Marie Simonin Ph.D
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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:
RESEARCH INTERESTS
Publications
CV

​Marie Simonin, Ph.D
​INRAE Researcher - Team EmerSys
Emergence, Systematics and Ecology of Plant Pathogenic Bacteria 

IRHS Lab - Research Institute in Horticulture and Seeds

Picture
Credit: Katherine G. Stember
Follow @MicrobialMarie
​​Contact Information
Email: marie.simonin[at] inrae.fr                             Links to my:   ResearchGate            Google Scholar            
ORCID page​
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Cover of our Conversation article on our research using environmental DNA to uncover the impact of coal mining on aquatic biodiversity
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Graphical abstract from Carley et al. 2020 ES&T.
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Graphical abstract of our wheat microbiome study (Simonin et al. 2020 FEMS Microbiology Ecology)
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Rice mesocosms inoculated with different bacterial bio-pesticides to control nematode infections (Cambodia)
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Sampling in the Outer Banks (NC) along a salinity gradient to study microbial community coalescence with Jenny Rocca
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eDNA biodiversity survey in 100 streams in WV to study the impact of surface coal mining - Panther Creek - WV with Jenny Rocca
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Sampling day at the CEINT wetland mesocosms. Credit: Nick Geitner
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​Sampling day at the terrestrial mesocosms in the Duke Forest (soil and plant biomass collection)
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Fishing spider! A spider eating a mosquito fish in the CEINT wetland mesocosm experiment
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Outreach with High school students from the North Carolina School of Science and Maths. Mini-Term "Stress and Microbes"(March 2017). Credit: Jenny Rocca
NEWS
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
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March 2022: Our Seed Microbiome meta-analysis is out in New Phytologist !
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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
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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)!
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​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 !
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August 2017: Talk at ESA 2017 (Portland) on the results of both the wetland and terrestrial mesocosm experiments!
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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).
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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)
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October 2015: PhD defense at the University of Lyon (France)
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