Project Objectives

The Plant-Microbe Interfaces (PMI) Science Focus Area seeks to develop a genome-informed understanding of plant-microbiome systems that enables their rational design for resilient biomass production, phytoming critical minerals, and the emerging bioeconomy. Over the next three years, PMI will determine how Populus and its associated microbiome respond to combined heat and drought stress, using this interaction for understanding plant resilience under increasingly variable and extreme environmental conditions. Grounded in genomic science, the program integrates systems biology, plant science, microbiology, ecology, and advanced computational approaches to connect genes to plant microbiome systems across variable environments. Populus provides an ideal model because of its ecological importance, extensive genomic resources, role as a bioenergy feedstock, and potential for critical material recovery. Three tightly integrated objectives guide the research: (1) identify the host genetic associations of microbiome-conferred resilience; (2) determine the molecular and ecological mechanisms linking microbiome assembly to host function; and (3) integrate these discoveries across laboratory, greenhouse, and field environments to establish a genome-informed, multi-scale modeling framework relating plant genetics, microbial traits, and environment to plant performance under variable environmental conditions. These advances will support DOE BER’s mission to understand, predict, and ultimately harness biological systems to advance feedstock production for biomass, phytomining, and bioproducts.

Overview of major objectives and flow of experimental information. Known genes and metabolites involved in Populus’ response to hot drought (hot drought), along with GWAS-based gene discovery will be used to define plant-microbe association traits. The mechanistic bases for system function will be defined and this information, combined with an AI-supplemented process model, will facilitate prediction of system response in field settings. Feedback from experimental findings will inform future studies.

Objective 1. Identify the genetic associations in Populus that lead to microbiome-conferred stress tolerance

Objective 1 research framework. This objective links three integrated tasks to identify host genetic and microbial drivers of stress tolerance in Populus. Task 1 identifies species-specific physiological thresholds in P. trichocarpa and P. deltoides to hot drought. Task 2 tests how within-species genetic variation interacts with microbial taxa to shape plant performance and multi-omic responses. Task 3 validates candidate plant genes and stress-responsive microbes in controlled systems. Together, these tasks connect automated phenotyping, host and microbiome multi-omics, and targeted validation to discover genes, metabolites, and microbial mechanisms underlying microbiome-conferred stress tolerance.

Objective 2. Determine the mechanisms linking microbiome assembly to stress response in Populus

Objective 2 research framework. This objective uses an iterative framework to resolve mechanisms by which root-associated microbiomes influence Populus responses to hot drought stress. Task 4 defines colonization, succession, and stability across stress conditions; Task 5 links microbial community states to microbe-responsive host stress pathways; and Task 6 integrates microbial traits, host responses, and community dynamics into predictive models for SynCom design. These tasks connect microbial assembly, host physiology, and trait-based prediction to identify mechanisms that support stress resilience.

Objective 3. Integrate information across variable environments to link Populus-microbiome interactions to field performance

Objective 3 research framework. This objective combines GI-PBM with multi-omic, phenotyping, greenhouse, and field datasets to predict Populus growth, resilience, and mortality. Task 7 builds predictive PBMs, and Task 8 parameterizes, refines, and validates those models across experimental and field contexts.