Breaking Down the Shutdown Deal: What It Means for Research, Agriculture, and Conservation

After 43 days of a partial federal government shutdown, Congress reached an agreement to reopen the government and move forward on key funding legislation. Following bipartisan passage in the Senate — with all Republicans and eight Democrats voting in favor — the House returned to Washington and voted to approve the same deal. President Trump signed the bill, officially reopening the government and restoring federal operations.

The legislative package includes a short-term continuing resolution through January, a full FY26 Agriculture–FDA appropriations bill, and a one-year Farm Bill extension. While additional funding decisions still lie ahead, this agreement provides clarity for agencies and programs that have been stalled for more than six weeks.

Below is a breakdown of what’s included and what it means for research institutions, nonprofits, agricultural producers, and conservation professionals.

1. Government Reopening: What’s in the Package?

The agreement ends the shutdown through a continuing resolution that maintains FY24 funding levels into January. It also includes:

• A full FY26 Agriculture–FDA budget

• A one-year Farm Bill extension

• Congressional direction to maintain core USDA research functions

• Immediate restoration of federal operations following the President’s signature

Back Pay for Furloughed Workers
According to a 2025 OPM guidance document, furloughed employees will receive back pay as soon as administratively possible, even if processed outside a normal pay period.

2. FY26 Appropriations: What’s Funded, What’s Not, and What’s New

The package includes full FY26 funding for Agriculture–FDA accounts (as well as VA and Legislative Branch budgets). Although many accounts fall below FY24 levels, others are protected or receive modest increases.

Key Research & Conservation Accounts

• Conservation Operations: $850,000,000 (-7.1% from FY24)

• Conservation Technical Assistance (CTA): $697,624,000 (-10.2% from FY24)

• NIFA Research & Education Activities: $1,075,810,000 (-0.02% from FY24)

• Ag and Food Research Initiative (AFRI): $435,000,000 (-2.25% from FY24)

• Sustainable Ag Research & Education (SARE): $48,000,000 (No change from FY24)

• Ag Research Service (ARS) - Salaries & Expenses: $1,793,063,000 (+0.28% from FY24)

• FPAC Business Center: $167,633,000 (-44.9% from FY24)

Notable Report Language: Congress rejected all proposed USDA research program terminations and laboratory closures from the President’s budget request. Both extramural and intramural research are expected to be funded at least at FY24 levels.

Contextual Notes: Many reductions reflect staffing capacity constraints at USDA rather than policy shifts. These numbers are lower than those in the Senate Agriculture Appropriations Subcommittee’s original draft but offer stability for the year ahead.

Shutdown Protection Moving Forward
Because the FY26 Agriculture–FDA bill is now law, these agencies will not face disruptions if another shutdown occurs in January.

Next Steps
Lawmakers now have until January 30 to negotiate the remaining nine FY26 appropriations bills.  Track updates via the AAAS R&D Dashboard. 

3. Farm Bill Extension: What’s Included and Why It Matters

The package includes a one-year Farm Bill extension through September 30, 2026, preventing disruptions across conservation, commodity, and nutrition programs while giving Congress additional time to negotiate a full reauthorization. The extension also ensures continued operation of programs that were not covered in the summer budget reconciliation bill.

Key Notes on Conservation and Agriculture

1. CRP Transition Incentive Program (TIP) Eliminated for 2025–2026
The extension eliminates funding for the CRP Transition Incentive Program (TIP) for the 2025 and 2026 program years. TIP has historically supported the transition of CRP land from retiring farmers to beginning, socially disadvantaged, and veteran farmers. The removal of TIP funding marks a notable change in conservation program support for underserved producers.

2. Limits Removed on EQIP and CSP Payments
The extension removes an existing limitation on payments from both the Environmental Quality Incentives Program (EQIP) and the Conservation Stewardship Program (CSP) to a single entity. This may allow larger operations to access a greater share of EQIP and CSP payments, raising questions about how funds will be distributed among producers of different sizes.

3. Coverage for Programs Not Addressed in Reconciliation
Because the summer reconciliation bill focused primarily on mandatory spending changes and IRA-related conservation funding, several Farm Bill-authorized programs were left without updated authority. This extension restores or maintains authority for those programs, ensuring continuity until Congress completes a full Farm Bill reauthorization.