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Marie Simonin

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Research Scientist at INRAE --- 42 Rue Georges Morel, 49070 Beaucouzé, France E-mail: marie.simonin\[at\]inrae.fr 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 Education --- ● 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**

Publications

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Cultivated and wild pearl millet display contrasting patterns of abundance and co-occurrence in their root mycobiome

Marie-Thérèse Mofini , Abdala Diedhiou , Marie Simonin , Donald Tchouomo Dondjou , Sarah Pignoly et al.
Scientific Reports, 2022, 12 (1), pp.207. ⟨10.1038/s41598-021-04097-8⟩
Journal articles hal-03576717v1
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Protist Predation Influences the Temperature Response of Bacterial Communities

Jennifer Rocca , Andrea Yammine , Marie Simonin , Jean Gibert
Frontiers in Microbiology, 2022, 13, pp.847964. ⟨10.3389/fmicb.2022.847964⟩
Journal articles hal-03701557v1

The impact of the rice production system (irrigated vs lowland) on root-associated microbiome from farmer's fields in western Burkina Faso

Mariam Barro , Issa Wonni , Marie Simonin , Abalo Itolou Kassankogno , Agnieszka Klonowska et al.
FEMS Microbiology Ecology, 2022, 98 (9), ⟨10.1093/femsec/fiac085⟩
Journal articles hal-03773237v1

Enrichment in biodiversity and maturation of the soil food web under conservation agriculture is associated with suppression of rice-parasitic nematodes

Anne-Sophie Masson , Marie-Liesse Vermeire , Vira Leng , Marie Simonin , Florent Tivet et al.
Agriculture, Ecosystems & Environment, 2022, 331, pp.107913. ⟨10.1016/j.agee.2022.107913⟩
Journal articles hal-03607685v1

Single seed microbiota: assembly and transmission from parent plant to seedling

Guillaume Chesneau , Béatrice Laroche , Anne Préveaux , Coralie Marais , Martial Briand et al.
mBio, 2022, pp.0164822. ⟨10.1128/mbio.01648-22⟩
Journal articles hal-03834661v1

Guided by Microbes: Applying Community Coalescence Principles for Predictive Microbiome Engineering

Jennifer Rocca , Mario Muscarella , Ariane Peralta , Dandan Izabel-Shen , Marie Simonin et al.
mSystems, 2021, 6 (4), pp.e00538-21. ⟨10.1128/mSystems.00538-21⟩
Journal articles hal-03541580v1

Deep modifications of the microbiome of rice roots infected by the parasitic nematode Meloidogyne graminicola in highly infested fields in Vietnam

Anne-Sophie Masson , Hai Ho Bich , Marie Simonin , Hue Nguyen Thi , Pierre Czernic et al.
FEMS Microbiology Ecology, 2020, 96 (7), pp.fiaa099. ⟨10.1093/femsec/fiaa099⟩
Journal articles hal-02770824v1

An extended root phenotype: the rhizosphere, its formation and impacts on plant fitness

Carla de La Fuente Cantó , Marie Simonin , Eoghan King , Lionel Moulin , Malcolm Bennett et al.
Plant Journal, 2020, 14 p. ⟨10.1111/tpj.14781⟩
Journal articles hal-02779134v1
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Rare microbial taxa emerge when communities collide: freshwater and marine microbiome responses to experimental mixing

Jennifer Rocca , Marie Simonin , Emily S Bernhardt , Alex D Washburne , Justin P Wright et al.
Ecology, 2020, 101 (3), ⟨10.1002/ecy.2956⟩
Journal articles hal-02958363v1

Long-Term Effects of Copper Nanopesticides on Soil and Sediment Community Diversity in Two Outdoor Mesocosm Experiments

Lauren N Carley , Renuka Panchagavi , Xin Song , Sade Davenport , Christina M Bergemann et al.
Environmental Science and Technology, 2020, 54 (14), pp.8878-8889. ⟨10.1021/acs.est.0c00510⟩
Journal articles hal-02945106v1
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Copper and Gold Nanoparticles Increase Nutrient Excretion Rates of Primary Consumers

Brittany G Perrotta , Marie Simonin , Jeffrey A Back , Steven M Anderson , Astrid Avellan et al.
Environmental Science and Technology, 2020, 54 (16), pp.10170-10180. ⟨10.1021/acs.est.0c02197⟩
Journal articles hal-02958354v1

Influence of plant genotype and soil on the wheat rhizosphere microbiome: evidences for a core microbiome across eight African and European soils

Marie Simonin , Cindy Dasilva , Valeria Terzi , Eddy L M Ngonkeu , Diégane Diouf et al.
FEMS Microbiology Ecology, 2020, 96 (6), pp.fiaa067. ⟨10.1093/femsec/fiaa067⟩
Journal articles hal-02941967v1

Chemistry of streams draining mined and unmined watersheds in the mountaintop mined landscape of Central Appalachia, USA

Jacqueline Gerson , Eric Moore , Laura Naslund , Jennifer Rocca , Marie Simonin et al.
Ecology, inPress, 101 (9), pp.e03093. ⟨10.1002/ecy.3093⟩
Journal articles hal-02798110v1
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Differential Reactivity of Copper- and Gold-Based Nanomaterials Controls Their Seasonal Biogeochemical Cycling and Fate in a Freshwater Wetland Mesocosm

Astrid Avellan , Marie Simonin , Steven M Anderson , Nicholas K Geitner , Nathan Bossa et al.
Environmental Science and Technology, 2019, 54 (3), pp.1533-1544. ⟨10.1021/acs.est.9b05097⟩
Journal articles hal-02958362v1
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Harmonizing Across Environmental Nanomaterial Testing Media for Increased Comparability of Nanomaterial Datasets

Nicholas K Geitner , Christine Ogilvie Hendren , Geert Cornelis , Ralf Kaegi , Jamie Lead et al.
Environmental science‎.Nano, inPress, ⟨10.1039/C9EN00448C⟩
Journal articles hal-02376852v1

Negative Effects of Copper Oxide Nanoparticles on Carbon and Nitrogen Cycle Microbial Activities in Contrasting Agricultural Soils and in Presence of Plants

Marie Simonin , Amélie A. M. Cantarel , Armelle Crouzet , Jonathan Gervaix , Jean Mf Martins et al.
Frontiers in Microbiology, 2018, ⟨10.3389/fmicb.2018.03102⟩
Journal articles hal-02479075v1

Engineered nanoparticles interact with nutrients to intensify eutrophication in a wetland ecosystem experiment

Marie Simonin , Benjamin P Colman , Steven M Anderson , Ryan S King , Matthew Ruis et al.
Ecological Applications, 2018, 28 (6), pp.1435-1449. ⟨10.1002/eap.1742⟩
Journal articles hal-03707300v1

Gold nanoparticle biodissolution by a freshwater macrophyte and its associated microbiome

Astrid Avellan , Marie Simonin , Eric Mcgivney , Nathan Bossa , Eleanor Spielman-Sun et al.
Nature Nanotechnology, 2018, 13 (11), pp.1072-1077. ⟨10.1038/s41565-018-0231-y⟩
Journal articles hal-03707302v1

Toxicity of TiO2 nanoparticles on soil nitrification at environmentally relevant concentrations: Lack of classical dose-response relationships

Marie Simonin , Jean M. F. Martins , Xavier Le Roux , Gaelle Uzu , Aude Calas et al.
Nanotoxicology, 2017, 11 (2), pp.247 - 255. ⟨10.1080/17435390.2017.1290845⟩
Journal articles hal-01602574v1
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Short-term responses and resistance of soil microbial community structure to elevated CO2 and N addition in grassland mesocosms

Marie Simonin , Naoise Nunan , Juliette Bloor , Valérie Pouteau , Audrey Niboyet et al.
FEMS Microbiology Letters, 2017, 364 (9), ⟨10.1093/femsle/fnx077⟩
Journal articles hal-01525344v1
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Titanium dioxide nanoparticles strongly impact soil microbial function by affecting archaeal nitrifiers

Marie Simonin , Agnès Richaume-Jolion , Julien P. Guyonnet , Audrey Dubost , Jean M. F. Martins et al.
Scientific Reports, 2016, 6, pp.1-10. ⟨10.1038/srep33643⟩
Journal articles hal-01602239v1
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Combined study of titanium dioxide nanoparticle transport and toxicity on microbial nitrifying communities under single and repeated exposures in soil columns

Marie Simonin , Jean M. F. Martins , Gaëlle Uzu , Erwann Vince , Agnès Richaume et al.
Environmental Science and Technology, 2016, 50 (19), pp.10693-10699. ⟨10.1021/acs.est.6b02415⟩
Journal articles hal-01604452v1

Impact of engineered nanoparticles on the activity, abundance, and diversity of soil microbial communities: a review

Marie Simonin , Agnès Richaume
Environmental Science and Pollution Research, 2015, 22 (18), pp.13710-13723. ⟨10.1007/s11356-015-4171-x⟩
Journal articles hal-01602179v1

Coupling Between and Among Ammonia Oxidizers and Nitrite Oxidizers in Grassland Mesocosms Submitted to Elevated CO2 and Nitrogen Supply

Marie Simonin , Xavier Le Roux , Franck Poly , Catherine Lerondelle , Bruce A. Hungate et al.
Microbial ecology, 2015, 70 (3), pp.809-818. ⟨10.1007/s00248-015-0604-9⟩
Journal articles hal-01569713v1

Influence of soil properties on the toxicity of TiO₂ nanoparticles on carbon mineralization and bacterial abundance

Marie Simonin , Julien P. Guyonnet , Jean M. F. Martins , Morgane Ginot , Agnès Richaume-Jolion et al.
Journal of Hazardous Materials, 2015, 283, pp.529-535. ⟨10.1016/j.jhazmat.2014.10.004⟩
Journal articles hal-01197005v1