My work falls in the fields of Microbiome and Stress Ecology and the overarching questions that motivate my research are:
- What are the processes driving microbiome diversity and functions, especially during disturbances?
- How do microbiomes influence host phenotypes, particularly their responses to abiotic and biotic stressors?
- Can we classify microbial taxa into ecological categories, similar to those developed for plants or animals, to better predict microbiome dynamics?

Current Research Projects at INRAE

Seed Microbiomes:
Drivers and Transmission
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With my colleagues from the EmerSys team, I'm studying the diversity and composition of seed microbiota from different crops (bean, radish, rapeseed) to identify the key parameters structuring these microbial assemblages. Check Rochefort et al. 2021 mSystemss on the coalescence of seed and soil microbiomes. And also Chesneau et al. 2022 mBio on single seed microbiota and Simonin et al. 2022 New Phytologist on our large scale seed microbiota meta-analysis and database

Inheritance of Stress Tolerance through Seed Microbiome Modification

In collaboration with Ashley Shade (MSU) and Matthieu Barret, I'm investigating if seed microbiota can promote plant resilience to abiotic stressors, like drought and nutrient stress.

Seed Microbiome Engineering to Improve Plant Health

Using a synthetic microbiome approach, I'm studying the influence of seed microbiota on plant germination, emergence and resistance to pathogens using automated plant phenotyping platforms (Phenotic). This research is performed in the framework of the SUCSEED project funded by PPR-CPA for 6 years (2021-2026)

Research Projects Initiated at IRD

Wheat Microbiome

As part of my postdoc at IPME, I studied plant microbiome interactions in different important crops (wheat, rice, pearl millet). I analyzed the results of a greenhouse experiment to identify the core microbiome of wheat (rhizosphere) across 13 genotypes of wheat grown on 8 contrasted soils from Europe and Africa. Results published in Simonin et al. (2020) FEMS Microbiology Ecology.

Rice Microbiome

I was involved in the JEAI HealthyRice project in Cambodia to develop sustainable rice production in an Agroecology framework. This work has for goal to gather basic knowledge on plant-microbiome interactions before proposing new solutions using microbiome engineering to make agriculture more sustainable and resilient to global change. Results published on the rice microbiome in Cambodia by Masson et al. (2020) FEMS Microbiology Ecology and Masson et al. (2022) AEE. Results in Burkina Faso in Barro et al. (2022) FEMS

The rhizosphere as an extended plant phenotype

With colleagues from the DIADE lab in Montpellier, we wrote a focused review paper in the Plant Journal: de la Fuente Cantó et al."An extended root phenotype: the rhizosphere, its formation and impacts on plant fitness".
This review covers how plants shape the rhizosphere and the benefits it confers to plant fitness.

Research Projects Initiated at Duke University

​The Microbiome Stress Project

In collaboration with scientists from Duke University (Jennifer Rocca, Firas Midani), the Institute for System Biology (Sean Gibbons), University of Montana (Joanna Blaszczak), University of New Hampshire (Jessica Ernakovich) and Montana State University (Alex Washburne), we are developing a large database to investigate how stressors (natural and anthropogenic) impact microbial community structure across multiple environments (soil, plant, biofilm, water, reactor, gut, sediment). This database is built with published/unpublished microbial data sets (using Illumina sequencing, 16S rRNA gene V4 region only) and we are developing a computational pipeline to identify microbial taxa specifically sensitive or resistant to these stressors. Check the paper presenting the methodology of the project and a pilot meta-analysis: Rocca et al. 2019, Frontiers in Microbiology.
​More info on the Microbiome Stress Project Website.
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Impact of emerging contaminants on wetland ecosystem functioning

I'm coordinating the ​CEINT Wetland Mesocosm experiment involving 11 labs in the US (Duke University, Baylor University, Carnegie Mellon University, Virginia Tech) looking at the long-term impact of nanomaterials in wetlands. Results published in Simonin et al. (2018) Ecological Applications and Geitner et al. (2018) ES&T and Avellan et al. (2018) Nature Nanotechnology and Avellan et al. (2020) ES &T and Perrotta et al. (2020) ES&T

Resistance and resilience of microbial communities to nanopesticides

I'm leading a terrestrial mesocosm experiment looking at the interactive effects  of nanopesticides and fertilization on plant community, soil fertility and microbial function over a year. Results published in Simonin et al. (2018) Frontiers in Microbiology and in Carley et al. (2020) ES&T which combines both wetland and terrestrial mesocosm results.

Microbial community coalescence in the context of seawater intrusions

In collaboration with Jennifer D. Rocca, I'm studying community assembly mechanisms (environmental filtering and biotic interactions) of microbial community coalescence events occurring during seawater intrusion in freshwater ecosystems on the North Carolina Coast. Results published in Rocca et al. 2020 Ecology

Identification of microbial indicator taxa along an urbanization gradient

In collaboration with Kris Voss (Regis University), I'm working on identifying microbial taxa negatively or positively impacted by urbanization and their environmental thresholds (change points). These results will be compared to macro-invertebrates change points more traditionally used as bioindicators. This project is conducted in 41 urban streams sampled in Central North Carolina. Results published in Simonin et al. (2019) Environmental Microbiology

Global biodiversity assessment in Appalachian streams using environmental DNA 

In collaboration with Noah Fierer and Jennifer D. Rocca, I'm conducting a large field environmental DNA sampling in Appalachian streams to assess the biodiversity of microorganisms, phytoplankton, arthropods and vertebrates. We are in particular looking at the impact of Mountain-top mining and landscape fragmentation on this hot spot of biodiversity. Results published in Simonin et al. (2021) Ecological Applications and in Jin et al. (2022) STOTEN. Data paper : Gerson et al. (2020) Ecology

Mercury contaminations in soils associated to artisanal gold mining in Senegal 

In collaboration with Jacqueline Gerson, I'm studying the response of microbial communities to a gradient of mercury contaminations in urban and agricultural soils exposed to artisanal gold mining in Senegal. I'm studying the distribution of sulfate-reducing bacteria to understand the presence of hot spots of methylmercury in specific locations.

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​Past Projects (PhD and Master)
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Soil collection in Burgundy (France)

Soil microcosm experiment (n=366 ! )

Impact of nanomaterials on carbon and nitrogen cycles in contrasted agricultural soils

During my PhD in the Microbial Ecology Lab (University of Lyon, France) and LTHE (University of Grenoble), I studied the influence of soil texture and organic matter content on TiO2-NPs and CuO-NPs toxicity on soil microbial function. We observed that soil respiration was especially affected in a silty-clay soil with a high organic matter content, while the other soils were not affected by the contamination (Simonin et al. 2015 JHazMat). In this silty-clay soil, N cycle was strongly altered by TiO2-NPs, due to the high sensitivity of ammonia-oxidizing archaea (AOA), a key player of the nitrification process (Simonin et al. 2016 Scientific Reports). New results on CuO toxicity in contrasting soils have been recently published (Simonin et al. 2018 Frontiers in Microbiology)

Cartoon summarizing the impacts of TiO2-NPs on the carbon and nitrogen cycles in an agricultural soil

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Graphical abstract of the paper published in ES&T

Soil Column experiment set-up

Influence of soil properties and of chronic exposures on nanomaterial’s fate and transport

​Also during my Ph.D, I studied the fate and transport of TiO2-NPs and CuO-NPs in contrasted agricultural soils using column experiments. We observed very limited transport of both nanoparticles in the different soils studied. Our findings suggest that these contaminants present a low risk of groundwater contamination whatever the surface soil but that they will likely be retained in soils in the long term, which may be problematic, especially in the case of agricultural soils (Simonin et al. 2021 STOTEN). I have also investigated the influence of TiO2-NP repeated exposures (acute vs chronic) on their transport and impact on soil microbial activity.  Our results suggest that under repeated exposures, the transport of TiO2-NPs to deep soil layers and groundwater is limited and that a chronic contamination is more harmful for the soil microbiological function than a single exposure (Simonin et al. 2016 ES&T). 

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Grassland Mesocosm experiment at University Paris Sud

Soil Nitrogen cycle and the key microbial functional groups involved in Nitrification

Combined effects of elevated CO2 and nitrogen fertilization on soil microbial communities in grasslands
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During my Master, I studied the interactive effects of two main components of global change: elevated CO2 and N fertilization on microbial communities in grasslands. ​In a mesocosm experiment conducted at the University Paris Sud (France), we looked at the consequences on soil N cycle and more specifically on the microbes involved in nitrification (Simonin et al. 2015, Microbial Ecology). Our results suggested that the couplings between ammonia and nitrite oxidizers are influenced by soil N availability. Multiple environmental changes may thus elicit rapid and contrasted responses between and among the soil ammonia and nitrite oxidizers due to their different ecological requirements.
We also studied the global impact of CO2 and N fertilization on the microbial community structure and the influence of the abundance of r- and K-strategist microorganisms on the resistance of the community (Simonin et al. 2017 FEMS Microbiology Letters). We observed that only N fertilization led to a shift in the microbial community (not CO2 or CO2 x N) and that the resistance of the community structure was positively correlated to the Gram + / Gram- bacteria ratio, a proxy of the relative abundance of K-strategists.