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Plateforme AME

Jonathan Gervaix



Activités principales

  • Mesures d’activités enzymatiques microbiennes sur souches/sols/sédiments
  • Compilation des résultats
  • Surveillance et maintenance des appareils
  • Gestion des stocks de consommables et commandes
  • Organisation du planning d’utilisation de la plateforme
  • Participation à des campagnes de prélèvement sur le terrain
  • Développement de protocoles

Activités secondaires

  • Membre du conseil de Laboratoire
  • Membre du conseil de Département de Biologie

Parcours scientifique

  • Technicien de recherche et d’enseignement, Laboratoire d’Ecologie Microbienne- Lyon depuis Octobre 2015
  • Assistant-Ingénieur en Ecologie Microbienne, Laboratoire d’Ecologie Microbienne- Lyon (Janvier-Octobre 2015)
  • Technicien de laboratoire, Institut des Sciences Analytiques/IRSTEA (Octobre 2013-Décembre 2014)
  • DUT Génie Biologique option Agronomie (Septembre 2013)


  • Préparation et encadrement technique de Travaux Pratiques en Master 1
  • Formation technique d’étudiants et de stagiaires aux techniques de mesures de la plateforme



  • Capdeville, C., Pommier, T., Gervaix, J., Fromards, F., Rols, J. - L., & Leflaive, J. (2018). Mangrove facies drives resistance and resilience of sediment microbes exposed to anthropic disturbance. Frontiers In Microbiology, 9. doi:10.3389/fmicb.2018.03337
    Résumé : Mangrove forests are coastal ecosystems continuously affected by various environmental stresses and organized along constraint gradients perpendicular to the coastline. The aim of this study was to evaluate the resistance and resilience of sediment microbial communities in contrasted vegetation facies, during and after exposure to an anthropic disturbance. Our hypothesis was that microbial communities should be the most stable in the facies where the consequences of the anthropic disturbance are the most similar to those of natural disturbances. To test this, we focused on communities involved in N-cycle. We used an in situ experimental system set up in Mayotte Island where 2 zones dominated by different mangrove trees are daily exposed since 2008 to pretreated domestic wastewater (PW) discharges. These freshwater and nutrients inputs should increase microbial activities and hence the anoxia of sediments. We monitored during 1 year the long-term impact of this disturbance, its short-term impact and the resilience of microbial communities on plots where PW discharges were interrupted. Microorganism densities were estimated by qPCR, the nitrification (NEA) and denitrification (DEA) enzyme activities were evaluated by potential activity measurements and pigment analyses were performed to assess the composition of microbial photosynthetic communities. At long-term PW discharges significantly modified the structure of phototrophic communities and increased the total density of bacteria, the density of denitrifying bacteria and DEA. Similar effects were observed at short-term, notably in the facies dominated by Ceriops tagals. The results showed a partial resilience of microbial communities. This resilience was faster in the facies dominated by Rhizophora mucronata, which is more subjected to tides and sediment anoxia. The higher stability of microbial communities in this facies confirms our hypothesis. Such information should be taken into account in mangrove utilization and conservation policies.
    Mots-clés : #5, #AME, Anthropic disturbance, Mangrove ecosystem, microbial communities, N-cycle, Wastewater discharge.

  • Simonin, M., Cantarel, A. A. M., Crouzet, A., Gervaix, J., Martins, J. M. F., & 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. doi:10.3389/fmicb.2018.03102
    Résumé : 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 soil microbial activities involved in the carbon and nitrogen cycles in five contrasting agricultural soils in a microcosm experiment over 90 days. Additionally, in a pot experiment, we evaluated the influence of plant presence on the toxicity of CuO-NPs on soil microbial activities. CuO-NPs caused significant reductions of the three microbial activities measured (denitrification, nitrification, and soil respiration) at 100 mg/kg dry soil, but the low concentrations (0.1 and 1 mg/kg) had limited effects. We observed that denitrification was the most sensitive microbial activity to CuO-NPs in most soil types, while soil respiration and nitrification were mainly impacted in coarse soils with low organic matter content. Additionally, large decreases in heterotrophic microbial activities were observed in soils planted with wheat, even at 1 mg/kg for soil substrate-induced respiration, indicating that plant presence did not mitigate or compensate CuO-NP toxicity for microorganisms. These two experiments show that CuO-NPs can have detrimental effects on microbial activities in soils with contrasting physicochemical properties and previously exposed to various agricultural practices. Moreover, we observed that the negative effects of CuO-NPs increased over time, indicating that short-term studies (hours, days) may underestimate the risks posed by these contaminants in soils.
    Mots-clés : #5, Agro-ecosystem, Denitrification, Metal-oxide nanomaterials, microbial ecotoxicology, Nitrification, plant-microorganism interactions, Soil respiration, wheat.

  • Srikanthasamy, T., Leloup, J., N'Dri, A. B., Barot, S., Gervaix, J., Koné, A. W., et al. (2018). Contrasting effects of grasses and trees on microbial N-cycling in an African humid savanna. Soil Biology And Biochemistry, 117, 153-163. doi:10.1016/j.soilbio.2017.11.016
    Résumé : African humid savannas are highly productive ecosystems, despite very low soil fertility, where grasses and trees coexist. Earlier results showed that some perennial grass species are capable of biological nitrification inhibition (BNI) while trees likely influence differently on nitrogen cycling. Here we assessed the impact of the dominant grass and tree species of the Lamto savanna (Ivory Coast) on soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively) and on the abundances of archaeal and bacterial ammonia oxidizers (AOA and AOB, respectively) and nitrite reducers. This is one of the first studies linking nitrifying and denitrifying activities and the abundances of the involved groups of microorganisms in savanna soils. NEA was 72-times lower under grasses than under trees while AOA and AOB abundances were 34- and 3-times lower. This strongly suggests that all dominant grasses inhibit nitrification while trees stimulate nitrification, and that archaea are probably more involved in nitrification than bacteria in this savanna. While nitrite reducer abundances were similar between locations and dominated by nirS genes, DEA was 9-times lower under grasses than trees, which is likely explained by BNI decreasing nitrate availability under grasses. The nirS dominance could be due to the ferruginous characteristics of these soils as nirS and nirK genes require different metallic co-enzymes (Fe or Cu). Our results show that the coexistence of grasses and trees in this savanna creates a strong heterogeneity in soil nitrogen cycling that must be considered to understand savanna dynamics and functioning. These results will have to be taken into account to predict the feedbacks between climate changes, nitrogen cycling and tree/grass dynamics at a time when savannas face worldwide threats.
    Mots-clés : #5, #AME, Biological nitrification inhibition (BNI), Denitrification, Nitrification, Perennial grasses, Trees, Tropical savanna.


  • Assémien, F. L., Pommier, T., Gonnety, J. T., Gervaix, J., & Le Roux, X. (2017). Adaptation of soil nitrifiers to very low nitrogen level jeopardizes the efficiency of chemical fertilization in west african moist savannas. Scientific Reports, 7(1). doi:10.1038/s41598-017-10185-5
    Mots-clés : #5.

  • Florio, A., Pommier, T., Gervaix, J., Bérard, A., & Le Roux, X. (2017). Soil C and N statuses determine the effect of maize inoculation by plant growth-promoting rhizobacteria on nitrifying and denitrifying communities. Scientific Reports, 7(1). doi:10.1038/s41598-017-08589-4
    Mots-clés : #5.

Chapitre d’ouvrages


Communications Orales


  • Cantarel, A. A. M., Andrieu, B., Allard, V., Enjalbert, J., Gervaix, J., Saint Jean, S., et al. (2016). Effects of agricultural wheat selection on plant trait variability and trait syndromes. Dans .
    Mots-clés : #5, #AME, #colloque.
  • Florio, A., Pommier, T., Gervaix, J., & Le Roux, X. (2016). Can we manage plant-microbes interactions belowground to increase the sustainability of cropping systems? The case of maize seed inoculation with the beneficial Azospirillum lipoferum CRT1 and its effects on the N-cycling rhizospheric microbial communities. Dans . Présenté à EcoSummit 2016 Ecological Sustainability.
    Mots-clés : #5, #AME, #colloque.
  • Hugoni, M., Cantarel, A. A. M., Allard, V., Enjalbert, J., Gervaix, J., Saint Jean, S., et al. (2016). Increasing wheat variety diversity within cropped fields can channel soil N dynamics in a favourable status for the sustainability of cropping systems. Dans .
    Mots-clés : #5, #AME, #colloque.



  • Crouzet, O., GOULAS, A., Richaume, A., Marrauld, C., Gervaix, J., Haudin, C. S., et al. (2016). Impact écotoxicologique d’un antibiotique sur les processus microbiens du cycle de l’azote, dans des sols amendés par des produits résiduaires organiques. Présenté à Congrès exotoxicomic, rovaltin.
    Mots-clés : #AME, #poster.
  • Lecomte, S., Haichar, F. Z., Guyonnet, J. P., Diel, B., Gervaix, J., & Hommais, F. (2016). Denitrification And Its Regulation In Agrobacterium fabrum C58.
    Mots-clés : #AME, #poster.
  • Vautrin, F., Le Floch, A., Gutbraut, E., Bergeron, E., Marjolet, L., Gleizal, A., et al. (2016). Nocardia, un pathogène au fil de l’eau.
    Mots-clés : #6, #AME, #poster.


  • Gervaix, J., Poly, F., Breil, P., & Namour, P. (2015). Measuring of the bacterial gaseous emission in river sediment. Présenté à Ecohydrologie 21-23/09/2015, Lyon, France.
    Mots-clés : #AME, #poster.
  • Jobin, L., Pommier, T., Jose, C., Pages, C., Gervaix, J., Raffin, G., & Namour, P. (2015). Influence of external resistor on denitrifying activity of a pure strain of Pseudomonas stutzeri in Microbial Fuel Cell. Présenté à Conférence international e“Ecohydrology, Lyon, France.
    Mots-clés : #AME, #poster.