Cécile Thion Environmental Microbial Genomics Group

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Laboratoire Ampere
Ecole Centrale de Lyon, Université de Lyon. France
(33) 472 18 61 18

Education | Research Interests | Publications | Curriculum Vitae | More...

  Cécile Thion

Environmental Microbial Genomics
Laboratoire Ampère, UMR CNRS 5005
Ecole Centrale de Lyon
36 avenue Guy de Collongue
69134 Ecully cedex

  Phone: (33) 4 72 18 62 37
Fax: (33) 4 78 43 37 17




  • 2012 Ph.D. in Geosciences, Université de Lorraine, Nancy, France
  • Masters Microbial Ecology, Université Claude Bernard Lyon1, Université de Lyon, France (valedictorian)
  • Bachelors Science and Technology, Université Claude Bernard Lyon1, Université de Lyon, France


As a microbial functional ecologist, I am interested in links between prokaryotic diversity - or community structure - and ecosystem functioning, in diverse systems, from glacier forefields to managed agricultural soils. 
Nitrogen cycle scene has just been shaken up by the entrance of ‘comammox’, Nitrospira bacteria able to perform complete nitrification (Daims et al. 2015, Nature 528). This was previously thought to involve the oxidation of ammonia into nitrite by ammonia oxidisers (AO), further oxidised into nitrate by nitrite oxidising bacteria (NOB), which also include members of the Nitrospira genus. A decade before, AO were supposed to be bacteria (AOB) only, when archaeal AO (AOA) were found; significant contribution of AOA, initially considered as accessory, to nitrification was since then repetitively shown. Now, exploring the ecology of comammox and their interaction with ammonia oxidisers in soils, where nitrification affects fertilisation yield, nitrate leaching and nitrous oxide emissions, is crucial for agricultural and environmental fields. My main project in Ampère aims at examining comammox relative contribution to nitrification in soils, as well as the environmental factors that modulate it. 
For my research, I use a variety of techniques including microcosm incubations, real-time PCR, fingerprinting, Illumina sequencing or DNA-SIP.


  • Ramirez K, Knight C […] Thion C, van der Heijden M & de Vries F. Detecting macroecological patterns in bacterial communities across independent studies of global soils. Nature Microbiology, doi:10.1038/s41564-017-0062-x
  • Catão E, Thion C, Krüger R & Prosser JI (2017). Ammonia oxidizers in a non-nitrifying Brazilian savanna soil. FEMS Microbiology Ecology, 93(11).
  • 1.     Lehtovirta-Morley L, Ross J, Hink L, Weber E, Gubry-Rangin C, Thion C, Prosser JI and Nicol G (2016). Isolation of ‘Candidatus Nitrosocosmicus franklandus’, a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration. FEMS Microbiology Ecology, 92(5), fiw057.
  • 2.     Thion C, Poirel J, Cornulier T, DeVries F, Bardgett R & Prosser JI (2016). Plant N-use strategy as a driver of rhizosphere archaeal and bacterial ammonia oxidiser abundance. FEMS Microbiology Ecology, 92, fiw091. (Editor’s choice).
  • 3.     De Boer W, Hundscheid M, Klein Gunnewiek P, de Ridder-Duine A, Thion C, van Veen J, van der Wal A (2015). Antifungal Rhizosphere Bacteria Can increase as Response to the Presence of Saprotrophic Fungi. PLoS ONE 10(9): e0137988. doi:10.1371/journal. pone.0137988
  • 4.     Thion C & Posser JI. (2014). Differential response of non-adapted ammonia oxidising archaea and bacteria to drying rewetting stress. FEMS Microbiology Ecology 90(2):380-9.
  • 5.     Thion C, Cébron A, Beguiristain T and Leyval C. (2013) Inoculation of PAH-degrading strains of Fusarium solani and Arthrobacter oxydans in rhizospheric sand and soil microcosms: persistence, microbial interactions and PAH dissipation. Biodegradation, 24(4):569-581
  • 6.     Thion C, Cébron A, Beguiristain T and Leyval C. (2012) Long-term in situ dynamics of the fungal communities in a heavy-metal and PAH polluted soil are mainly driven by plants. FEMS Microbiology Ecology. 82(1):169-181
  • 7.     Thion C, Cébron A, Beguiristain T and Leyval C. (2012) PAH biotransformation and sorption by Fusarium solani and Arthrobacter oxydans in axenic cultures or mixed cocultures. International Biodeterioration & Biodegradation, 68(1): 28-35
  • 8.     Cébron A, Cortet J, Criquet S, Biaz A, Calvert V, Caupert C[1], Pernin P and Leyval C. (2011) Biological functioning of PAH-polluted and thermal desorption-treated soils assessed by fauna and microbial bioindicators. Research in Microbiology, 162(9):896-907
  • 9.     Thuillier A, Ngadin A, Thion C, Billard P, Jacquot JP, Gelhaye E and Morel M. (2011) Functional diversification of fungal glutathione transferases from the Ure2p class. International Journal of Evolutionary Biology, doi:10.4061/2011/938308
  • 10.  Ouvrard S, Barnier C, Bauda P, Beguiristain T, Biache C, Bonnard M, Caupert C, Cébron A, Cortet J, Cotelle S, Dazy M, Faure F, Masfaraud JF, Nahmani J, Palais F, Poupin P, Raoult N, Vasseur P, Morel JL and Leyval C. (2011) In situ assessment of phytotechnologies for multicontaminated soil management. International Journal of Phytoremediation, 13(S1):245–263
  • [1] Caupert was husband's name

top CURRICULUM VITAE (CV available here in French)

2016- present Post-doc Environmental Microbial Genomics, Laboratoire Ampere, Ecole Centrale de Lyon, Université de Lyon, Ecully, France

2013-2015 Post-doc, University of Aberdeen, Aberdeen, Scotland

2008-2012 Docotrante Geosciences, Université de Lorraine, Nancy, France

2008 Masters Internship Environmental Microbial Genomics, Laboratoire Ampere, Ecole Centrale de Lyon, Université de Lyon, Ecully, France

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