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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 d’UFR

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



  • Cantarel, A.A.M., Allard, V., Andrieu, B., Barot, S., Enjalbert, J., Gervaix, J., Goldringer, I., Pommier, T., Saint-Jean, S., Le Roux, X., 2020. Plant functional trait variability and trait syndromes among wheat varieties: the footprint of artificial selection. Journal of Experimental Botany.
    Résumé : Although widely used in ecology, trait-based approaches are seldom used to study agroecosystems. In particular, there is a need to evaluate how functional trait variability among varieties of a crop species compares to the variability among wild plant species and how variety selection can modify trait syndromes. Here, we quantified 18 above- and below-ground functional traits for 57 varieties of common wheat representative of different modern selection histories. We compared trait variability among varieties and among Pooideae species, and analyzed the effect of selection histories on trait values and trait syndromes. For traits under strong selection, trait variability among varieties was less than 10% of the variability observed among Pooideae species. However, for traits not directly selected, such as root N uptake capacity, the variability was up to 75% of the variability among Pooideae species. Ammonium absorption capacity by roots was counter-selected for conventional varieties compared with organic varieties and landraces. Artificial selection also altered some trait syndromes classically reported for Pooideae. Identifying traits that have high or low variability among varieties and characterizing the hidden effects of selection on trait values and syndromes will benefit the selection of varieties to be used especially for lower N input agroecosystems.
    Mots-clés : #5, #ame.

  • Cantarel, A.A.M., Rouifed, S., Simon, L., Bourg, J., Gervaix, J., Blazère, L., Poussineau, S., Creuzé des Châtelliers, C., Piola, F., 2020. In Nitrate-Rich Soil, Fallopia x bohemica Modifies Functioning of N Cycle Compared to Native Monocultures. Diversity 12, 156.
    Résumé : The effects of invasive species at the ecosystem level remain an important component required to assess their impacts. Here, we conducted an experimental study with labeled nitrogen in two types of soil (low and high nitrate conditions), investigating the effects of (1) the presence of Fallopia x bohemica on the traits of three native species (Humulus lupulus, Sambucus ebulus, and Urtica dioica) and (2) interspecific competition (monoculture of the invasive species, monoculture of the native species, and a mixture of invasive/native species) on nitrification, denitrification, and related microbial communities (i.e., functional gene abundances). We found that the species with the higher nitrate assimilation rate (U. dioica) was affected differently by the invasive species, with no effect or even an increase in aboveground biomass and number of leaves. F. x bohemica also decreased denitrification, but only in the soil with high nitrate concentrations. The impacts of the invasive species on nitrification and soil microorganisms depended on the native species and the soil type, suggesting that competition for nitrogen between plants and between plants and microorganisms is highly dependent on species traits and environmental conditions. This research highlights that studies looking at the impacts of invasive species on ecosystems should consider the plant–soil–microorganism complex as a whole.
    Mots-clés : #5, #AME, #PGE, abundances of functional genes, denitrification, invasive and native species, isotopes, labeled-N, nitrification, nitrogen (N) cycle, plant-soil competition for soil N.


  • Capdeville, C., Pommier, T., Gervaix, J., Fromard, F., Rols, J.-L., Leflaive, J., 2019. Mangrove Facies Drives Resistance and Resilience of Sediment Microbes Exposed to Anthropic Disturbance. Frontiers in Microbiology 9, 3337.
    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.

  • Florio, A., Bréfort, C., Gervaix, J., Bérard, A., Le Roux, X., 2019. The responses of NO2−- and N2O-reducing bacteria to maize inoculation by the PGPR Azospirillum lipoferum CRT1 depend on carbon availability and determine soil gross and net N2O production. Soil Biology and Biochemistry 136, 107524.
    Résumé : Seed inoculation by plant growth promoting rhizobacteria (PGPRs) is an agronomic practice that stimulates root carbon (C) exudation and nitrogen (N) uptake. Inoculation thus increases and decreases C and N availabilities to denitrifiers in the rhizosphere, respectively. Hence, denitrification rates in the rhizosphere can be positively or negatively influenced by root activity depending on the balance between these two processes. We assumed that inoculation effect on denitrifiers could strongly differ according to soil conditions. Would denitrifiers be mostly limited by C, inoculation would increase denitrifier abundance and activity through increased labile C availability. Would denitrifiers be limited by N rather than C, inoculation would decrease denitrifier abundance and activity through increased competition for N. Here we manipulated denitrification limitation by C and N (i) in a field trial through the use of different fertilization levels, and (ii) in a growth chamber experiment by mimicking root exudate inputs. We analyzed how the effects of maize inoculation by the PGPR Azospirillum lipoferum CRT1 on potential gross and net N2O production rates and NO2−- and N2O-reducer abundances were related to C and N limitation levels. An increase in potential gross (up to +113%) and to a lesser extent net (+37%) N2O production was observed for soils where denitrification was highly limited by C. This was explained by strong and moderate increases in the abundances of NO2−- and N2O-reducers, respectively. In contrast, when denitrification was weakly limited by C, gross and net N2O productions were negatively affected by inoculation (−15 and −40%, respectively). Our results show that the inoculation practice should be evaluated in term of possible increased crop yield but also possible modified N2O emission, paying much attention to cropland soils where denitrifiers are highly limited by C.
    Mots-clés : #5, #AME, Plant-microbes competition for nitrate, Root exudates.

  • Galland, W., Piola, F., Burlet, A., Mathieu, C., Nardy, M., Poussineau, S., Blazère, L., Gervaix, J., Puijalon, S., Simon, L., Haichar, F.Z., 2019. Biological denitrification inhibition (BDI) in the field: A strategy to improve plant nutrition and growth. Soil Biology and Biochemistry 136, 107513.
    Résumé : Nitrogen is one of the factors limiting in plant growth, is naturally present in soils, and is mainly assimilated as nitrate and ammonium by plants. However, soil nitrate is also used by denitrifying bacteria, which reduce it to N2O (a greenhouse gas) and N2. Therefore, plants are in direct competition with these bacteria for the assimilation of nitrate. Recently, our research team has highlighted a strategy developed by some plants consisting of the production of secondary metabolites (procyanidins) that inhibit the denitrification activity of microbial communities in soils, referred to as BDI for biological denitrification inhibition (BDI). This strategy could make nitrate more available in the soil, which may then be used by plants for their growth. However, the extent to which procyanidins can affect plant growth and nutrition via BDI under field conditions has not yet been investigated. In this study, we tested the effect of procyanidins exogenously applied in the field on the nutrition and growth of cos or romaine lettuce crops (Lactuca sativa) nutrition and growth. Procyanidins were added to growing lettuce at 8, 42, 83 and 210 kg ha−1. Soil denitrification enzyme activity (DEA), nitrate concentration, above- and below-ground lettuce traits and the abundance of total bacteria and denitrifiers were measured in lettuces treated or untreated with procyanidins. Our results showed that the addition of procyanidins in the field at 210 kg ha−1 resulted in: (1) the inhibition of microbial denitrification activity and counter-selection of denitrifiers in the root-adhering soil of lettuce and (2) an increase in available nitrate and a significant gain in plant productivity. This study allowed us to propose for the short term the development of a more environmentally friendly method of sustainable agriculture by limiting fertilizer inputs, nitrogen losses from the soil, and greenhouse gas emissions while increasing plant growth and productivity.
    Mots-clés : #4, #AME, Biological denitrification inhibition, Denitrifiers, Field experiment, Lettuce, Nitrate, Plant traits, Productivity, Rhizosphere.


  • 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.
    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., Koffi, K.F., Le Roux, X., Raynaud, X., Lata, J.-C., 2018. Contrasting effects of grasses and trees on microbial N-cycling in an African humid savanna. Soil Biology and Biochemistry 117, 153-163.
    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.
    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.
    Mots-clés : #5.

Chapitre d’ouvrages


Communications Orales


  • Cantarel, A.A.M., Andrieu, B., Allard, V., Enjalbert, J., Gervaix, J., Saint Jean, S., Pommier, T., Pope, C., Le Roux, X., 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., Pommier, T., Le Roux, X., 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., Benoit, P., Nazaret, S., 2016. Impact écotoxicologique d’un antibiotique sur les processus microbiens du cycle de l’azote, dans des sols amendés par des produits résiduaires organiques.
    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., Gervaix, J., Cournoyer, B., Winiarski, T., Rodriguez-Nava, V., 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.
    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.
    Mots-clés : #AME, #poster.