Systems Biology of Bioenergy Relevant Microbes to Enable Production of Next Generation Biofuels | Apply Online

Frequently Asked Questions (FAQs)

1. What agency is offering this grant opportunity?

This funding opportunity was released by the Department of Energy (DOE) Office of Science through its Office of Biological and Environmental Research (BER).

2. What program area does this funding opportunity support?

The opportunity supports research under DOE BER's Genomic Science program, with a focus on microbes that can help enable next generation biofuels.

3. What is the main purpose of this FOA?

The core purpose is to fund fundamental and enabling research that uses systems biology and genomics-driven approaches to better understand, build, and optimize bioenergy-relevant microorganisms so they can produce advanced fuels more efficiently, more reliably, and at meaningful scales for energy production.

4. What is the Funding Opportunity Number?

The Funding Opportunity Number is DE-FOA-0001060.

5. What CFDA program is associated with this opportunity?

This opportunity is listed under CFDA 81.049, the Office of Science Financial Assistance Program.

6. What type of grant opportunity is this described as?

It is described as a discretionary grant opportunity in the Science and Technology and other R&D category.

7. What research topics or directions are supported?

The FOA calls for applications in three main research directions: (1) development of promising new model organisms relevant to biofuels production, (2) development of novel microbial functional capabilities and biosynthetic pathways directly relevant to producing advanced biofuels, and (3) development of analytical technologies or high-throughput screening approaches that enable the organism and pathway work.

8. What does DOE mean by developing "new model organisms" for biofuels?

In this FOA, developing new model organisms means moving beyond common lab organisms by establishing new microbes as tractable, well-characterized experimental models. Examples of activities include improving genetic tools, generating foundational omics datasets, mapping regulatory and metabolic networks, and demonstrating predictable outcomes from engineering changes.

9. What kinds of microbes are of interest for the new model organism direction?

DOE signaled interest in microbes that naturally perform chemistry useful for biofuels, such as organisms that tolerate harsh industrial conditions, consume complex biomass-derived substrates, or naturally produce fuel-like compounds, but that need better experimental accessibility and systems-level understanding.

10. What does the FOA mean by "novel microbial functional capabilities" for advanced biofuels?

This direction includes designing, introducing, or optimizing biosynthetic pathways that generate higher-value fuel molecules beyond conventional ethanol, along with improving underlying cellular functions that make production feasible.

11. What underlying microbial functions are specifically called out as important for fuel production?

The FOA highlights functions such as carbon utilization, electron and redox balancing, tolerance to solvents or inhibitors, secretion, and overall metabolic efficiency.

12. What metabolic or engineering challenges does DOE expect applicants to address?

The FOA specifically emphasizes challenges that can arise when pathways are modified, including growth defects, buildup of toxic intermediates, regulatory bottlenecks, cofactor imbalances, and tradeoffs between cell fitness and product formation.

13. What approaches are implied to be competitive for diagnosing and overcoming these constraints?

Competitive projects would typically propose systems biology measurements to diagnose constraints and then use integrative strategies to overcome them, such as rational design, dynamic control, adaptive evolution, or related approaches.

14. What kinds of technology development does DOE want in the third research direction?

DOE invites new analytical technologies and high-throughput screening approaches that enable the organism and pathway work. Examples mentioned include faster and more informative phenotype/product assays, scalable methods to measure pathway fluxes or metabolite pools, improved single-cell or time-resolved analytics, automated strain construction/testing workflows, and screening platforms for large engineered variant libraries under relevant conditions.

15. Does technology development need to be connected to biological goals?

Yes. The FOA emphasizes that technology development should be tied directly to the biological goals, meaning tools should help discover mechanisms, select better strains, and validate models for biofuel-relevant traits.

16. How many awards did DOE anticipate making?

DOE anticipated making about 25 awards.

17. What was the estimated total funding available for the program?

The estimated total program funding level was $8,000,000.

18. What was the expected award size range?

Individual awards were expected to range from $750,000 (floor) to $1,500,000 (ceiling).

19. Is cost sharing required?

No. Cost sharing was not required.

20. Who is eligible to apply?

Eligibility was broadly open to most entity types, with specific exclusions noted by the FOA.

21. Which entities were explicitly excluded from applying?

The FOA states that other federal agencies, Federally Funded Research and Development Center (FFRDC) contractors, and 501(c)(4) nonprofit organizations that engaged in lobbying activities after December 31, 1995 were not eligible to apply as applicants.

22. Are collaborations with DOE National Laboratories or other federal laboratories allowed?

Yes. Collaborations with federal laboratories and FFRDCs, including DOE National Laboratories, were explicitly allowed and encouraged when they fill critical gaps in expertise.

23. Is there a cap on how much of the budget can go to federal labs or FFRDCs?

Yes. The FOA constrained federal laboratory and FFRDC participation to no more than 50 percent of the total project budget.

24. What does the 50 percent budget constraint imply about the role of the primary applicant?

It reinforces DOE's expectation that the primary applicant team will carry the majority of the work and budget, even when national labs or FFRDCs are included as collaborators.

25. When was this funding opportunity posted?

The FOA was posted on December 20, 2013.

26. What was the application deadline?

The application deadline was March 14, 2014.

27. When was the FOA archived?

The archive date listed was June 16, 2014.

28. What is the scientific emphasis of the FOA: applied demonstrations or fundamental research?

The FOA is aimed at fundamental and enabling research, especially work that links genome-level understanding to measurable function and can translate into improved microbial performance for fuel-related bioconversion.

29. What kind of linkage between biology and outcomes is the FOA emphasizing?

It emphasizes connecting genome-level understanding (genomics and systems biology) to measurable function, with the end goal of making microbial performance for advanced fuel production more predictable and improvable.

30. Are there DOE contacts for administrative and technical questions?

Yes. The listing provided points of contact at DOE for both grants administration and programmatic questions, indicating applicants could engage DOE to interpret requirements and align proposed research with Genomic Science program priorities.