Marie Simonin

61
Documents

Présentation

Research Scientist at INRAE


42 Rue Georges Morel, 49070 Beaucouzé, France

E-mail: marie.simonin[at]inrae.fr

Research interests


Impact of abiotic and biotic disturbances on microbial activity and diversity

Interactive effects of different agents of global change (contaminants, nutrient pollution, CO2)

Plant-microbiome interactions and microbiome engineering

Resistance and resilience of microbiomes to these disturbances

Education


● Ph.D (2012 –2015):Microbial Ecology Laboratory (University Claude Bernard - Lyon, France) and Laboratory of Transfer in Hydrology and Environment (University Joseph Fourier - Grenoble, France)

Advisors: Pr Agnès Richaume-Jolion and Dr Jean Martins

● MSc. Degree in Ecology, Biodiversity, Evolution (2010–2012): University Pierre & Marie Curie

Paris VI, France. Specialty: Biodiversity and Functioning of Ecosystems – Ecological engineering

● BSc. Degrees(2007 – 2010): University of Caen-Basse Normandie, France

- License of Biology of organisms and License of Geography

Professional experiences


● Research Scientist (Oct 2019 - Present): INRAE - IRHS in EmerSys team (Angers, France) Characterization of seed microbiomes and their resistances to abiotic and biotic stressors.

● Postdoctoral associate (Jan 2019 - Sept 2019):IRD - Interaction Plant - Microorganism - Environment Lab (Montpellier, France) Impact of biotic disturbances and agricultural practices on the plant microbiome of diverse crops in West Africa and South-East Asia.Supervisor: Lionel Moulin

● Postdoctoral associate (2016 - 2018):Biology Department (Duke University, NC, USA)

Impact of anthropogenic disturbances on the diversity and function of microbial communities in aquatic and terrestrial ecosystems.Supervisor: Emily Bernhardt

● Graduate researcher(2012- 2015): Microbial Ecology Laboratory (University Claude Bernard - Lyon) and Laboratory of Transfer in Hydrology and Environment (University Joseph Fourier - Grenoble)

Thesis title: Dynamic, reactivity and ecotoxicity of metal oxide nanoparticles in soil: impact on functions and diversity of microbial communities.Advisors: Pr Agnès Richaume-Jolion and Dr Jean Martins

Articles / Presentations / Posters


● Published articles and Pre-prints

24 articles published in peer-reviewed journal (Rank A)

1 pre-print

Publications

Publications

Sowing success: ecological insights into seedling microbial colonisation for robust plant microbiota engineering

Oscar Joubert , Gontran Arnault , Matthieu Barret , Marie Simonin

Trends in Plant Science, 2025, 30 (1), pp.21-34. ⟨10.1016/j.tplants.2024.09.004⟩

Article dans une revue hal-05081372v1

Transient microbial architects: tracing the legacy effects of ephemeral taxa during plant microbiome assembly

Logan Suteau , Louna Colaert-Sentenac , Simon Law , Marie Simonin

Current Opinion in Microbiology, 2025, 88, pp.102664. ⟨10.1016/j.mib.2025.102664⟩

Article dans une revue (article de synthèse) hal-05535812v1

A cross-systems primer for synthetic microbial communities

Elijah Mehlferber , Gontran Arnault , Bishnu Joshi , Laila Partida-Martinez , Kathryn Patras et al.

Nature Microbiology, 2024, 9 (11), pp.2765-2773. ⟨10.1038/s41564-024-01827-2⟩

Article dans une revue hal-05081398v1
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The type VI secretion system of Stenotrophomonas rhizophila CFBP13503 limits the transmission of Xanthomonas campestris pv. campestris 8004 from radish seeds to seedlings

Tiffany Garin , Chrystelle Brin , Anne Préveaux , Agathe Brault , Martial Briand et al.

Molecular Plant Pathology, 2024, 25 (1), pp.e13412. ⟨10.1111/mpp.13412⟩

Article dans une revue hal-04688341v1
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Interactions shape aquatic microbiome responses to Cu and Au nanoparticle treatments in wetland manipulation experiments

Zhao Wang , Christina Bergemann , Marie Simonin , Astrid Avellan , Phoebe Kiburi et al.

Environmental Research, 2024, 252, pp.118603. ⟨10.1016/j.envres.2024.118603⟩

Article dans une revue hal-04579728v1
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Stable, multigenerational transmission of the bean seed microbiome despite abiotic stress

Abby Sulesky-Grieb , Marie Simonin , A. Fina Bintarti , Brice Marolleau , Matthieu Barret et al.

mSystems, 2024, 9 (11), ⟨10.1128/msystems.00951-24⟩

Article dans une revue hal-04688340v1
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Seedling microbiota engineering using bacterial synthetic community inoculation on seeds

Gontran Arnault , Coralie Marais , Anne Préveaux , Martial Briand , Anne-Sophie Poisson et al.

FEMS Microbiology Ecology, 2024, 100 (4), ⟨10.1093/femsec/fiae027⟩

Article dans une revue hal-04688333v1
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T6SS-mediated competition by Stenotrophomonas rhizophila shapes seed-borne bacterial communities and seed-to-seedling transmission dynamics

Tiffany Garin , Agathe Brault , Coralie Marais , Martial Briand , Anne Préveaux et al.

mSystems, 2024, 10 (8), pp.e00457-25. ⟨10.1101/2024.07.22.604635⟩

Article dans une revue hal-05293005v1

Chronic Engineered Nanoparticle Additions Alter Insect Emergence and Result in Metal Flux from Aquatic Ecosystems into Riparian Food Webs

Brittany G Perrotta , Marie Simonin , Benjamin P Colman , Steven M Anderson , Ethan Baruch et al.

Environmental Science and Technology, 2023, 57 (21), pp.8085-8095. ⟨10.1021/acs.est.3c00620⟩

Article dans une revue hal-04111816v1
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Density declines, richness increases, and composition shifts in stream macroinvertebrates

Samantha Rumschlag , Michael Mahon , Devin Jones , William Battaglin , Jonny Behrens et al.

Science Advances , 2023, 9 (18), pp.eadf4896. ⟨10.1126/sciadv.adf4896⟩

Article dans une revue hal-04097465v1

At the interfaces of the hydrologic sciences: Connecting water, elements, ecosystems, and people through the major contributions of Dr. Emily Bernhardt

Ashley Helton , Jennifer Morse , Elizabeth Sudduth , Marcelo Ardón , Raven Bier et al.

Journal of Hydrology, 2023, 619, pp.129251. ⟨10.1016/j.jhydrol.2023.129251⟩

Article dans une revue (article de synthèse) hal-04292325v1

Mean species responses predict effects of environmental change on coexistence

Frederik de Laender , Camille Carpentier , Timoteo Carletti , Chuliang Song , Samantha Rumschlag et al.

Ecology Letters, 2023, 26 (9), pp.1535-1547. ⟨10.1111/ele.14278⟩

Article dans une revue hal-04494294v1
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Transmission of synthetic seed bacterial communities to radish seedlings: impact on microbiota assembly and plant phenotype

Marie Simonin , Anne Préveaux , Coralie Marais , Tiffany Garin , Gontran Arnault et al.

Peer Community Journal, 2023, 3, pp.e95. ⟨10.24072/pcjournal.329⟩

Article dans une revue hal-04688330v1
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Seasonal Differences and Grazing Pressure Alter the Fate of Gold Nanoparticles in a Microcosm Experiment

Christina Bergemann , Astrid Avellan , Brittany Perrotta , Emily Bernhardt , Marie Simonin

Environmental Science and Technology, 2023, 57 (37), pp.13970-13979. ⟨10.1021/acs.est.3c01839⟩

Article dans une revue hal-04208811v1
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The impact of the rice production system (irrigated vs lowland) on root-associated microbiome from farmer's fields in western Burkina Faso

Mariam Barro , Issa Wonni , Marie Simonin , Abalo Itolou Kassankogno , Agnieszka Klonowska et al.

FEMS Microbiology Ecology, 2022, 98 (9), ⟨10.1093/femsec/fiac085⟩

Article dans une revue hal-03773237v1

Alkaline mine drainage drives stream sediment microbial community structure and function

Lingrong Jin , Jacqueline R Gerson , Jennifer D Rocca , Emily S Bernhardt , Marie Simonin

Science of the Total Environment, 2022, 805, pp.150189. ⟨10.1016/j.scitotenv.2021.150189⟩

Article dans une revue hal-04688338v1
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Protist Predation Influences the Temperature Response of Bacterial Communities

Jennifer D.. Rocca , Andrea Yammine , Marie Simonin , Jean P. Gibert

Frontiers in Microbiology, 2022, 13, pp.847964. ⟨10.3389/fmicb.2022.847964⟩

Article dans une revue hal-03701557v1
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Enrichment in biodiversity and maturation of the soil food web under conservation agriculture is associated with suppression of rice-parasitic nematodes

Anne-Sophie Masson , Marie-Liesse Vermeire , Vira Leng , Marie Simonin , Florent Tivet et al.

Agriculture, Ecosystems & Environment, 2022, 331, pp.107913. ⟨10.1016/j.agee.2022.107913⟩

Article dans une revue hal-03607685v1
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Single seed microbiota: assembly and transmission from parent plant to seedling

Guillaume Chesneau , Béatrice Laroche , Anne Préveaux , Coralie Marais , Martial Briand et al.

mBio, 2022, 13 (6), pp.0164822. ⟨10.1128/mbio.01648-22⟩

Article dans une revue hal-03834661v1

Author Correction: Cultivated and wild pearl millet display contrasting patterns of abundance and co-occurrence in their root mycobiome

Marie-Thérèse Mofini , Abdala Diedhiou , Marie Simonin , Donald Tchouomo Dondjou , Sarah Pignoly et al.

Scientific Reports, 2022, 12 (1), pp.1639. ⟨10.1038/s41598-022-05899-0⟩

Article dans une revue hal-05194267v1
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Cultivated and wild pearl millet display contrasting patterns of abundance and co-occurrence in their root mycobiome

Marie-Thérèse Mofini , Abdala Diedhiou , Marie Simonin , Donald Tchouomo Dondjou , Sarah Pignoly et al.

Scientific Reports, 2022, 12 (1), pp.207. ⟨10.1038/s41598-021-04097-8⟩

Article dans une revue hal-03576717v1

Seed microbiota revealed by a large-scale meta-analysis including 50 plant species

Marie Simonin , Martial Briand , Guillaume Chesneau , Aude Rochefort , Coralie Marais et al.

New Phytologist, 2022, 234 (4), pp.1448-1463. ⟨10.1111/nph.18037⟩

Article dans une revue hal-03299446v1

Consistent declines in aquatic biodiversity across diverse domains of life in rivers impacted by surface coal mining

Marie Simonin , Jennifer Rocca , Jacqueline Gerson , Eric Moore , Alexander Brooks et al.

Ecological Applications, 2021, Early Access, pp.e02389. ⟨10.1002/eap.2389⟩

Article dans une revue hal-03313219v1
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Low mobility of CuO and TiO2 nanoparticles in agricultural soils of contrasting texture and organic matter content

Marie Simonin , Jean M.F. Martins , Gaëlle Uzu , Lorenzo Spadini , Aline Navel et al.

Science of the Total Environment, 2021, 783, pp.146952. ⟨10.1016/j.scitotenv.2021.146952⟩

Article dans une revue hal-03301328v1
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Toward a Generalizable Framework of Disturbance Ecology Through Crowdsourced Science

Emily Graham , Colin Averill , Ben Bond-Lamberty , Joseph Knelman , Stefan Krause et al.

Frontiers in Ecology and Evolution, 2021, 9, ⟨10.3389/fevo.2021.588940⟩

Article dans une revue (article de synthèse) hal-03220658v1

Microbiome Composition and Function in Aquatic Vertebrates: Small Organisms Making Big Impacts on Aquatic Animal Health

Ludek Sehnal , Elizabeth Brammer-Robbins , Alexis Wormington , Ludek Blaha , Joe Bisesi et al.

Frontiers in Microbiology, 2021, 12, pp.567408. ⟨10.3389/fmicb.2021.567408⟩

Article dans une revue (article de synthèse) hal-03238365v1
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Transmission of Seed and Soil Microbiota to Seedling

Aude Rochefort , Marie Simonin , Coralie Marais , Anne-Yvonne Guillerm-Erckelboudt , Matthieu Barret et al.

mSystems, 2021, 6 (3), pp.00446-21. ⟨10.1128/msystems.00446-21⟩

Article dans une revue hal-03299428v1

Guided by Microbes: Applying Community Coalescence Principles for Predictive Microbiome Engineering

Jennifer Rocca , Mario Muscarella , Ariane Peralta , Dandan Izabel-Shen , Marie Simonin

mSystems, 2021, 6 (4), pp.e00538-21. ⟨10.1128/mSystems.00538-21⟩

Article dans une revue hal-03541580v1

Long-Term Effects of Copper Nanopesticides on Soil and Sediment Community Diversity in Two Outdoor Mesocosm Experiments

Lauren N Carley , Renuka Panchagavi , Xin Song , Sade Davenport , Christina M Bergemann et al.

Environmental Science and Technology, 2020, 54 (14), pp.8878-8889. ⟨10.1021/acs.est.0c00510⟩

Article dans une revue hal-02945106v1

Chemistry of streams draining mined and unmined watersheds in the mountaintop mined landscape of Central Appalachia, USA

Jacqueline Gerson , Eric Moore , Laura Naslund , Jennifer Rocca , Marie Simonin

Ecology, In press, 101 (9), pp.e03093. ⟨10.1002/ecy.3093⟩

Article dans une revue (data paper) hal-02798110v1
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Influence of plant genotype and soil on the wheat rhizosphere microbiome: evidences for a core microbiome across eight African and European soils

Marie Simonin , Cindy Dasilva , Valeria Terzi , Eddy L M Ngonkeu , Diégane Diouf et al.

FEMS Microbiology Ecology, 2020, 96 (6), pp.fiaa067. ⟨10.1093/femsec/fiaa067⟩

Article dans une revue hal-02941967v1

Deep modifications of the microbiome of rice roots infected by the parasitic nematode Meloidogyne graminicola in highly infested fields in Vietnam

Anne-Sophie Masson , Hai Ho Bich , Marie Simonin , Hue Nguyen Thi , Pierre Czernic et al.

FEMS Microbiology Ecology, 2020, 96 (7), pp.fiaa099. ⟨10.1093/femsec/fiaa099⟩

Article dans une revue hal-02770824v1
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Rare microbial taxa emerge when communities collide: freshwater and marine microbiome responses to experimental mixing

Jennifer Rocca , Marie Simonin , Emily S Bernhardt , Alex D Washburne , Justin P Wright

Ecology, 2020, 101 (3), ⟨10.1002/ecy.2956⟩

Article dans une revue hal-02958363v1
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An extended root phenotype: the rhizosphere, its formation and impacts on plant fitness

Carla de La Fuente Cantó , Marie Simonin , Eoghan King , Lionel Moulin , Malcolm Bennett et al.

The Plant Journal, 2020, 14 p. ⟨10.1111/tpj.14781⟩

Article dans une revue (article de synthèse) hal-02779134v1
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Copper and Gold Nanoparticles Increase Nutrient Excretion Rates of Primary Consumers

Brittany G Perrotta , Marie Simonin , Jeffrey A Back , Steven M Anderson , Astrid Avellan et al.

Environmental Science and Technology, 2020, 54 (16), pp.10170-10180. ⟨10.1021/acs.est.0c02197⟩

Article dans une revue hal-02958354v1
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Differential Reactivity of Copper- and Gold-Based Nanomaterials Controls Their Seasonal Biogeochemical Cycling and Fate in a Freshwater Wetland Mesocosm

Astrid Avellan , Marie Simonin , Steven M Anderson , Nicholas K Geitner , Nathan Bossa et al.

Environmental Science and Technology, 2019, 54 (3), pp.1533-1544. ⟨10.1021/acs.est.9b05097⟩

Article dans une revue hal-02958362v1
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Harmonizing Across Environmental Nanomaterial Testing Media for Increased Comparability of Nanomaterial Datasets

Nicholas K Geitner , Christine Ogilvie Hendren , Geert Cornelis , Ralf Kaegi , Jamie Lead et al.

Environmental science‎.Nano, 2019, ⟨10.1039/C9EN00448C⟩

Article dans une revue hal-02376852v1
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Size-Based Differential Transport, Uptake, and Mass Distribution of Ceria (CeO 2 ) Nanoparticles in Wetland Mesocosms

Nicholas Geitner , Jane Cooper , Astrid Avellan , Benjamin Castellon , Brittany Perrotta et al.

Environmental Science and Technology, 2018, 52 (17), pp.9768-9776. ⟨10.1021/acs.est.8b02040⟩

Article dans une revue hal-03707279v1
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Gold nanoparticle biodissolution by a freshwater macrophyte and its associated microbiome

Astrid Avellan , Marie Simonin , Eric Mcgivney , Nathan Bossa , Eleanor Spielman-Sun et al.

Nature Nanotechnology, 2018, 13 (11), pp.1072-1077. ⟨10.1038/s41565-018-0231-y⟩

Article dans une revue hal-03707302v1

Negative Effects of Copper Oxide Nanoparticles on Carbon and Nitrogen Cycle Microbial Activities in Contrasting Agricultural Soils and in Presence of Plants

Marie Simonin , Amélie A. M. Cantarel , Armelle Crouzet , Jonathan Gervaix , Jean Mf Martins et al.

Frontiers in Microbiology, 2018, ⟨10.3389/fmicb.2018.03102⟩

Article dans une revue hal-02479075v1
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Engineered nanoparticles interact with nutrients to intensify eutrophication in a wetland ecosystem experiment

Marie Simonin , Benjamin P Colman , Steven M Anderson , Ryan S King , Matthew Ruis et al.

Ecological Applications, 2018, 28 (6), pp.1435-1449. ⟨10.1002/eap.1742⟩

Article dans une revue hal-03707300v1
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Short-term responses and resistance of soil microbial community structure to elevated CO2 and N addition in grassland mesocosms

Marie Simonin , Naoise Nunan , Juliette Bloor , Valérie Pouteau , Audrey Niboyet

FEMS Microbiology Letters, 2017, 364 (9), ⟨10.1093/femsle/fnx077⟩

Article dans une revue hal-01525344v1

Toxicity of TiO2 nanoparticles on soil nitrification at environmentally relevant concentrations: Lack of classical dose-response relationships

Marie Simonin , Jean M. F. Martins , Xavier Le Roux , Gaelle Uzu , Aude Calas et al.

Nanotoxicology, 2017, 11 (2), pp.247 - 255. ⟨10.1080/17435390.2017.1290845⟩

Article dans une revue hal-01602574v1
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Titanium dioxide nanoparticles strongly impact soil microbial function by affecting archaeal nitrifiers

Marie Simonin , Agnès Richaume-Jolion , Julien P. Guyonnet , Audrey Dubost , Jean M. F. Martins et al.

Scientific Reports, 2016, 6, pp.1-10. ⟨10.1038/srep33643⟩

Article dans une revue hal-01602239v1
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Combined study of titanium dioxide nanoparticle transport and toxicity on microbial nitrifying communities under single and repeated exposures in soil columns

Marie Simonin , Jean M. F. Martins , Gaëlle Uzu , Erwann Vince , Agnès Richaume

Environmental Science and Technology, 2016, 50 (19), pp.10693-10699. ⟨10.1021/acs.est.6b02415⟩

Article dans une revue hal-01604452v1

Coupling Between and Among Ammonia Oxidizers and Nitrite Oxidizers in Grassland Mesocosms Submitted to Elevated CO2 and Nitrogen Supply

Marie Simonin , Xavier Le Roux , Franck Poly , Catherine Lerondelle , Bruce A. Hungate et al.

Microbial ecology, 2015, 70 (3), pp.809-818. ⟨10.1007/s00248-015-0604-9⟩

Article dans une revue hal-01569713v1

Influence of soil properties on the toxicity of TiO₂ nanoparticles on carbon mineralization and bacterial abundance

Marie Simonin , Julien P. Guyonnet , Jean M. F. Martins , Morgane Ginot , Agnès Richaume-Jolion

Journal of Hazardous Materials, 2015, 283, pp.529-535. ⟨10.1016/j.jhazmat.2014.10.004⟩

Article dans une revue istex hal-01197005v1

Impact of engineered nanoparticles on the activity, abundance, and diversity of soil microbial communities: a review

Marie Simonin , Agnès Richaume

Environmental Science and Pollution Research, 2015, 22 (18), pp.13710-13723. ⟨10.1007/s11356-015-4171-x⟩

Article dans une revue (article de synthèse) hal-01602179v1
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Characterisation of the spermosphere of the common bean seed (Phaseolus vulgaris)

Chandrodhay Saccaram , Marie Simonin , Stéphanie Boutet , Céline Brosse , Tracy François et al.

Journée annuelle des Jeunes Chercheuses et Chercheurs (JJC) 2023, Apr 2023, Clermont-Ferrand, France

Poster de conférence hal-04528599v1
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Contribution of floral transmission to the assembly and health impact of bacterial communities in watermelon seeds

Gillian Bergmann , Kacie Lui , Carina Lopez , Alexander Velasco , Coralie Marais et al.

2025

Pré-publication, Document de travail hal-05293161v1
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Evaluating the legacy of drought exposure on root and rhizosphere bacterial microbiomes over two plant generations

A. Fina Bintarti , Abby Sulesky-Grieb , Joanna Colovas , Brice Marolleau , Tristan Boureau et al.

2025

Pré-publication, Document de travail hal-05290191v1
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Synthetic Community Inoculation on Seeds Revealed its Transient Colonization Capacity but Legacy Effects on Plant Microbiota Assembly

Gontran Arnault , Louna Colaert-Sentenac , Coralie Marais , Alain Sarniguet , Matthieu Barret et al.

2025

Pré-publication, Document de travail hal-05292992v1
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Evaluating the legacy of drought exposure on root and rhizosphere bacterial microbiomes over two plant generations

A Fina Bintarti , Abby Sulesky-Grieb , Joanna Colovas , Brice Marolleau , Tristan Boureau et al.

2026

Pré-publication, Document de travail hal-05481592v1

Single seed microbiota: assembly and transmission from parent plant to seedling

Guillaume Chesneau , Béatrice Laroche , Anne Préveaux , Coralie Marais , Martial Briand et al.

2021

Pré-publication, Document de travail (preprint/prepublication) hal-03299438v1
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Asymmetric outcome of community coalescence of seed and soil microbiota during early seedling growth

Aude Rochefort , Marie Simonin , Coralie Marais , Anne-Yvonne Guillerm-Erckelboudt , Matthieu Barret et al.

2020

Pré-publication, Document de travail (preprint/prepublication) hal-03045727v1