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Home > Research Teams > Actinorhizal symbiosis

Actinorhizal symbiosis

Team leader : NORMAND Philippe
co-leader : BOUBAKRI Hasna

Team :

Permanent members

BOUBAKRI Hasna Lecturer (MCF), UCB
FERNANDEZ Maria Professor (PR), UCB
FOURNIER Pascale Technician (T), CNRS
HAY-DE BETTIGNIES Anne-Emmanuelle Lecturer (MCF), UCB
HERRERA-BELAROUSSI Aude Lecturer (MCF), UCB
NORMAND Philippe Research Director (DR), CNRS
PUJIC Petar Research Engineer (IR), CNRS

Non permanent members

GASSER Mélanie Phd student

Presentations :

Bacteria of genus Frankia belong to the class of actinobacteria, sub-order Frankineae. These bacteria have a Gram positive cell wall and a large genome with a high percent of DNA bases G and C (G+C%). Other well known actinobacteria are Mycobacterium (agents of tuberculosis and leprosy) and Streptomyces (soil bacteria that synthesize numerous antibiotics). Twelve genomic groups called genomospecies have been described so far in Frankia. These bacteria have a morphology typical of actinobacteria with branched and segmented hyphae, multilocular sporangia and vesicles where nitrogenase synthesis takes place, both in vitro (photos) and in symbiosis.
 
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Figure 1: Frankia alni with on the left a sporangium and a vesicle, where nitrogen fixation takes place (Photo P. Normand), in the middle a scanning electron micrograph of a Frankia alni sporangium (Photos Y. Prin, LSTM Montpellier). On the right, a malachite/safranine staining highlights septa in Frankia alni (Photo P. Pujic).
 
These bacteria fix nitrogen in symbiosis with a large spectrum of dicotyledonous plants, collectively called actinorhizal that belong to 24 genera spread into 8 families among which the Betulaceae (alder), the Myricaceae (bayberry, bog myrtle, sweet gale), and the Casuarinaceae (she-oak, ironwood, australian pine). These plants, with their symbiotic bacteria, are collectively responsible for about 15% of the input of nitrogen biologically fixed on Earth. These actinorhizal plants are found in different ecosystems where nitrogen is limiting, for example glacial moraines, gravel slopes, volcanic ashes, mine spoils or burned forests.
 
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Figure 2: On the left, Alnus crispa planted in Northern Quebec to stabilize hydro dam dykes (photo M. Lessard), in the center Alnus glutinosa growing on the Rhone river banks in Lyon ; photo on the right, Hippophae rhamnoides growing above the Aiguebelette lake in Savoy (Photos P. Normand)
 
Actinorhizal plants are cultivated for their fruits, for instance sea buckthorn, or as ornamentals such as autumn olive. They are used to stabilize unstable slopes, to set wind breaks, interplanted with more valuable species to supply them with nitrogen. Some (Hippophae, Myrica) are used for their pharmaco-dynamic properties, as a source of vitamins, anti-oxydants, etc.
 
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Figure 3 : An alder root hair deformed following contact with Frankia hyphae (Photo Y. Prin, LSTM Montpellier). Photo on the right, a branched root hair of alder together with Frankia hyphae (Photo P. Pujic). This reaction is also triggered simply by the application of a Frankia cells supernatant..
 
Bacteria of genus Frankia have branched hyphae, multilocular sporangia and diazo-vesicles, cells specialized for nitrogen fixation due to a thick wall that forms a barrier against oxygen diffusion that would otherwise inhibit nitrogenase. Following contact with its host plant, the bacterium Frankia induces deformation of alder root hairs, penetrates roots where it induces cell divisions and eventually a perenial dichotomous nodule whence giant cortical cells are filled with Frankia cells.
 
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Figure 4 : A cortex swelling called « prenodule », that constitutes the first step in the establishment of the nodule, longitudinal cut of an alder nodule, stained with cotton blue in order to visualize cortical cells full of Frankia vesicles. The photo on the right shows a Dryas drummondii seedling from Gaspé (Canada) with a nodule (photos P. Normand).
 

Research themes :

Nos axes de recherche sont la physiologie et la génétique de l’interaction et l’évolution et l’écologie des symbioses.
Our research themes are the physiology and genetics of the interaction and evolution and ecology of symbioses. We aim to understand the physiological bases of this symbiosis by analyzing the modifications that occur upon establishment of the symbiosis. Because of the lack of genetic transformation tools for Frankia, knowledge of the genes involved in symbiosis is being carried out through study of the genome : project Genoscope. Through studies of the biodiversity and the phylogeny, at the level of the bacterial partner as well as at that of the host-plant, we aim to understand the modalities of the evolution of the symbiosis. Concerning Frankia, strains with differing hosts spectra are compared with close phylogenetic neighbors such as the acidothermophilic bacterium Acidothermus cellulolyticus recovered from hot springs in Yellowstone park and Geodermatophilus spp. recovered in different dry soils and on different surfaces.
 
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Figure 5: Circular representation of the Frankia alni genome, with a few known regions, in particular those involved in symbiosis : glnB/amtB involved in assimilation of ammonium, shc1 et shc2 involved in the synthesis of hopanoid lipids that form a barrier to diffusion of oxygen, hup1 and hup2 that permits recycling of hydrogen, a by-product of nitrogen fixation, sod that permits to cope with superoxide ions, suf that permits synthesis of iron-sulfur and nif that codes for nitrogenase (Normand et. coll., 2007).
 
We are interested in particular in the genome of Frankia alni, looking for symbiotic determinants. Given that Frankia is not genetically transformable, this aspect is broached through a gain-of-function approach in the actinobacterium Streptomyces. The first biological screen used is deformation of root hairs, the first step in the establishment of the symbiosis.
 
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Figure 6 : Alnus glutinosa seedlings growing in growth pouches (width 16cm) without mineral nitrogen. On the left, following inoculation with Frankia alni, there are root nodules and the seedlings have leaves and shoots that are more important. On the right, non-inoculated seedlings have small shoots but more important, longer root systems (Photo P. Pujic).
 
 
 
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Figure 7 : Effect of Myrica gale extracts on the growth of incompatible (A) or compatible (B et C) Frankia strains (Popovici et al., 2011).
 
From a larger perspective, we also aim to understand what are the effects of Frankia on ecosystems functions, and what are the modifications of the communities of soil bacteria following different treatments.

Bibliography :

2019



  • Béthencourt, L., Boubakri, H., Taib, N., Normand, P., Armengaud, J., Fournier, P., Brochier-Armanet, C., Herrera-Belaroussi, A., 2019. Comparative genomics and proteogenomics highlight key molecular players involved in Frankia sporulation. Research in Microbiology. https://doi.org/10.1016/j.resmic.2019.04.002


  • Bethencourt, L., Vautrin, F., Taib, N., Dubost, A., Castro-Garcia, L., Imbaud, O., Abrouk, D., Fournier, P., Briolay, J., Nguyen, A., Normand, P., Fernandez, M.P., Brochier-Armanet, C., Herrera-Belaroussi, A., 2019. Draft genome sequences for three unisolated <i>Alnus</i> -infective <i>Frankia</i> Sp+ strains, AgTrS, AiOr and AvVan, the first sequenced <i>Frankia</i> strains able to sporulate <i>in-planta</i>. Journal of Genomics 7, 50-55. https://doi.org/10.7150/jgen.35875


  • Gasmi, M., Kitouni, M., Carro, L., Pujic, P., Normand, P., Boubakri, H., 2019. Chitinolytic actinobacteria isolated from an Algerian semi-arid soil: development of an antifungal chitinase-dependent assay and GH18 chitinase gene identification. Annals of Microbiology 69, 395-405. https://doi.org/10.1007/s13213-018-1426-z


  • Pujic, P., Alloisio, N., Fournier, P., Roche, D., Sghaier, H., Miotello, G., Armengaud, J., Berry, A.M., Normand, P., 2019. Omics of the early molecular dialogue between <i>Frankia alni</i> and <i>Alnus glutinosa</i> and the cellulase synton. Environmental Microbiology. https://doi.org/10.1111/1462-2920.14606


  • Selak, G.V., Raboteg, M., Dubost, A., Abrouk, D., Žanić, K., Normand, P., Pujić, P., 2019. Whole-Genome Sequence of a Pantoea sp. Strain Isolated from an Olive (Olea europaea L.) Knot. Microbiology Resource Announcements 8. https://doi.org/10.1128/MRA.00978-19

2018



  • Bertrand, J.-C., Caumette, P., Normand, P., Ollivier, B., Sime-Ngando, T., 2018. Prokaryote/Eukaryote Dichotomy and Bacteria/Archaea/Eukarya Domains: Two Inseparable Concepts, in: Bertrand, J.-C., Normand, P., Ollivier, B., Sime-Ngando, T. (Eds.), Prokaryotes And Evolution. Springer International Publishing, Cham, p. 1-21.


  • Ghedira, K., Harigua-Souiai, E., Hamda, C., Fournier, P., Pujic, P., Guesmi, S., Guizani, I., Miotello, G., Armengaud, J., Normand, P., Sghaier, H., 2018. The PEG-responding desiccome of the alder microsymbiont Frankia alni. Scientific Reports 8, 759. https://doi.org/10.1038/s41598-017-18839-0

  • Griesmann, M., Chang, Y., Liu, X., Song, Y., Haberer, G., Crook, M.B., Billault-Penneteau, B., Lauressergues, D., Keller, J., Imanishi, L., Roswanjaya, Y.P., Kohlen, W., Pujic, P., Battenberg, K., Alloisio, N., Liang, Y., Hilhorst, H., Salgado, M.G., Hocher, V., Gherbi, H., Svistoonoff, S., Doyle, J.J., He, S., Xu, Y., Xu, S., Qu, J., Gao, Q., Fang, X., Fu, Y., Normand, P., Berry, A.M., Wall, L.G., Ané, J.-M., Pawlowski, K., Xu, X., Yang, H., Spannagl, M., Mayer, K.F.X., Wong, G.K.-S., Parniske, M., Delaux, P.-M., Cheng, S., 2018. Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis. Science (New York, N.Y.). https://doi.org/10.1126/science.aat1743


  • Lurthy, T., Alloisio, N., Fournier, P., Anchisi, S., Ponsero, A., Normand, P., Pujic, P., Boubakri, H., 2018. Molecular response to nitrogen starvation by Frankia alni ACN14a revealed by transcriptomics and functional analysis with a fosmid library in Escherichia coli. Research in Microbiology 169, 90-100. https://doi.org/10.1016/j.resmic.2017.12.002


  • Myronovskyi, M., Rosenkränzer, B., Nadmid, S., Pujic, P., Normand, P., Luzhetskyy, A., 2018. Generation of a cluster-free Streptomyces albus chassis strains for improved heterologous expression of secondary metabolite clusters. Metabolic Engineering 49, 316-324. https://doi.org/10.1016/j.ymben.2018.09.004


  • Normand, P., Caumette, P., 2018. Phylogeny and Biodiversity of Prokaryotes, in: Bertrand, J.-C., Normand, P., Ollivier, B., Sime-Ngando, T. (Eds.), Prokaryotes And Evolution. Springer International Publishing, Cham, p. 23-55.


  • Normand, P., Nouioui, I., Pujic, P., Fournier, P., Dubost, A., Schwob, G., Klenk, H.-P., Nguyen, A., Abrouk, D., Herrera-Belaroussi, A., Pothier, J.F., Pflüger, V., Fernandez, M.P., 2018. Frankia canadensis sp. nov., isolated from root nodules of Alnus incana subspecies rugosa. International Journal of Systematic and Evolutionary Microbiology 68, 3001-3011. https://doi.org/10.1099/ijsem.0.002939


  • Pozzi, A.C., Bautista-Guerrero, H.H., Abby, S.S., Herrera-Belaroussi, A., Abrouk, D., Normand, P., Menu, F., Fernandez, M.P., 2018. Robust Frankia phylogeny, species delineation and intraspecies diversity based on Multi-Locus Sequence Analysis (MLSA) and Single-Locus Strain Typing (SLST) adapted to a large sample size. Systematic and Applied Microbiology. https://doi.org/10.1016/j.syapm.2018.03.002

  • Pozzi, A.C., Roy, M., Nagati, M., Schwob, G., Manzi, S., Gardes, M., Moreau, P.-A., Fernandez, M.P., 2018. Patterns of diversity, endemism and specialization in the root symbiont communities of alder species on the island of Corsica. The New Phytologist. https://doi.org/10.1111/nph.14996


  • Riesco, R., Carro, L., Román-Ponce, B., Prieto, C., Blom, J., Klenk, H.-P., Normand, P., Trujillo, M.E., 2018. Defining the species Micromonospora saelicesensis and Micromonospora noduli under the framework of genomics. Frontiers in Microbiology 9. https://doi.org/10.3389/fmicb.2018.01360


  • Schwob, G., Roy, M., Pozzi, C.A., Herrera-Belaroussi, A., Fernandez, M.P., 2018. <i>In planta</i> sporulation of <i>Frankia</i> as a determinant of alder-symbionts interactions. Applied and Environmental Microbiology. https://doi.org/10.1128/AEM.01737-18


  • Wielgoss, S., Leblond, P., Masson-Boivin, C., Normand, P., 2018. Evolution Underway in Prokaryotes, in: Bertrand, J.-C., Normand, P., Ollivier, B., Sime-Ngando, T. (Eds.), Prokaryotes And Evolution. Springer International Publishing, Cham, p. 339-391.

2017



  • Bernardin Souibgui, C., Zoropogui, A., Voisin, J., Ribun, S., Vasselon, V., Pujic, P., Rodriguez-Nava, V., Belly, P., Cournoyer, B., Blaha, D., 2017. Virulence test using nematodes to prescreen <i>Nocardia</i> species capable of inducing neurodegeneration and behavioral disorders. PeerJ 5, e3823. https://doi.org/10.7717/peerj.3823


  • Hay, A.E., Boubakri, H., Buonomo, A., Rey, M., Meiffren, G., Cotin-Galvan, L., Comte, G., Herrera-Belaroussi, A., 2017. Control of Endophytic Frankia Sporulation by Alnus Nodule Metabolites. Molecular Plant-Microbe Interactions 30, 205-214. https://doi.org/10.1094/MPMI-11-16-0235-R


  • Normand, P., Van Nguyen, T., Battenberg, K., Berry, A.M., Heuvel, B.V., Fernandez, M.P., Pawlowski, K., 2017. Proposal of'Candidatus Frankia californiensis', the uncultured symbiont in nitrogen-fixing root nodules of a phylogenetically broad group of hosts endemic to western North America. International journal of systematic and evolutionary microbiology 67, 3706-3715. https://doi.org/10.1099/ijsem.0.002147
  • Petar, P., Philippe, N., Anita, S., 2017. Nitrogenase and hydrogenase of the actinomycete Frankia: From gene expression to proteins. Journal of Microbiology Research 7, 79–92.


  • Roy, M., Pozzi, A.C., Gareil, R., Nagati, M., Manzi, S., Nouioui, I., Sharikadze, N., Jargeat, P., Gryta, H., Moreau, P.-A., Fernandez, M.P., Gardes, M., 2017. Alder and the Golden Fleece: high diversity of Frankia and ectomycorrhizal fungi revealed from Alnus glutinosa subsp. barbata roots close to a Tertiary and glacial refugium. PeerJ 5, e3479. https://doi.org/10.7717/peerj.3479


  • Schwob, G., Roy, M., Manzi, S., Pommier, T., Fernandez, Mp., 2017. Green alder (Alnus viridis) encroachment shapes microbial communities in subalpine soils and impacts its bacterial or fungal symbionts differently. Environmental Microbiology n/a-n/a. https://doi.org/10.1111/1462-2920.13818

2016



  • Carro, L., Persson, T., Pujic, P., Alloisio, N., Fournier, P., Boubakri, H., Pawlowski, K., Normand, P., 2016. Organic acids metabolism in Frankia alni. Symbiosis 70, 37–48. https://doi.org/10.1007/s13199-016-0404-0
  • Carro, L., Pujic, P., Alloisio, N., Fournier, P., Boubakri, H., Poly, F., Rey, M., Heddi, A., Normand, P., 2016. Physiological effects of major up-regulated Alnus glutinosa peptides on Frankia sp. ACN14a. Microbiology 162, 1173–1184.


  • Cotin-Galvan, L., Pozzi, A.C., Schwob, G., Fournier, P., Fernandez, M.P., Herrera-Belaroussi, A., 2016. In-planta Sporulation Capacity Enhances Infectivity and Rhizospheric Competitiveness of Frankia Strains. Microbes and Environments 31, 11-18. https://doi.org/10.1264/jsme2.ME15090


  • Franche, C., Normand, P., Pawlowski, K., Tisa, L.S., Bogusz, D., 2016. An update on research on Frankia and actinorhizal plants on the occasion of the 18th meeting of the Frankia-actinorhizal plants symbiosis. Symbiosis 70, 1-4. https://doi.org/10.1007/s13199-016-0431-x


  • Nouioui, I., Ghodhbane-Gtari, F., Montero-Calasanz, M. del C., Göker, M., Meier-Kolthoff, J.P., Schumann, P., Rohde, M., Goodfellow, M., Fernandez, M.P., Normand, P., Tisa, L.S., Klenk, H.-P., Gtari, M., 2016. Proposal of a type strain for Frankia alni (Woronin 1866) Von Tubeuf 1895, emended description of Frankia alni, and recognition of Frankia casuarinae sp. nov. and Frankia elaeagni sp. nov. International Journal of Systematic and Evolutionary Microbiology 66, 5201–5210. https://doi.org/10.1099/ijsem.0.001496


  • Nouioui, I., Gtari, M., Göker, M., Ghodhbane-Gtari, F., Tisa, L.S., Fernandez, M.P., Normand, P., Huntemann, M., Clum, A., Pillay, M., Varghese, N., Reddy, T.B.K., Ivanova, N., Woyke, T., Kyrpides, N.C., Klenk, H.-P., 2016. Draft Genome Sequence of Frankia Strain G2, a Nitrogen-Fixing Actinobacterium Isolated from Casuarina equisetifolia and Able To Nodulate Actinorhizal Plants of the Order Rhamnales. Genome Announcements 4, e00437-16. https://doi.org/10.1128/genomeA.00437-16


  • Persson, T., Van Nguyen, T., Alloisio, N., Pujic, P., Berry, A.M., Normand, P., Pawlowski, K., 2016. The N-metabolites of roots and actinorhizal nodules from Alnus glutinosa and Datisca glomerata: can D. glomerata change N-transport forms when nodulated? Symbiosis 70, 149–157. https://doi.org/10.1007/s13199-016-0407-x


  • Sarkar, I., Normand, P., Tisa, L.S., Gtari, M., Bothra, A., Sen, A., 2016. Characterization of PAS domains in Frankia and selected Actinobacteria and their possible interaction with other co-domains for environmental adaptation. Symbiosis 70, 69–78. https://doi.org/10.1007/s13199-016-0413-z