Plant Microbiota

In nature, healthy plants are intimately associated with a staggering diversity of commensal microbes, collectively called the microbiota, which are thought to provide fitness benefits to their host. In the past several years, we have contributed to develop plant microbiota science as novel research field and aim at exploring microbiota functions using reductionist approaches.

We have shown that

i) soil type is a major driver of the composition of root-inhabiting bacterial communities and a fraction of soil microbes serves as main seeding source of the microbiota (Bulgarelli et al., Nature 2012; Schläppi et al., PNAS 2014; Bulgarelli et al., Cell Host&Microbe, 2015),

ii) the majority of bacterial and fungal taxa of the leaf and root microbiota can be cultured (Bai et al., Nature 2015; Duran et al., Cell 2018)

iii) the plant microbiota can be reconstituted with germ-free plants and synthetic microbial communities in laboratory environments (Bai et al., Nature 2015, Duran et al., Cell 2018)

iv) the bacterial root microbiota is essential for plant survival in soil and protects plants against root-associated fungi and oomycetes (Duran et al., Cell 2018).

Based on this understanding, the stage is now set for us to probe the plant and bacterial cues that underlie the establishment and activities of a core of bacterial lineages that are ubiquitously found on plant hosts (core microbiota). To this end, we apply pioneering approaches, involving microbiota reconstitution with gnotobiotic plant systems, and combine these with computational, genome-based, and genetic tools.

We hypothesize that the innate immune system of plants plays an important role in microbiota establishment and we aim to identify the underlying molecules and pathways (Hacquard et al., Ann Rev Plant Path 2017; Garrido-Oter et al., Cell Host&Microbe 2018). To understand the inner working of the microbial assemblages, we explore metabolic diversity and metabolic interdependencies among commensal members and with the plant host as potential determinants of community stability and microbial services. These community services (traits) include indirect pathogen protection, mineral nutrient mobilization, and abiotic stress tolerance.

Fundamental knowledge in this research field is expected to enable the development of rational probiotics for future low-input agricultural ecosystems with reduced chemical control of plant pathogens and decreased application of synthetic fertilizer.


Current projects in the group


Role of root exudates in triggering the formation of distinct bacterial communities (Kathrin Wippel). Analysis of the composition of root and rhizosphere microbiomes in various plant species has shown that different species grown in the same soil – i.e., in the same initial microbial environment – accommodate distinct microbial consortia. Using a customized hydroponic system and a novel millifluidics system, we are testing the hypotheses that exudates, biologically active compounds secreted from the host root, play a key role in shaping microbial community composition and that these exudates determine plant species-specific divergence of bacterial assemblages. By linking the chemical exudate profile to the functional traits of the associated bacteria, we aim to provide new insights into the molecular mechanisms underlying plant-microbiota interactions.


Interplay between coumarins and the plant microbiota in promoting plant growth under iron-limiting conditions (CJ Harbort). Iron is often a limiting factor for plant growth. In soils with poor iron availability, plants secrete coumarins, compounds that complex with iron and mobilize it for reduction and import. The root microbiome is an important contributor to plant nutrition, and may also play a role in iron acquisition. By combining experiments in complex natural soils with reductionist approaches using defined synthetic bacterial communities, we aim to elucidate the mechanistic interplay between coumarins and plant-associated bacteria that allows plants to thrive under iron-poor conditions.


Role of the microbiota in influencing invasion by bacterial wilt-causing bacteria (Alicia Jimenez Fernandez). Bacterial wilt caused by Ralstonia species is one of the most devastating and economically significant infectious diseases of plants and current control strategies are far from ideal. In this project we aim to determine the role of root microbiota composition in Ralstonia invasion. Our goal is to understand how Ralstonia invades taxonomically diverse SynComs and to elucidate the impact of these communities on Ralstonia root colonization. We hope that our findings may suggest novel microbiota-based strategies for how to control this destructive disease.


Influence of abiotic and biotic factors in shaping the root microbiota in maize (Amelia Bourceret). Plant fitness in the wild is determined by a complex interplay between abiotic factors such as pH and nutrient availability and other living organisms such as the members of the root and soil microbiota. With the overall aim of improving maize yield in low-nutrient soil, we are undertaking large-scale sampling of soil and several host genotypes of maize plants from contrasting soil managements over different developmental stages and applying amplicon sequencing to characterize the associated bacterial, fungal, and oomycetal communities.

Emerging roles of the root microbiota in balancing plant growth and defense for microbe-host homeostasis (Ka-Wai Ma). The plant immune system and MAMP-triggered immunity (MTI) restrict microbial proliferation, and both commensal and pathogenic microbes modulate plant responses to allow successful plant colonization. Activation of plant defense responses generally comes at the price of growth. In this project, we are investigating the ability of members of the root microbiota to influence this trade-off between growth and defense. To this end, we are surveying the impact of Arabidopsis root culture collection (At-R-sphere) members on pathogen-elicited root growth inhibition (RGI). By dissecting the host pathway(s) involved, we hope to identify factors that could be targeted to promote plant resistance and growth.


Interactions between plants and bacteria that shape root microbiome composition (Charles Copeland). The importance of the plant innate immune system in plant-microbe interactions means that balanced activation and suppression of MAMP-triggered immunity (MTI) by the root microbial community is likely to be required for balanced community composition. However, the mechanisms by which commensal bacteria may target MTI signaling are unknown. With the aim of better understanding plant-bacteria crosstalk and plant signaling modules that govern microbiota composition, I aim to identify plant MTI signaling components that are targeted by commensal microbes as well as MTI-independent mechanisms that modulate growth of the root microbiota.


The genetic basis of immune suppression by microbiota members (Jana Ordon). Plants mount defensive responses against surrounding microbes/pathogens after detecting conserved microbe-associated molecular patterns (MAMPs) on the plant cell surface. However, a multitude of bacteria are found in association with roots and a subset seem to be able to suppress basal immunity by yet unknown mechanisms. Forward genetic approaches will be used to identify genetic elements required for the suppression of defense responses.. Since the suppressive activity is found to be isolate-specific, a subset of root-derived bacteria will be barcoded to reveal the biological relevance of suppressive isolates during the colonisation process.


Involvement of the bacterial root microbiota of Arabidopsis thaliana in the trade-off between plant growth and defense (Ryohei Thomas Nakano). The genomes of the commensal microbes associated with plant roots encode conserved microbial epitopes, designated MAMPs, which are predicted to be perceived by the plant immune system. Chronic activation of MAMP-triggered plant responses results in root growth inhibition (RGI), which is thought to be consequence of a plant growth-defense trade-off. However, it remains unclear how plants coordinate growth and immunity in natural environments in the presence of commensals. We have identified commensal bacteria from the root microbiota of Arabidopsis thaliana that interfere with host responses to the well-characterized MAMP flg22 peptide, and  our analysis suggests that commensal bacteria can influence the trade-off between plant growth and defense.


Molecular mechanisms by which plant-associated bacteria allow Arabidopsis thaliana to overcome root growth suppression mediated by the DAMP Pep1 (Jia Yong). Using a panel of plant-associated bacteria and employing DNA isolation, cloning and protein purification approaches, I have identified bacterial commensals and proteins that may mediate this effect. In further screening experiments, I now aim to confirm these findings.


Structural analysis of plant immune receptors (Dongli Yu). NLR receptors were discovered in plants more than two decades ago, and since then, much progress has been made in understanding their functions. However, we still lack structures for any of these proteins. In this project, we aim to unravel the structural basis of pre- and post-activation of plant NLR complexes. To this end, we are employing heterogeneous expression of different plant NLRs in various systems, studying the biochemical property of these proteins, and using crystallization or Cryo-EM to solve their structures.


Identification of the Rhizobiales mechanisms involved in microbiota colonization and persistence (Julien Thouin). One of the most abundant groups of the core root microbiota is the bacterial order Rhizobiales. In this project, we aim to identify the mechanisms employed by the Rhizobiales to colonize and persist in plant roots. To achieve this, we will take advantage of the large number of sequenced Rhizobiales strains available in-house. A significant number of these strains will be DNA-barcoded to enable a precise analysis of their root colonization and persistence. The identification of candidate genes will be conducted using a genome-wide association study approach. Candidate genes identified in this way will be validated by reverse genetics.


Plant Innate Immunity

Another major strand of our work is focused on elucidating molecular mechanisms of innate immunity in plants against pathogenic microbes. We investigate how immune receptors that reside inside plant cells detect the presence of pathogen-delivered molecules, called effectors, and activate powerful immune responses that terminate pathogen growth. The immune receptors are encoded by plant disease resistance (R) genes that are often used by plant breeders to select resistant crop varieties. Immunity mediated by these receptors is typically associated with host cell death at sites of attempted pathogen invasion. The diversified receptors in plants comprise a protein family, designated Nucleotide-Binding Domain and Leucine-Rich Repeat containing proteins (NLRs). Intriguingly, plant NLRs are structurally related to intracellular receptors of the innate immune system in animals and humans (Maekawa and Schulze-Lefert, Nature Immunology 2011).

We primarily use the crop barley and the model plant Arabidopsis thaliana to address the co-evolutionary dynamics between host and pathogen at the level of populations and conservation of receptor function across different plant lineages (Maekawa et al., PNAS 2012; Maekawa et al., MPMI 2018). A particular recent highlight has been our finding that highly sequence-related MLA receptor variants in barley directly detect unrelated pathogen effectors of the powdery mildew fungus, a widespread pathogen of cereals (Lu et al., PNAS 2016; Saur, Bauer et al. eLIFE 2019). This discovery provides the basis for ongoing biochemical studies to reveal the mechanism underlying MLA receptor activation upon effector binding using cryo-EM technology in collaboration with Jijie Chai’s structural biology laboratory at the MPIPZ. Our recent findings also suggest it may be feasible to rationally design synthetic receptors to detect pathogen effectors that escape surveillance by the plant immune system.

We study mechanisms of cell death in plant cells upon pathogen recognition and MLA receptor activation. The N-terminal coiled-coil domain of MLA receptors is capable to form homodimers and/or higher-order oligomers and defines a minimal functional unit for triggering cell death (Maekawa et al., Cell Host&Microbe 2011). We test the hypothesis that this module serves as cell death executor rather than signaling domain, probably by pore formation in host cell membranes. A further experimental line investigates whether MLA receptors can act as autonomous cell death machine in plant and animal cells.



Parallels between plant and animal immunity (Takaki Maekawa). Over the past decades, growing evidence has highlighted remarkable similarities between the innate immune systems in the plant and animal kingdoms. These ‘shared’ innate immunity systems include intracellular receptors as exemplified by NLRs. My work aims at unveiling the underlying mechanistic parallels of plant and animal immune components with emphasis on protein structure and function.


Characterization of the interactions between plant NLRs and pathogen effectors (Isabel Saur). Intracellular sensing of pathogen-secreted effector molecules by nucleotide-binding domain and leucine-rich repeat (NLR)-containing proteins is the cornerstone of a plant’s immune strategy against invading microbes. Despite this, the mechanisms underlying NLR recognition of effectors remains incompletely understood. In the prevailing view, direct binding of effectors by NLR receptors is rather a rare event in plant-pathogen interactions, and it has been thought instead that in most cases recognition proceeds via other host proteins that are modified by the pathogen. Our recent large-scale characterization of MLA-Bgh NLR-effector pairs in barley instead suggests that direct physical interactions between host and fungal proteins are more widespread in immunity to fungal pathogens. These findings may have important implications for engineering disease resistance in crop species.