I am a Microbial Ecologist studying plant-microbiome interactions and the effects of disturbances (pathogens, climate, contaminants) on ecosystem health.
I am developing microbiome engineering approaches for a more sustainable agriculture. 

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

Credit: Katherine G. Stember

​​Contact Information
Email: marie.simonin[at] inrae.fr                             Links to my:   ResearchGate            Google Scholar            ORCID page​
Follow me  on Bluesky

Massive greenhouse experiment led by PhD student Gontran Arnault and Master student Louna Colaert-Sentenac. We study the transmission of SynComs from seed to seed

Figure from Simonin et al. 2023 PCI Microbiology - showing the effect of single bacterial strains and SynComs on seedling phenotypes

Cover of our Conversation article on our research using environmental DNA to uncover the impact of coal mining on aquatic biodiversity

Graphical abstract from Carley et al. 2020 ES&T.

Graphical abstract of our wheat microbiome study (Simonin et al. 2020 FEMS Microbiology Ecology)

Rice mesocosms inoculated with different bacterial bio-pesticides to control nematode infections (Cambodia)

Sampling in the Outer Banks (NC) along a salinity gradient to study microbial community coalescence with Jenny Rocca

eDNA biodiversity survey in 100 streams in WV to study the impact of surface coal mining - Panther Creek - WV with Jenny Rocca

Sampling day at the CEINT wetland mesocosms. Credit: Nick Geitner

​Sampling day at the terrestrial mesocosms in the Duke Forest (soil and plant biomass collection)

Fishing spider! A spider eating a mosquito fish in the CEINT wetland mesocosm experiment

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
April - May 2025: I'm happy to welcome 2 new postdocs in the team! Tristan Lafont Rapnouil will work on the ANR INHERSEED project to study microbial inheritance through seeds across 60 plant species. Kenji Maurice will join the Biodiversa + Grass4fun project to study plant-soil microbiome diversity of crops/grasslands and conservation status at the European level
​
September 2024: Two opinion papers accepted: One  lead by my Master student Oscar Joubert in Trends in Plant Science and another by Eli Mehlferber in Nature Microbiology!

July 2024: With colleagues from LEM and LEHNA lab in Lyon, we received funding of the ANR PRC for the Plant-MANA project (2025-2029): Plant-Driven Microbiome Management through Biological Denitrification Inhibition: a New Strategy to Limit Nitrogen Loss in Agroecosystems. 

April 2024: New publication of PhD student Gontran Arnault on Seedling microbiota engineering using bacterial synthetic community inoculation on seeds in FEMS Microbiology Ecology

February 2024: Kick-off of the European project Grass4Fun (Biodiversa+) to monitor and conserve soil and plant microbiome across Europe in response to multiple stressors (2024-2027)

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 JCJC 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 PhD student 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!
​
​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.

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!