PUBLICATIONS
​
 For up-to-date Publications and Citations information, see my Google Scholar profile.  

49. Oscar Joubert, Gontran Arnault, Matthieu Barret, Marie Simonin (2024). Sowing success: ecological insights into seedling microbial colonisation for robust plant microbiome engineering. Trends In Plant Science. Accepted

48. Elijah C Mehlferber, Gontran Arnault, Bishnu Joshi, Laila P Partida-Martinez, Katy A Patras, Marie Simonin, Britt Koskella. A cross-systems primer for designing, deploying, and evaluating synthetic microbial communities. Nature Microbiology. Accepted

47. Wang, Z., Bergemann, C. M., Simonin, M., Avellan, A., Kiburi, P., & Hunt, D. E. (2024). Interactions shape aquatic microbiome responses to Cu and Au nanoparticle treatments in wetland manipulation experiments. Environmental Research, 252, 118603.

46. Arnault, G., Marais, C., Préveaux, A., Briand, M., Poisson, A. S., Sarniguet, A., ... & Simonin, M. (2024). Seedling microbiota engineering using bacterial synthetic community inoculation on seeds. FEMS Microbiology Ecology, 100(4), fiae027.

45. Cantarel, A. A., Signoret, A., Gervaix, J., Beligon, C., Béraud, C., Boisselet, C., ... & Simonin, M., Piola, F. (2024). Biological inhibition of denitrification (BDI): an early plant strategy for Fallopia× bohemica seedling development. Annals of Botany, 133(4), 533-546.

44. Garin, T., Brin, C., Préveaux, A., Brault, A., Briand, M., Simonin, M., ... & Sarniguet, A. (2024). The type VI secretion system of Stenotrophomonas rhizophila CFBP13503 limits the transmission of Xanthomonas campestris pv. campestris 8004 from radish seeds to seedlings. Molecular Plant Pathology, 25(1), e13412.

43. Simonin M, Préveaux A, Marais C, Garin T, Arnault G, Sarniguet A, & Barret M. (2023). Transmission of synthetic seed bacterial communities to radish seedlings: impact on microbiota assembly and plant phenotype. Peer Community Journal, 3.

42. Bergemann CM, Avellan A, Perrotta BG, Bernhardt ES, & Simonin M. (2023). Seasonal Differences and Grazing Pressure Alter the Fate of Gold Nanoparticles in a Microcosm Experiment. Environmental Science & Technology, 57(37), 13970-13979.

41. De Laender, F, Carpentier C, Carletti T, Song C, Rumschlag SL, Mahon MB, Simonin M, ... & Barabás G. (2023). Mean species responses predict effects of environmental change on coexistence. Ecology Letters.

40. Rumschlag SL, Mahon MB, Jones DK, Battaglin W, Behrens J, Bernhardt, ES, ... Simonin M, ... & Rohr JR. (2023). Density declines, richness increases, and composition shifts in stream macroinvertebrates. Science Advances, 9(18), eadf4896.

39. Perrotta BG, Simonin M, Colman BP, Anderson SM, Baruch E, Castellon BT, ... & King RS. (2023). Chronic Engineered Nanoparticle Additions Alter Insect Emergence and Result in Metal Flux from Aquatic Ecosystems into Riparian Food Webs. Environmental Science & Technology.

38. Helton, AM, Morse JL, Sudduth EB, Ardón M, Bier R, Voss KA, ... Simonin M, ... & Vlah, M. J. (2023). At the interfaces of the hydrologic sciences: Connecting water, elements, ecosystems, and people through the major contributions of Dr. Emily Bernhardt. Journal of Hydrology, 129251.

37. Chesneau G, Laroche B, Préveaux A, Marais C, Briand M, Marolleau B, Simonin M, Barret M. (2022). Single seed microbiota: assembly and transmission from parent plant to seedling. mBio, e01648-22.

36. Barro M, Wonni I, Simonin M, Kassankogno AI, Klonowska A, Moulin L., Bena G, Somda I, Brunel C, Tollenaere C. (2022). The impact of the rice production system (irrigated vs lowland) on root-associated microbiome from farmer's fields in western Burkina Faso. FEMS Microbiology Ecology, 98(9), fiac085.

35. Rocca, JD, Yammine A, Simonin M, Gibert JP. (2022). Predation by protists influences the temperature response of microbial communities. Frontiers in Microbiology. doi: 10.3389/fmicb.2022.847964

34. Simonin, M., Briand, M., Chesneau, G., Rochefort, A., Marais, C., Sarniguet, A., & Barret, M. (2022). Seed microbiota revealed by a large-scale meta-analysis including 50 plant species. New Phytologist. doi: 10.1111/nph.18037 -> Link to PDF
​
33. Masson AS, Vermeire ML, Leng V, Simonin M, Tivet F, Nguyen Thi H, Brunel C, Suong M, Kuok F, Moulin L, Bellafiore S. (2022). Enrichment in biodiversity and maturation of the soil food web under conservation agriculture is associated with suppression of rice-parasitic nematodes.  Agriculture, Ecosystems and Environment, 331, 107913

32. Mofini MT, Diedhiou AG, Simonin M, Tchouomo D, Pignoly S, Ndiaye C, Min D , Vigouroux Y, Laplaze L, Kane A. (2022). Cultivated and Wild Pearl Millet Display Contrasting Patterns of Abundance and Co-occurrence in their root mycobiome. Scientific Reports, 12, 1639 ​

31. Jin L, Gerson JR, Rocca JD, Bernhardt ES, Simonin M. (2022). Alkaline mine drainage drives stream sediment microbial community structure and function. Science of The Total Environment, 805, 150189.

30. Rocca JD, Muscarella ME, Peralta AL, Izabel-Shen D, Simonin M. (2021). Guided by Microbes: Applying Community Coalescence Principles for Predictive Microbiome Engineering. mSystems, 6(4), e00538-21.

29. Rochefort A, Simonin M, Marais C, Guillerm-Erckelboudt AY,  Barret M, Sarniguet A. (2021). Transmission of Seed and Soil Microbiota to Seedling. mSystems, https://doi.org/10.1128/mSystems.00446-21

28. Simonin M, Richaume A, Uzu G, Navel A, Dumay A, Martins JMF. (2021) Very limited transport of TiO2 and CuO nanoparticles in contrasted natural soils.  Science of the Total Environment. 783, 146952

27. Simonin M, Rocca JD, Gerson JR, Moore E, Brooks AC, Czaplicki L, Ross MRV, Fierer N,  Craine JM,  Bernhardt E.S. (2021) Consistent declines in aquatic biodiversity across diverse domains of life in rivers impacted by surface coal mining. Ecological Applications,  31 (6), e02389
-> See the associated The Conversation article

26. Graham EB, Averill C, Bond-Lamberty B, Knelman JE, Krause S, Peralta AL, ... Simonin M, ...& Freund C. (2021). Towards a unifying framework of disturbance ecology through crowdsourced science. Frontiers in Ecology and Evolution. doi: 10.3389/fevo.2021.588940

25. Sehnal L, Brammer-Robbins E, Wormington A, Blaha L, Bisesi J, Larkin I, Martiniuk C, Simonin M, & Adamovsky O. (2021). Microbiome composition and function in aquatic vertebrates: small organisms making big impacts on aquatic animal health. Frontiers in Microbiology, 12, 358.

24. Perrotta B, Simonin M, Back J, Anderson SM, Bergemann CM, Castellon B, Colman B, Matson C, Bernhardt ES, King R. (2020) Copper and Gold Nanoparticles Increase Nutrient Excretion Rates of Primary Consumers. Environmental Science & Technology

23. Masson AS, Ho Bich, H, Simonin M, Nguyen Thi H; Czernic P, Moulin L, Bellafiore S. (2020).  Deep modifications of the microbiome of rice roots infected by the parasitic nematode Meloidogyne graminicola in highly infested fields in Vietnam. FEMS Microbiology Ecology, 96, 7, fiaa099

22. Simonin M, Dasilva C, Terzi V, Ngonkeu ELM, Diouf D, Kane A, Bena G, Moulin L (2020). Influence of plant genotype and soil on the wheat rhizosphere microbiome: identification of a core microbiome across eight African and European soils. FEMS Microbiology Ecology, fiaa067.

21. Carley LN, Panchagavi R, Song X, Davenport S, Bergemann CM, McCumber AW, Gunsch CK, Simonin M. (2020) Long-term effects of copper nanopesticides on soil and sediment community diversity in two outdoor mesocosm experiments.  Environmental Science& Technology. 54 (14), 8878-8889

20. de la Fuente Canto C, Simonin M, King E, Moulin L, Bennett M, Castrillo G, Laplaze L (2020). An extended root phenotype: the rhizosphere, its formation and impacts on plant fitness.  The Plant Journal, doi:10.1111/tpj.14781.

19. Gerson  JR, Moore E, Naslund LC, Rocca JD, Simonin M. (2020) Chemistry of streams draining mined and unmined watersheds in the mountaintop mined landscape of Central Appalachia, USA,  Ecology e03093

18.  Avellan A, Simonin M,  Anderson SM, Geitner NK, Bossa N, Spielman-Sun E,  Bernhardt ES, Castellon BT,  Colman BP, Cooper JL, Ho M,  Hochella MF, Hsu-Kim H, Inoue S, King RS, Laughton SN, Matson CW, Perrotta B, Richardson C, Unrine JM,  Wiesner MR, Lowry GV. (2020). Differential Reactivity of Copper- and Gold-Based Nanomaterials Controls Their Seasonal Biogeochemical Cycling and Fate in a Freshwater Wetland Mesocosm. Environmental Science and Technology. 10.1021/acs.est.9b05097
​
17. Rocca JD, Simonin M, Wright JP, Washburne A, Bernhardt ES. (2020). Rare Microbial Taxa Emerge When Communities Collide: Freshwater and Marine Microbiome Responses to Experimental Seawater Intrusion.  Ecology,  doi: 10.1002/ecy.2956

16. Geitner NK, Hendren, CO, et al, Simonin, M...& Wiesner M  (2020). Harmonizing across environmental nanomaterial testing media for increased comparability of nanomaterial datasets. Environmental Science: Nano, 7, 13-36

15. Simonin M, Voss KA, Hassett BA, Rocca JD, Wang SY, Bier RL, Violin CR, Wright JP, Bernhardt ES (2019). In search of microbial indicator taxa: shifts in stream bacterial communities along an urbanization gradient. Environmental Microbiology, doi: 10.1111/1462-2920.14694

14. Brandt JE, Simonin M, Di Giulio RT, Bernhardt ES (2019). Beyond selenium: Coal combustion residuals lead to multi-element enrichment in receiving lake food webs. Environmental Science and Technology, doi:10.1021/acs.est.9b00324
​
13. Rocca JD, Simonin M, Blaszczak JR, Ernakovich JG, Gibbons SM,  Midani FS, Washburne AD (2019). The Microbiome Stress Project: towards a global meta-analysis of environmental stressors and their effects on microbial communities. Frontiers in Microbiology, 9:3272. doi: 10.3389/fmicb.2018.03272 

12. Simonin M, Cantarel AAM,  Crouzet A, Gervaix J, Martins JMF, Richaume A (2018). Negative effects of copper oxide nanoparticles on carbon and nitrogen cycle microbial activities in contrasting agricultural soils and in presence of plants. Frontiers in Microbiology, 9:3102.doi: 10.3389/fmicb.2018.03102

11. Avellan A, Simonin M, McGivney E, Bossa N, Spielman-Sun E, Rocca JD, Bernhardt ES, Geitner NK, Wiesner MR,  Lowry GV (2018). Gold nanoparticle biodissolution by a freshwater macrophyte and its associated microbiome. Nature Nanotechnology,  https://doi.org/10.1038/s41565-018-0231-y 

10. Geitner NK, Cooper JR, Avellan A, Castellon BT, Perrotta BG, Bossa N, Simonin M, Anderson SM, Inoue S, Hochella MF, Richardson CJ, Bernhardt ES, Lowry GV, Ferguson PL, Matson CW, King RS, Unrine JM, Wiesner MR, Hsu-Kim H. (2018) Size-based differential transport, uptake, and mass distribution of ceria (CeO2) nanoparticles in wetland mesocosms. Environmental Science and Technology, doi: 10.1021/acs.est.8b02040

9. Simonin M, Colman BP, Tang W, Judy JD, Anderson SM, Bergemann CM, Rocca JD, Unrine JM, Cassar N, Bernhardt ES, (2018) Plant and microbial responses to repeated Cu(OH)2 nanopesticide exposures under different fertilization levels in an agro-ecosystem. Frontiers in Microbiology, 9:1769. doi: 10.3389/fmicb.2018.01769

8. Simonin M, Colman BP, Anderson SM, King RS, Ruis MT, Avellan A, Bergemann, CM, Perrotta BG, Geitner NK, Ho M. de la Barrera B, Richardson CJ, Wiesner MR, Bernhardt ES, (2018) Engineered nanoparticles interact with nutrients to intensify eutrophication in a wetland ecosystem experiment. Ecological Applications, https://doi.org/10.1002/eap.1742

7. Simonin M, Nunan N, Bloor J, Pouteau V, Niboyet A, (2017) Short-term responses and resistance of soil microbial community structure to elevated CO2 and N addition in grassland mesocosms. FEMS Microbiology Letters, doi: 10.1093/femsle/fnx077
​
6. Simonin M, Martins JMF, Calas A, Uzu G, Richaume A, (2017)  Toxicity of TiO2  nanoparticles on soil nitrification at environmentally relevant concentrations: Lack of classical dose–response relationships. Nanotoxicology, doi: 10.1080/17435390.2017.1290845
 
5. Simonin M, Richaume A, Dubost A, Guyonnet JP, Martins JMF, Pommier T, (2016) Titanium dioxide nanoparticles strongly impact soil microbial function by affecting archaeal nitrifiers. Scientific reports, 6, 33643, doi: 10.1038/srep33643

4. Simonin M, Martins JMF, Uzu G, Vince E, Richaume A, (2016) Combined study of titanium dioxide nanoparticle transport and toxicity on microbial nitrifying communities under single and repeated exposures in soil columns. Environmental Science & Technology, doi: 10.1021/acs.est.6b02415

3. Simonin M, Le Roux X, Poly F, Lerondelle C, Hungate BA, Nunan N, Niboyet A, (2015) Coupling between and among ammonia oxidizers and nitrite oxidizers in grassland mesocosms submitted to elevated CO2 and nitrogen supply. Microbial Ecology, doi: 10.1007/s00248-015-0604-9

2. Simonin M, Richaume A, (2015) Impact of engineered nanoparticles on the activity, abundance and diversity of soil microbial communities: a review. Environmental Science and Pollution Research, doi: 10.1007/s11356-015-4171-x

​1. Simonin M, Guyonnet JP, Martins JMF, Ginot M, Richaume A, (2015). Influence of soil properties on the toxicity of TiO2 nanoparticles on carbon mineralization and bacterial abundance. Journal of Hazardous Material, 283: 529-535