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Research Scientist at INRAE




42 Rue Georges Morel, 49070 Beaucouzé, France                                                                                          

E-mail: marie.simonin[at]


Research interests


Impact of abiotic and biotic disturbances on microbial activity and diversity

Interactive effects of different agents of global change (contaminants, nutrient pollution, CO2)

Plant-microbiome interactions and microbiome engineering

Resistance and resilience of microbiomes to these disturbances




●  Ph.D (2012 –2015):Microbial Ecology Laboratory (University Claude Bernard - Lyon, France) and Laboratory of Transfer in Hydrology and Environment (University Joseph Fourier - Grenoble, France)

Advisors: Pr Agnès Richaume-Jolion and Dr Jean Martins


  ●    MSc. Degree in Ecology, Biodiversity, Evolution (2010–2012): University Pierre & Marie Curie 

        Paris VI, France. Specialty: Biodiversity and Functioning of Ecosystems – Ecological engineering  


   ●    BSc. Degrees(2007 – 2010): University of Caen-Basse Normandie, France

-       License of Biology of organisms and License of Geography   

Professional experiences


Research Scientist (Oct 2019 - Present): INRAE - IRHS in EmerSys team (Angers, France) Characterization of seed microbiomes and their resistances to abiotic and biotic stressors. 


●  Postdoctoral associate (Jan 2019 - Sept 2019):IRD - Interaction Plant - Microorganism - Environment Lab  (Montpellier, France) Impact of biotic disturbances and agricultural practices on the plant microbiome of diverse crops in West Africa and South-East Asia.Supervisor: Lionel Moulin


●   Postdoctoral associate (2016 - 2018):Biology Department  (Duke University, NC, USA)

Impact of anthropogenic disturbances on the diversity and function of microbial communities in aquatic and terrestrial ecosystems.Supervisor: Emily Bernhardt


●  Graduate researcher(2012- 2015): Microbial Ecology Laboratory (University Claude Bernard - Lyon) and Laboratory of Transfer in Hydrology and Environment (University Joseph Fourier - Grenoble)

Thesis title: Dynamic, reactivity and ecotoxicity of metal oxide nanoparticles in soil: impact on functions and diversity of microbial communities.Advisors: Pr Agnès Richaume-Jolion and Dr Jean Martins


Articles / Presentations / Posters


      Published articles and Pre-prints

24 articles published in peer-reviewed journal (Rank A)

1 pre-print

Journal articles17 documents

  • Jacqueline Gerson, Eric Moore, Laura Naslund, Jennifer Rocca, Marie Simonin. Chemistry of streams draining mined and unmined watersheds in the mountaintop mined landscape of Central Appalachia, USA. Ecology, Ecological Society of America, In press, 101 (9), pp.e03093. ⟨10.1002/ecy.3093⟩. ⟨hal-02798110⟩
  • Jennifer Rocca, Marie Simonin, Emily Bernhardt, Alex Washburne, Justin Wright. Rare microbial taxa emerge when communities collide: freshwater and marine microbiome responses to experimental mixing. Ecology, Ecological Society of America, 2020, 101 (3), ⟨10.1002/ecy.2956⟩. ⟨hal-02958363⟩
  • Marie Simonin, Cindy Dasilva, Valeria Terzi, Eddy Ngonkeu, Diégane Diouf, et al.. Influence of plant genotype and soil on the wheat rhizosphere microbiome: evidences for a core microbiome across eight African and European soils. FEMS Microbiology Ecology, Wiley-Blackwell, 2020, 96 (6), pp.fiaa067. ⟨10.1093/femsec/fiaa067⟩. ⟨hal-02941967⟩
  • Carla de la Fuente Cantó, Marie Simonin, Eoghan King, Lionel Moulin, Malcolm Bennett, et al.. An extended root phenotype: the rhizosphere, its formation and impacts on plant fitness. Plant Journal, Wiley, 2020, 14 p. ⟨10.1111/tpj.14781⟩. ⟨hal-02779134⟩
  • Brittany Perrotta, Marie Simonin, Jeffrey Back, Steven Anderson, Astrid Avellan, et al.. Copper and Gold Nanoparticles Increase Nutrient Excretion Rates of Primary Consumers. Environmental Science and Technology, American Chemical Society, 2020, 54 (16), pp.10170-10180. ⟨10.1021/acs.est.0c02197⟩. ⟨hal-02958354⟩
  • Anne-Sophie Masson, Hai Ho Bich, Marie Simonin, Hue Nguyen Thi, Pierre Czernic, et al.. Deep modifications of the microbiome of rice roots infected by the parasitic nematode Meloidogyne graminicola in highly infested fields in Vietnam. FEMS Microbiology Ecology, Wiley-Blackwell, 2020, 96 (7), pp.fiaa099. ⟨10.1093/femsec/fiaa099⟩. ⟨hal-02770824⟩
  • Lauren Carley, Renuka Panchagavi, Xin Song, Sade Davenport, Christina Bergemann, et al.. Long-Term Effects of Copper Nanopesticides on Soil and Sediment Community Diversity in Two Outdoor Mesocosm Experiments. Environmental Science and Technology, American Chemical Society, 2020, 54 (14), pp.8878-8889. ⟨10.1021/acs.est.0c00510⟩. ⟨hal-02945106⟩
  • Nicholas Geitner, Christine Ogilvie Hendren, Geert Cornelis, Ralf Kaegi, Jamie Lead, et al.. Harmonizing Across Environmental Nanomaterial Testing Media for Increased Comparability of Nanomaterial Datasets. Environmental science‎.Nano, Royal Society of Chemistry, In press, ⟨10.1039/C9EN00448C⟩. ⟨hal-02376852⟩
  • Astrid Avellan, Marie Simonin, Steven Anderson, Nicholas Geitner, Nathan Bossa, et al.. Differential Reactivity of Copper- and Gold-Based Nanomaterials Controls Their Seasonal Biogeochemical Cycling and Fate in a Freshwater Wetland Mesocosm. Environmental Science and Technology, American Chemical Society, 2019, 54 (3), pp.1533-1544. ⟨10.1021/acs.est.9b05097⟩. ⟨hal-02958362⟩
  • Marie Simonin, Amélie A. M. Cantarel, Armelle Crouzet, Jonathan Gervaix, Jean Mf Martins, et al.. Negative Effects of Copper Oxide Nanoparticles on Carbon and Nitrogen Cycle Microbial Activities in Contrasting Agricultural Soils and in Presence of Plants. Frontiers in Microbiology, Frontiers Media, 2018, ⟨10.3389/fmicb.2018.03102⟩. ⟨hal-02479075⟩
  • Marie Simonin, Naoise Nunan, Juliette Bloor, Valérie Pouteau, Audrey Niboyet. Short-term responses and resistance of soil microbial community structure to elevated CO2 and N addition in grassland mesocosms. FEMS Microbiology Letters, Wiley-Blackwell, 2017, 364 (9), ⟨10.1093/femsle/fnx077⟩. ⟨hal-01525344⟩
  • Marie Simonin, Jean M. F. Martins, Xavier Le Roux, Gaelle Uzu, Aude Calas, et al.. Toxicity of TiO2 nanoparticles on soil nitrification at environmentally relevant concentrations: Lack of classical dose-response relationships. Nanotoxicology, Taylor & Francis, 2017, 11 (2), pp.247 - 255. ⟨10.1080/17435390.2017.1290845⟩. ⟨hal-01602574⟩
  • Marie Simonin, Jean M. F. Martins, Gaëlle Uzu, Erwann Vince, Agnès Richaume. Combined study of titanium dioxide nanoparticle transport and toxicity on microbial nitrifying communities under single and repeated exposures in soil columns. Environmental Science and Technology, American Chemical Society, 2016, 50 (19), pp.10693-10699. ⟨10.1021/acs.est.6b02415⟩. ⟨hal-01604452⟩
  • Marie Simonin, Agnès Richaume-Jolion, Julien P. Guyonnet, Audrey Dubost, Jean M. F. Martins, et al.. Titanium dioxide nanoparticles strongly impact soil microbial function by affecting archaeal nitrifiers. Scientific Reports, Nature Publishing Group, 2016, 6, pp.1-10. ⟨10.1038/srep33643⟩. ⟨hal-01602239⟩
  • Marie Simonin, Agnès Richaume. Impact of engineered nanoparticles on the activity, abundance, and diversity of soil microbial communities: a review. Environmental Science and Pollution Research, Springer Verlag, 2015, 22 (18), pp.13710-13723. ⟨10.1007/s11356-015-4171-x⟩. ⟨hal-01602179⟩
  • Marie Simonin, Xavier Le Roux, Franck Poly, Catherine Lerondelle, Bruce A. Hungate, et al.. Coupling Between and Among Ammonia Oxidizers and Nitrite Oxidizers in Grassland Mesocosms Submitted to Elevated CO2 and Nitrogen Supply. Microbial Ecology, Springer Verlag, 2015, 70 (3), pp.809-818. ⟨10.1007/s00248-015-0604-9⟩. ⟨hal-01569713⟩
  • Marie Simonin, Julien P. Guyonnet, Jean M. F. Martins, Morgane Ginot, Agnès Richaume-Jolion. Influence of soil properties on the toxicity of TiO₂ nanoparticles on carbon mineralization and bacterial abundance. Journal of Hazardous Materials, Elsevier, 2015, 283, pp.529-535. ⟨10.1016/j.jhazmat.2014.10.004⟩. ⟨hal-01197005⟩

Preprints, Working Papers, ...1 document

  • Aude Rochefort, Marie Simonin, Coralie Marais, Anne-Yvonne Guillerm-Erckelboudt, Matthieu Barret, et al.. Asymmetric outcome of community coalescence of seed and soil microbiota during early seedling growth. 2020. ⟨hal-03045727⟩

Theses1 document

  • Marie Simonin. Dynamique, réactivité et écotoxicité des nanoparticules d’oxydes métalliques dans les sols : impact sur les fonctions et la diversité des communautés microbiennes. Ecotoxicologie. Université Claude Bernard - Lyon I, 2015. Français. ⟨NNT : 2015LYO10164⟩. ⟨tel-01272111⟩