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

The beneficial association of plants and microbes exemplifies a complex, multiorganismal system that is
shaped by the participating organisms and the environmental forces acting on them. Often these plant-microbe
interactions can benefit plant productivity and performance by, for example, (1) affecting nutrient uptake and growth allocation, (2) influencing plant hormone signaling, (3) inducing catabolism of toxic compounds, and (4) conferring resistance to pathogens. In both natural and engineered systems, plants and microbes function collectively to determine the responses of terrestrial ecosystems to global changes as well as to offer potential as dedicated feedstocks in a renewable, carbon-neutral economy.


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.  Populus was chosen as the first tree genome to be sequenced, and numerous tools for manipulating its genetics and physiology are available. Further, Populus is a leading candidate for bioenergy production and provides researchers with ecosystem-scale insights into the central role of plants in carbon sequestration and cycling in terrestrial ecosystems. As a perennial woody plant, Populus also is among only a few plant species that host both endo- and ectomycorrhizal fungal associates. Numerous other types of microorganisms can be found within, or closely associated with, various Populus tissues, and these organisms 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.  Specifically, elucidating the mechanisms involved in energy, information, and material transduction across interfaces will be critical for interpreting environmental responses based on genomic signatures.  Three interrelated scientific aims create integrating themes for this SFA and drive needed advances in analytical and computational technologies.

Objective 1: Understanding the progression of molecular events involved in selecting and maintaining a mutualistic relationship between Populus and specific members of its microbiome

Objective 1 addresses the question of how Populus selects specific microbial mutualists from a biologically diverse environment.  We have defined a specific genetic determinant that regulates interactions between Populus and Laccaria bicolor, a fungal symbiont.  Additionally, we have defined small secreted proteins in both Populus and Laccaria bicolor.  In L. bicolor, these small proteins are critical for negotiating symbiotic interactions and for reprogramming the host’s immune response.  We will take advantage of bacterial and fungal sequence information as well as a combination of advanced -omics techniques that will determine the succession of molecular and functional invents that lead to selective mutualistic partnerships and identify the key determinant software bacterial recognition and selection. 

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Objective 2: Defining the chemical environment and molecular signals that influence community structure and function

Objective 2, addresses the question of how the microbial community is structured. We will sort out microbial community structure and its distribution across host cells and tissues and its temporally-dependent changes.  Sorting out these collective contributions and defining general chemical determinants and specific signals operating between the component members will reveal functional roles of the involved organisms and potentially the reasons for their recruitment.  We will use -omics techniques, imaging and directed analytical methodologies as well as recently developed experimental platforms that permit the spatial and temporal sampling necessary to interrogate and monitor how these complex communities form, how they function and respond to perturbations, and how they change over time. 

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Objective 3: Understanding the dynamic relationship and extrinsic stressors that shape microbiome composition and affect host performance

Objective 3 will address the question of how the microbiome responds to host maturation and an assortment of biological and environmental stresses that occur over developmental time and reveal whether  microbiomes have the ability to complement host genetic predispositions to defense and growth trade-off strategies.  We will use stable-isotope chambers, common garden field plus and natural clonal stands as well as advanced analytical capabilities to evaluate short-term events in a high-resolution, molecular genomic manner and to extend those finds to the longer-term forces that shape the microbiome and ultimately host performance. 

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