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Equipe de Recherche Groupes fonctionnels du cycle de l’azote

Thomas Pommier


  • Thèmes de recherches :
    1. Relations Diversité - Fonctionnement des écosystèmes
    2. Biogéographie des micro-organismes et de leur diversité

Parcours scientifique

  • depuis novembre 2009 : CR - INRA
  • 01/2008-11/2009 Stage postdoctoral CNRS avec T. Bouvier, UMR 5119 ECOLAG, Montpellier.
  • 09/2006-12/2007 Stage postdoctoral (Réseau d’Excellence "Marine Genomics Europe") avec C. Pedrós-Alió - Instituto de Ciencias del Mar, Barcelone (Espagne).
  • 01/2006-08/2006 Assistant de recherche avec Â. Hagström, HIK, Kalmar (Suède)





  • Alonso, L., Creuzé-des-Châtelliers, C., Trabac, T., Dubost, A., Moënne-Loccoz, Y., & Pommier, T. (2018). Rock substrate rather than black stain alterations drives microbial community structure in the passage of Lascaux Cave. Microbiome, 6(1), 216. doi:10.1186/s40168-018-0599-9
    Résumé : The World-famous UNESCO heritage from the Paleolithic human society, Lascaux Cave (France), has endeavored intense microclimatic perturbations, in part due to high touristic pressure. These perturbations have resulted in numerous disturbances of the cave ecosystem, including on its microbial compartment, which resulted in the formation of black stains especially on the rock faces of the passage. We investigated the cave microbiome in this part of Lascaux by sampling three mineral substrates (soil, banks, and inclined planes) on and outside stains to assess current cave microbial assemblage and explore the possibility that pigmented microorganisms involved in stain development occur as microbial consortia.
    Mots-clés : #3, #5, #ibio.

  • 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.

  • Le, H. T., Rochelle-Newall, E., Auda, Y., Ribolzi, O., Sengtaheuanghoung, O., Thébault, E., et al. (2018). Vicinal land use change strongly drives stream bacterial community in a tropical montane catchment. Fems Microbiology Ecology, 94(11). doi:10.1093/femsec/fiy155
    Mots-clés : #5.

  • Pommier, T., Cantarel, A. A. M., Grigulis, K., Lavorel, S., Legay, N., Baxendale, C., et al. (2018). The added value of including key microbial traits to determine nitrogen-related ecosystem services in managed grasslands. (M. Isaac, Éd.)Journal Of Applied Ecology, 55(1), 49-58. doi:10.1111/1365-2664.13010
    Résumé : * Despite playing central roles in nutrient cycles and plant growth, soil microbes are generally neglected in the study of ecosystem services (ES), due to difficulties to assess their diversity and functioning. However, to overcome these hurdles, new conceptual approaches and modern tools now provide a means to assess the role of micro-organisms in the evaluation of ES. * In managed grasslands, soil microbes are central in providing nitrogen (N)-related ES such as maintenance of soil fertility and retention of mineral forms of N. Here, we applied state-of-the-art techniques in microbial ecology and plant functional ecology to uncover the intrinsic link between N-related bacterial functional groups, important plant functional traits, environmental factors and three proxies of maintenance of soil fertility and potential for N-leaching across managed grasslands in three regions of Europe. * By constructing well-defined structural equation modelling, we showed that including key microbial traits improve on average more than >50% of the total variances of ES proxies, that is, ammonium (NH4+) or nitrate (NO3−) leaching, and soil organic matter content. Geographic differences arose when considering the direct relationships of these ES proxies with specific microbial traits: nitrate leaching was positively correlated to the maximum rate of nitrification, except in the Austrian site and potentially leached NH4+–N was negatively correlated to the fungi/bacteria ratio, with the exception of the French site. * Synthesis and applications. The integration of soil microbial functional traits in the assessment of nitrogen-related grassland ecosystem services has direct contributions for understanding sustainable management of grassland ecosystems. The fundamental aspects of this study suggest that integrating a soil microbial component in grassland management may enhance sustainability of such grass-based agroecosystems.
    Mots-clés : #5, above- and below-ground interactions, agroecology, ecosystem services, functional traits, grass-based agroecosystems, N-cycle, nitrogen retention, soil fertility, subalpine grassland.


  • 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.

  • Legay, N., Piton, G., Arnoldi, C., Bernard, L., Binet, M. - N., Mouhamadou, B., et al. (2017). Soil legacy effects of climatic stress, management and plant functional composition on microbial communities influence the response of Lolium perenne to a new drought event. Plant And Soil, 1-22. doi:10.1007/s11104-017-3403-x
    Résumé : Background and aimsDrought events, agricultural practices and plant communities influence microbial and soil abiotic parameters which can feedback to fodder production. This study aimed to determine which soil legacies influence plant biomass production and nutritional quality, and its resistance and recovery to extreme weather events.MethodsIn a greenhouse experiment, soil legacy effects on Lolium perenne were examined, first under optimal conditions, and subsequently during and after drought. We used subalpine grassland soils previously cultivated for two years with grass communities of distinct functional composition, and subjected to combinations of climatic stress and simulated management.ResultsThe soil legacy of climatic stress increased biomass production of Lolium perenne and its resistance and recovery to a new drought. This beneficial effect resulted from higher nutrient availability in soils previously exposed to climatic stresses due to lower competitive abilities and resistance of microbial communities to a new drought. This negative effect on microbial communities was strongest in soils from previously cut and fertilized grasslands or dominated by conservative grasses.ConclusionIn subalpine grasslands more frequent climatic stresses could benefit fodder production in the short term, but threaten ecosystem functioning and the maintenance of traditional agricultural practices in the long term.
    Mots-clés : #5.

  • Schwob, G., Roy, M., Manzi, S., Pommier, T., & Fernandez, Mp. (2017). Green alder (Alnus viridis) encroachment shapes microbial communities in subalpine soils and impacts its bacterial or fungal symbionts differently. Environmental Microbiology, n/a-n/a. doi:10.1111/1462-2920.13818
    Résumé : Since the mid twentieth-century, subalpine grasslands undergo a progressive encroachment by Alnus viridis shrubs. Thanks to its rapid vegetative reproduction, its nitrogen fixing symbiosis with Frankia and its ectomycorrhizal cohorts, green alders are vigorous colonizers that quickly form mosaic of alder patches that evolves into a close canopy shrub community. To better understand how alder encroachment might influence microbial communities in this successional sequence, symbiont distribution, microbial richness and community structure in both soils and nodules were analyzed at three successional stages: grassland, mosaic and forest. Soil analyses were performed in association with measures of nitrification and denitrification, as well as DNA metabarcoding of three bacterial genes (16S rDNA, nifH and amoA) and one fungal gene (ITS1). Our results show that (i) Alnus viridis encroachment is associated with soil microbial community changes that are in turn, linked to certain soil properties (i.e. pH, C/N ratio and organic matter content), (ii) both taxonomic and N related functional gene structures of bacteria are modified by alder encroachment, and (iii) the distribution in soils of its bacterial symbionts (Frankia) is apparently weakly influenced by alder establishment while Alnus-specific ectomyccorrhizae increase with the increase in alder shrub density. This article is protected by copyright. All rights reserved.
    Mots-clés : #1, #5, Bacteria, Environmental genomics, functional diversity, fungi, microbial ecology, Symbionts.


  • Le, H. T., Ho Tu, C., Trinh, Q. H., Trinh, D. A., Luu, M. T. N., Tran, H. S., et al. (2016). Responses of aquatic bacteria to terrestrial runoff: effects on community structure and key taxonomic groups. Aquatic Microbiology, 7, 889. doi:10.3389/fmicb.2016.00889
    Résumé : Organic fertilizer application is often touted as an economical and effective method to increase soil fertility. However, this amendment may increase dissolved organic carbon (DOC) runoff into downstream aquatic ecosystems and may consequently alter aquatic microbial community. We focused on understanding the effects of DOC runoff from soils amended with compost, vermicompost or biochar on the aquatic microbial community of a tropical reservoir. Runoff collected from a series of rainfall simulations on soils amended with different organic fertilizers was incubated for 16 days in a series of 200 liters mesocosms filled with water from a downstream reservoir. We applied 454 high throughput pyrosequencing for bacterial 16S rRNA genes to analyze microbial communities. After 16 days of incubation, the richness and evenness of the microbial communities present decreased in the mesocosms amended with any organic fertilizers, except for the evenness in the mesocosms amended with compost runoff. In contrast, they increased in the reservoir water control and soil-only amended mesocosms. Community structure was mainly affected by pH and DOC concentration. Compared to the autochthonous organic carbon produced during primary production, the addition of allochthonous DOC from these organic amendments seemed to exert a stronger effect on the communities over the period of incubation. While the Proteobacteria and Actinobacteria classes were positively associated with higher DOC concentration, the number of sequences representing key bacterial groups differed between mesocosms particularly between the biochar runoff addition and the compost or vermi-compost runoff additions. The genera of Propionibacterium spp. and Methylobacterium spp. were highly abundant in the compost runoff additions suggesting that they may represent sentinel species of complex organic carbon inputs. Overall, this work further underlines the importance of studying the off-site impacts of organic fertilizers as their impact on downstream aquatic systems is not negligible.
    Mots-clés : #5, Aquatic microbial community, biochar, Compost, DOC, mesocosm experiments.

  • Legay, N., Lavorel, S., Baxendale, C., Krainer, U., Bahn, M., Binet, M. - N., et al. (2016). Influence of plant traits, soil microbial properties, and abiotic parameters on nitrogen turnover of grassland ecosystems. Ecosphere, 7(11), n/a-n/a. doi:10.1002/ecs2.1448
    Résumé : Although it is known that multiple interactions among plant functional traits, microbial properties, and abiotic soil parameters influence the nutrient turnover, the relative contribution of each of these groups of variables is poorly understood. We manipulated grassland plant functional composition and soil nitrogen (N) availability in a multisite mesocosm experiment to quantify their relative effects on soil N turnover. Overall, root traits, arbuscular mycorrhizal colonization, denitrification potential, as well as N availability and water availability, best explained the variation in measured ecosystem properties, especially the trade-off between nutrient sequestration and plant biomass production. Their relative contributions varied with soil N availability. In relatively N-poor soils (10–20 μg·N·g−1 soil), N turnover was mainly controlled by microbial properties and abiotic soil parameters, whereas in the relatively N-rich soils (110–120 μg·N·g−1 soil), N turnover was mainly controlled by plant traits and microbial properties. This experiment is a strong demonstration of the importance of functional characteristics of both plants and soil microbes, and their interplay with soil N availability, for N turnover in grassland soils.
    Mots-clés : #5, ammonia-oxidizing archaea and bacteria, arbuscular mycorrhizal colonization, ecosystem properties, Grasslands, leaf traits, nitrite oxidizers, nitrite reducers, nutrient availability, root traits, water availability.

  • Simonin, M., Richaume, A., Guyonnet, J. P., Dubost, A., Martins, J. M. F., & Pommier, T. (2016). Titanium dioxide nanoparticles strongly impact soil microbial function by affecting archaeal nitrifiers. Scientific Reports, 6, 33643. doi:10.1038/srep33643
    Mots-clés : #5, #ibio.


  • Cabrol, L., Poly, F., Malhautier, L. C., Pommier, T., Lerondelle, C., Verstraete, W., et al. (2015). Management of microbial communities through transient disturbances enhances the functional resilience of nitrifying gas-biofilters to future disturbances. Environmental Science & Technology. doi:10.1021/acs.est.5b02740
    Mots-clés : #5.

  • Cantarel, A. A. M., Pommier, T., Desclos-Theveniau, M., Diquélou, S., Dumont, M., Grassein, F., et al. (2015). Using plant traits to explain plant-microbe relationships involved in nitrogen acquisition. Ecology, 96(3), 788-799. doi:10.1890/13-2107.1
    Résumé : It has long been recognized that plant species and soil microorganisms are tightly linked, but understanding how different species vary in their effects on soil is currently limited. In this study, we identified those plant characteristics (identity, specific functional traits or resource acquisition strategy) that were the best predictors of nitrification and denitrification processes. Ten plant populations representing eight species collected from three European grassland sites were chosen for their contrasting plant trait values and resource acquisition strategies. For each individual plant, leaf and root traits and the associated potential microbial activities (i.e. denitrification rate (DEA), maximal nitrification rate (NEA) and NH4+/NH3 affinity of microbial community (NHScom)) were measured at two fertilization levels under controlled growth conditions. Plant traits were powerful predictors of plant-microbe interactions, but relevant plant traits differed in relation to the microbial function studied. Whereas denitrification was linked to the relative growth rate of plants, nitrification was strongly correlated to root trait characteristics (comprising: specific root length, root nitrogen concentration and plant affinity for NH4+) linked to plant N cycling. The "leaf economics spectrum" (LES) that commonly serves as an indicator of resources acquisition strategies was not correlated to microbial activity. These results suggest that the LES alone is not a good predictor of microbial activity, whereas root traits appeared critical in understanding plant-microbe interactions.
    Mots-clés : #5, Denitrification, leaf economics spectrum, Nitrification, plant strategy for N resource acquisition, plant traits, rhizosphere.

  • Legay, N., Grassein, F., Binet, M. N., Arnoldi, C., Personeni, E., Perigon, S., et al. (2015). Plant species identities and fertilization influence on arbuscular mycorrhizal fungal colonisation and soil bacterial activities. Applied Soil Ecology. doi:10.1016/j.apsoil.2015.10.006
    Mots-clés : #5.

  • Trinh, D. A., Luu, T. N. M., Trinh, Q. H., Tran, H. S., Tran, T. M., Le, T. P. Q., et al. (2015). Impact of terrestrial runoff on organic matter, trophic state, and phytoplankton in a tropical, upland reservoir. Aquatic Sciences, 1-13. doi:10.1007/s00027-015-0439-y
    Résumé : The impact of organic matter inputs from agricultural, forest and domestic sources on aquatic processes has been considerably less studied in tropical reservoirs relative to temperate systems despite the high number of these small aquatic systems in the tropics. Here we present the results of an in situ mesocosm study that examined the impact of allochthonous organic matter on a headwater reservoir in Northern Vietnam. We examined the impact of wastewater and soils from floodplain paddies, Acacia mangium plantations and from upland slopes on the metabolic status of the reservoir. The addition of floodplain paddy soils to the reservoir water led to a rapid switch in metabolic status from net autotrophic to net heterotrophic. In contrast, the addition of wastewater in low concentrations had less impact on the metabolic status of the reservoir, reflecting the low population density in the area. The addition of floodplain paddy soils also increased phytoplankton diversity and evenness relative to the control. In summary, soils from floodplain paddies and from A. mangium plantations had the highest impact on the reservoir, with upland soils and wastewater having less of an impact. We also found that primary production in this reservoir was nitrogen limited. In order to avoid accelerating the impact of runoff on the reservoir, future management options should perhaps focus on minimizing water and sediment runoff from upstream paddy fields and from A. mangium plantations. These results also underline the importance of studying these upland tropical water bodies that can contribute an important but, on the whole, ignored part of the global carbon balance.
    Mots-clés : #5, Aquatic mesocosm, ecology, Freshwater & Marine Ecology, Incubation, Life Sciences, general, Limiting factor, Marine & Freshwater Sciences, Oceanography, Vietnam.


  • Bardon, C., Piola, F., Bellvert, F., Haichar, F. Z., Comte, G., Meiffren, G., et al. (2014). Evidence for biological denitrification inhibition (BDI) by plant secondary metabolites. New Phytologist, 204(3), 620-630. doi:10.1111/nph.12944
    Résumé : * Previous studies on the effect of secondary metabolites on the functioning of rhizosphere microbial communities have often focused on aspects of the nitrogen (N) cycle but have overlooked biological denitrification inhibition (BDI), which can affect plant N-nutrition. Here, we investigated the BDI by the compounds of Fallopia spp., an invasive weed shown to be associated with a low potential denitrification of the soil. * Fallopia spp. extracts were characterized by chromatographic analysis and were used to test the BDI effects on the metabolic and respiratory activities of denitrifying bacteria, under aerobic and anaerobic (denitrification) conditions. The BDI of Fallopia spp. extracts was tested on a complex soil community by measuring denitrification enzyme activity (DEA), substrate induced respiration (SIR), as well as abundances of denitrifiers and total bacteria. * In 15 strains of denitrifying bacteria, extracts led to a greater BDI (92%) than respiration inhibition (50%). Anaerobic metabolic activity reduction was correlated with catechin concentrations and the BDI was dose dependent. In soil, extracts reduced the DEA/SIR ratio without affecting the denitrifiers: total bacteria ratio. * We show that secondary metabolite(s) from Fallopia spp. inhibit denitrification. This provides new insight into plant–soil interactions and improves our understanding of a plant's ability to shape microbial soil functioning.
    Mots-clés : #3, #5, #cesn, biological inhibition, catechin derivates, Denitrification, Fallopia spp., nitrogen cycle, rhizosphere, secondary metabolites, weeds.

  • Baxendale, C., Orwin, K. H., Poly, F., Pommier, T., & Bardgett, R. D. (2014). Are plant–soil feedback responses explained by plant traits? New Phytologist, n/a-n/a. doi:10.1111/nph.12915
    Résumé : * Plant–soil feedbacks can influence plant growth and community structure by modifying soil biota and nutrients. Because most research has been performed at the species level and in monoculture, our ability to predict responses across species and in mixed communities is limited. As plant traits have been linked to both soil properties and plant growth, they may provide a useful approach for an understanding of feedbacks at a generic level. * We measured how monocultures and mixtures of grassland plant species with differing traits responded to soil that had been conditioned by model grassland plant communities dominated by either slow- or fast-growing species. * Soils conditioned by the fast-growing community had higher nitrogen availability than those conditioned by the slow-growing community; these changes influenced future plant growth. Effects were stronger, and plant traits had greater predictive power, in mixtures than in monocultures. In monoculture, all species produced more above-ground biomass in soil conditioned by the fast-growing community. In mixtures, slow-growing species produced more above-ground biomass, and fast-growing species produced more below-ground biomass, in soils conditioned by species with similar traits. * The use of a plant trait-based approach may therefore improve our understanding of differential plant species responses to plant–soil feedbacks, especially in a mixed-species environment.
    Mots-clés : #5, competition, competitive ability, plant traits, plant–soil feedback responses, soil conditioning.

  • Legay, N., Baxendale, C., Grigulis, K., Krainer, U., Kastl, E., Schloter, M., et al. (2014). Contribution of above- and below-ground plant traits to the structure and function of grassland soil microbial communities. Annals Of Botany, mcu169. doi:10.1093/aob/mcu169
    Résumé : Background and Aims Abiotic properties of soil are known to be major drivers of the microbial community within it. Our understanding of how soil microbial properties are related to the functional structure and diversity of plant communities, however, is limited and largely restricted to above-ground plant traits, with the role of below-ground traits being poorly understood. This study investigated the relative contributions of soil abiotic properties and plant traits, both above-ground and below-ground, to variations in microbial processes involved in grassland nitrogen turnover. Methods In mountain grasslands distributed across three European sites, a correlative approach was used to examine the role of a large range of plant functional traits and soil abiotic factors on microbial variables, including gene abundance of nitrifiers and denitrifiers and their potential activities. Key Results Direct effects of soil abiotic parameters were found to have the most significant influence on the microbial groups investigated. Indirect pathways via plant functional traits contributed substantially to explaining the relative abundance of fungi and bacteria and gene abundances of the investigated microbial communities, while they explained little of the variance in microbial activities. Gene abundances of nitrifiers and denitrifiers were most strongly related to below-ground plant traits, suggesting that they were the most relevant traits for explaining variation in community structure and abundances of soil microbes involved in nitrification and denitrification. Conclusions The results suggest that consideration of plant traits, and especially below-ground traits, increases our ability to describe variation in the abundances and the functional characteristics of microbial communities in grassland soils.
    Mots-clés : #5, Ammonia-oxidizing archaea, Bacteria, denitrifiers, leaf traits, nitrite oxidizers, nitrite reducers, nutrient availability, Plant functional traits, root traits, soil microbial community.

  • Pommier, T., Merroune, A., Bettarel, Y., Got, P., Janeau, J. - L., Jouquet, P., et al. (2014). Off-site impacts of agricultural composting: role of terrestrially derived organic matter in structuring aquatic microbial communities and their metabolic potential. Fems Microbiology Ecology, n/a-n/a. doi:10.1111/1574-6941.12421
    Résumé : While considered as sustainable and low-cost agricultural amendments, the impacts of organic fertilizers on downstream aquatic microbial communities remain poorly documented. We investigated the quantity and quality of the dissolved organic matter leaching from agricultural soil amended with compost, vermicompost or biochar and assessed their effects on lake microbial communities, in terms of viral and bacterial abundances, community structure and metabolic potential. The addition of compost and vermicompost significantly increased the amount of dissolved organic carbon in the leachate compared to soil alone. Leachates from these additions, either with or without biochar were highly bioavailable to aquatic microbial communities, though reducing the metabolic potential of the community and harboring more specific communities. Although not affecting bacterial richness or taxonomic distributions, the specific addition of biochar affected the original lake bacterial communities resulting in a strongly different community. This could be partly explained by viral burst and converging bacterial abundances throughout the samples. These results underline the necessity to include off-site impacts of agricultural amendments when considering their cascading effect on downstream aquatic ecosystems. This article is protected by copyright. All rights reserved.
    Mots-clés : #5, Lakes, Metabolic potential, Off-site effects, Soil leachates.


  • Crespo, B. G., Pommier, T., Fernández-Gómez, B., & Pedrós-Alió, C. (2013). Taxonomic composition of the particle-attached and free-living bacterial assemblages in the Northwest Mediterranean Sea analyzed by pyrosequencing of the 16S rRNA. Microbiologyopen, 2(4), 541-552. doi:10.1002/mbo3.92
    Résumé : Free-living (FL) and particle-attached (PA) bacterial assemblages in the Northwest Mediterranean Sea were studied using pyrosequencing data of the 16S rRNA. We have described and compared the richness, the distribution of Operational Taxonomic Units (OTUs) within the two fractions, the spatial distribution, and the taxonomic composition of FL and PA bacterial assemblages. The number of OTUs in the present work was two orders of magnitude higher than in previous studies. Only 25% of the total OTUs were common to both fractions, whereas 49% OTUs were exclusive to the PA fraction and 26% to the FL fraction. The OTUs exclusively present in PA or FL assemblages were very low in abundance (6% of total abundance). Detection of the rare OTUs revealed the larger richness of PA bacteria that was hidden in previous studies. Alpha-Proteobacteria dominated the FL bacterial assemblage and gamma-Proteobacteria dominated the PA fraction. Bacteroidetes were important in the PA fraction mainly at the coast. The high number of sequences in this study detected additional phyla from the PA fraction, such as Actinobacteria, Firmicutes, and Verrucomicrobia.
    Mots-clés : #5, Marine bacteria, microbial communities, microbial ecology, particle attached, pyrosequencing.

  • Grigulis, K., Lavorel, S., Krainer, U., Legay, N., Baxendale, C., Dumont, M., et al. (2013). Relative contributions of plant traits and soil microbial properties to mountain grassland ecosystem services. Journal Of Ecology, 101(1), 47–57. doi:10.1111/1365-2745.12014
    Résumé : Summary * Plant functional diversity and soil microbial community composition are tightly coupled. Changes in these interactions may influence ecosystem functioning. Links between plant functional diversity, soil microbial communities and ecosystem functioning have been demonstrated in experiments using plant monocultures and mixtures, using broad plant and microbial functional groups, but have not been examined in diverse natural plant communities. * We quantified the relative effects of plant and microbial functional properties on key ecosystem functions. We measured plant functional diversity, soil microbial community composition and parameters associated with nitrogen (N) cycling and key nutrient cycling processes at three grassland sites in different parts of Europe. Because plant structure and function strongly influence soil microbial communities, we determined relationships between ecosystem properties, plant traits and soil community characteristics following a sequential approach in which plant traits were fitted first, followed by the additional effects of soil micro-organisms. * We identified a continuum from standing green biomass and standing litter, linked mostly with plant traits, to potential N mineralization and potential leaching of soil inorganic N, linked mostly with microbial properties. Plant and microbial functional parameters were equally important in explaining % organic matter content in soil. A parallel continuum ran from plant height, linked with above-ground biomass, to plant quality effects captured by the leaf economics spectrum, which were linked with the recycling of carbon (C) and N. * More exploitative species (higher specific leaf area, leaf N concentrations and lower leaf dry matter content) and taller swards, along with soil microbial communities dominated by bacteria, with rapid microbial activities, were linked with greater fodder production, but poor C and N retention. Conversely, dominance by conservative species (with opposite traits) and soil microbial communities dominated by fungi, and bacteria with slow activities, were usually linked with low production, but greater soil C storage and N retention. * Synthesis – Grassland production, C sequestration and soil N retention are jointly related to plant and microbial functional traits. Managing grasslands for selected, or multiple, ecosystem services will thus require a consideration of the joint effects of plant and soil communities. Further understanding of the mechanisms that link plant and microbial functional traits is essential to achieve this.
    Mots-clés : #5, denitrifying and nitrifying microbial communities, ecosystem service trade-offs, grassland management, long-term ecological research sites, microbial functioning, nitrogen cycling, plant economics spectrum, plant functional diversity, plant–soil (below-ground) interactions, plant–soil microbe interactions.

  • Michalet, S., Rohr, J., Warshan, D., Bardon, C., Roggy, J. - C., Domenach, A. - M., et al. (2013). Phytochemical analysis of mature tree root exudates <i>in situ</i> and their role in shaping soil microbial communities in relation to tree N-acquisition strategy. Plant Physiology And Biochemistry, 72, 169-177. doi:10.1016/j.plaphy.2013.05.003
    Résumé : Abstract Eperua falcata (Aublet), a late-successional species in tropical rainforest and one of the most abundant tree in French Guiana, has developed an original strategy concerning N-acquisition by largely preferring nitrate, rather than ammonium [1].Given the preference of this species for nitrate, we hypothesized that root exudates would promote nitrate availability by a) enhancing nitrate production by stimulating ammonium oxidation or b) minimizing nitrate losses by inhibiting denitrification. Root exudates were collected in situ in monospecific planted plots. The phytochemical analysis of these exudates and of several of their corresponding root extracts was achieved using UHPLC/DAD/ESI-QTOF and allowed the identification of diverse secondary metabolites belonging to the flavonoid family. Our results show that (i) the distinct exudation patterns observed are related to distinct root morphologies, and this was associated with a shift in the root flavonoid content, (ii) a root extract representative of the diverse compounds detected in roots showed a significant and selective metabolic inhibition of isolated denitrifiers in vitro, and (iii) in soil plots the abundance of nirK-type denitrifiers was negatively affected in rhizosphere soil compared to bulk. Altogether this led us to formulate hypothesis concerning the ecological role of the identified compounds in relation to N-acquisition strategy of this species.
    Mots-clés : #3, #5, #8, #cesn, Chemical Ecology, Denitrification, Eperua falcata, Flavonoids, Metabolic Profiling, Mycorrhizae, Plant-Microbes Interactions, Root Exudates.


  • Bouvier, T., Venail, P., Pommier, T., Bouvier, C., Barbera, C., & Mouquet, N. (2012). Contrasted Effects of Diversity and Immigration on Ecological Insurance in Marine Bacterioplankton Communities. (S. Thrush, Éd.)Plos One, 7(6), e37620. doi:10.1371/journal.pone.0037620
    Mots-clés : #5.

  • Cantarel, A., Bloor, J. M. G., Pommier, T., Guillaumaud, N., Moirot, C., Soussana, J. F., & Poly, F. (2012). Four years of experimental climate change modifies the microbial drivers of N<sub>2 </sub>O fluxes in an upland grassland ecosystem. Global Change Biology, 18(8), 2520-2531. doi:10.1111/j.1365-2486.2012.02692.x
    Mots-clés : #5.

  • Ghiglione, J. - F., Galand, P. E., Pommier, T., Pedrós-Alió, C., Maas, E. W., Bakker, K., et al. (2012). Pole-to-pole biogeography of surface and deep marine bacterial communities. Proceedings Of The National Academy Of Sciences, 109(43), 17633-17638. doi:10.1073/pnas.1208160109
    Résumé : The Antarctic and Arctic regions offer a unique opportunity to test factors shaping biogeography of marine microbial communities because these regions are geographically far apart, yet share similar selection pressures. Here, we report a comprehensive comparison of bacterioplankton diversity between polar oceans, using standardized methods for pyrosequencing the V6 region of the small subunit ribosomal (SSU) rRNA gene. Bacterial communities from lower latitude oceans were included, providing a global perspective. A clear difference between Southern and Arctic Ocean surface communities was evident, with 78% of operational taxonomic units (OTUs) unique to the Southern Ocean and 70% unique to the Arctic Ocean. Although polar ocean bacterial communities were more similar to each other than to lower latitude pelagic communities, analyses of depths, seasons, and coastal vs. open waters, the Southern and Arctic Ocean bacterioplankton communities consistently clustered separately from each other. Coastal surface Southern and Arctic Ocean communities were more dissimilar from their respective open ocean communities. In contrast, deep ocean communities differed less between poles and lower latitude deep waters and displayed different diversity patterns compared with the surface. In addition, estimated diversity (Chao1) for surface and deep communities did not correlate significantly with latitude or temperature. Our results suggest differences in environmental conditions at the poles and different selection mechanisms controlling surface and deep ocean community structure and diversity. Surface bacterioplankton may be subjected to more short-term, variable conditions, whereas deep communities appear to be structured by longer water-mass residence time and connectivity through ocean circulation.
    Mots-clés : #5, Biodiversity, bipolar, microbial ecology, next-generation sequencing.

  • Gravel, D., Bell, T., Barbera, C., Combe, M., Pommier, T., & Mouquet, N. (2012). Phylogenetic constraints on ecosystem functioning. Nature Communications, 3, 1117. Consulté de
    Mots-clés : #5.

  • Pommier, T., Douzery, E. J. P., & Mouillot, D. (2012). Environment drives high phylogenetic turnover among oceanic bacterial communities. Biology Letters, 8(4), 562–566. Consulté de
    Mots-clés : #5.

  • Zinger, L., Gobet, A., & Pommier, T. (2012). Two decades of describing the unseen majority of aquatic microbial diversity. Molecular Ecology. Consulté de
    Mots-clés : #5.


  • Venail, P. A., Kaltz, O., Olivieri, I., Pommier, T., & Mouquet, N. (2011). Diversification in temporally heterogeneous environments: effect of the grain in experimental bacterial populations. Journal Of Evolutionary Biology, 24(11), 2485-2495. doi:10.1111/j.1420-9101.2011.02376.x
    Mots-clés : #5.


  • Gravel, D., Bell, T., Barbera, C., Bouvier, T., Pommier, T., Venail, P., & Mouquet, N. (2010). Experimental niche evolution alters the strength of the diversity–productivity relationship. Nature, 469(7328), 89-92. doi:10.1038/nature09592
    Mots-clés : #5.

  • Pommier, T., Neal, P., Gasol, J., Coll, M., Acinas, S., & Pedrós-Alió, C. (2010). Spatial patterns of bacterial richness and evenness in the NW Mediterranean Sea explored by pyrosequencing of the 16S rRNA. Aquatic Microbial Ecology, 61(3), 221-233. doi:10.3354/ame01484
    Mots-clés : #5.


  • Pommier, T., Canback, B., Lundberg, P., Hagstrom, A., & Tunlid, A. (2009). RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities. Bioinformatics, 25(6), 736-742. doi:10.1093/bioinformatics/btp051
    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.



  • 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.


  • Simonin, M. (2014). Disturbance of soil nitrogen cycle by titanium dioxide (TiO2) nanoparticles. Dans . BES Lille.
    Mots-clés : #5, #ibio, #poster.