Marie Simonin

Marie Simonin
French National Institute for Agriculture, Food, and Environment (INRAE) | INRAE · IRHS - Team EmerSys

PhD in Microbial Ecology

About

42
Publications
11,392
Reads
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1,171
Citations
Introduction
I'm a microbial ecologist studying plant-microbiome interactions and the effects of disturbances on ecosystem health. Main interests in: - Plant and Rhizosphere Microbiomes - Seed Microbiome: Structuration, Succession, Transmission - Resistance and Resilience of Microbial Communities to Acute and Chronic disturbances - Impact of land-use change and pollution on aquatic and terrestrial biodiversity
Additional affiliations
October 2019 - present
French National Institute for Agriculture, Food, and Environment (INRAE)
Position
  • Researcher
January 2019 - October 2020
Institute of Research for Development (IRD)
Position
  • PostDoc Position
Description
  • Studying Plant-Microbiome interactions in various crops exposed to abiotic and biotic disturbances
February 2016 - January 2019
Duke University
Position
  • PostDoc Position

Publications

Publications (42)
Article
Full-text available
Meloidogyne spp. and Hirschmanniella spp. are among the most damaging plant-parasitic nematodes (PPNs). They threaten rice production, the main staple food in Asia. Cropping systems that promote natural biocontrol and plant tolerance to diseases are put forward as sustainable solutions to protect rice from these pests. In particular, cropping syste...
Article
Full-text available
Temperature strongly influences microbial community structure and function, in turn contributing to global carbon cycling that can fuel further warming. Recent studies suggest that biotic interactions among microbes may play an important role in determining the temperature responses of these communities. However, how predation regulates these micro...
Preprint
As a consequence of its potential applications for food safety, there is a growing interest in rice root-associated microbial communities, but some systems remain understudied. Here, we compare the assemblage of root-associated microbiota in rice sampled in 19 small farmers fields from irrigated and rainfed lowlands in western Burkina Faso, using a...
Article
Seed microbiota constitutes a primary inoculum for plants that is gaining attention due to its role for plant health and productivity. Here, we performed a meta‐analysis on 63 seed microbiota studies covering 50 plant species to synthesize knowledge on the diversity of this habitat. Seed microbiota are diverse and extremely variable, with taxa rich...
Article
Full-text available
Fungal communities associated with roots play a key role in nutrient uptake and in mitigating the abiotic and biotic stress of their host. In this study, we characterized the roots mycobiome of wild and cultivated pearl millet [ Pennisetum glaucum (L.) R. Br., synonym: Cenchrus americanus (L.) Morrone] in three agro-ecological areas of Senegal foll...
Poster
Full-text available
Root-knot nematodes (Meloidogyne spp.) are among the most damaging plant parasitic nematodes (PPNs) worldwide. They are obligate and polyphageous soilborne parasites affecting the root morphology and physiology and making plants more susceptible to other diseases and abiotic stresses. Meloidogyne graminicola is particularly widespread in Asia where...
Article
With advances in eDNA metabarcoding, environmental microbiomes are increasingly used as cost-effective tools for monitoring ecosystem health. Stream ecosystems in Central Appalachia, heavily impacted by alkaline drainage from mountaintop coal mining, present ideal opportunities for biomonitoring using stream microbiomes, but the structural and func...
Article
Full-text available
Every seed germinating in soils, wastewater treatment, and stream confluence exemplify microbial community coalescence-the blending of previously isolated communities. Here, we present theoretical and experimental knowledge on how separated microbial communities mix, with particular focus on managed ecosystems. We adopt the community coalescence fr...
Article
Full-text available
The seed microbial community constitutes an initial inoculum for plant microbiota assembly. Still, the persistence of seed microbiota when seeds encounter soil during plant emergence and early growth is barely documented. We characterized the encounter event of seed and soil microbiota and how it structured seedling bacterial and fungal communities...
Preprint
Full-text available
Seed microbiota constitutes a primary inoculum for plants that is gaining attention due to its role for plant health and productivity. Here, we performed a meta-analysis on 63 seed microbiota studies covering 50 plant species to synthesize knowledge on the diversity of this habitat. Seed microbiota are diverse and extremely variable, with taxa rich...
Article
The rivers of Appalachia (USA) are among the most biologically diverse freshwater ecosystems in the temperate zone and are home to numerous endemic aquatic organisms. Throughout the Central Appalachian ecoregion, extensive surface coal mines generate alkaline mine drainage that raises the pH, salinity and trace element concentrations in downstream...
Preprint
Full-text available
Gaining basic understanding of processes involved in seed microbiota assembly is a prerequisite for improving crop establishment. Investigation of microbiota structure during seed development revealed that individual seeds of bean and radish were associated with a dominant bacterial taxon representing more than 75% of all reads. The identity of thi...
Preprint
Full-text available
Temperature strongly influences microbial community structure and function, which in turn contributes to the global carbon cycle that can fuel further warming. Recent studies suggest that biotic interactions amongst microbes may play an important role in determining the temperature responses of these communities. However, how microbial predation re...
Article
The fate of nanoparticles (NPs) in soil under relevant environmental conditions is still poorly understood. In this study, the mobility of two metal-oxide nanoparticles (CuO and TiO2) in contrasting agricultural soils was investigated in water-saturated soil columns. The transport of TiO2 and CuO-NPs were assessed in six soils with three different...
Article
Full-text available
Aquatic ecosystems are under increasing stress from global anthropogenic and natural changes, including climate change, eutrophication, ocean acidification, and pollution. In this critical review, we synthesize research on the microbiota of aquatic vertebrates and discuss the impact of emerging stressors on aquatic microbial communities using two c...
Article
Freshwater ecosystems are exposed to engineered nanoparticles through municipal and industrial wastewater-effluent discharges and agricultural non-point source runoff. Because previous work has shown that engineered nanoparticles from these sources can accumulate in freshwater algal assemblages, we hypothesized that nanoparticles may affect the bio...
Article
Full-text available
Meloidogyne graminicola, also known as the rice root-knot nematode, is one of the most damaging plant-parasitic nematode, especially on rice. This obligate soilborne parasite induces gall formation that disturb the root morphology and physiology. Its impact on the root microbiome is still not well described. Here, we conducted a survey in Northern...
Article
Mountaintop removal coal mining is the predominant form of surface mining in the Appalachian Region, USA and leads to elevated levels of chemical constituents in streams draining mined watersheds. This data set contains measurements of water chemistry in the mountaintop mined landscape of Central Appalachia, USA. These data were collected to determ...
Article
Full-text available
Plants forage soil for water and nutrients, whose distribution is patchy and often dynamic. To improve their foraging activities, plants have evolved mechanisms to modify the physicochemical properties and microbial communities of the rhizosphere, i.e. the soil compartment under the influence of the roots. This dynamic interplay in root‐soil‐microb...
Article
Full-text available
Here, we assessed the relative influence of wheat genotype, agricultural practices (conventional vs organic) and soil type on the rhizosphere microbiome. We characterized the prokaryotic (archaea, bacteria) and eukaryotic (fungi, protists) communities in soils from four different countries (Cameroon, France, Italy, Senegal) and determined if a rhiz...
Conference Paper
Full-text available
Meloidogyne graminicola, also known as the rice root-knot nematode, is the most damaging plant parasitic nematode, especially on rice in Asia. This obligate soilborne parasite creates galls that disturb the root morphology and physiology, making plants more susceptible to other diseases (e.g. BLAST) and / or abiotic stress (e.g. water stress). Sinc...
Article
Reliable predictions of the environmental fate and risk of engineered nanomaterials (ENMs) require a better understanding of ENM reactivity in complex, biologically active systems for chronic low-concentration exposure scenarios. Here, simulated freshwater wetland mesocosms were dosed with ENMs to assess how their reactivity and seasonal changes in...
Article
Whole microbial communities regularly merge with one another, often in tandem with their environments, in a process called community coalescence. Such events impose substantial changes: abiotic perturbation from environmental blending and biotic perturbation of community merging. We used an aquatic mixing experiment to independently unravel the eff...
Article
The chemical composition and properties of environmental media determine nanomaterial (NM) transport, fate, biouptake, and organism response. To compare and interpret experimental data, it is essential that sufficient context be provided for describing the physical and chemical characteristics of the setting in which a nanomaterial may be present....
Presentation
Full-text available
Microbiomes are not only keystones of soil fertility, water quality and performance of engineered ecosystems but also major drivers of plant and animal health. Due to a recent decrease of sequencing cost, there are an increasing number of a broad spectrum of toxicologists that study the effect of stressors on microbiome. In our session, researchers...
Article
A majority of environmental studies describe microbiomes at coarse scales of taxonomic resolution (bacterial community, phylum), ignoring key ecological knowledge gained from finer‐scales and microbial indicator taxa. Here, we characterized the distribution of 940 bacterial taxa from 41 streams along an urbanization gradient (0‐83% developed waters...
Article
Effluents from coal-fired power plant ash ponds are a major source of environmental contamination, annually loading more than a million metric tons of pollutants to aquatic ecosystems in the U.S. alone. Though this waste stream is characterized by elevated concentrations of numerous inorganic constituents, decades of previous research effort has fo...
Article
Full-text available
Microbial community structure is highly sensitive to natural (e.g., drought, temperature, fire) and anthropogenic (e.g., heavy metal exposure, land-use change) stressors. However, despite an immense amount of data generated, systematic, cross-environment analyses of microbiome responses to multiple disturbances are lacking. Here, we present the Mic...
Article
Full-text available
Metal-oxide nanoparticles (NPs) such as copper oxide (CuO) NPs offer promising perspectives for the development of novel agro-chemical formulations of pesticides and fertilizers. However, their potential impact on agro-ecosystem functioning still remains to be investigated. Here, we assessed the impact of CuO-NPs (0.1, 1, and 100 mg/kg dry soil) on...
Article
Full-text available
Predicting nanoparticle fate in aquatic environments requires mimicking of ecosystem complexity to observe the geochemical processes affecting their behaviour. Here, 12 nm Au nanoparticles were added weekly to large-scale freshwater wetland mesocosms. After six months, ~70% of Au was associated with the macrophyte Egeria densa, where, despite the t...
Article
Trace metals associated with nanoparticles are known to possess reactivities that are different from their larger-size counterparts. However, the relative importance of small relative to large particles for the overall distribution and biouptake of these metals is not as well studied in complex environmental systems. Here, we have examined differen...
Article
Full-text available
The environmental fate and potential impacts of nanopesticides on agroecosystems under realistic agricultural conditions are poorly understood. As a result, the benefits and risks of these novel formulations compared to the conventional products are currently unclear. Here, we examined the effects of repeated realistic exposures of the Cu(OH)2 nano...
Article
Despite the rapid rise in diversity and quantities of engineered nanomaterials produced, the impacts of these emerging contaminants on the structure and function of ecosystems have received little attention from ecologists. Moreover, little is known about how manufactured nanomaterials may interact with nutrient pollution in altering ecosystem prod...
Article
Nitrogen (N) addition is known to affect soil microbial communities, but the interactive effects of N addition with other drivers of global change remain unclear. The impacts of multiple global changes on the structure of microbial communities may be mediated by specific microbial groups with different life-history strategies. Here, we investigated...
Article
Titanium-dioxide nanoparticles (TiO2-NPs) are increasingly released in agricultural soils through, e.g. biosolids, irrigation or nanoagrochemicals. Soils are submitted to a wide range of concentrations of TiO2-NPs depending on the type of exposure. However, most studies have assessed the effects of unrealistically high concentrations, and the dose-...
Article
Full-text available
Soils are facing new environmental stressors, such as titanium dioxide nanoparticles (TiO 2-NPs). While these emerging pollutants are increasingly released into most ecosystems, including agricultural fields, their potential impacts on soil and its function remain to be investigated. Here we report the response of the microbial community of an agri...
Article
Full-text available
Soils are exposed to nanoparticles (NPs) due to their increasing use in many commercial products. Adverse effects of NPs on soil microorganisms have been reported in several ecotoxicological studies using microcosms. Although repeated exposures are more likely to occur in soils, most of these previous studies were performed as a single exposure to...
Thesis
Full-text available
Les nanoparticules métalliques manufacturées (NPs) sont des polluants émergents dont la concentration augmente dans les sols en raison de leur utilisation croissante dans de nombreux produits commerciaux de la vie courante (cosmétiques, aliments, peintures…). Des études in vitro ont montré la toxicité des NPs pour les microorganismes, mais il exist...
Article
Full-text available
Many studies have assessed the responses of soil microbial functional groups to increases in atmospheric CO2 or N deposition alone and more rarely in combination. However, the effects of elevated CO2 and N on the (de)coupling between different microbial functional groups (e.g., different groups of nitrifiers) have been barely studied, despite poten...
Article
Full-text available
This report presents an exhaustive literature review of the effects of engineered nanoparticles on soil microbial communities. The toxic effects on microbial communities are highly dependent on the type of nanoparticles considered. Inorganic nanoparticles (metal and metal oxide) seem to have a greater toxic potential than organic nanoparticles (ful...

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Projects

Projects (3)
Project
Which processes are involved in seed microbiota assembly? What arethe main transmission pathways used by seed-borne taxa ? Are seed-borne taxa transmitted to seedling ? Can we used seed microbiota to inhibit the seed-borne pathogen Xanthomonas campestris pv. campestris.
Project
Website: https://ecotoxicomic.org/ EcotoxicoMic aims at establishing and fostering contacts and scientific partnerships within the community of microbial ecotoxicologists, at improving the visibility of research and innovation in the field of Microbial Ecotoxicology and at promoting the transfer of knowledge between the scientific community, the environmental managers and the society. Becoming a member of the international EcotoxicoMic Network is free-of-charge. The only thing you need to join the EcotoxicoMic Community is to fill online a membership form. We are waiting for you !
Project
i)Understanding what shapes microbial communities of two major crops, rice and wheat. ii) Identify microbes with biocontrol properties against phytopathogens