PMI Project Aims

The goal of the Plant-Microbe Interfaces SFA is to gain a deeper understanding of the diversity and functioning of mutually beneficial interactions between plants and microbes in the rhizosphere. The plant-microbe interface is the boundary across which a plant senses, interacts with, and may alter its associated biotic and abiotic environments. Understanding the exchange of energy, information, and materials across the plant-microbe interface at diverse spatial and temporal scales is our ultimate objective. Our ongoing efforts focus on characterizing and interpreting such interfaces using systems comprising plants and microbes, in particular the poplar tree (Populus) and its microbial community in the context of favorable plant microbe interactions. We seek to define the relationships among these organisms in natural settings, dissect the molecular signals and gene-level responses of the organisms using natural and model systems, and interpret this information using advanced computational tools.

The advances anticipated here will set the stage for detailed understanding of other symbiotic relationships and of natural routes to ecosystem response to climate change, the cycling and sequestration of carbon in terrestrial environments, and the development and management of renewable energy sources.

Importance of plant-microbe interfaces

Often plant-microbe interactions can benefit plant health and productivity by 1) affecting nutrient uptake and growth allocation, 2) influencing plant hormone signaling, 3) inducing catabolism of toxic compounds, and/or 4) conferring resistance to pathogens. In both natural and engineered systems, plants and microbes function together to determine responses of terrestrial ecosystems to climate change, influence global fluxes of carbon cycling, and offer potential as renewable, carbon neutral or negative, alternative energy sources.


Populus, is a dominant perennial component of temperate forests, has the broadest geographic distribution of any North American tree genus and is the model woody perennial organism. The Populus genome was the first tree genome to be sequenced, and numerous tools for manipulating its genetics and physiology are available. Further, Populus is one of the leading candidates for bioenergy production and provides researchers with ecosystem-scale insights into the central role of plants in carbon sequestration and cycling in terrestrial ecosystems. Populus is also among only a few plant species that hosts both endo- and ectomycorrhizal fungal associates and numerous other types of microorganisms can be found within Populustissues and/or closely associated with the roots that may range from highly beneficial to pathogenic with respect to host fitness. Ultimately, an improved fundamental understanding of plant-microbe interfaces will enable the use of indigenous or engineered systems to address challenges as diverse as bioenergy production, environmental remediation, and carbon cycling and sequestration.

Three interrelated scientific aims create integrating themes for this SFA and drive needed advances in analytical and computational technologies.

Aim 1: Characterizing host drivers of the Populus microbiome

Aim 1 addresses two complementary questions: How do features of the Populus niche (i.e., tissue compartmentalization), environment, genotype, and phenotype influence microbial community structure and function? Second, how do genomic features of the microbial community affect Populus development?

Read More

Aim 2: Molecular mechanisms underpinning the Populus-microbe interface

In Aim 2, we focus on confirming microbial functions related to plant performance and will elucidate at a molecular level how these functions may operate to impact Populus biology. We already have developed several tractable fungal and bacterial experimental systems to dissect molecular mechanisms involved in host recognition and root colonization. In addition, we will characterize additional microbial functions that are likely to be important in plant-microbe interactions, including nutrient cycling and bacteria-host plant signaling.

Read More

Aim 3: Constructed communities for gaining insights into collective plantmicrobiome function

In Aim 3, we continue to advance experimental systems for understanding collective plantmicrobiome function using constructed communities. We mine the rich biological space afforded by our microbial collection that contains greater than 200 sequenced strains and 1084 resequenced Populus genomes to design constructed communities of defined complexity.

Read More