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HIGHLIGHTS

Développement durable

Le Projet TERO proposé en réponse à l’AAP pépinière RSE INRAE a été évalué favorablement : « Projet solide, innovant, participatif et très pertinent, dont le caractère pilote est avéré ». Ce projet (20 k€) impliquant le LIPME, AGIR, UE APC, la FR-AIB et le LRSV vise à créer une filière de gestion des déchets de culture sur le centre. Et oui, ce sont près de 35 tonnes de terreau/jiffy qui partent à l’incinération tous les ans, rien que pour le LIPME, sans parler des dizaines de milliers de pots.

Contacts :

Mathieu Hanemian et Carine Chauveau

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Portrait: Guilhem Reyt, new CNRS researcher in the SMS team

- IM: Hello, can you introduce yourself?

- GR: My name is Guilhem Reyt, I am 34 years old and I arrived at LIPME in November on a post of

CNRS researcher. I did most of my studies in Montpellier, IUT, license, Master, thesis and ATER.

I did my thesis at the B&PMP laboratory (Biochemistry and Molecular Physiology of Plants),

Mixed Research Unit (CNRS/INRAE/SupAgro/Montpellier University) whose work aims to

elucidate the fundamental mechanisms governing the hydro-mineral nutrition of plants and their

responses to the abiotic constraints of the environment, in particular those related to change

climatic. During my thesis, I worked under the supervision of Frédéric Gaymard and Jean-François

Briat on iron nutrition in arabidopsis. I showed how the roots adapt their development

in response to iron.

- What made you want to do a thesis in plant biology?

- I think what made me want to start a thesis and pursue research is my curiosity, the desire to answer fundamental questions for the understanding of life. I chose the plant domain because I have always been fascinated by the diversity of shapes, organs and sizes of different plant species.

- What has been your career path since your thesis?

- During my thesis, I realized that plants have great developmental plasticity,

which allows them to adapt to very contrasting environments. This is particularly the case

roots that show significant phenotypic plasticity in response to different stresses

nutritional. This is why I decided to work on root developmental processes

controlling nutrition. For this I carried out a post-doctorate in the group of Professor David Salt at

the University of Aberdeen and Nottingham. I studied the formation and function of barriers

roots which are essential to control water and nutrient flows in the root, at the level

of the endodermis.

During my post-doc, I also realized that there was another level of complexity that I had

not considered, the contribution of soil microorganisms. I therefore studied, in collaboration with

Gabriel Castrillo, how these microorganisms that live with plants can influence the

formation of root barriers and how this allows plants to be more resilient to

nutritional stresses.

- Would you define yourself as a biochemist or a molecular biologist?

- I would say that I have more training in molecular biology, but I do not consider myself completely in these terms. I consider myself more of a plant biologist interested in developmental processes. I can use biochemical or molecular biology techniques to answer my questions.

-  Following your post-doctoral experience in the United Kingdom, what are the differences that strike you the most between the French and English labs?

- No very significant differences. The scientific animation of the laboratory is organized in a rather similar way. I am impressed by the organization of the laboratory which provides many common resources (eg equipment, consumables) and the possibility of interacting with different groups with diverse themes. The Toulouse environment is also very conducive to the study of interactions with microorganisms with many experts in these fields.

-  What is your research project in the SMS team at LIPME and what skills do you bring to the team?

- My research project is a continuation of my post-doc, while taking advantage of the tools and resources available at LIPME. Its objective is to characterize the role of root barriers in the context of pathogenic (Ralstonia) and symbiotic (Rhizobium and arbuscular mycorrhiza) interactions. For this, I will use the model plant Arabidopsis thaliana for pathogen interactions and the model legume Medicago truncatula for symbiotic interactions. I will develop and bring different microscopy techniques to visualize how root barriers influence the colonization of different microorganisms in the root. The mechanisms described in this project should create a useful knowledge base to generate varieties of cultivated plants that are more resistant to biotic and abiotic stresses.

- What are your hobbies?

- I like cycling, hiking, gardening and cooking. Now that I am settled in the region, I want to participate in Adas activities in the centre.

             

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When a bacterium repairs its damaged DNA to adapt to its environment


DNA is subjected to numerous physicochemical constraints of intracellular or extracellular origin, which lead to the regular appearance of lesions, including DNA breaks. Faced with this, bacteria develop repair strategies which can have surprising consequences on the bacteria's ability to adapt to their environment. This is what researchers from the Laboratory of Interactions-Plants-Microorganisms, LIPM (INRAE-CNRS) showed in an article published on December 04, 2018 in the journal Nucleic Acids Research.

DNA (deoxyribonucleic acid), a biological macromolecule constituting chromosomes, is formed from the linear sequence of several million / billion nucleotides, the nature and very precise order of which determine the genetic information of living beings. Maintaining the integrity of this molecule is therefore a priority for living beings to ensure the expression and faithful transmission of their genetic heritage. At the level of a cell, the slightest chromosome break, if it is not repaired, can have irreversible consequences, including the death of the cell.

How does a bacterium adapt to its environment?


Living beings have therefore developed mechanisms for repairing DNA breaks, one of which, called NHEJ (for Non-Homologous End-Joining) consists of bringing together and "re-gluing" the ends of DNA, restoring thus the integrity of the molecule.

Unlike other more faithful repair mechanisms, NHEJ repairs chromosomes sometimes at the cost of "tinkering" at the repair junction, which can lead to a modification of the local nucleotide composition and therefore sometimes to a change. the meaning of genetic information (we speak of mutations).

An outstanding DNA repairer

By studying the NHEJ repair mechanism in a soil bacterium, Sinorhizobium meliloti, two surprising observations were made:

  • The ability of bacteria to repair NHEJ breaks increases under stressful environmental conditions, such as when ambient temperature rises.

  • On the other hand, among the “tinkering” of the NHEJ repair system, it can happen to accidentally integrate a DNA fragment of foreign origin at the level of the repaired break.

These observations made in the laboratory could find an echo in nature: when bacteria are in unfavorable environmental conditions, the increase in their DNA repair capacity by NHEJ would lead to an increase in the frequency of appearance of mutations in their cells. genome. In addition, stimulating their ability to integrate foreign DNA would make it easier for them to acquire genetic information from other organisms (this is referred to as "horizontal gene transfer").

These mechanisms, present in many bacterial species, could thus allow them to increase their potential for genetic evolution, and therefore their ability to adapt to new environmental conditions.

This work was carried out within the Laboratory of Plants-Microorganisms Interactions ( LIPM ), and was supported by INRAE ​​through a young scientist contract with Pierre Dupuy, and funding from the Department of Plant Health and Environment.

                                                                                                                                                                             

                                                                                                                                                                             

 

                                                                                                                                                                           © INRAE

Dupuy, P., Sauviac, L., and Bruand, C. Stress-inducible NHEJ in bacteria: function in DNA repair and acquisition of heterologous DNA. Nucleic Acids Research, 2018 Dec 4. https://doi.org/10.1093/nar/gky1212


https://www.inrae.fr/actualites/quand-bacterie-repare-son-adn-endommage-sadapter-son-environnement

Polygale à feuille de myrte infectée par Xylella fastidiosa (sous-espèce multiplex). Les symptômes visibles sont le jaunissement et dessèchement des feuilles. Xylella fastidiosa peut entrainer la mort de la plante.

The slow growth of the bacteria Xylella fastidiosa:

metabolic accident or epidemic strategy?

Xylella fastidiosa is a bacterium which causes many diseases affecting plants. It has preoccupied European agriculture since its emergence in Italy, where it caused the death of many olive trees. Better understanding how this bacteria works helps fight it. A collaboration between the Plant Microbes Environment Interactions Laboratory of INRAE ​​Occitanie-Toulouse and the Horticulture and Seeds Research Institute of INRAE ​​Pays de la Loire studied its metabolic network using systems biology and modeling tools . This work appeared in the American Society for Microbiology Journals mSystems.

                                                                                                      © Marie-Agnès Jacques, INRAE

How are this expansion and virulence possible when this pathogen has a growth described as fastidious because it is very slow?

So slow that it complicates its diagnosis in plants and its study in the laboratory. This physiological characteristic, shared with several pathogenic bacteria of man, seems paradoxical. This slow growth is an intrinsic characteristic of the organism. A research team from the Laboratory of Plant Microbes Environment Interactions (INRAE-CNRS) and researchers from the Horticulture and Seeds Research Institute of INRAE ​​in Angers, worked together to better understand the metabolism of this bacterium.

Using tools from systems biology and modeling, the researchers discovered that the metabolic network of Xylella fastidiosa is, unexpectedly, complete but reduced to its essentials. It has, for example, half as many reactions as the reference organism Escherichia Coli. Thus, the redundant pathways of metabolism have disappeared, especially those promoting rapid and efficient growth. The metabolic network of Xylella fastidiosa is therefore inefficient and fragile. The synthesis of exopolysaccharide, one of its virulence factors, has also been shown to be ineffective, even becoming a burden for growth.

A weakness that becomes a strength

It seems that this fastidious growth results from an evolution of this pathogenic agent, undoubtedly allowing it to escape the mechanisms of detection and defense of the plants. Strategy which seems to be winning, in view of the increasing dissemination of Xylella fastidiosa in the world.

To better understand the metabolism of Xylella fastidiosa, work is continuing with the study of several genes in order to understand their involvement in fastidious growth.

Scientists are trying to better understand how this slow growth affects the spread of the bacteria in host plants. All these advances are necessary to better fight against the bacteria.

 


Gerlin L, Cottret L, Cesbron S, Taghouti G, Jacques MA, Genin S, Baroukh C. 2020. Genome-scale investigation of the metabolic determinants generating bacterial fastidious growth. ASM Journals, mSystems Vol. 5, No. 2 : e00698-19.

https://doi.org/10.1128/mSystems.00698-19

The slow growth of the bacterium Xylella fastidiosa: metabolic accident or epidemic strategy? | INRAE ​​INSTIT

©Marie-Agnès Jacques, INRAE

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Cooperation within the fungal network allows Sclerotinia to diversify its victims

White rot Sclerotinia sclerotiorum causes disease in hundreds of plant species. During infection, cells in the network of mycelial filaments produce toxins to dismantle plant cells, while their neighbors constitute reserves with the nutrients thus released. This discovery illustrates how cooperation can generate complex traits such as the infectivity of a parasitic fungus.

The number of different species that a pathogen is able to infect in nature plays a key role in the spread of disease. While many parasitic fungi are specialized on one host species, Sclerotinia sclerotiorum is a plant pathogenic fungus known for its ability to infect a wide variety of plant species.

 

Global transcriptome sequencing reveals that S. sclerotiorum gene expression differs markedly in cells located at the base and at the end of the filaments during infection. To better understand these differences, the researchers reconstructed a genome-wide metabolic model of the fungus and analyzed metabolic fluxes. A form of division of labor between cells along the filaments has been demonstrated. The benefit of cooperative functioning increases with the plant's ability to defend itself. These conclusions are supported by the observation of reduced invasive growth when the continuity between the central and apical compartments of the fungal filaments is interrupted, and more markedly when the host plant is more resistant.

 

These results show that cooperation between cells is a mechanism favoring diseases caused by fungal pathogens. These exchanges modify the stresses acting on the cells of pathogens in their natural environment and should be taken into account in the design of disease management strategies.

​​

Remi Peyraud ,  Malick Mbengue ,  Adelin Barbacci ,  Sylvain Raffaele  Intercellular cooperation in a fungal plant pathogen facilitates host colonization. . 2019 Feb 19;116(8):3193-3201. Proc Natl Acad Sci US A.

DOI: 10.1073/pnas.1811267116

Advances on plant-pathogen interactions from molecular toward systems biology perspectives.

Peyraud R, Dubiella U, Barbacci A, Genin S, Raffaele S, Roby D. Plant J. 2017 May;90(4):720-737.

doi: 10.1111/tpj.13429. Epub 2017 Feb 10.

SPE Intranet - 10 years of SPE Research (inrae.fr)

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When a bacterium repairs its damaged DNA to adapt to its environment


DNA is subjected to numerous physicochemical constraints of intracellular or extracellular origin, which lead to the regular appearance of lesions, including DNA breaks. Faced with this, bacteria develop repair strategies which can have surprising consequences on the bacteria's ability to adapt to their environment. This is what researchers from the Laboratory of Interactions-Plants-Microorganisms, LIPM (INRAE-CNRS) showed in an article published on December 04, 2018 in the journal Nucleic Acids Research.

DNA (deoxyribonucleic acid), a biological macromolecule constituting chromosomes, is formed from the linear sequence of several million / billion nucleotides, the nature and very precise order of which determine the genetic information of living beings. Maintaining the integrity of this molecule is therefore a priority for living beings to ensure the expression and faithful transmission of their genetic heritage. At the level of a cell, the slightest chromosome break, if it is not repaired, can have irreversible consequences, including the death of the cell.

How does a bacterium adapt to its environment?


Living beings have therefore developed mechanisms for repairing DNA breaks, one of which, called NHEJ (for Non-Homologous End-Joining) consists of bringing together and "re-gluing" the ends of DNA, restoring thus the integrity of the molecule.

Unlike other more faithful repair mechanisms, NHEJ repairs chromosomes sometimes at the cost of "tinkering" at the repair junction, which can lead to a modification of the local nucleotide composition and therefore sometimes to a change. the meaning of genetic information (we speak of mutations).

An outstanding DNA repairer

By studying the NHEJ repair mechanism in a soil bacterium, Sinorhizobium meliloti, two surprising observations were made:

  • The ability of bacteria to repair NHEJ breaks increases under stressful environmental conditions, such as when ambient temperature rises.

  • On the other hand, among the “tinkering” of the NHEJ repair system, it can happen to accidentally integrate a DNA fragment of foreign origin at the level of the repaired break.

These observations made in the laboratory could find an echo in nature: when bacteria are in unfavorable environmental conditions, the increase in their DNA repair capacity by NHEJ would lead to an increase in the frequency of appearance of mutations in their cells. genome. In addition, stimulating their ability to integrate foreign DNA would make it easier for them to acquire genetic information from other organisms (this is referred to as "horizontal gene transfer").

These mechanisms, present in many bacterial species, could thus allow them to increase their potential for genetic evolution, and therefore their ability to adapt to new environmental conditions.

This work was carried out within the Laboratory of Plants-Microorganisms Interactions ( LIPM ), and was supported by INRAE ​​through a young scientist contract with Pierre Dupuy, and funding from the Department of Plant Health and Environment.

                                                                                                                                                                             

                                                                                                                                                                             

 

                                                                                                                                                                           © INRAE

Dupuy, P., Sauviac, L., and Bruand, C. Stress-inducible NHEJ in bacteria: function in DNA repair and acquisition of heterologous DNA. Nucleic Acids Research, 2018 Dec 4. https://doi.org/10.1093/nar/gky1212


https://www.inrae.fr/actualites/quand-bacterie-repare-son-adn-endommage-sadapter-son-environnement

© INRAE

Interviews of doctoral students carried out for the 40th anniversary of LIPME

Tessa Acar, Phyllosym team

Thi-Bich Luu , SMS Team

Noe Arroyo-Velez , Team SIX