Microbial Communities in Continental ecosystems "CoMIC" Team - iEES Paris

The CoMiC team studies microbial communities in continental terrestrial and aquatic ecosystems in an interdisciplinary framework that combines microbiology, comparative genomics, metagenomics, chemistry, ecology, health, environmental sciences and social sciences.

More specifically, our research focuses on (i) the vulnerability of microbial communities to disturbances and pollutants induced by human activity (ii) the flows and diversity of pathogens (human or plant) in the environment, (iii) the development of new tools for monitoring aquatic ecosystems and new approaches to ensure sustainable management of these ecosystems.

Our work, structured around the “one health/ecohealth” concept, is developed along two main lines:

Structural and functional biodiversity of microbial communities, their interactions and their roles in the function of the ecosystems where we are studying :

Prolifération de cyanobactéries
Caption:Cyanobacterial blooms potentially toxic in Aghien lagoon (Ivory Cost) – J.-F. HUMBERT
  1. The relationship between the structure and composition of microbial communities and the fluxes of organic carbon and nitrogen or pollutants in ecosystems.
  2. The impact of local and global changes on the dynamics and structure of microbial communities and on the microbial processes involved in the dynamics of the C and N cycles.
  3. The consequences of these changes in microbial communities on the ecosystem services provided by ecosystems and on the uses made of them.
 

Ecological quality of continental ecosystems and (dys)-functioning of microbial communities and associated risks for human health and plant pro

duction where we study :

Eaux de surface non traitées
Caption:Domestic use of untreated surface water – O. RIBOLZI
  1. The relationship between the ecological quality of continental ecosystems (organic matter, trophic level, structure and composition of microbial communities, …) and the survival and/or development of bacteria pathogenic to plants or humans.
  2. The proliferation of cyanobacteria in continental aquatic ecosystems and the production of toxins, from understanding the processes (implementation, synergy with heterotrophic microorganisms, etc.) to the development of tools for monitoring these proliferations and the development of new approaches for the management of aquatic ecosystems.
  3. The risks of human exposure to bacterial pathogens and cyanobacterial toxins in relation to the uses of soils and aquatic environments.
  4. The adaptation of pathogens to the environment through comparative genomics approaches.

In a context of local and global change, present and future, CoMiC researchers are committed to :

  • place our work within a solid theoretical and conceptual framework ;
  • provide targeted answers to specific societal and stakeholder needs in developed, emerging and developing countries.

Team members are all heavily involved in teaching activities, particularly at Sorbonne University, but also in other Universities (UPEC, University of Paris) or in agronomic schools (Agroparistech, ISARA in Lyon) as well as in Southern countries (Ivory Coast, Uganda, Laos, Niger, Senegal, Vietnam, Thailand) and in the continuing education of researchers and scientific staff in Southern countries.

Team publications

Only applies to publications from 2017 to present. To see all the publications go to the Publications page.

RéférenceDOI, liens hal et pdfJournalÉquipes et départements impliqués
​Bettarel Y, Boudin E, Halary S, Auguet J, Péronnin J, Bouvier T, Rochelle-Newall E*, Bui V` and Desnues C (2021) The Hungry Snail, the Fragile Coral, and the Friendly Microbe. Front. Young Minds. 9:573856. doi: 10.3389/frym.2021.57385610.3389/frym.2021.573856Frontiers for Young MindsCoMiCDCFE
​Nakhle, P.; Boithias, L.; Pando-Bahuon, A*.; Thammahacksa,C.`; Gallion, N.; Sounyafong, P`.; Silvera, N*.; Latsachack, K.`; Soulileuth,B.`; Rochelle-Newall, E.J*.; Marcangeli, Y;* Pierret, A*; Ribolzi, O*. Decay Rate of Escherichia coli in a
Mountainous Tropical Headwater Wetland. Water 2021, 13, 2068., https://doi.org/10.3390/w13152068
10.3390/w13152068WaterBioDISDCFE ; CoMiCDCFE ; EMSDCFE ; FESTSols_ZC
​Srikanthasamy T.~,Barot S.*,Koffi F.`,Tambosco K^,Marcangeli Y*,Carmignac D.*,N’Dri A. B.`,Gervaix J.,Le Roux X.,Lata J-C.* (2021) Short-term impact of fire on the total soil microbial and nitrifier communities in a wet savanna, Ecology and Evolution

10.1002/ece3.7661Ecology and EvolutionEMSDCFE ; CoMiCDCFE
​Pédron J*, Schaerer S, Kellenberger I, Van Gijsegem F* (20021) Early Emergence of Dickeya solani Revealed by Analysis of Dickeya Diversity of Potato Blackleg and Soft Rot Causing Pathogens in Switzerland. Microorganisms 2021, 9, 1187, 10.3390/microorganisms9061187
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MicroorganismsCoMiCDCFE
​Audry, S., H. Ateba Bessa, J.-P. Bedimo Bedimo, J.-L. Boeglin, L. Boithias, J.-J. Braun, B. Dupre, M. Faucheux, C. Lagane, J.-C. Marechal, J. R. Ndam-Ngoupayou`, B. Nka Nnomo`, J. Nlozoa`, J.-C. Ntonga`, O. Ribolzi, J. Riotte, E. Rochelle-Newall* and L. Ruiz (2021). “The Multiscale TROPIcal CatchmentS critical zone observatory M-TROPICS dataset I: The Nyong River Basin, Cameroon.” Hydrological Processes: e14138. 10.1002/hyp.14138Hydrological ProcessesCoMiCDCFE
​Riotte, J., Ruiz, L., Audry, S., Baud, B., Bedimo Bedimo, J.-P., Boithias, L., Braun, J.-J., Dupre, B., Faucheux, M., Lagane, C., Marechal, J.-C., Moger, H., Mohan Kumar, M.S.`, Parate, H., Ribolzi, O., Rochelle-Newall, E.*, Sriramulu, B.`, Varma, M.R.R.` and Sekhar, M`.  2021.  The Multiscale TROPIcal CatchmentS critical zone observatory M-TROPICS dataset III: hydro-geochemical monitoring of the Mule Hole catchment, south India. 2021. Hydrological Processes, e14196. 10.1002/hyp.14196Hydrological ProcessesCoMiCDCFE
​Mathias Koffi Ahoutou, Rosine Yao Djeha, Eric Kouamé Yao, Catherine Quiblier, Julie Niamen-Ebrottié, Sahima Hamlaoui, Kevin Tambosco^, Jean-Louis Perrin, Marc Troussellier, Cécile Bernard, Luc Seguis, Marc Bouvy, Jacques Pédron*, Felix Koffi Konan, Jean-François Humbert*, Julien Kalpy Coulibaly (2021) Assessment of some key indicators of the ecological status of an African freshwater lagoon (Lagoon Aghien, Ivory Coast). Plos One, 10.1371/journal.pone.0251065
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PLoS ONECoMiCDCFE
Noémie Pascault, Olivier Rué, Valentin Loux, Jacques Pédron*, Véronique Martin, Jennifer Tambosco, Cécile Bernard, Jean‐François Humbert*, Julie Leloup* (2021) Insights into the cyanosphere: capturing the respective metabolisms of cyanobacteria and chemotrophic bacteria in natural conditions? Env. Mic. Reports. 10.1111/1758-2229.12944
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Environmental Microbiology ReportsCoMiCDCFE ; EMSDCFE
​Michelet C., Zeppilli, D., Hubas, C., Baldrighi, E., Cuny, P., Dirberg, G., Militon, C., Lamy, D.*, Jézéquel, R., Receveur, J., Gilbert, F., El Houssainy, A., Dufour, A., Heimbürger-Boavida, L-E., Bihannic, I., Sylvi, L., Vivier, B., Michaud, E. (2021) First assessment of the benthic meiofauna sensitivity to low human-impacted mangroves in french Guiana. Forests, 12:33810.3390/f12030338
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ForestsCoMiCDCFE
Laurie Boithias, Yves Auda, Stéphane Audry, Jean-Pierre Bricquet, Alounsavath Chanhphengxay`, Vincent Chaplot,  Anneke de Rouw*, Thierry Henry des Tureaux*, Sylvain Huon*, Jean-Louis Janeau*, Keooudone Latsachack`, Yann Le Troquer*, Guillaume Lestrelin, Jean-Luc Maeght, Pierre Marchand, Pierre Moreau, Andrew Noble, Anne Pando-Bahuon*, Kongkeo Phachomphon`, Khambai Phanthavong`, Alain Pierret*, Olivier Ribolzi, Jean Riotte, Henri Robain*, Emma Rochelle-Newall*, Saysongkham Sayavong`, Oloth Sengtaheuanghoung`, Norbert Silvera*, Nivong Sipaseuth`, Bounsamay Soulileuth`, Xaysatith Souliyavongsa`, Phapvilay Sounyaphong`, Sengkeo Tasaketh`, Chanthamousone Thammahacksa`, Jean-Pierre Thiebaux, Christian Valentin*, Olga Vigiak, Marion Viguier^, Khampaseuth Xayyathip`.(2021) The Multiscale TROPIcal CatchmentS critical zone observatory M-TROPICS dataset II: Land use, hydrology and sediment production monitoring in Houay Pano, northern Lao PDR. Hydrological Processes. 2021;35:e14126.10.1002/hyp.14126
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Hydrological ProcessesBioDISDCFE ; CoMiCDCFE ; FESTSols_ZC ; F2ZCSols_ZC
​Mügler, C., O. Ribolzi, M. Viguier, J.-L. Janeau*, E. Jardé, K. Latsachack`, T. Henry-Des-Tureaux*, C. Thammahacksa`, C. Valentin*, O. Sengtaheuanghoung` and E. Rochelle-Newall* (2021). “Experimental and modelling evidence of splash effects on manure borne Escherichia coli washoff.” Environmental Science and Pollution Research: 1-12.10.1007/s11356-021-13011-8
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Environmental Science and Pollution ResearchCoMiCDCFE ; FESTSols_ZC ; F2ZCSols_ZC
​David, G. M., P. López-García, D. Moreira, B. Alric, P. Deschamps, P. Bertolino, G. Restoux, E. Rochelle-Newall, E. Thébault, M. Simon and L. Jardillier “Small freshwater ecosystems with dissimilar microbial communities exhibit similar temporal patterns.” Molecular Ecology 10.1111/mec.15864Molecular EcologyCoMiCDCFE ; EERIDCFE
​Nakhle P., Ribolzi O., Boithias L., Rattanavong S., Auda Y., Sayavong S., Zimmermann R., Soulileuth B., Pando A*., Thammahacksa C., Rochelle-Newall E.J.*, Santini W., Martinez J-M., Gratiot N., Pierret A*.(2021) “Effects of hydrological regime and land use on in-stream Escherichia coli concentration in the Mekong basin, Lao PDR”. Scientific Reports, 11:3460.10.1038/s41590-021-82891-0Scientific ReportsBioDISDCFE ; CoMiCDCFE
​Sisouvanh P’, Trelo-Ges V’., Isarangkool Na Ayutthaya S’., Pierret A.*, Nunan N*., Silvera N.*, Xayyathip K’., Hartmann C*. (2021) Can organic amendments improve soil physical characteristics and increase maize performances in contrasting soil water regimes? Agriculture, 11, 132.10.3390/agriculture11020132AgricultureCoMiCDCFE ; BioDISDCFE ; F2ZCSols_ZC
​David F., Meziane T., Marchand C., Rolland G., Pham A., Thanh-Nho N., Lamy, D.* (2021) Prokaryotic abundance, cell size and extracellular enzymatic acrivity in a human impacted and mangrove dominated tropical estuary (Can Gio, Vietnam). Estuarine, Coastal and Shelf Science, 251: 10725310.1016/j.ecss.2021.107253
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Estuarine, Coastal and shelf ScienceCoMiCDCFE
Nakhle P., Ribolzi O., Boithias L., Rattanavong S.’, Auda Y., Sayavong S.’, Zimmermann R.E., Soulileuth B.’, Pando A*., Tammahacksa C’., Rochelle-Newall E.*, Santinin W., Martinez J.-M., Gratiot N., Pierret A.* (2021) Effects of hydrological regime and land use on in-stream Escherichia coli concentration in the Mekong basin, Lao PDR, Scientific Reports – Nature 11:3460 10.1038/s41598-021-82891-0​Scientific ReportsCoMiCDCFE ; BioDISDCFE
​Boithias, L., O. Ribolzi, G. Lacombe, C. Thammahacksa*, N. Silvera*, K. Latsachack*, B. Soulileuth*, M. Viguier, Y. Auda, E. Robert, O. Evrard, S. Huon*, T. Pommier, C. Zouiten, O. Sengtaheuanghoung` and E. Rochelle-Newall* (2021). “Quantifying the effect of overland flow on Escherichia coli pulses during floods: Use of a tracer-based approach in an erosion-prone tropical catchment.” Journal of Hydrology 594: 125935. 10.1016/j.jhydrol.2020.125935
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Journal of HydrologyCoMiCDCFE ; F2ZCSols_ZC
 Liechti N., Zimmermann R.E., Zopfi J., Robinson M., Pierret A*, Ribolzi O., Rattanavong S’., Davong V.’, Newton P.N., Wittwer M., Dance D.A.B. (2021) Whole-genome assemblies of 16 Burkholderia pseudomallei isolates from rivers in Laos. Microbiol Resour Announc 10:e01226-20,10.1128/MRA.01226-20​
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Microbiology Resources AnnouncementsCoMiCDCFE
​Anh, H. Q., T. P. Q. Le`, N. Da Le, X. X. Lu, T. T. Duong`< /span>, J.Garnier, E. Rochelle-Newall*, S. Zhang, N.-H. Oh, C. Oeurng`, C. Ekkawatpanit, T. D. Nguyen, Q. T. Nguyen, T. D. Nguyen, T. N. Nguyen, T. L. Tran, T. Kunisue, R. Tanoue, S. Takahashi, T. B. Minh, H. T. Le, T. N. M. Pham and T. A. H. Nguyen (2020). “Antibiotics in surface water of East and Southeast Asian countries: A focused review on contamination status, pollution sources, potential risks, and future perspectives.” Science of The Total Environment: 14286510.1016/j.scitotenv.2020.142865Science of the Total EnvironmentCoMiCDCFE
Portier P., Pédron J.*, Taghouti G., Dutrieux C., Barny MA.* (2020) Updated taxonomy of Pectobacterium genus in the CIRM-CFBP bacterial collection: when newly described species reveal “old” endemic population. Microorganism 8 :144110.3390/microorganisms8091441
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MicroorganismsCoMiCDCFE
​Song, L.’, Boithias, L., Sengtaheuanghoung, O.’, Oeurng C.’, Valentin C*., Souksavath B’., Sounyafong P.’, De Rouw A*., Soulileuth B.’, Silvera N.*, Lattanavongkhot B.’, Pierret A*., Ribolzi O. (2020) Understorey vegetation limits surface runoff and soil loss in teak plantation-based systems of Northern Lao PDR. Water10.3390/w12092327WaterCoMiCDCFE ; F2ZCSols_ZC
El Hayany B., El Fels L., Quenea K., Dignac M.-F.*, Rumpel C.*, Gupta V.K., Hafidi M. 2020. Microplastics from lagooning sludge to composts as revealed by Fluorescent staining- Image analysis, Raman spectroscopy and Pyrolysis-GC/MS. Journal of Environmental Management 275 111249.10.1016/j.jenvman.2020.111249​
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Journal of Environmental ManagementCoMiCDCFE ; FESTSols_ZC
Pédron J.*, Guyon L., Lecomte A.°, Blottière L.^, Chandeysson C., Rochelle-Newall E.*, Raynaud X.*, Berge O., Barny MA*. (2020) Comparison of Environmental and Culture-Derived Bacterial Communities through 16S Metabarcoding: A Powerful Tool to Assess Media Selectivity and Detect Rare Taxa. Microorganisms 27:E112910.3390/microorganisms8081129
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MicroorganismsCoMiCDCFE ; EMSDCFE
​El Hayany B., El Fels L., Dignac M.-F.*, Quenea K., Rumpel C.*, Hafidi M. (2020) Pyrolysis-GCMS as a tool for maturity evaluation of compost from sewage sludge and green waste. Waste and biomass Valorization.10.1007/s12649-020-01184-1
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Waste and Biomass ValorizationCoMiCDCFE ; FESTSols_ZC
Panettieri M., Courtier-Murias D., Rumpel C.,* Dignac M.-F.*, Almendros G., Chabbi A. 2020. Land-use perturbations in ley grassland decouple the degradation of ancient soil organic matter from the storage of newly derived carbon inputs. SOIL Discussions, 1-31.10.5194/soil-2020-16​
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SOIL DiscussionsCoMiCDCFE ; FESTSols_ZC
​Arrieta-Escobar J., Derrien D., Ouvrard S., Asadollahi-Yazdi E., Hassan A., Boly V., Tinet A.-J., Dignac M.-F.* 2020. 3D Printing: an emerging opportunity for soil science. Geoderma. 378 114588.10.1016/j.geoderma.2020.114588
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GeodermaCoMiCDCFE
Le Mer G.~, Barthod J.~, Dignac M.-F.,* Barré P., Baudin F., Rumpel C.* 2020. Inferring earthworms’ impact on the stability of organo-mineral associations by Rock-Eval pyrolysis and 13C NMR spectroscopy. Organic Geochemistry, 104016.10.1016/j.orggeochem.2020.104016
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Organic GeochemistryCoMiCDCFE ; FESTSols_ZC
Vidal A., Lenhart T., Dignac M.F*, Biron P.*, Höschen C., Barthod J., Vedere C., Vaury V.*, Bariac T.*, Rumpel C.* (2020): Promoting plant growth and carbon transfer to soil with with organic amendments produced with mineral additives. Geoderma.Volume 374, 1 September 2020, 11445410.1016/j.geoderma.2020.114454
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GeodermaEMSDCFE ; CoMiCDCFE ; FESTSols_ZC ; F2ZCSols_ZC
Sayavong, S’., Kaewjampa, N’., Katawatin, R’., Boonthai Iwai C’., Moukomla S.’, Oszwald J., Pierret A*. (2020) Recent Co-occurring Expansion of Rubber Tree Plantations and Land Use/Land Cover Change in Luangnamtha District, Northern Laos. International Journal of Geoinformatics, 16(1), 85-10110.52939/ijg.v16i11843International Journal of GeoinformaticsCoMiCDCFE
Barthod J.~, Dignac M.-F.*, Le Mer G.~, Bottinelli N.*, Watteau F., Kögel-Knabner I., Rumpel C.* (2020) How do earthworms affect organic matter decomposition in the presence of clay-sized minerals? Soil Biology and Biochemistry
10.1016/j.soilbio.2020.107730
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Soil Biology and BiochemistryCoMiCDCFE ; FESTSols_ZC
​Thorup-Kistensen K., Halberg N., Nicolaisen M., Eivind-Olsen J., Crews T.E., Hinsinger P., Kirkegaard J. Pierret A*., Bodin-Dresbøll D (2020) Digging Deeper for Agricultural Resources, the Value of Deep Rooting.Trends in Plant Science.10.1016/j.tplants.2019.12.007
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Trends in Plant ScienceCoMiCDCFE
Paradelo R., Lerch T.Z.*, Houot S., Dignac M.-F.* (2019) Composting modifies the patterns of incorporation of OC and N from plant residues into soil aggregates. Geoderma, 353: 415-422. 10.1016/j.geoderma.2019.07.025
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GeodermaCoMiCDCFE ; BioDISDCFE
Portier P, Pédron J*, Taghouti G`, Fischer-Le Saux M, Caullireau E, Bertrand C^, Laurent A, Chawki K, Oulgazi S`, Moumni M`, Andrivon D​, Dutrieux C, Faure D​, Hélias V, Barny MA* (2019) Elevation of Pectobacterium carotovorum subsp. odoriferum to species level as Pectobacterium odoriferum sp. nov., proposal of Pectobacterium brasiliense sp. nov. and Pectobacterium actinidiae sp. nov., emended description of Pectobacterium carotovorum and description of Pectobacterium versatile sp. nov.,isolated from streams and symptoms on diverse plants. Int J Syst Evol Microbiol. 69(10):3214-2310.1099/ijsem.0.003611
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International Journal of Systematic and Evolutionary MicrobiologyCoMiCDCFE
Lerch T.Z.*, Dignac M.-F.*, Thevenot M., Mguerchi C.°, Houot S. (2019) Chemical changes during composting of plant residues reduce their mineralisation in soil and cancel the priming effect. Soil Biology and Biochemistry, 136: 107525. 10.1016/j.soilbio.2019.107525
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Soil Biology and BiochemistryCoMiCDCFE ; BioDISDCFE
Oulghazi S`, Pédron J*, Cigna J, Lau YY, Moumni M`, Van Gijsegem F*, Chan KG, Faure D (2019) Dickeya undicola sp. nov., a novel species for pectinolytic isolates from surface waters in Europe and Asia. Int J Syst Evol Microbiol. 69(8): 2440-244410.1099/ijsem.0.003497
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International Journal of Systematic and Evolutionary MicrobiologyCoMiCDCFE
Le H.T.~, Rochelle-Newall E.*, Ribolzi O., Janeau J.L.*, Huon S.*, Latsachack K.`, Pommier T. (2020). Land use strongly influences soil organic carbon and bacterial community loss in runoff in tropical Uplands. Land  Degradation Development  10.1002/ldr.3433
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Land Degradation & DevelopmentF2ZCSols_ZC ; CoMiCDCFE ; FESTSols_ZC
Pédron J*, Van Gijsegem F* (2019) Diversity in the Bacterial Genus Dickeya Grouping Plant Pathogens and Waterways Isolates. OBM Genetics 2019, Volume 3, Issue 4.10.21926/obm.genet.1904098OBM GeneticsCoMiCDCFE
Duong, T. T.`, T. T. H. Hoang`, T. K. Nguyen`, T. P. Q. Le`, N. D. Le`, D. K. Dang`, X. Lu`, M. H. Bui`, Q. H. Trinh`, T. H. V. Dinh`, T. D. Pham` & E. Rochelle-newall, 2019. Factors structuring phytoplankton community in a large tropical river: Case study in the Red River (Vietnam). Limnologica 76:82-93
10.1016/j.limno.2019.04.003
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LimnologicaCoMiCDCFE
​Clement, C~., Pierret A*., Maeght JL., Hartmann C*., Xayyathip K’., Soulileuth B’., Sounyafong P.’, Latsachack K’., Thammahacksa C’., Sengtaheuanghoung O’.  (2019) Linking tree‐rooting pro les to leaf phenology: a first attempt on Tectona Grandis Linn F. Trees 33, pages 1491–1504 (2019).10.1007/s00468-019-01876-9
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TreesCoMiCDCFE ; BioDISDCFE
​Zeitoun V., Auetrakulvit P’., Zazzo A., Pierret A*., Frere S., Forestier H. (2019) Discovery of an outstanding Hoabinhian site from the Late Pleistocene at Doi Pha Kan (Lampang province, northern Thailand), Archaeological Research in Asia, 18, 1-16,10.1016/j.ara.2019.01.002
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Archaeological Research in AsiaCoMiCDCFE
Daviere A, Sotomski M, Audibert A, Carol P*, Hubert S, Lebreton S*, Louvet-Vallee S, Pedron J, PuyaubertJ, Kraepiel Y, Lacoste J.(2019) Synergistic toxicity between glyphosate and 2,4-dinitrophenol on budding yeast is not due to H2O2-mediated oxidative stress. Matters 5 (4), e201903000030
10.19185/matters.201903000030MattersAPCEIPE ; EMSDCFE ; CoMiCDCFE
Mugler, C., Ribolzi, O., Janeau, J.L.*, Rochelle-Newall, E.*, Latsachack, K.`, Thammahacksa, C.`, Viguier, M., Jarde, E., Henri-Des-Tureaux*, T., Sengtaheuanghoung, O.`, Valentin, C.*, 2019. Experimental and modelling evidence of short-term effect of raindrop impact on hydraulic conductivity and overland flow intensity. Journal of Hydrology 570, 401-410.10.1016/j.jhydrol.2018.12.046
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Journal of HydrologyFESTSols_ZC ; F2ZCSols_ZC ; CoMiCDCFE
Barot, S*., L. Abbadie*, A. Auclerc, C. Barthélémy, E. Bérille, P. Billet, P. Clergeau, J.-N. Consales, M. Deschamp-Cottin, A. David~, C. Devigne, V. Dham, Y. Dusza~, A. Gaillard, E. Gonzalez, M. Hédont, D. Labarraque, A.-M. Le Bastard, J.-L. Morel, Y. Petit-Berghem, E. Rémy, E. Rochelle-Newall* & M. Veyrières, 2019. Urban ecology, stakeholders and the future of ecology. Science of The Total Environment 667:475-48410.1016/j.scitotenv.2019.02.410
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Science of the Total EnvironmentCoMiCDCFE ; EMSDCFE
​Berg, J.S., Jézéquel, D., Duverger, A., Lamy, D.*,  Laberty-Robert, C., Miot, J. (2019) Microbial diversity involved in iron and cryptic sulfur cycling in the ferruginous, low-sulfate waters of Lake Pavin. PlosOne, 14:e021278710.1371/journal.pone.0212787
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PLoS ONECoMiCDCFE
Pédron J*, Bertrand C^, Taghouti G, Portier P, Barny MA*. (2019) Pectobacterium aquaticum sp. nov., isolated from waterways. Int J Syst Evol Microbiol. 69(3): 745-751​10.1099/ijsem.0.003229
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International Journal of Systematic and Evolutionary MicrobiologyCoMiCDCFE
​Zeitoun V., Bourdon E., Latsachack K.O.’, Pierret A*, Singthong S’, Baills H., Forestier H. (2019) Discovery of a new open-air Hoabinhian site in Luang Prabang province (Lao PDR). Dating and technological study of the lithic assemblage. Comptes Rendus Palevol, 18, 142-157.10.1016/j.crpv.2018.05.003
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Comptes rendus PalevolCoMiCDCFE
Alič Š, Pédron J*, Dreo T, Van Gijsegem F* (2019) Genomic characterisation of the new Dickeya fangzhongdai species regrouping plant pathogens and environmental isolates. BMC Genomics. 20(1): 3410.1186/s12864-018-5332-3
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BMC GenomicsCoMiCDCFE
Essarts YR des, Pédron J*, Blin P, Dijk EV, Faure D, Gijsegem FV* (2019) Common and distinctive adaptive traits expressed in Dickeya dianthicola and Dickeya solani pathogens when exploiting potato plant host. Environmental Microbiology.21(3), 1004–101810.1111/1462-2920.14519
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Environmental MicrobiologyCoMiCDCFE
Watteau F., Dignac M.-F.*, Bouchard A., Revallier A., Houot S. 2018. Microplastic detection in soil amended with municipal solid waste composts as revealed by transmission electronic microscopy and Pyrolysis/GC/MS. Frontiers in Sustainable Food Systems, 2: 8110.3389/fsufs.2018.00081
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Frontiers in Sustainable Food SystemsCoMiCDCFE
Ribolzi, O., Lacombe, G., Pierret, A.*, Robain, H.*, Sounyafong, P.`, de Rouw, A.*, Soulileuth, B.`, Mouche, E., Huon, S.*, Silvera, N.*, Latxachak, K.O.`, Sengtaheuanghoung, O.`, Valentin, C.* Interacting land use and soil surface dynamics control groundwater outflow in a montane catchment of the lower Mekong basin. Agric. Ecosyst. Environ. 268, 90–102​10.1016/j.agee.2018.09.005
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Agriculture Ecosystems & EnvironmentF2ZCSols_ZC ; CoMiCDCFE
​Dance D.A.B., Knappik M., Dittrich S., Viengmon D., Silisouk J.’, Vongsouvath M.’, Rattanavong S.,’ Pierret A.*, Newton P.N.,  Amornchai P’, Vanaporn Wuthiekanun’, Langla S., Limmathurotsakul D’. (2018) Evaluation of consensus method for the culture of Burkholderia pseudomallei in soil samples from Laos. Wellcome Open Research.10.12688/wellcomeopenres.14851.2
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Wellcome Open ResearchCoMiCDCFE
Le H.T.~, Rochelle-Newall E.*, Auda Y., Ribolzi O., Sengtaheuanghoung O.’, Thébault E.*, Soulileuth B.’, Pommier T. (2018) Vicinal land use change strongly drives stream bacterial community in a tropical montane catchment. FEMS microbiology ecology, 94, fiy155.​10.1093/femsec/fiy155
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FEMS Microbiology EcologyEERIDCFE ; CoMiCDCFE
Faye P`, Bertrand C^, Pédron J*, Barny MA* (2018) Draft genomes of “Pectobacterium peruviense” strains isolated from fresh water in France. Stand Genomic Sci. 13: 2710.1186/s40793-018-0332-0
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Standards in Genomic Sciences CoMiCDCFE
Barthod J.~, Rumpel C.*, Calabi-Floody M., Mora M-L., Bolan N., Dignac M-F.* (2018) Adding worms during composting with red mud and fly ash reduces CO2 emissions and increases plant available nutrient contents. Journal of Environmental Management, 222: 207-21510.1016/j.jenvman.2018.05.079
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Journal of Environmental ManagementCoMiCDCFE ; FESTSols_ZC
Van Gijsegem F*, Bitton F, Laborie A-L, Kraepiel Y*, Pédron J* (2018) Characterization of the early response of Arabidopsis thaliana to Dickeya dadantii infection using expression profiling. bioRxiv 415380; 10.1101/415380
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BioRxivCoMiCDCFE ; EMSDCFE
Sengtaheuanghoung O., Ribolzi O., Rochelle-Newall E. J.*, Boithias L., Evrard O., Henri-des-Tureaux T.*, Huon S.*, Janeau J.-L*., Latsachack K*., Lefèvre I., Mouche E., Robain H.*, de Rouw A.*, Xayyathip K.*, Silvera N.*, Sisouvanh P~., Soulileuth B.*, Sounyafong P*., Thammahacksa C*., Viguier M., Lacombe G., Valentin C. & Pierret. A.*, Interactions between land use, fluxes of water and sediments, and the spread of bacterial contaminants in the uplands of northern Lao PDR. In: Nations, F. A. O. (ed) Proceedings of the Global Symposium on Soil Pollution 2018, Rome, Italy, 2018. FAO, p 976.FAO EditionsCoMiCDCFE ; BioDISDCFE ; F2ZCSols_ZC ; FESTSols_ZC
Nkwain Y.F., Demyan M. S., Rasche F., Dignac M.-F.*, Schulz E., Kätterer T., Müller T., Cadisch G. (2018) Coupling pyrolysis with mid-infrared spectroscopy (Py-MIRS) to fingerprint biochemical quality of soil organic matter. Journal of Analytical and Applied Pyrolysis, 133: 176-18410.1016/j.jaap.2018.04.004
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Journal of Analytical and Applied PyrolysisCoMiCDCFE
Riera, E., Lamy, D.*, Goulard, C.,Francour, P.,Hubas, C. (2018) ​Biofilm monitoring as a tool to assess the efficiency of artificial reefs as substrates : Toward 3D printed reefs. Ecological Engineering, 120:230-237
10.1016/j.ecoleng.2018.06.005
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Ecological EngineeringCoMiCDCFE
Fouilland, E., A. Trottet, C. Alves-de-Souza, D. Bonnet, T. Bouvier, M. Bouvy, S. Boyer, L. Guillou, E. Hatey, H. Jing, C. Leboulanger, E. Le Floc’h, H. Liu, S. Mas, B. Mostajir, J. Nouguier, D. Pecqueur, E. Rochelle-Newall*, C. Roques, C. Salles, M.-G. Tournoud, C. Vasseur & F. Vidussi, 2017. Significant Change in Marine Plankton Structure and Carbon Production After the Addition of River Water in a Mesocosm Experiment. Microbial Ecology 74(2):289-30110.1007/s00248-017-0962-6
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Microbial EcologyCoMiCDCFE
Le, T. P. Q., N. D. Le, V. N. Dao, E. Rochelle-Newall*, T. M. H. Nguyen~, C. Marchand, T. T. Duong & T. X. B. Phung, 2018. Change in carbon flux (1960–2015) of the Red River (Vietnam). Environmental Earth Sciences 77(18):658 10.1007/s12665-018-7851-2
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Environmental Earth Sciences CoMiCDCFE
Zimmermann R. E., Ribolzi O., Pierret A,* Rattanavong S.’, Robinson M. T., Newton P. N., Davong V.’, Auda Y., Zopfi J., Dance D. A. B. (2018) Rivers as carriers and potential sentinels for Burkholderia pseudomallei in Laos. Scientific Reports – Nature, 2018, 8, p. art. 8674 [7p.]. ISSN 2045-2322.10.1038/s41598-018-26684-y​
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Scientific ReportsCoMiCDCFE
Alic S, Van Gijsegem F,  Pédron J*,  Ravnikar M and  Dreo T (2018) Diversity within the novel Dickeya fangzhongdai sp., isolated from infected orchids, water and pears. Plant Pathology 67: 1612-1620.​10.1111/ppa.12866
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Plant PathologyCoMiCDCFE
Rochelle-Newall E.*, Niboyet A.*, Jardillier L., Fiorini S., Chollet S., Llavata M., de Santis E., Barot S.*, Lacroix G.* (2018)Impacts of elevated atmospheric CO2 concentration on terrestrial-aquatic carbon transfer and a downstream aquatic microbial community. Aquatic Sciences, 80, Article Number: 2710.1007/s00027-018-0577-0
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Aquatic SciencesEERIDCFE ; CoMiCDCFE ; EMSDCFE
Nguyen, T. M. H.~, G. Billen, J. Garnier, T. P. Q. Le, Q. L. Pham, S. Huon* & E. Rochelle Newall*, 2018. Organic carbon transfers in the subtropical Red River system (Viet Nam): insights on CO2 sources and sinks. Biogeochemistry 138(3):277-295.
10.1007/s10533-018-0446-x
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BiogeochemistryCoMiCDCFE ; F2ZCSols_ZC
Barthod J.~, Rumpel C.*, Dignac M-F.* (2018) Improving the environmental footprint and properties of compost and vermicomposts through mineral, organic and biological additives. A review. Agronomy for Sustainable Development, 38:17​10.1007/s13593-018-0491-9
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Agronomy for Sustainable DevelopmentCoMiCDCFE ; FESTSols_ZC
Pédron J*, Chapelle E, Alunni B, Van Gijsegem F* (2018) Transcriptome analysis of the Dickeya dadantii PecS regulon during the early stages of interaction with Arabidopsis thaliana. Mol Plant Pathol. 19(3): 647-663​10.1111/mpp.12549
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Molecular Plant PathologyCoMiCDCFE
​Lacombe G., Valentin C*, Sounyafong P.’, De Rouw A*, Soulileuth B.’, Silvera N*, Pierret A*, Sengtaheuanghoung O.’, Ribolzi O (2018). Linking crop structure, throughfall, soil surface conditions, runoff and soil detachment : 10 land uses analyzed in Northern Laos. Science of the Total Environment, 2018, 616, p. 1330-1338. ISSN 0048-9697.10.1016/j.scitotenv.2017.10.185
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Science of the Total EnvironmentCoMiCDCFE ; CoMiCDCFE ; F2ZCSols_ZC
​Pierret A.*, Lacombe G. (2018) Hydrologic regulation of plant rooting depth : breakthrough or observational conundrum ?. Proceedings of the National Academy of Sciences of the United States of America, 2018, 115 (12), p. E2669-E2670. ISSN 0027-8424.10.1073/pnas.1801721115Proceeding of the National Academy of Sciences of the United States of America – PNASCoMiCDCFE
Toussaint A., Van Gijsegem F.* (2017) Extension of the transposable bacterial virus family: two genomic organisations among phages and prophages with a Tn552-related transposase. Research in Microbiology, 169: 9

10.1016/j.resmic.2017.11.002
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Research in MicrobiologyCoMiCDCFE
Pengerud A., Dignac M.-F.*, Certini G., Strand L.T., Forte C., Rasse D.P. (2017) Soil organic matter molecular composition and state of decomposition in three locations of the European Arctic. Biogeochemistry 135: 277–292. 10.1007/s10533-017-0373-2
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BiogeochemistryCoMiCDCFE
Rochelle Newall, E*., L. Boithias, C. Bouet*, O. Malam-Issa*, A. Pierret*, O. Ribolzi & E. Roberts, 2017. Accès à l’eau, usage des terres et dégradation des sols: un triptyque qui favorise l’émergence des maladies diarrhéiques. In Loireau, M. & N. Ben Khatra (eds) Désertification et Système Terre, de la (re)connaissance à l’action//Liason Energie-Francophonie. vol 106. Institut de la Francophonie pour le Developpement Durable et l’Organisation International de la Francophonie, Quebec, Canada, 83-85.
🔗 HAL Liason Energie-FrancophonieF2ZCSols_ZC ; CoMiCDCFE
Morris C., Barny MA.*, Berge O., Kinkel LL.,  and Lacroix C.(2017) Frontiers for research on the ecology of plant pathogenic bacteria: Fundamentals for sustainability. Mol plant pathol : 18(2)10.1111/mpp.12508
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Molecular Plant PathologyCoMiCDCFE
Ribolzi O., Evrard O., Huon S.*, de Rouw A.*, Silvera N.*, Latsachack K.O.`, Soulileuth B.`, Lefèvre I., Pierret A.*, Lacombe G., Sengtaheuanghoung O.`, Valentin C.* (2017) From shifting cultivation to teak plantation: effect on overland flow and sediment yield in a montane tropical catchment. Scientific Reports, 7: 398710.1038/s41598-017-04385-2
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Scientific ReportsF2ZCSols_ZC ; CoMiCDCFE ; FESTSols_ZC
Kim, M.`, L. Boithias, K. H. Cho`, N. Silvera, C. Thammahacksa, K. Latsachack*, E. Rochelle-Newall*, O. Sengtaheuanghoung, A. Pierret*, Y. A. Pachepsky & O. Ribolzi, 2017. Hydrological modeling of Fecal Indicator Bacteria in a tropical mountain catchment. Water Research 119:102-113 10.1016/j.watres.2017.04.038
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Water ResearchCoMiCDCFE ; F2ZCSols_ZC
Le, T. P. Q., V. N. Dao°, E. Rochelle-Newall*, J. Garnier, X. Lu, G. Billen, T. T. Duong, C. T. Ho, H. Etcheber, T. M. H. Nguyen~, T. B. N. Nguyen, B. T. Nguyen, N. Da Le & Q. L. Pham, 2017. Total organic carbon fluxes of the Red River system (Vietnam). Earth Surface Processes and Landforms 42:1329-1341 10.1002/esp.4107Earth Surface Processes and LandformsCoMiCDCFE
Manivanh, L`., A. Pierret*, S. Rattanavong`, O. Kounnavongsa, Y`. Buisson, I. Elliott, J.-L. Maeght*, K. Xayyathip`, J. Silisouk`, M. Vongsouvath`, R. Phetsouvanh`, P. N. Newton, G. Lacombe, O. Ribolzi, E. Rochelle-Newall* & D. A. B. Dance, 2017. Burkholderia pseudomallei in a lowland rice paddy: seasonal changes and influence of soil depth and physico-chemical properties. Scientific Reports 7:3031 10.1038/s41598-017-02946-z
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Scientific ReportsCoMiCDCFE ; F2ZCSols_ZC
Lerch T.Z.*, Chenu C., Dignac M.-F.*, Barriuso E., Mariotti A. (2017) Biofilm vs planktonic lifestyle: consequences on pesticide 2,4-D biodegradation by Cupriavidus necator JMP134.  Frontiers in Microbiology 8 : 9010.3389/fmicb.2017.00904
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Frontiers in MicrobiologyBioDISDCFE ; CoMiCDCFE
MANIVANH, L.’, PIERRET A.*, RATTANAVONG, S.’, KOUNNAVONGSA, O.’, BUISSON, Y., ELLIOTT, I., MAEGHT, J.-L.*, XAYYATHIP, K., SILISOUK, J.’, VONGSOUVATH, M.’, PHETSOUVANH, R.’, NEWTON, P.N., LACOMBE, G., RIBOLZI, O., ROCHELLE-NEWALL*, E., DANCE, D.A.B. (2017) Burkholderia pseudomallei in a lowland rice paddy: seasonal changes and influence of soil depth and physico-chemical properties. Scientific Reports – Nature, 2017, 7, p. art. 3031 [11 p.].10.1038/s41598-017-02946-z​
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Scientific ReportsCoMiCDCFE
IMDIRAKPHOL S.’, ZAZZO A., AUETRAKULVIT P.’, TIAMTINKRIT C.’, PIERRET A.*, FORESTIER H., ZEITOUN V. (2017) The perforated stones of the Doi Pha Kan burials (Northern Thailand): A Mesolithic singularity? Comptes rendus Palevol (2017) Volume 16, Issue 3, April–May 2017, Pages 351-36110.1016/j.crpv.2016.12.003
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Comptes rendus PalevolCoMiCDCFE
KIM, J.H., FOURCAUD, T., JOURDAN, C., MAEGHT*, J.-L., MAO, Z., METAYER, J., MEYLAN, L., PIERRET A*., RAPIDEL, B., ROUPSARD, O., de ROUW, A.*, VILLATORO SANCHEZ, M., WANG, Y., STOKES, A. (2017) Vegetation drives slope stability and its variability through hydrological impacts. Geophys. Res. Lett., 44: 4897-4907. 10.1002/2017gl073174
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Geophysical Research LettersCoMiCDCFE ; F2ZCSols_ZC
Van Gijsegem F.*, Pédron J.*, Patrit O., Simond-Côte E., Maia-Grondard A., Pétriacq P., Gonzalez R., Blottière L.^, Kraepiel Y.* (2017) Manipulation of ABA content in Arabidopsis thaliana modifies sensitivity and oxidative stress response to Dickeya dadantii and influences peroxidase activity. Front. Plant Sci.: 8 : 45610.3389/fpls.2017.00456
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Frontiers in Plant ScienceEMSDCFE ; CoMiCDCFE
Pancrace P., Barny MA.*, Ueoka R., Calteau A., Scalvenzi T., Pédron J.*, Barbe V., Piel J., Humbert JF.*, Gugger M (2017) Insights into the Planktothrix genus: Genomic and metabolic comparison of benthic and planktic strains. Scientific reports.7, 4118110.1038/srep41181
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Scientific ReportsCoMiCDCFE
​Vojvoda, J., Lamy, D.*, Sintes, E., Garcia, J.A.L, Turk, V., Herndl, G.J. (2014) Seasonal variation in marine-snow-associated and ambient-water prokaryotic communities in the northern Adriatic Sea. Aquatic Microbial Ecology, 73:211-224.Aquatic Microbial EcologyCoMiCDCFE
​Swan, B.K., Martinez-Garcia, M., Preston, C.M., Sczyrba, A., Woyke, T., Lamy, D.*, Reinthaler, T., Poulton, N.J., Masland, E.D.P., Lluesma Gomez, M., Sieracki, M.E., DeLong, E.F., Herndl, G.J, Stepanauskas, R. (2011).Ubiquitous dark ocean bacteria fix carbon and contain RuBisCO and sulfur oxidation genes. Science, 333:1296-1300ScienceCoMiCDCFE

🔗 All publications of iEES Paris

Team members

Nom PrénomCorpsEmployeurDépartement et ÉquipeAdresseTéléphoneMél
BARNY Marie-AnneDRINRAEÉquipe CoMiC du Département DCFEJussieu
Tour 44-45 – 4 étage – bureau : 408
(+33) 01 44 27 32 94marie-anne.barny@upmc.fr
BEN MOUSSA HajarDoctoranteSorbonne UniversitéÉquipe CoMiC du Département DCFECampus Pierre et Marie Curie – Paris 5e
Tour 44-45 – 4e étage – bureau : 413
(+33) 01 44 27 23 49hajar.ben_moussa@etu.upmc.fr
DIGNAC Marie-FranceDRINRAEÉquipe CoMiC du Département DCFECampus Pierre et Marie Curie – Paris 5e
Tour 44-34 – 5e étage – bureau : 504
(+33) 01 44 27 51 71marie-france.dignac@inrae.fr
GASQUE Mégane
Doctorante
IRD
Équipe CoMiC du Département DCFE
Campus Pierre et Marie Curie – Paris 5e
Tour 44-45 – 4e étage – bureau : 0
(+33) 06 25 95 72 52
megane.gasque@ird.fr
HUMBERT Jean-FrancoisDRINRAEÉquipe CoMiC du Département DCFECampus Pierre et Marie Curie – Paris 5e
Tour 44-45 – 4e étage – bureau : 511
(+33) 01 44 27 41 67jean-francois.humbert@upmc.fr
LAMY Dominique
MC
Sorbonne Université
Équipe CoMiC du Département DCFE
Campus Pierre et Marie Curie – Paris 5e
Tour 44-45 – 4e étage – bureau : 408
(+33) 01 44 27 32 94
dominique.lamy@sorbonne-universite.fr
MITROI VeronicaCDD ChercheurSorbonne UniversitéÉquipe CoMiC du Département DCFECampus Pierre et Marie Curie – Paris 5e
Tour 44-45 – 4e étage – bureau : 410
(+33) 01 44 27 41 67veronica.mitroi@enpc.fr
PEDRON JacquesMCSorbonne UniversitéÉquipe CoMiC du Département DCFECampus Pierre et Marie Curie – Paris 5e
Tour 44-45 – 4e étage – bureau : 410
(+33) 01 44 27 41 67jacques.pedron@upmc.fr
PIERRET AlainCRIRDÉquipe CoMiC du Département DCFEDepartement of Agricultural Land Management (DALaM)
– – – étage – bureau : –
(+ 856) 20 52 97 60 04alain.pierret@ird.fr
ROCHELLE-NEWALL EmmaDRIRDÉquipe CoMiC du Département DCFE
Campus Pierre et Marie Curie – Paris 5e
Tour 44-45 – 4e étage – bureau : 404
(+33) 01 44 27 38 26
emma.rochelle-newall@ird.fr
TREVISAN DominiqueIRINRAEÉquipe CoMiC du Département DCFECampus Pierre et Marie Curie – Paris 5e
Tour 44-45 – 4e étage – bureau : 1
(+33) 01 44 27 32 11dominique.trevisan@inrae.fr

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