I am a Microbial Ecologist studying plant-microbiome interactions and the effects of disturbances (pathogens, climate, contaminants) on ecosystem health.
For more information, check out the following sections:
Marie Simonin, Ph.D
INRAE Researcher - Team EmerSys
Emergence, Systematics and Ecology of Plant Pathogenic Bacteria
IRHS Lab - Research Institute in Horticulture and Seeds
November 2023: Check our new paper in PCI Microbiology on synthetic community inoculation on seeds and their impact on seedling microbiota and phenotype. Simonin et al. 2023
October 2023: I'm happy to welcome 2 new PhD students! Louna Colaert-Sentenac and Logan Suteau both working on plant microbiome engineering using SynComs, as part of the SUCSEED project
August 2023: New paper in Ecology Letters led by Frederik De Leander on species coexistence under environmental change. De Leander et al. 2023
July 2023: Really happy to be awarded an ANR Young Researcher grant for 4 years. the INHERSEED project will investigate the contribution of vertical transmission to plant microbiome assembly across 50 crops.
December 2022: New paper on single seed microbiota: from parental plant to seedlings: Chesneau et al. mBio
September 2022: 3 new papers on the plant microbiome:
- Barro et al. FEMS Rice microbiota in Burkina Faso
- Masson et al AEE Conservation agriculture to control phytoparasitic nematodes in Cambodia
- Mofini et al. Sci Rep Root mycobiome of pearl millet in Senegal
March 2022: Our Seed Microbiome meta-analysis is out in New Phytologist !
October 2021: Happy to welcome Gontran Arnault as my first official INRAE PhD student as part of the SUCSEED project.
September 2021: Two new papers on our work at Duke University on the impact of surface coal mining on biodiversity in Appalachia:
- Simonin et al. 2021 Eco Apps - Biodiversity loss across the tree of life
see the associated The Conversation article
- Jin et al. 2022 STOTEN - Impact on sediment microbiome
August 2021: Our perspective paper on how we can use community coalescence for microbiome engineering is out in mSystems (Rocca et al. 2021)!
June 2021: 1 paper in MSystems and 2 BioRxiv preprints on our seed microbiota research in the EmerSys team!
Rochefort et al. Msystems: seed and soil coalescence
Chesneau et al. BioRxiv single seed microbiota
Simonin et al BioRxiv Seed Microbiota meta-analysis
April 2021: A new paper in Science of the Total Environment from my PhD on the transport of nanomaterials in agricultural soils
February 2021: A new review paper accepted in Frontiers in Microbiology on the role of microbiomes for aquatic vertebrates health and an opinion paper presenting a generalizable framework for disturbance ecology in Frontiers in Ecology and Evolution
July 2020: Check our new paper in FEMS led by Anne-Sophie Masson (IPME-IRD) on the impact of parasitic nematodes on the rice microbiome
June 2020: A new paper published in ES&T about the long-term effects of Cu nanopestides on soil and sediment microbiomes. This paper is the result student project realized during the interdisciplinary graduate training program IBIEM at Duke.
April 2020: Two new papers accepted!
- Our study in FEMS on the wheat microbiome four countries and the identification of a shared core microbiome
- A review paper in the Plant Journal on the rhizosphere as an extended phenotype of plants
February 2020: Finishing our SynCom (Synthetic Community) experiment manipulating the seed microbiome to try to limit the invasion of pathogenic Xanthomonas bacteria!
January 2020: I was at the Plant-Bacteria meeting in Aussois to talk about how we can move from individual studies to generalizable patterns in plant microbiome research.
September 2019: Check out our new preprint on the characterization of the wheat microbiome in 4 countries (Cameroon, France, Italy, Senegal)!
August 2019: I will start a research scientist position at INRA in Angers, France in October! I will join the EmerSys team in the IRHS research institute to work on plant microbiome assembly processes.
May 2019: A new paper published in Environmental Microbiology on the impact of urbanization on river microbiomes and the identification of indicator taxa.
- I was in Cambodia for the kick-off meeting of the JEAI HealthyRice project and to start mesocosm and field trials to study rice microbiomes and biocontrol of phytoparasitic nematodes.
-Also I was at SETAC Europe in Helsinki as the chairman of a session on the impact of chemicals on environmental microbiomes.
April 2019: A new paper in ES&T on the fate of coal combustion residuals in lake food webs with Jess Brandt.
Also I presented a talk at EGU 2019 in Vienna about the impact of surface coal mining on biodiversity (using eDNA).
January 2019: Goodbye Duke! After 3 awesome years in the Bernhardt Lab, I will start a new postdoc at IPME (IRD, Montpellier, France) on plant-microbiome interactions with Lionel Moulin, Laurent Laplaze (DIADE) and Laurent Cournac (Eco&Sols).
January 2019: The paper presenting the methodology and a preliminary meta-analysis of the Microbiome Stress Project is out in Frontiers in Microbiology!
December 2018: New paper in Frontiers in Microbiology on the effects of copper oxide nanomaterials on soil microbial activities.
August 2018: New paper published in Nature Nanotechnology on the fate of gold nanomaterials in wetlands and their biodissolution by plant periphyton!
I will be at the ISME meeting in Leipzig to present a poster on the Microbiome Stress Project
July 2018: New paper in Frontiers in Microbiology on the effects of nanopesticides on plant and soil microorganisms in an agro-ecosystem + 2 papers accepted on the wetland mesocosm experiment! 1 in Nature Nanotechnology and the other in ES&T!
June 2018: New paper in Ecological Applications! Nanomaterials + Nutrient pollution intensify eutrophication and cause algal blooms. See press release here. Our article featured as top story on NSF Science news!
May 2018: SETAC Europe meeting in Rome to present our results on the identification of bacterial indicator taxa along an urbanization gradient
March 2018: Field work in West Virginia to perform eDNA survey in 100 streams to assess the impact of mountain-top mining on biodiversity
November 2017: Going to the 1st Microbial Ecotoxicology Conference (EcotoxicoMic) in Lyon France !
August 2017: Talk at ESA 2017 (Portland) on the results of both the wetland and terrestrial mesocosm experiments!
June 2017 : At the SFS meeting 2017 (Raleigh, NC)!
Co-chair of the special session "Stressing the Eco in Freshwater Ecotoxicology".
June 2017 : Final sampling (Day 365) of our terrestrial mesocosm experiment looking at the impact of nanopesticides on agro-ecosystems!
May 2017: A new paper in FEMS Microbiology Letters! Short-term responses and resistance of soil microbial community structure to elevated CO2 and N addition in grassland mesocosms (pdf).
April 2017: Seminar at Baylor University thanks to the award of the CEINT Scholar Steering committee. See here the CEINT news!
February 2017: A new paper in Nanotoxicology! Titanium dioxide nanoparticles cause non-classical dose-response on soil nitrification (pdf).
January 2017: Take a look at the NSF video of Science Nation that highlights our work at the CEINT Mesocosm experiment facility!
October 2016: Final sampling of the CEINT wetland mesocosm experiment! See here the CEINT news
September 2016: 2 papers accepted on the same day!
One in ES&T: Transport and toxicity of repeated TiO2 exposures in soil (pdf)
The second in Scientific Reports: TiO2-NPs cause a disruption of the soil N cycle.
May 2016: Talk at SETAC Europe (Nantes, France) about unlinear dose-response curves associated to nanomaterials
January 2016: Starting a new postdoc at Duke University with Emily Bernhardt and Ben Colman (University of Montana)
October 2015: PhD defense at the University of Lyon (France)