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Grants to USA Entities for Scientific Research
on Microbial Processes in the Ecosystem

Systems Biology Enabled Microbiome Research to Facilitate Predictions of Interactions and Behavior in the Environment

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U.S. Department of Energy (DOE) - Office of Science (SC) - Biological and Environmental Research (BER)

LOI Date:


Deadline Date:

04/04/22 11:59 PM ET


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Grants to USA and territories entities and teams for basic scientific research that will enhance understanding of different microbial processes in the ecosystem. Applicants must submit a pre-application in order to be considered for funding. Required registrations may take several weeks to complete.

The DOE SC program in Biological and Environmental Research (BER) hereby announces its interest in receiving applications for research within the Biological System Science Division (BSSD) Genomic Science Program (GSP) mission-space. This FOA solicits applications for basic research that will fundamentally enhance or transform our understanding of microbial processes in terrestrial ecosystems. Of interest to the Program are interdisciplinary projects grounded in holistic, systems-level approaches to understand microbial community interactions and biogeochemical cycling. Specifically, the Program seeks to elucidate fundamental principles that advance our understanding of regulatory, metabolic, and signaling networks among microbes, in microbe-plant interactions, the cycling and long-term storage or sequestration of carbon in soils, and the biogeochemical conversion of other elements, including nutrients, particularly as they relate to rapidly changing environmental conditions.

Proposed studies might include, but are not limited to the following topic areas:

  • Systems biology studies that leverage omics and modeling approaches to understand the rate and magnitude of the role of microbes in biogeochemical cycles (e.g., carbon, nitrogen, phosphorus, sulfur, and other elements) in the environment and to understand feedbacks with and responses to global change. Proposed studies should focus on environmental processes but may include research on model microbes or consortia with demonstrable relevance to biogeochemical processes in terrestrial ecosystems. Of particular interest are studies that seek to develop fundamental ecological principles that allow scaling and modeling of processes beyond the molecular realm.
  • Studies that provide insight into the mechanisms of microbial interactions with other microbes and with plants, signaling, resource sharing, and communication at the molecular, cellular, and community scales. Such studies may include inquiries into microbial community-scale metabolic and regulatory models and could examine fundamental ecological principles that govern the exchange of energy and metabolites in soil environments, including the breakdown of complex organic matter, such as lignocellulose. Applications that leverage high-throughput cultivation and reconstruction of microbial communities to reconcile observed, environmental community behavior are welcome.
  • The development of frameworks and techniques to manipulate environmental microbiomes for the purpose of understanding and predicting their behavior, including bioenergy crop sustainability and productivity, as well as soil carbon storage. This may include studies of complex interkingdom biological dependencies among soil microbial community members (e.g., bacteria, fungi, archaea, viruses, and protists) and the spheres they inhabit (e.g., phycosphere and rhizosphere) and might consider the impact of climate, precipitation, gas exchange, or environmental stressors.
  • Research on the development of novel environmental omics-based techniques for the interrogation of microbial communities. Such projects should address the adaptation of genome-enabled techniques (e.g. community-scale -omics, isotope tracing, visualization and quantification of activities etc.) to interrogate BER-relevant processes. Requisite projects are strengthened by field applications or use of model consortia with relevance to biogeochemical cycling processes or the breakdown of complex organic matter.

For further information, see

GrantWatch ID#:

GrantWatch ID#: 200657

Estimated Total Program Funding:


Number of Grants:

Approximately 10 to 14 awards are expected.

Estimated Size of Grant:

Award Ceiling: $1,200,000 per year
Award Floor: $250,000 per year

A multi-institutional team is limited to a request of no more than $1,200,000 per year.

Term of Contract:

DOE anticipates making awards with a project period of three years.

DOE is interested in seeing projects supported under this FOA begin work by August 2022.

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.

Additional Eligibility Criteria:

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.

Federally affiliated entities must adhere to the eligibility standards listed here:

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 for assistance. Individuals from underrepresented groups as well as individuals with disabilities are always encouraged to apply for assistance.

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

DOE/National Nuclear Security Administration (NNSA) National Laboratories, other Federal agencies, and another Federal agency’s FFRDCs, if participating in a team led by another institution, must be proposed as subrecipient.

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

Pre-Application Information:

- Submission Deadline for Pre-Applications: January 14, 2022 at 5:00 PM Eastern Time. A Pre-Application is required.
- Pre-Application Response Date: January 28, 2022 at 5:00 PM Eastern Time
- Submission Deadline for Applications: April 4, 2022 at 11:59 PM Eastern Time
- It is anticipated that the award selection will be completed by June 2022. It is expected that awards will be made in Fiscal Year 2022.

The Department of Energy (DOE) Office of Science (SC) encourages you to register in all systems as soon as possible. You are also encouraged to submit letters of intent (LOIs), pre-applications, and applications well before the deadline.

Organizations must have a Data Universal Numbering System (DUNS) Number, active System for Award Management (SAM) registration, and account to apply for grants.

Applicant institutions are limited to no more than one pre-application or applications for each PI at the applicant institution. The PI on a pre-application or application may also be listed as a senior or key personnel on separate submissions without limitation.

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For a list of relevant application documents, go to the Package tab (press Preview) on the link above.

Contact Information:

Before starting your grant application, please review the funding source's website listed below for updates/changes/addendums/conferences/LOIs.

Submit pre-application online:

Technical/Scientific Program Contact:
Dr. Boris Wawrik Customer Support:
800-518-4726 (toll-free)

PAMS Customer Support:
855-818-1846 (toll-free)

CFDA Number:


Funding or Pin Number:


URL for Full Text (RFP):

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