Requirements, Cost Principles, and Audit Requirements for Federal Awards, codified at 2 CFR 200 U.S. Department of Energy Financial Assistance Rules, codified at 2 CFR 910 U.S. Department of Energy, Office of Science Financial Assistance Program Rule, codified at 10

CFR 605

H. Program History

You can learn about SC’s history at https://science.osti.gov/About/History. You can read about our achievements at https://science.osti.gov/Science-Features/Science-Highlights. You can find information about all of our awards at https://pamspublic.science.energy.gov/WebPAMSExternal/interface/awards/AwardSearchExtern al.aspx.

I. Other Information

ANTICIPATED AWARD SIZE

The award size will depend on the number of meritorious applications and the availability of appropriated funds.

PERIOD OF PERFORMANCE

DOE anticipates making awards with a project period of up to five (5) years. Please note that the project period is independent of the yearly award size which is up to $3,000,000 per year.

Continuation funding (funding for the second and subsequent budget periods) is contingent on:

(1) availability of funds appropriated by Congress and future year budget authority; (2) progress towards meeting the objectives of the approved application; (3) submission of required reports;

and (4) compliance with the terms and conditions of the award.

AWARD BUDGET PERIODS

SC is committed to distributing workloads (internally and externally) across as much of the calendar as is practical. Accordingly, awards made under this NOFO will generally be made with budget periods that end between December 1 and June 30. New awards may be made with a first budget period of more than 12 months.

Applicants should prepare budgets with 12-month budget periods. Actual start dates and cycle dates will be negotiated if an application is recommended for award. Budget periods will generally not be made for less than nine (9) months or more than 18 months.

https://science.osti.gov/About/History https://science.osti.gov/Science-Features/Science-Highlights https://pamspublic.science.energy.gov/WebPAMSExternal/interface/awards/AwardSearchExternal.aspx https://pamspublic.science.energy.gov/WebPAMSExternal/interface/awards/AwardSearchExternal.aspx

IV. Application Contents and Format

A. Preliminary Submissions

1. Letter of Intent (LOI)

Not applicable.

2. Pre-application

Pre-Application Due Date The pre-application due date is printed on the cover of the NOFO.

ENCOURAGE/DISCOURAGE DATE

The pre-application response date is printed on the cover of the NOFO.

A pre-application is required and must be submitted by the date indicated on the cover of the

NOFO.

Pre-applications will be reviewed for responsiveness of the proposed work to the research topics identified in this NOFO. DOE will send a response by email to each applicant encouraging or discouraging the submission of an application by the date indicated on the cover of the NOFO.

Applicants who have not received a response regarding the status of their pre-application by this date are responsible for contacting the program to confirm this status.

Applications that have not been encouraged by DOE may be declined without merit review.

The pre-application must begin with a title page that will not count toward the pre-application page limitation. Include, at the top of the first page, the following information:

Title of Pre-application PI Name, Job Title [Lead] Institution

PI Phone Number, PI Email Address NOFO Number: Include the NOFO Number indicated on the cover of this NOFO

Include a list of all senior/key personnel at the applicant institution.

Include a list of all senior/key personnel at the applicant and team member institutions.

List of Collaborating Institutions Including Subrecipients [if applicable] PI Names and Job Titles at the Collaborating Institutions Including Subrecipients

The material listed here defines the required content of a title page. Additional material is not allowed.

The first page of the pre-application must specify at least one scientific hypothesis whose investigation motivates the proposed work, using no more than 100 words, in a box with a black border. For any hypothesis that is not itself innovative, the pre-application must describe at least one innovative insight into how the hypothesis can be investigated that may be exploited by the planned research.

This information must be followed by a clear and concise description of the objectives and technical approach of the proposed research. The pre-application may not exceed three pages, when printed using standard letter-size (8.5-inch x 11-inch) paper with 1-inch margins (top, bottom, left, and right). The body text font must not be smaller than 11 point. Figures and references, if included, must fit within the three-page limit. Pre-applications that exceed the page limit will be discouraged. It is the responsibility of the applicant to include sufficient information in the pre-application to enable evaluation of responsiveness to this announcement.

In addition, the pre-application must include a listing of senior/key personnel and a listing of individuals who should not serve as merit reviewers of a subsequent application. Detailed instructions for how to craft the required listings are provided in Section IX of this NOFO. Note that the listing of individuals who should not serve as merit reviewers is rarely empty because the instructions contain mandatory inclusions requirements. This listing will not count toward the pre-application’s page limit. The list of individuals must be included as an “Additional Attachment” to your pre-application in the Portfolio Analysis and Management System (PAMS).

The pre-application may include a list of suggested reviewers (including email address and organizational affiliation) who they believe are especially well qualified to review the application. DOE is under no obligation to consider any suggested reviewers.

The pre-application must be machine-readable. Do not submit a scanned image of a printed document.

PRE-APPLICATION REVIEW

Those pre-applications that are encouraged will be used to help SC begin planning for the application peer review process. SC’s intent in discouraging submission of certain applications is to save the time and effort of applicants in preparing and submitting applications not responsive to this NOFO.

The PI will be automatically notified when the pre-application is encouraged or discouraged.

PAMS will send an email to the PI from PAMS.Autoreply@science.doe.gov, and the status of the pre-application will be updated at the PAMS website https://pamspublic.science.energy.gov/.

Notifications are sent as soon as the decisions to encourage or discourage are finalized.

PRE-APPLICATION SUBMISSION

Pre-applications are created in the software system of your choice and must be submitted electronically through the DOE SC PAMS website https://pamspublic.science.energy.gov/. You cannot draft or edit a pre-application in PAMS. Do not submit a pre-application through FedConnect or Grants.gov.

mailto:PAMS.Autoreply@science.doe.gov https://pamspublic.science.energy.gov/ https://pamspublic.science.energy.gov/ https://www.fedconnect.net/ https://www.grants.gov/

Pre-applications may be submitted by a PI or by other users at the PI’s institution with the “Submit to DOE” privilege in PAMS.

Applicants are strongly encouraged to inform their DOE Program Manager if teaming arrangements, proposed personnel, topics, or the anticipated title change between submitting the pre-application and when an application is submitted, to ensure that their application is properly linked to their pre-application and that reviewers are properly assigned to the application.

Detailed instructions about how to submit a pre-application are in Section IX of this NOFO.

B. Application

Applications in response to this NOFO must be submitted through Grants.gov. Detailed instructions for registering in and using Grants.gov are in Section IX of this NOFO.

C. Component Pieces of the Application

LETTERS OF COLLABORATION OR ACCESS

Letters from collaborators or from institutions providing access to data, models, software, equipment and/or facilities may be appended to your project narrative and are not considered part of the project narrative’s page limit. Please ensure that letters from collaborators or from institutions providing access to data, models, software, equipment and/or facilities only describe the nature of the collaboration or the access to data, models, software, equipment and/or facilities. Letters of recommendation are not allowed in applications under this NOFO.

All letters may be addressed “To Whom It May Concern:”.

Letters of collaboration or access should be placed in Appendix 8 (Other Attachments). Letters of collaboration or access must not be written as recommendation or endorsement letters, which are not allowed. Each letter of collaboration or access may contain two and only two sentences and must use the following format:

Dear <Principal Investigator Name>:

If your application entitled, “<Application Name>,” is selected for funding under the NOFO Name, it is my intent to collaborate in this research by <Complete sentence with a very short description of what the collaborator offers to do or provide>.

Thank you for the opportunity to participate.

Sincerely, <Collaborator’s Name and Signature Block.>

SCIENTIFIC USER FACILITIES

Documentation from any SC scientific user facility (https://science.osti.gov/User-Facilities) may be provided with other letters of collaboration or access in Appendix 8 (Other Attachments).

1. SF-424 (R&R)

Complete this form first to populate data in other forms. Complete all the required fields in accordance with the pop-up instructions on the form. The list of certifications and assurances referenced in Field 17 is available on the DOE Financial Assistance Forms Page at https://energy.gov/management/office-management/operational-management/financial-assistance/financial-assistance-forms under Certifications and Assurances4. Applicants are bound by their representations and certifications in SAM.gov.

TYPE OF SUBMISSION (FIELD 1)

Select the checkbox for “Application” for an initial submission. Select the checkbox for “Changed/Corrected Application” if submitting an updated version of an application. Do not submit pre-applications via Grants.gov: Do not select the checkbox for “Pre-application.”

IDENTIFYING NUMBERS (FIELD 4)

UEI AND EIN NUMBERS (FIELDS 5 AND 6)

The Uniform Entity Identifier (UEI) and Employer Identification Number (EIN) fields on the SF-424 (R&R) form are used in PAMS to confirm the identity of the individual or organization submitting an application.

• Enter the UEI as a 12-digit alpha-numerical sequence.

• Enter the EIN as a nine-digit number.

• Do not use hyphens or dashes.

• SC does not use the 12-digit EIN format required by some other agencies.

• Applications will not be rejected if an applicant’s system-to-system service uses a…