Marie Simonin

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

Yeasts are known to be fantastic biotechnological resources for medical, food, and industrial applications, but their potential remains untapped in agriculture, especially for plant biostimulation and biocontrol. In particular, yeasts have been reported as part of the core microbiome of seeds using next generation sequencing methods, but their dive...

Microbiota that originate in the seed can have consequences for the education of the plant immune system, competitive exclusion of pathogens from the host tissue, and host access to critical nutrients. Our research objective was to investigate the consequences of the environmental conditions of the parent plant for bacterial seed microbiome assembl...

The design and use of synthetic communities, or SynComs, is one of the most promising strategies for disentangling the complex interactions within microbial communities, and between these communities and their hosts. Compared to natural communities, these simplified consortia provide the opportunity to study ecological interactions at tractable sca...

Seeds harbor diverse microbial communities important for plant growth and health. During germination, seed exudation triggers intense microbial competition, shaping the communities transmitted to seedlings. This study explores the role of the bacterial type VI secretion system (T6SS)-mediated interference competition in seed microbiota transmission...

Seed microbiomes initiate plant microbiome assembly, but the consequences of environmental conditions of the parent plant for seed microbiome assembly and transmission are unknown. We tracked endophytic seed bacterial communities of common bean lines exposed to drought or excess nutrients, and discovered stable transmission of 22 bacterial members...

Synthetic Communities (SynComs) are being developed and tested to manipulate plant microbiota and improve plant health. To date, only few studies proposed the use of SynCom on seed despite its potential for plant microbiota engineering. We developed and presented a simple and effective seedling microbiota engineering method using SynCom inoculation...

In natural systems, organisms are embedded in complex networks where their physiology and community composition is shaped by both biotic and abiotic factors. Therefore, to assess the ecosystem-level effects of contaminants, we must pair complex, multi-trophic field studies with more targeted hypothesis-driven approaches to explore specific actors a...

Stenotrophomonas rhizophila CFBP13503 is a seedborne commensal bacterial strain, which is efficiently transmitted to seedlings and can outcompete the phytopathogenic bacterium Xanthomonas campestris pv. campestris (Xcc8004). The type VI secretion system (T6SS), an interference contact‐dependent mechanism, is a critical component of interbacterial c...

Synthetic Communities (SynComs) are being developed and tested to manipulate plant microbiota and improve plant health. To date, only few studies proposed the use of SynCom on seed despite its potential for plant microbiota engineering. We developed and presented a simple, reproducible and effective seedling microbiota engineering method using SynC...

Background and Aims The successful plant Fallopia x bohemica presents interesting capacities for the control of soil nitrogen cycle at the adult stage, named the biological denitrification inhibition (BDI). BDI strategy allows the plant, through the production of secondary metabolites (procyanidins), to compete with denitrifying microbial community...

Gold nanoparticles (AuNPs) are used as models to track and predict NP fates and effects in ecosystems. Previous work found that aquatic macrophytes and their associated biofilm primarily drove the fate of AuNPs within aquatic ecosystems and that seasonality was an important abiotic factor in the fate of AuNPs. Therefore, the present work aims to st...

Stenotrophomonas rhizophila CFBP13503 is a seed-borne commensal bacterial strain, which is efficiently transmitted to seedlings and can outcompete the phytopathogenic bacteria Xanthomonas campestris pv. campestris (Xcc8004). The type VI Secretion System (T6SS), an interference contact-dependent mechanism, is a critical component of interbacterial c...

Environmental change research is plagued by the curse of dimensionality: the number of communities at risk and the number of environmental drivers are both large. This raises the pressing question if a general understanding of ecological effects is achievable. Here, we show evidence that this is indeed possible. Using theoretical and simulation‐bas...

Freshwater ecosystems are exposed to engineered nanoparticles (NPs) through discharge from wastewater and agricultural runoff. We conducted a 9-month mesocosm experiment to examine the combined effects of chronic NP additions on insect emergence and insect-mediated contaminant flux to riparian spiders. Two NPs (copper, gold, plus controls) were cro...

Documenting trends of stream macroinvertebrate biodiversity is challenging because biomonitoring often has limited spatial, temporal, and taxonomic scopes. We analyzed biodiversity and composition of assemblages of >500 genera, spanning 27 years, and 6131 stream sites across forested, grassland, urban, and agricultural land uses throughout the Unit...

Seed-borne microorganisms can be pioneer taxa during germination and seedling emergence. Still, the identity and phenotypic effects of these taxa that constitute a primary inoculum of plant microbiota is mostly unknown. Here, we studied the transmission of bacteria from radish seeds to seedlings using the inoculation of individual seed-borne strain...

The seed acts as the primary inoculum source for the plant microbiota. Understanding the processes involved in its assembly and dynamics during germination and seedling emergence has the potential to allow for the improvement of crop establishment. Changes in the bacterial community structure were tracked in 1,000 individual seeds that were collect...

Due to their 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 farmer's fields from irrigated and rainfed lowlands in Burkina Faso, using an amplicon metabar...

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...

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...

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...

Seed microbiota constitutes a primary inoculum for plants that is gaining attention owing 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 ri...

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...

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...

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...

The rivers of Appalachia (United States) 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...

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...

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...

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...

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...

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...

Disturbances fundamentally alter ecosystem functions, yet predicting their impacts remains a key scientific challenge. While the study of disturbances is ubiquitous across many ecological disciplines, there is no agreed-upon, cross-disciplinary foundation for discussing or quantifying the complexity of disturbances, and no consistent terminology or...

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...

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...

The use of novel pesticides containing nanomaterials (nanopesticides) is growing and is considered a promising approach to reduce the impacts of agriculture on the environment and human health. However, the environmental effects of these novel agrochemicals are not fully characterized, and more research is needed to determine the benefits and risks...

Mountaintop removal coal mining is the predominant form of surface mining in the Appalachian Region of the United States 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. These data were collecte...

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...

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...

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...

Disturbances fundamentally alter ecosystem functions; yet predicting the impacts of disturbances remains a key scientific challenge. The study of disturbances is ubiquitous across almost all ecological disciplines, yet varying terminology and methodologies have led to the lack of an agreed upon, cross-disciplinary foundation for discussing and quan...

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 unravel the effects of these...

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...

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...

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....

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...

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...

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...

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...

Whole microbial communities regularly merge with one another, often in tandem with their environments, in a process called community coalescence. Such events allow us to address a central question in ecology — what processes shape community assembly. We used a reciprocal transplant and mixing experiment to directly and independently unravel the eff...

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...

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...

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...

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...

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...

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...

Emerging contaminants are agents for ecosystem change on a global scale. Our understanding of how engineered nanomaterials (ENM) contribute to global change is no different. Originating in human dominated landscapes (e.g. agriculture, consumer products, biomedical applications) ENM are transported downstream via wastewater treatment affluent and bi...

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...

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-...

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...

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...

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...

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...

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...