Plant-microbiota, evolution and ecology

Microorganisms constitute by far the major diversity reservoir on earth. The huge microbial-species richness and diversity found in a variety of microbiota is theoretically unexpected because within a shared habitat competition is expected to lead to competitive exclusion. I am developing research to explain this observed paradox by assessing (i) the rules of assembly and ecological filters both biotic and abiotic (ii) the evolution of dependencies and specialisation (iii) the microbiota composition dynamics (iv) the division of labor in microbiota.

Sustainable interactions among (micro)organisms are resulting from evolutionary processes. Among these interactions, symbiosis has many forms and includes relationships ranging from cooperation to parasitism. Symbioses interactions are widespread in the biosphere and are major components of macro- and micro-evolution processes because of their impact on both individual and population fitness. As a consequence, these interactions also impact the higher hierarchical ecological levels (i.e. communities and ecosystems).

My current research is focusing on the plant microbiota. We (my group) have developed a new ecological knowledge of the plant root endosphere (i.e. microorganisms within roots) and new conceptual frameworks (see publications). In relation to this, we are studying the evolution of plant symbioses and develop a new understanding of the plant holobiont and hologenome concept. From a more applied perspective, the fundamental researches developed have the ambition to provide new directions for a more sustainable and productive agriculture.

My current research interests are  :

1-Symbiosis evolution :

How did cooperation behavior evolve ? What rules the persistence of mutualism, trade-off, other evolutionary and functional processes ?
How evolution of dependancies could explain microbiota complexity and steady state interactions among free leaving microorganisms ?
How the agricultural practices could impact the evolutionary trajectories of plant symbionts ?

2-Understanding the plant microbiota

What is the composition of the endospheric plant microbiota ? What rules the microbiota community assembly ?
Is it possible to transpose landscape ecology concepts at microscale to address the plant microbiota rules of community assembly
To what extend the plant microbiota is heritable ?

3- New concepts

Should we have to consider a plant as an holobiont ? Is it possible to evaluate the hologenome concept ?

 

Very last published or accepted papers :

Plant holobiont

Biget M, Wang T, Mony C, Xu Q, Lecoq L, Chable V, Theis KR, Ling N, Vandenkoornhuyse P (2023) Evaluating the hologenome concept by analyzing the root-endosphere microbiota of chimeric plants. iScience 26, 106031

Vannier N, Mony C, Bittebière A-K, Theis K, Rosenberg E, Vandenkoornhuyse P (2019) Clonal plants as metaholobionts. mSystems 4: e00213-18

Vannier N, Mony C, Bittebière AK, Michon-Codouel S, Biget M, Vandenkoornhuyse P (2018) A microorganisms’ journey between plant generations. Microbiome 6:79

Vandenkoornhuyse P, Quaiser A, Duhamel M, Le Van A, Dufresne A (2015) The importance of the microbiome of the plant holobiont. New Phytologist 206: 1196-1206

Theis KR, Dheilly NM, Klassen JL, Brucker RM, Baines JF, Bosch TCG, Cryan JF, Gilbert SF, Goodnight CJ, Lloyd EA, Sapp J, Vandenkoornhuyse P, Zilber-Rosenberg I, Rosenberg E, Bordenstein SR (2016) Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes. mSystems 1: e00028-16

Symbiosis evolution, rules of assembly and plant microbiota (a selection of publications)

Mony C, Uroy L, Khalfallah F, Haddad N, Vandenkoornhuyse P (2022) Landscape connectivity for the invisibles. Ecography 8:e06041 

Xu Q, Vandenkoornhuyse P, Li L, Guo J, Zhu C, Guo S, Ling N, Shen Q (2022) Microbial generalists and specialists differently contribute to the community diversity in farmland soils. Journal of Advanced Research 40:17-27

Guo J, Ling N, Li Y, Li K, Ning H, Shen Q, Guo S, Vandenkoornhuyse P (2021) Seed‐borne, endospheric and rhizospheric core microbiota as predictor for plant functional traits across rice cultivars are dominated by deterministic processes. New Phytologist,230: 2047–2060

Xu Q, Ling N, Chen H, Duan Y, Wang S, Shen Q, Vandenkoornhuyse P (2020) Long-term chemical-only fertilization indices a diversity decline and deep selection on the soil microbiota. mSystems 5:e00337-20

Guo JJ, Ling N, Chen ZJ, Xue C, Li L, Liu LS, Gao LM, Wang M, Ruan JY, Guo SW, Vandenkoornhuyse P, Shen, QR (2020) Soil fungal assemblage complexity is dependent on soil fertility and dominated by deterministic processes. New Phytologist, 226:232-243.

Mony C, Brunellière P, Vannier N, Bittebière AK, Vandenkoornhuyse P (2020) Effect of floristic composition and configuration on plant root mycobiota: a landscape transposition at a small scale. New Phytologist 225:1777-1787

Bittebiere AK, Vandenkoornhuyse P, Maluenda E, Gareil A, Dheilly A, Coudouel S, Bahin M, Mony C (2019) Past spatial structure of plant communities determines arbuscular mycorrhizal fungal community assembly. Journal of Ecology 108:546-560.

Vannier N, Mony C, Bittebière AK, Michon-Codouel S, Biget M, Vandenkoornhuyse P (2018) A microorganisms’ journey between plant generations. Microbiome 6:79 

Lê Van A, Quaiser A, Duhamel M, Michon-Coudouel S, Dufresne A, Vandenkoornhuyse P (2017) Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera. Peer Journal 5:e3454

Vannier N, Bittebiere AK, Vandenkoornhuyse P, Mony C (2016) Arbuscular Mycorhizal fungi patchiness and the clonal growth of Glechoma hederacea in heterogeneous environment. Scientific Reports 6:37852

Mas A, Jamshidi S, Lagadeuc Y, Eveillard D, Vandenkoornhuyse P (2016) Beyond the Black Queen Hypothesis. ISME Journal 10: 2085-2091 

Vandenkoornhuyse P, Quaiser A, Duhamel M, Le Van A, Dufresne A (2015) The importance of the microbiome of the plant holobiont. New Phytologist 206: 1196-1206

Jamshidi S, Behm JE, Eveillard D, Kiers ET, Vandenkoornhuyse P (2015) Using hybrid automata modelling to study phenotypic plasticity and allocation strategies in the plant mycorrhizal mutualism. Ecological Modelling 311: 11-19

Duhamel M, Vandenkoornhuyse P 2013 Sustainable agriculture: possible trajectories from mutualistic symbiosis and plant neodomestication. Trends in Plant Science 18:597-600

Duhamel M, Pel R, Ooms A, Bücking H, Jansa J, Ellers J, van Straalen NM Tjiaf Wouda, Vandenkoornhuyse P, Kiers ET 2013. Do fungivores trigger the transfer of protective metabolites from host plants to arbuscular mycorrhizal hyphae? Ecology 94:2009-2029

Kiers ET, Duhamel M, Beesetty Y, Mensah JA, Franken O, Verbruggen E, Fellbaum CR, Kowalchuk GA, Hart MM, Bago A, Palmer TM, West SA, Vandenkoornhuyse P, Jansa J, Bucking H 2011. Reciprocal Rewards Stabilize Cooperation in the Mycorrhizal Symbiosis Science 333, 880-882.

Review & perspectives

Mauger S, Monard C, Thion C, Vandenkoornhuyse P (2022) Contribution of single-cell omics to microbial ecology. Trends in Ecology and Evolution 37:67-78.

Mony C, Uroy L, Khalfallah F, Haddad N, Vandenkoornhuyse P (2022) Landscape connectivity for the invisibles. Ecography https://doi.org/10.1111/ecog.06041

Mas A, Lagadeuc Y, Vandenkoornhuyse P (2020) Reflections on the Predictability of Evolution: Toward a Conceptual Framework. iScience 23, 101736,

Mony C, Vandenkoornhuyse P, Bohannan BJM, Peay K, Leibold MA (2020) A landscape of opportunities for microbial ecology research. Frontiers in Microbiology 11 : Article 561427

Vandenkoornhuyse P, Quaiser A, Duhamel M, Le Van A, Dufresne A (2015) The importance of the microbiome of the plant holobiont. New Phytologist 206: 1196-1206

Duhamel M, Vandenkoornhuyse P (2013) Sustainable agriculture: possible trajectories from mutualistic symbiosis and plant neodomestication. Trends in Plant Science 18: 597-600.

PhD positions:

-If you are entering your final MSc year and are contemplating a PhD in my group please get in touch to discuss.

-Visiting PhDs are welcome

Postdoctoral Researchers:

We are looking for Postdoctoral Fellows – I am particularly interested in applying for Marie Curie funding etc… To get in touch don't hesitate to Email me

(philippe [dot] vandenkoornhuyseuniv-rennes1 [dot] fr)

Head of genomics facility at University of Rennes.
For details visit the following website :
EcogenO (https://osur.univ-rennes1.fr/ecogeno)
 

Detailed methodologies to perform SIP-RNA experiments are now detailed in : Le Van A, Duhamel M, Quaiser A, Vandenkoornhuyse P (2015) SIP-RNA to study the plant/fungi interaction. In Microbial Environmental Genomics, Methods in Molecular Biology series. Springer
 

Our curated SSU rRNA and EF1-alpha sequence database (~11.000 and ~1200 sequences respectively) :

Database - PHYMYCO-DB : A Curated Database for Analyses of Fungal Diversity and Evolution (link)

Reference:

Mahe S, Duhamel M, Le Calvez T, Guillot L, Sarbu L, Bretaudeau A, Collin O, Dufresne A, Kiers ET, Vandenkoornhuyse P 2012. PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and Evolution. PLoS ONE 7 : e43117 (link)
 

Phylogenetic tool - Influence functions for robust phylogenetic trees

Reference

Bar-Hen A, Madriassou M, Poursat M.A., Vandenkoornhuyse P 2008 Influence functions for robust phylogenetic trees. Mol Biol Evol 25:869-873. (link)

Scientific events

2019
Nov 26 – 27th 2019 - 4th Adam Kondorosi Symposium - Frontiers in Symbiosis 2019. Paris (France) https://symposium.inra.fr/ak2019/

Nov 6 – 9th 2019 - IXe Colloque de l'Association Francophone d'Ecologie Microbienne. Bussang (France). https://colloque.inra.fr/afem2019/

Oct 8 – 10th 2019 – Colloque Génomique Environnementale. La Rochelle (France). https://apps.univ-lr.fr/cgi-bin/WebObjects/Colloque.woa/1/wa/colloque?code=2401

July 7-11th 8th Congress of European Microbiologists, Glasgow scotland - https://fems2019.org/

Sept 3-4th Workshop Single Cell analyses (Scenion, Cellenion), Lyon (France)

2018
Oct 22nd-25th, International Conference on Ecological Sciences, Rennes - https://sfecologie2018.sciencesconf.org/

June 14th-15th 2018, Journées Condorcet 2018 'Etude du microbiote associé aux plantes et son implication en agroécologie' - http://sfr-condorcet.fr/spip.php?article1390

June 1st 2018, 'Systems ecology : which advances towards ecosystems understanding ?' - http://www.js.univ-nantes.fr/navigation/cl10-systems-ecology-which-advances-towards-ecosystems-understanding--2184302.kjsp?RH=1486401620746

Jan 15th-19th, JCC2018 Aussois (France) - https://colloque.inra.fr/jjc2018/

2017
Nov 9th-10th Réunion annuelle du réseau PhytoMic (ex Phytobiome)

Noc 6th-8th Interdisciplinary Workshop on Holobionts - https://www.immuconcept.org/holobiont-workshop/#1495533739053-ce74f35c-99c9

Oct 17th-20th Microbiomes: des environnements naturels à l'homme

Sept 13rd-15th Colloque Génomique Environnementale

Aug 20th-25th ESEB, symposium Coevolution of hosts and their microbiome

Apr 19th-21st International conference on Holobionts

22nd-25th Aug European Society for Evolutionary Biology (ESEB XVI congress)

Feb 20th-21st VISCEA meeting: Plant nutrition growth & environment interactions

2013
Colloque génomique environnementale

2011
Jacques Monod Conferences : Integrative ecological genomics
15th-19th Oct 2011 (link)