In this work, we will investigate how the pine seed microbiome confers resilience to lodgepole pine forests common throughout the western US

The Department of Agriculture National Institute of Food and Agriculture awarded Colorado State University $849,998 on February 1, 2026, under the Agriculture and Food Research Initiative (AFRI) to investigate how the pine seed microbiome confers resilience to lodgepole pine forests throughout the western United States.

The research employs genome-resolved metagenomics, metatranscriptomics, germination tests, and greenhouse seedling bioassays to test whether the seed microbiome acts as a source of microorganisms that colonize root tissues and the rhizosphere post-fire, providing beneficial services to seedlings. The work examines how global change disturbances—varying fire severities and bark beetle-induced tree mortality—influence seed microbiome viability and post-fire tree recovery. The project will identify specific seed microbiome members that promote plant growth through recovery of environmental isolates from Pinus contorta seeds. Results are intended to provide insights into microbiome processes governing forest resilience post-disturbance and offer biological solutions to enhance vegetation regeneration efforts.

Performance runs from February 1, 2026, through January 31, 2029, at Fort Collins, Colorado. Colorado State University's Sponsored Programs division serves as the recipient. The US Forest Service participates as a sub-grantee, with Dr. Rhoades contributing to study design, site selection, and data analysis for germination and seedling bioassays; coordinating pinecone collection and greenhouse assays; and serving as liaison with US Forest Service land management staff on the Medicine Bow-Routt National Forest. The sub-award was executed June 16, 2026.

The work will leverage preliminary data identifying bacteria in pinus contorta seeds and hinting at strategies that these communities may utilize to colonize burned soils. Employing a research approach incorporating genome-resolved metagenomics and metatranscriptomics, germination tests, and greenhouse seedling bioassays, we will test the hypothesis that the seed microbiome acts as a source of microorganisms that colonize root tissues and the rhizosphere post-fire, occupying niches made available by fire disturbance and providing beneficial services to seedlings. Furthermore, we will investigate how global change disturbances (varying fire severities, bark beetle-induced tree mortality) influence the viability of the seed microbiome, with implications for post-fire tree recovery. Finally, we will identify specific seed microbiome members that promote plant-growth through the recovery of environmental isolates from P. Contorta seeds. Together, results from this work will provide new insights into microbiome processes that could govern forest resilience post-disturbance and offer biological solutions that may enhance vegetation regeneration efforts.