BIOADAPT - Adaptation - des gènes aux populations.Génétique et biologie de l'adaptation aux stress et aux perturbations

Shaping new rhizobia by experimental evolution: insights into bacterial adaptation to the plant environment – SHAPE

Towards the design of new nitrogen fixing symbionts

Elucidate how the capacity to establish a nitrogen fixing symbiosis with legumes has been acquired by new bacterial taxons via a lab-evolution experiment should allow developping the required know-how for the design of new symbionts.

Deciphering adaptive mechanisms leading to the rhizobium-legume symbiosis

Contrary to cereals and most cultivated plants, legumes do not require nitrogen fertilizers for growth thanks to their ability to enter a symbiosis with nitrogen-fixing microorganisms, called rhizobia. Symbiosis includes four major steps: nodule formation, bacterial infection, bacterial maintenance and nitrogen fixation. Recent major scientific advances have renewed interest and hope in bioengineering N2-fixing cereals. Bioengineering nodulating cereals will necessitate better understanding of key traits of the symbiotic interaction, i.e. nodulation competitiveness, intracellular infection, bacterial maintenance and nitrogen fixation as well as the parallel design of symbiotic bacterial partners adapted to these new plants. The SHAPE projecs aims at elucidating bacterial adaptive mechanisms leading to symbiosis as well as paving the way to experimental evolution-based strategies to design new rhizobia, e.g. adapted to new host plants.

We will take advantage of the previous experimental evolution of a pathogenic Ralstonia solanacearum chimera carrying the symbiotic plasmid of the rhizobium Cupriavidus taiwanensis into legume symbionts (in its primary sense «which lives with«) and will exploit the generated biological material evolved under legume selection pressure. The evolution of key phenotypic traits – including nodulation competitiveness and intracellular infection quality and persistence- along the evolution experiment will be analyzed using high resolution phenotyping at the cellular, transcriptomic and metabolic level. Experimental strategies to emerge N2-fixing Ralstonia, a trait not acquired along the evolution experiment. will be explored using the reference C. taiwanensis rhizobium Genomic changes and mechanisms underlying the adaptive process will be analyzed using whole genome resequencing (Illumina technology) and genetic reconstruction.

The project is starting.

Although developed in a rhizobium-legume context, the knowledge acquired in SHAPE should benefit plant-microbe interactions in general, and provide general insights into how bacterial genomes evolve under environmental constraints and how to shape plant-associated bacteria with beneficial traits in a sustainable agriculture perspective.

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The increasing world population together with global environmental threats urgently calls for a low-input agriculture in which traditional pesticides and fertilizers are less and better used and innovative, environment-friendly, products are designed. Plant-microbe interactions, either pathogenic or symbiotic (mutualistic), have a major impact on plant growth and health. Recent molecular advances in their understanding offers new opportunities for controlling plant yield in a sustainable agriculture perspective. At the same time, elucidating how these biotic interactions adapt to challenging anthropogenic or natural conditions is crucial to the long-term management of agro- and ecosystems.
Contrary to cereals and most cultivated plants, legumes do not require nitrogen fertilizers for growth thanks to their ability to enter a symbiosis with nitrogen-fixing microorganisms, called rhizobia. Symbiosis includes four major steps: nodule formation, bacterial infection, bacterial maintenance and nitrogen fixation. The last two decades have seen tremendous progress in our understanding of the molecular mechanisms that control nodulation and early infection, renewing realistic hope in bioengineering N2-fixing cereals in the coming decades. This however requires that other key stages and traits of the symbiotic interaction, i.e. nodulation competitiveness, intracellular infection, bacterial maintenance and nitrogen fixation are better understood. In addition, bioengineering nodulating cereals will necessitate the parallel design of symbiotic bacterial partners adapted to these new plants. This requires better understanding of how the rhizobium-legume symbioses have evolved along evolutionary times, a topic that has received little attention so far.
SHAPE addresses these two major objectives as it aims at
- elucidating bacterial adaptive mechanisms leading to legume symbiosis
- paving the way to experimental evolution-based strategies to design new rhizobia e.g. adapted to new host plants.
SHAPE follows an original approach based on experimental evolution that, coupled to Next Generation Sequencing (NGS), is a powerful tool for deciphering adaptive mechanisms to changing environments. We initiated this approach in a former ANR project called SYMPA that established the experimental system -i.e. the conversion of a plant root bacterial pathogen, Ralstonia solanacearum, into a legume (Mimosa) symbiont-, generated biological material evolved under legume selection pressure and opened up new lines of research that will be explored in SHAPE.
First, SHAPE will analyze the evolution of key phenotypic traits – including nodulation competitiveness and intracellular infection quality and persistence- along the evolution experiment and their contribution to the striking increase in fitness observed between ancestors and final clones. Second, it will analyze the high number of genomic changes that took place during the adaptation process in order to decipher the underlying adaptive and evolutionary mechanisms. Third, SHAPE will characterize an original phenomenon of transient and high mutability that was evidenced in the evolution experiment. Last, it will explore experimental strategies to emerge N2-fixing Ralstonia.
Three partners with expertise in rhizobium-legume symbiosis, bioinformatics and evolutionary genomics are mobilized to the project. A 4-year length time is needed to successfully realize this project.
SHAPE is pioneer in exploring the power of experimental evolution-NGS coupling in the field of complex plant-microbe interactions. Behind its primary scope on rhizobium-legume symbiosis, SHAPE aims at providing general insights into how bacterial genomes adapt to environmental constraints and at developing innovative strategies for designing plant-associated bacteria with beneficial traits in a sustainable agriculture and environment perspective.

Project coordinator

Madame CATHERINE MASSON (Laboratoire des Interactions Plantes Micro-organismes) – catherine.masson@inra.fr

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.

Partner

LIPM Laboratoire des Interactions Plantes Micro-organismes
Institut Pasteur Microbial Evolutionary Genomics
CEA / DSV / IG / CNS / LABGeM Commissariat à l'Energie Atomique et aux énergies alternatives / Direction des Sciences Du Vivant / Institut de Génomique /

Help of the ANR 500,000 euros
Beginning and duration of the scientific project: December 2012 - 48 Months

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