IHPE – Transversal Holobiont

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TRANSVERSAL CHALLENGE
« Dynamics of the holobiont and fitness »
Head Eve TOULZA & Caroline MONTAGNANI

Event : october 15-16 2018 :
Workshop Integrated immunity in holobionts

 

 

The concept of holobiont has extended our vision of organisms to the whole (microbial) community living in association with them. These metaorganisms, considered as communities of species, would thus be the true unit of evolution. In this context, the hologenome is defıned as the sum of the genetic information of the host and its symbiotic microorganisms. The hologenome theory of evolution proposes that the object of natural selection is not the individual organism, but the holobiont, i.e. the organism together with its associated microbial communities.
This concept has gained more and more attention for many issues on the functioning, homeostasis or evolution of living organisms. These questions, however, remain open in many taxonomic groups. The goal of this research axis, is to develop collaborative projects to study the extent of these concepts in different model species. The various invertebrates studied in the IHPE laboratory indeed give us today the unique opportunity to explore the impact of the nature and dynamics of the microbiota on their health status and survival as well as their adaptive capabilities (defense against parasites or opportunistic pathogens, resistance to environmental variations).
HOLOBIONTE-fig1 Holobiont exploration in IHPE invertebrate models (c)IHPE-Montagnani-Toulza-2015
 HOLOBIONTE-fig2  A metagenome (c)http:/armbrustlab.ocean.washington.eduseastar

The concept of holobiont has extended the notion of organism to all internal and surface microbial communities associated with it. These organisms would then be considered as communities of species, metaorganisms that would be the true unity of evolution resulting from the interaction of their own genome with that of their microbiota. Thus, the hologenome theory defined for the first time in corals by Eugene Rosenberg, considers the holobiont and its hologenome (all interacting genomic entities) as the target of natural selection.
The significance of this concept has become more and more important as the studies showing the impact of the microbial compartment on the fitness of the host and its role in many physiological functions, from reproduction to development, operation of epithelial barriers, immunity, etc. have accumulated. Disruptions of this association could affect the adaptive capabilities and therefore the fitness of the species assemblage.
Another new interesting aspect highlighted by this theory is that of the interaction between a slow evolving macroorganism and a labile microbial community that can change and adapt quickly (microbiota) and from new selective traits may emerge thus influencing the adaptability of this species. In stressful environmental conditions, the symbiotic community can change quickly and this plasticity may play an important role both in the acclimatization and evolution of organisms.
This concept has gained more and more attention for many issues on the functioning, homeostasis or evolution of living organisms. These questions, however, remain open in many taxonomic groups. The goal of this research axis, is to develop collaborative projects to study the extent of these concepts in different model species. The various invertebrates studied in the IHPE laboratory indeed give us the opportunity today to explore the impact of the nature and dynamics of the microbiota on their health status and survival as well as their adaptive capabilities (defense against parasites or opportunistic pathogens, resistance to environmental variations).
In most of these models, it will be necessary to first carry out an inventory of species composing the microbiota, characterize their specificity, and determine their stability over generations. We would then discuss their dynamics in response to environmental stresses, biotic or abiotic. Integrative approaches associating field sampling, controlled environment experiments and high-throughput molecular analysis methods, both at the taxonomic and functional levels (barcoding, metagenomics metatranscriptomics) should allow us to determine the importance of the microbiota in the functioning of these interactions in the light of major ecological crises affecting recurrently some of our models of interest facing global changes.

Research programs
Publications
Communications
Methodologies
Doctoral and post-doctoral fellowships’support

2018 Research programs

- « MICROTRANS»: Crassostrea gigas microflora transmission (C. Cosseau ; C. Montagnani, E. Toulza)
- « Characterization and specificity of the microbiota of Schistosome » (C. Huot, E. Toulza, R. Galinier, O. Rey, B. Gourbal , J.F Allienne , J. Boissier)
- « Characterization and dynamics of the microbiota of susceptible and resistant phenotypes of a strain of Biomphalaria glabrata originating from Brazil in the face of infection with the parasite Schistosoma mansoni from Venezuela » (C. Huot, A. Rognon, E. Toulza, R. Galinier, D. Duval)

2017 Research programs

- « PASEO » : Protists in microbiotes (C. Clerissi, J.-M. Escoubas, B. Gourbal, E. Toulza)
- « Oyster RNAi »: development of the invalidation of antimicrobial peptide genes and impact on the microbiota in C. gigas (C. Montagnani)

2016 Research programs

- « RESIVIR » : Resident viromes in our model organisms: the Pacific oyster  Crassostrea gigas, the coral Pocillocora damicornis, the freshwater snail  Biomphalaria glabrata and its trematode parasite Schistosoma mansoni (C. Chaparro, R. Galinier, J.-M. Escoubas, A. Passerieux (Master 1), C. Montagnani, E. Toulza)
- « AMIGO » : Association MIcrobiota – GenOtype : specificity and stability in healthy and diseased oysters (E. Toulza, C. Clerissi)
- «BIOGENO» : Biogeography of the coral holobiont (K. Brenner-Rafalli, J. Vidal-Dupiol, G. Mitta, E. Toulza)

2015 Programmes de recherche

- « HEMO-MICROBIOTE » : Microbial diversity and dynamics of the hemo-microbiota in our C. gigas  (J.-M. Escoubas, E. Toulza, S. Dupont)
- « MICROBIOMPH» : Dynamics of the microbiota during an allopatric or sympatric infection and after priming in Biomphalaria glabrata/Schistosoma mansoni interaction  (A. Portet, E. Toulza, B. Gourbal)

Publications

- Galinier R., Tetreau G., Portet A., Pinaud S., Duval D., Gourbal B. (2017). First characterization of viruses from freshwater snails of the genus Biomphalaria, the intermediate host of the parasite Schistosoma mansoni. Acta Tropica, 167 : 196-203.
– Brener-Raffalli, K., Clerissi, C., Vidal-Dupiol, J., Adjeroud, M., Bonhomme, F., Pratlong, M., Aurelle, D., Mitta, G., and Toulza, E. (2018) “Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato”. Microbiome , 6(1), 39.

Communications

Marine holobionts-concepts and challenges, euromarine european marine research network, March 27-28, 2018- Roscoff, France : Eve Toulza
Interdisciplinary Workshop on holobiont, November 6-8, 2017, Bordeaux, France
– Dupont S, Petton B, Lokmer A, Toulza E, Corre E, Montagnani C, Pecqueur D, Guillou L, Desnues C, De Lorgeril J, Mitta G, Gueguen Y, Escoubas JM. A holistic approach to investigate the establishment and dynamics of the blood-microbiota (bacteria, protists and viruses) in a marine invertebrate.
– Brener-Raffalli K, Clerissi C, Vidal-Dupiol J, Adjeroud M, Bonhomme F, Pratlong M, Aurelle D, Bramanti L, Bosserelle P, Mitta G, Toulza E. Thermal regime and host clade, rather than biogeography, drive symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora sp.
– Clerissi C, Petton B, Escoubas JM, Gueguen Y, Mitta G, De Lorgeril J, Toulza E. Deciphering links between osyter fitness and microbiota composition.
Seminars « Environmental Genomics », September 13-15, 2017, Marseille, France
– Brener Raffalli K., Clerissi C., Vidal-Dupiol J., Adjeroud M., Bonhomme F., Pratlong M., Aurelle D., Bramanti L., Bosserrelle P., Mitta G., Toulza E. Thermal regime and host clade, rather than biogeography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora sp.
Immuninv congress (Immunity in Invertebrates) 2017, June 7-9, 2017, Lyon, France
– Galinier R. ssRNA viruses discovery in the freshwater snail Biomphalaria, the intermediate host of intestinal Schistosomiasis.
– Lucasson A. et al. An integrative approach to decipher the summer mortality syndrome affecting Pacific oysters.
– De Lorgeril, J.*, Lucasson, A.*, Petton, B., Toulza, E., Haffner, P., Destoumieux-Garzon, D., Chaparro, C., Galinier, R., Clerissi, C., Montagnani, C., Escoubas, J.M., Vergnes, A., Leroy, M., Degrémont, L., Vidal-Dupiol, J., Chiarello, M., Pérignon, A., Alunno-Bruscia, M., Boudry, P., Le Roux, F., Gueguen, Y., Mitta, G. An integrative approach to decipher the summer mortality syndrome affecting pacific oysters (POSTER).
Workshop 2017 VIVALDI European project (annual meeting), May 9-12, 2017, L’Ampolla, Spain
– Dupont S, Petton B, Toulza E, Lokmer A, Montagnani C, Desdevises Y, Pecqueur D, Salmeron C, Guillou L, Desnues C, La Scola B, De Lorgeril J, Mitta G, Gueguen Y, Escoubas JM. The blood microbiota of oysters : viruses, bacteria, and protists. What else?
International Conference on Holobionts, April 19-21, 2017, Paris, France
– Brener-Raffalli K. Integrative analysis of the coral holobiont thermotolerance under contrasted thermal environment.
– De Lorgeril, J.*, Lucasson, A.*, Petton, B., Toulza, E., Haffner, P., Destoumieux-Garzon, D., Chaparro, C., Galinier, R., Clerissi, C., Montagnani, C., Escoubas, J.M., Vergnes, A., Leroy, M., Degrémont, L., Vidal-Dupiol, J., Chiarello, M., Pérignon, A., Alunno-Bruscia, M., Boudry, P., Le Roux, F., Gueguen, Y., Mitta, G. An integrative approach to decipher the summer mortality syndrome affecting pacific oysters (POSTER).
– Dupont S. et al. Involvement of the environment and genetic background in the composition and dynamics of microbial communities hosted by the hemolymph of the pacific oyster (POSTER).
– Clerissi C, Petton B, Escoubas JM, Gueguen Y, Mitta G, De Lorgeril J, Toulza E. Specificity and stability of microbial communities associated to healthy and diseased Crassostrea gigas oysters (POSTER)
– Dupont S, Petton B, Toulza E, Lokmer A, Montagnani C, Desdevises Y, Pecqueur D, Salmeron C, Guillou L, Desnues C, La Scola B, De Lorgeril J, Mitta G, Gueguen Y, Escoubas JM. Oyster’s blood microbiota : bacteria, protists and viruses, what else ? (POSTER)
Annual meeting of the REID network « Ecology of Sustainable Interactions », March 22-24, 2017, Toulouse, France
– Huot C., Portet A., Galinier R., Gourbal B., Duval D., Toulza E. Characterization and role of Biomphalaria glabrata‘s microbiota in its host-parasite interaction with Schistosoma mansoni (POSTER)
– Portet A., Duval D., Toulza E., Huot C., Lokmer A., Galinier R., Gourbal B. Characterization and analysis of bacterial community changes in Biomphalaria glabrata following infection by Schistosoma mansoni (POSTER)
– De Lorgeril, J.*, Lucasson, A.*, Petton, B., Toulza, E., Haffner, P., Destoumieux-Garzon, D., Chaparro, C., Galinier, R., Clerissi, C., Montagnani, C., Escoubas, J.M., Vergnes, A., Leroy, M., Degrémont, L., Vidal-Dupiol, J., Chiarello, M., Pérignon, A., Alunno-Bruscia, M., Boudry, P., Le Roux, F., Gueguen, Y., Mitta, G. An integrative approach to decipher the summer mortality syndrome affecting pacific oysters (POSTER).
– Dupont S, Petton B, Toulza E, Lokmer A, Montagnani C, Desdevises Y, Pecqueur D, Salmeron C, Guillou L, Desnues C, La Scola B, De Lorgeril J, Mitta G, Gueguen Y, Escoubas JM. Composition and dynamics of the oyster Crassostrea gigas microbiota: role of the environment and the genetic background of animals
8th IMH Network days (Interactions Microorganisms-Hosts) & 2nd day of the CEMEB labex « Microbiota Initiative », November 14, 2016, Montpellier, France
– Dupont S. et al. Composition and dynamics of the oyster microbiota Crassostrea gigas: role of the environment and the genetic background of animals.
– Brener Raffalli K. Multiscale analysis of the coral holobiont response under thermal stress: intra- and inter-populational comparisons.
SIP 2016 (Society for Invertebrate Pathology), July 24-28, 2016, Tours, France
– Galinier, R., Kinoo, A., Tetreau, G., Portet, A., Pinaud, S., Duval, D., Gourbal, B. ssRNA viruses discovery in the fresh water snail Biomphalaria sp, the intermediate host of intestinal Schistosomiasis (POSTER)
13th International Coral Reef Symposium (IRCS 2016), June 19-24, 2016, Honolulu, Hawaii , USA
– Brener Raffalli, K., Pratlong, M., Vidal-Dupiol, J., Adjeroud, M., Romans, P., Pillot, R., Feuillassier, L., Aurelle, D., Pontarotti, P., Haguenauer, A., Mitta, G., Toulza, E. Coral plasticity and holobiont dynamics under thermal stress: intrapopulational, interpopulational and interspecific variability.
Symposium « Marine Biotic Interactions», June 2, 2016, Banyuls-sur-Mer, France
– Toulza E. Dynamics of holobionts under stress.
Seminars CeMEB « Environment, society and climate change: impacts and scenarios », September 28-29, 2015, Montpellier, France
– Toulza E. Increase in the thermo-tolerance of the holobionte in the scleractinic coral Pocillopora damicornis subjected to recurrent thermal stress: analysis of molecular mechanisms.
Conference Jacques Monod “ Marine Eco-systems biology”, June 22-26, 2015, Roscoff , France
-Toulza E. What drives increased thermo-tolerance in the tropical coral Pocillopora damicornis submitted to recurrent thermal stresses?

Methodologies

- 16S barcoding MiSeq, ITS2,
– viral metagenomics,
– host RNAseq and immunome analyses,
– metranscriptomics

Doctoral and Post-doctoral fellowships’support

- Post-doctoral fellowship – Samuel Dupont (2015-2016): « Hemo-microbiota of Crassostrea gigas: microbial and dynamic diversity during experimental pathogenesis »
- Inititation of PhD project – Camille Huot (2016-2018) : « Characterization and role of microbiota in host interaction  Biomphalaria glabrata et Schistosoma mansoni, vector of schistosomiasis »
- Inititation of PhD project – J. Delmotte (2017-2020): « Characterization of the diversity and dynamics of Crassostrea gigas virome and analysis of its interaction with the antiviral response of the oyster »

- 2018, october 15-16: Workshop Integrated immunity in holobionts
- 2016 : Co-organization of the 8th IMH Network days (Interactions Microorganisms-Hosts) & 2nd days of the CEMEB labex « Microbiota initiative », November 14, 2016, Montpellier, France download program
- 2015: Workshop «holobiont dynamics and impact on fitness», November 2-3, 2015,  Montpellier, France. International keynote speaker: S. Fraune, Christian-Albrechts Universiy, Kiel, Germany, “Cnidarian microbiome, coevolution and function
download program

Eve TOULZA (ECOEVI team), eve.toulza@univ-perp.fr
Caroline MONTAGNANI (MIMM team), cmontan@ifremer.fr