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Plant Interactions with Microbes: Discerning Friend from Foe

Research Summary

Jeff Dangl studies the molecular control of plant-microbe communication. Some of these intimate associations provide nutrition to the plant or protection from other microbial infections. But other microbes are pathogenic, and the plant needs to tell the difference between friend and foe at the molecular level in order to fine-tune its response. The Dangl lab studies the genetic and molecular mechanisms underlying the plant immune system’s extraordinary ability to discriminate between friend and foe in a complex environment.

My group and I are interested in how plants respond to interactions with pathogens and turn that molecular recognition into a successful innate immune response. We would also like to understand how plants assemble a population of beneficial microbes on and inside their root systems that can provide them with nutrients and protection from pathogens. Thus, we study the plant immune system, and we study how it intersects with assemblage of the plant microbiome. We use the tools of genetics, genomics, and molecular, structural, and cellular biology in our research, and we inform these studies with inferences from evolutionary genomics.

Plants are in contact with diverse microbes blown by the wind, delivered via the water cycle, and recruited to their roots and leaves from the soil. Many of these microbes are unable to start their life cycle in association with a living plant. Others are potential pathogens, potential symbionts, or harmless commensals. The ultimate outcome of plant-microbe interactions is tuned by host and microbe genotypes and by the environmental context. All land plants grow in intimate association with complex microbial communities. These attach to, and inhabit, both the roots (rhizosphere) and aboveground organs (phyllosphere) as epiphytes or endophytes. Plant-derived exudates and secreted secondary metabolites are implicated in encouraging specific microbial colonization. Host plants often rely on the associated microbiome for one or more critical nutrients, such as fixed nitrogen. The plant, in turn, can provide fixed atmospheric carbon to some members of the microbiome, thus acting as a carbon sequestration niche.

Plant interactions with microbes are important in the context of plant health and global food security. Yield losses due to microbial pathogens and pests can be up to 30 percent worldwide, and much of this loss takes place after the freshwater input required to grow a crop. Thus, if we could better combat microbial infection of plants via rational deployment of the plant immune system, we could save significant amounts of water and spare significant acreage from the plow. Additionally, if we could better understand and deploy the plant immune system, we could diminish or eliminate the use of chemicals in the control of plant disease.

My lab currently focuses on the following questions:

  1. How do plant intracellular nucelotide-binding leucine-rich repeat (NB-LRR) innate immune receptors recognize pathogen virulence effectors, and how are they activated?
  2. What is the structural and functional diversity of type III effectors from a single but widespread bacterial species, Pseudomonas syringae?
  3. Do virulence effectors from two pathogens with very different lifestyles, P. syringae and the obligate biotrophic haustorial oomycete parasite Hyaloperonospora arabidopsidis, converge onto a core set of host immune system targets?
  4. Can we expand our understanding of plant-microbe interactions to include the plant-associated microbiome and understand how the metagenome influences plant health and disease resistance?

The Plant Immune System
Plants express a two-tiered immune system that has analogies to the mammalian innate immune system. Microbes express microbial-associated molecular patterns (MAMPs) on their surfaces. MAMPs can be sensed specifically by plant cell-surface pattern-recognition receptors (PRRs). Plant PRRs described to date are cell-surface receptors featuring an ectodomain, most commonly a leucine-rich repeat (LRR), a transmembrane domain, and a cytosolic kinase domain. Plant PRRs are analogous to the familiar TLR receptors of the animal innate immune system. MAMP recognition leads to signal transduction and transcriptional reprogramming, resulting in the initiation of MAMP-triggered immunity (MTI). MTI is sufficient to halt the growth of most microbes. Hence, most microbes are not pathogens.

Successful pathogens evolve or acquire, via horizontal gene transfer, genes encoding virulence factors that, among other things, suppress MTI. Successful symbionts, also recognized via their own MAMPs, are likely to do the same. Pathogen-encoded virulence factors from bacteria, fungi, oomycetes, and insects (generically, "effectors") are delivered into the host cell by various molecular mechanisms. Effectors disrupt host defense signaling, help the microbe access plant-derived nutrients, and enhance microbial dissemination. Plant genomes, in turn, have evolved a second immune system tier. They encode and express polymorphic intracellular receptors called NB-LRR proteins that "recognize" effectors, thereby activating effector-triggered immunity (ETI). Plant NB-LRR proteins are analogous to mammalian NLR intracellular immune receptors that also function as microbial sensors and regulators of inflammatory responses. ETI is a more rapid, higher amplitude version of MTI that can also be associated with a localized programmed cell death at the site of infection and with the generation of systemic signals that lead to a poised state that allows rapid response to subsequent infection on distal plant surfaces, known as systemic acquired resistance (SAR).

NB-LRR proteins are encoded by disease resistance genes and have been manipulated by plant breeders for more than a century. Every domesticated crop has been bred to incorporate NB-LRR disease resistance genes, typically from wild relatives. Our work, and that of many of our colleagues, has helped make breeding with these genes easier.

NB-LRR–dependent recognition of pathogen effectors can be indirect, driven by effector-mediated alteration of a plant target. For example, several effectors are proteases. They cleave one or more host targets. The cleavage products of a single host target can activate an associated NB-LRR receptor. Hence, NB-LRR proteins can recognize "modified-self" molecules. There are three important corollaries of this "guard hypothesis," which Jonathan Jones (Sainsbury Laboratory, UK) and I have articulated. First, the NB-LRR proteins (~125 in Arabidopsis) monitor the integrity of host effector targets. Second, if particular host machines are critical for immune function, then independent evolution of virulence factors should repeatedly target them. Third, if pathogen effectors repeatedly target the same host machine but use independently evolved mechanisms to do so, then that particular machine could associate with different NB-LRR protein "guards." We are contributing evidence for each of these three corollaries, and we continue to dig deeper into plant immune system function.

Since NB-LRR proteins are analogous to animal innate immune receptors, our elucidation of this model has had a direct impact on mammalian immunology. The guard hypothesis is somewhat analogous to activation of animal innate immune responses by "danger signals."

The Plant Microbiome
All land plants grow in intimate association with a complex root microbiota that is distinct from the microbial community present in bulk soil. These interactions are driven by the influence of root physiology and metabolism, which influence the rhizoplane (the 1 mm surrounding the root) environment through adjusting the soil pH changing soil structure and oxygen availability, producing antimicrobials and quorum-sensing mimics that manipulate microbial communication, providing an energy source in the form of dead root material and carbon-rich exudates, and more. In fact, between 5 and 33 percent of fixed atmospheric carbon is sequestered in the rhizosphere. The microbial communities that inhabit this niche can have a net beneficial or net detrimental impact on plant health, and shifting this balance is of major agronomic interest. Various mutualistic rhizosphere microbes provide the host plant with physiologically accessible nutrients; improve plant growth through production of phytohormones; help plants withstand heat, salt, and drought; act as protectants against phytopathogens; and more.

Microbial community structure differs across plant species and also among some inbred genotypes within single species grown in a common soil. Studies abound in a variety of systems to address the host genetic effect on the microbiome for various crops and other plants. Rhizosphere and microbial community analysis studies in Arabidopsis are also becoming more common, although these lack power because they use methods that are not readily comparable among studies, use low-resolution phylotyping techniques, and suffer from small sample sizes.

Our goal is to define a robust system in which host genes important in shaping definable microbial phenotypes could be subsequently identified. Such host genes would constitute practical targets for intervention in crop plants to promote plant health in particular soil and climate conditions. One critical question is whether the gain and loss of effectors, and their subsequent recognition, play a role in the evolution or interconversion of pathogens and mutualists. Another is to what degree the known components of the plant immune system modulate the assemblage of the root microbiome. These new projects will benefit from integration with our ongoing studies of both effector diversity and plant immune function.

Using Arabidopsis thaliana inbreds and related Brassicaceae, we applied multiplexed pyrosequencing of microbial 16S rRNA genes from the root systems of hundreds of individual plants to test the hypothesis that the microbiota of a plant grown in wild soils is sufficiently dependent on host genotype to vary among related inbred individuals. We found distinct microbial communities in bulk soil, rhizosphere, and endophyte fractions that are influenced by soil type and plant developmental stage. We also found that plant genotype directs the assembly of robust microbial phenotypes, setting the stage for genetic dissection of responsible host loci.

This project is expanding significantly to include technology development of new high-throughput 16S ribotyping, metagenome and metatranscriptome analyses in controlled conditions, and development of new model systems. These systems will feature various levels of both genetic and genomic resources, which will help us to identify host loci shaping the microbiome and to understand the consequences of local adaptation to climate alterations on the root microbiome.

Grants from the National Institutes of Health, the National Science Foundation, and the Department of Energy provided partial support for these projects.

As of May 30, 2012

Scientist Profile

Investigator
The University of North Carolina at Chapel Hill
Microbiology, Plant Biology