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Research

Research on plants and their naturally associated microorganisms is in a prime position to provide new perspectives and concepts for understanding plant function, performance and plant growth under limited input conditions. This will provide opportunities to reduce the environmental footprint as well as the potential to define breeding targets and develop applications through microbial interventions. To reach this goal, InRoot uses an interdisciplinary approach combining plant and bacterial genetics, protein biochemistry, analytical chemistry and plant physiology with bacterial and plant population biodiversity studies and advanced modeling.

 

The aim of InRoot is to provide knowledge and tools for evidenced-based development of new resilient crops and associated microbial interventions that will improve productivity, reduce the need for fertilizers and pesticides, and alleviate negative environmental impacts accompanying food production. To achieve this InRoot investigates both the plant and bacterial contributions to crop resiliency.

 

Research Areas

InRoot is organized around six research area that combine investigations of the natural diversity, host controlled rhizosphere and endosphere interactions, root responses, plant physiology and advanced modeling in a tightly interconnected and iterative workflow.

1. Natural diversity and adaptation

Plants’ adaptation to local microbiota is poorly understood but this research area aims to untangle the effects of climate and soil type from the impact of root-microbe interactions. A combination of transplantation experiments and exploitation of natural variation will be used to find the plant genetic components responsible for plant adaptation to local microbiota.

We will overlay population differentiation signatures derived from contrasting three distinct subpopulations with GWAS analysis of fitness traits measured in transplantation field experiments. This approach intersects and integrates phenotype-independent data from population differentiation signatures with the results of the trait- and phenotype-dependent GWA methodology in a uniquely suited population.


Stig U Andersen

Associate Professor

Heike Sederoff

Professor

Ronnie de Jonge

Assistant Professor

Shusei Sato

Associate Professor

2. Molecular programs that control plant-microbial association in the rhizosphere.

The second research area will identify key plant and microbial functions controlling state transitions in plant and microbial phenotypes in specific environmental conditions. The role of these functions will be tested using plant genetics and tailored microbial ecosystems with reduced complexity (for Lotus) and during intercropping or in rotation (for wheat). These model legumes will be used to identify the principles guiding microbiota assembly in the rhizosphere and for identifying and studying root-associated microbes.


Simona Radutoiu

Associate Professor

Simon Kelly

Assistant Professor

Marianne Glasius

Associate Professor

Henrik Scheller

Professor

3. Molecular programs that control root infection and endosphere colonization

The plant and microbial components that contribute to the enrichment of core microbiota and host-specific microbiota are unknown, as is their function in plant growth, development and resilience. To help unravel this we will use comparative analysis to identify core and host-specific endophytes. We will then identify the microbial genes controlling the core and host-specific associations by performing comparative genome and transcriptome analysis as well as establishing an unbiased large-scale genetic screen for several endophytic strains using the insertion sequencing (INSeq) strategy. Parallel studies will also be performed on the hosts to identify plant genes controlling endophytic interactions as well as those involved in intercellular infection.


Ronnie de Jonge

Assistant Professor

Simona Radutoiu

Associate Professor

Simon Kelly

Assistant Professor

Jens Stougaard

Professor

Henrik Scheller

Professor

4. Cellular responses in roots

The fourth research area will investigate the modulation of plant responses, plant hormone signaling, nutrient acquisition, and root system architecture that are potential means for microbes to promote plant resilience to environmental stresses. It is thought that microbes might induce and/or exploit these plant responses in order to provide an advantageous environment for their colonization or to obtain novel carbon sources to support their growth.

Genetic resources will be developed to determine the role of plant hormones in root colonization by microbial communities and how plant growth responses to microbial colonization are orchestrated by plant hormone signaling. These experiments will be carried out in soil and the tailored SynComs. We will also identify differentially regulated components in bacteria-plant communication using TRAP-RNAseq and study the function of plant genes using Lotus and Arabisopsis mutant resources or CRISPR in barley for reverse genetics. Biochemical approaches will also be used to complete pathway identification and characterization and elucidate transcriptional networks.


Jens Stougaard

Professor

Dugald Reid

Assistant Professor

Kasper Rødkjær Andersen

Assistant Professor

Ronnie de Jonge

Assistant Professor

5. Integration of reciprocal signaling into plant physiological responses to sustain growth and stress resilience

In this research area we will focus on elucidating the mechanisms of intra- and inter-organismal communication, signaling and resource allocation that regulate the local and systemic responses of selected Lotus accessions and their specific interactions with SynComs. This will lead to an understanding of the molecular mechanisms integrating root-microbe interactions into whole-plant physiology.

Peptides, RNAs, hormones, metabolites and other molecules involved in systematic and local responses will be analyzed to identify and characterize the mobile signals/molecules that provide information between plant organs and between plant root and microbiome. InRoot will develop new sensor and chip technologies to overcome current limitations in sensitivity, resolution and throughput of hormone and metabolite changes and movements. In addition, plant resiliency will be assessed non-invasively through the use of the automated, high-throughput controlled environment phenotyping facility PhenoLab.


Thomas Roitsch

Professor

Heike Sederoff

Professor

Manuel Kleiner

Assistant Professor

Dugald Reid

Assistant Professor

Stig U Andersen

Associate Professor

Jan Madsen

Professor

Winnie Edith Svendsen

Professor

Paul Pop

Professor

6. Multiscale modeling of Plant-Microbe interactions for improved plant performance

The sixth research area will integrate the data on experimentally controlled variation with the quantified plant and microbial responses and combine mechanistic and data-driven modeling approaches to capture the drivers of plant yield and resilience resulting from changes in the microbiota structure and function. The goal is to develop a multiscale model to capture changes in plant yield and resilience in response to 1) genes and associated mechanisms that are associate with natural diversity and adaptation; 2) microbial targets associated with the microbe-microbe and microbe-host machinery that affect rhizosphere microbiota; and 3) plant targets associated with reciprocal root to shoot signaling.


Cranos Williams

Associate Professor

Stig U Andersen

Associate Professor

Paul Pop

Professor

Jan Madsen

Professor

Simona Radutoiu

Associate Professor