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Accueil > Pages Perso > Philippe Normand

Equipe de Recherche Symbiose actinorhizienne

Philippe Normand

Directeur de recherche CNRS

Activité

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Les bactéries du genre Frankia appartiennent à la classe des actinobactéries,ordre des Frankiales. Ces bactéries ont une paroi à Gram positif et un génome de grande taille avec un pourcentage élevé en bases G et C (haut G+C%). On retrouve parmi les actinobactéries notamment Mycobacterium (agents de la tuberculose et de la lèpre) et Streptomyces (bactéries du sol, à l’origine de nombreux antibiotiques). Douze groupes génomiques qui ont rang d’espèces sont décrites à ce jour chez Frankia. Ces bactéries ont une morphologie typique des actinobactéries avec des hyphes ramifiées et segmentées, des sporanges multiloculaires et des vésicules où des vésicules synthétisent la nitrogénase, in vitro et en symbiose. L’utilisation récente des séquences génomiques a permis de proposer un réarrangement taxonomique.

L’étude des génomes de Frankia aussi permis de montrer l’absence de gènes nod canoniques et d’ilôt symbiotique, mais la surexpression dans les nodules symbiotiques des gènes nif, suf, hup et shc. D’autres gènes qui ont un rôle dans la symbiose sont les lectines qui augmentent le nombre de nodules formés en situation de faible densité microbienne. La situation du côté de la plante est contrastée avec la démonstration de la présence chez l’aulne et le filao de la quasi-totalité des gènes de la cascade de signalisation connue chez les légumineuses. De nombreux autres gènes mis en évidence lors d’études de transcriptomique sont en cours d’analyse.


Publications

2018


  • Griesmann, M., Chang, Y., Liu, X., Song, Y., Haberer, G., Crook, M. B., et al. (2018). Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis. Science (New York, N.y.). doi:10.1126/science.aat1743
    Résumé : The root nodule symbiosis of plants with nitrogen-fixing bacteria impacts global nitrogen cycles and food production but is restricted to a subset of genera within a single clade of flowering plants. To explore the genetic basis for this scattered occurrence, we sequenced the genomes of ten plant species covering the diversity of nodule morphotypes, bacterial symbionts and infection strategies. In a genome-wide comparative analysis of a total of 37 plant species, we discovered signatures of multiple independent loss-of-function events in the indispensable symbiotic regulator NODULE INCEPTION (NIN) in ten out of 13 genomes of non-nodulating species within this clade. The discovery that multiple independent losses shaped the present day distribution of nitrogen-fixing root nodule symbiosis in plants reveals a phylogenetically wider distribution in evolutionary history and a so far underestimated selection pressure against this symbiosis.
    Mots-clés : #1.


  • Lurthy, T., Alloisio, N., Fournier, P., Anchisi, S., Ponsero, A., Normand, P., et al. (2018). Molecular response to nitrogen starvation by Frankia alni ACN14a revealed by transcriptomics and functional analysis with a fosmid library in Escherichia coli. Research In Microbiology, 169(2), 90-100. doi:10.1016/j.resmic.2017.12.002
    Résumé : The transcriptome of Frankia alni strain ACN14a was compared between in vitro ammonium-replete (N-replete) and ammonium-free dinitrogen-fixing (N-fixing) conditions using DNA arrays. A Welch-test (p < 0.05) revealed significant upregulation of 252 genes under N-fixing vs. N-replete (fold-change (FC) ≥ 2), as well as significant downregulation of 48 other genes (FC ≤ 0.5). Interestingly, there were 104 Frankia genes upregulated in vitro that were also significantly upregulated in symbiosis with Alnus glutinosa, while the other 148 genes were not, showing that the physiology of in vitro fixation is markedly different from that under symbiotic conditions. In particular,in vitro fixing cells were seen to upregulate genes identified as coding for a nitrite reductase, and amidases that were not upregulated in symbiosis. Confirmatory assays for nitrite reductase showed that Frankia indeed reduced nitrite and used it as a nitrogen source. An Escherichia coli fosmid clone carrying the nirB region was able to grow better in the presence of 5 mM nitrite than without it, confirming the function of the genome region. The physiological pattern that emerges shows that Frankia undergoes nitrogen starvation that induces a molecular response different from that seen in symbiosis.
    Mots-clés : #1, fosmid library, Nitrite reductase, nitrogen fixation, nitrogen stress.


  • Myronovskyi, M., Rosenkränzer, B., Nadmid, S., Pujic, P., Normand, P., & Luzhetskyy, A. (2018). Generation of a cluster-free Streptomyces albus chassis strains for improved heterologous expression of secondary metabolite clusters. Metabolic Engineering, 49, 316-324. doi:10.1016/j.ymben.2018.09.004
    Mots-clés : #1.


  • Normand, P., Nouioui, I., Pujic, P., Fournier, P., Dubost, A., Schwob, G., et al. (2018). Frankia canadensis sp. nov., isolated from root nodules of Alnus incana subspecies rugosa. International Journal Of Systematic And Evolutionary Microbiology, 68(9), 3001-3011. doi:10.1099/ijsem.0.002939
    Mots-clés : #1, #ibio.


  • Riesco, R., Carro, L., Román-Ponce, B., Prieto, C., Blom, J., Klenk, H. - P., et al. (2018). Defining the species Micromonospora saelicesensis and Micromonospora noduli under the framework of genomics. Frontiers In Microbiology, 9. doi:10.3389/fmicb.2018.01360
    Résumé : The type isolates of species Micromonospora saelicesensis and Micromonospora noduli are Gram-stain positive actinobacteria that were originally isolated from nitrogen fixing nodules of the legumes Lupinus angustifolius and Pisum sativum, respectively. These two species are very closely related and questions arise as to whether they should be merged into a single species. To better delineate the relationship of M. saelicesensis and M. noduli, ten strains isolated from plant tissue (nodules and leaves) and identified by their 16S rRNA gene sequences as either M. saelicensesis or M. noduli, based on a cut-off value of >99.5% were selected for whole-genome sequencing and compared with the type strains of M. saelicesensis Lupac 09T and M. noduli GUI43T using overall genome relatedness indices (OGRI) which included ANI, OrthoANI and digital DNA-DNA hybridization. Whole- and core-genome phylogenomic analyses were also carried out. These results were compared with the topologies of the 16S rRNA and gyrB gene phylogenies. Good correlation was found between all trees except for the 16S rRNA gene. Overall results also supported the current classification of M. saelicesensis and M. noduli as separate species. Especially useful was the core-genome phylogenetic analyses based on 92 genes and the dDDH results which were highly correlated. The importance of using more than one strain for a better definition of a species was also shown. A series of in-vitro phenotypic assays performed at different times were compared with in-silico predictions based on genomic data. In-vitro phenotypic tests showed discrepancies among the independent studies, confirming the lack of reproducibility even when tests were performed in the same laboratory. On the other hand, the use of in-silico predictions proved useful for defining a stable phenotype profile among the strains analyzed. These results provide a working framework for defining Micromonospora species at the genomic and phenotypic level.
    Mots-clés : #1, Genome sequencing, Micromonospora, nitrogen-fixing nodule, phylogenomic analysis, species delimitation, Taxonomy.

2016



  • Carro, L., Persson, T., Pujic, P., Alloisio, N., Fournier, P., Boubakri, H., et al. (2016). Organic acids metabolism in Frankia alni. Symbiosis, 70(1-3), 37–48. doi:10.1007/s13199-016-0404-0
    Résumé : Trophic exchanges constitute the bases of the symbiosis between the nitrogen-fixing actinomycete Frankia and its host plant Alnus, but the identity of the compounds exchanged is still poorly known. In the current work, previously published transcriptomic studies of Alnus nodules and of symbiotic Frankia were reexamined for TCA cycle related genes. The bacterial TCA enzyme genes were all upregulated, especially the succinyl-CoA synthase and the citrate synthase while on the plant side, none was significantly modified in nodules relative to non-inoculated roots. A preliminary metabolomics approach permitted to see that citrate, 2-oxoglutarate, succinate, malate and fumarate were all more abundant (FC (Fold change) = 5–70) in mature nitrogen-fixing nodules than in roots. In the evaluation of the uptake and metabolism of these organic acids, a significant change was observed in the morphology of nitrogen fixing vesicles in vitro: the dicarboxylates malate, succinate and fumarate induced the formation of larger vesicles than was the case with propionate. Moreover, the production of spores was also modified depending on the organic acid present. The assays showed that most C4 dicarboxylates were taken up while C6 tricarboxylates were not and citrate even partially blocked catabolism of reserve carbon. Tests were performed to determine if the change in membrane permeability induced by Ag5, a peptide previously shown to modify the membranes of Frankia, increased the uptake of specific organic acids. No effect was observed with citrate while an increase in nitrogen fixation was seen with propionate.
    Mots-clés : #1, developmental biology, Dicarboxylates, ecology, evolutionary biology, Frankia, Microbiology, nitrogen fixation, Plant Sciences, Propionate, Respiration, Vesicles.


  • Franche, C., Normand, P., Pawlowski, K., Tisa, L. S., & Bogusz, D. (2016). An update on research on Frankia and actinorhizal plants on the occasion of the 18th meeting of the Frankia-actinorhizal plants symbiosis. Symbiosis, 70(1-3), 1-4. doi:10.1007/s13199-016-0431-x
    Mots-clés : #1.


  • Nouioui, I., Ghodhbane-Gtari, F., Montero-Calasanz, M. del C., Göker, M., Meier-Kolthoff, J. P., Schumann, P., et al. (2016). Proposal of a type strain for Frankia alni (Woronin 1866) Von Tubeuf 1895, emended description of Frankia alni, and recognition of Frankia casuarinae sp. nov. and Frankia elaeagni sp. nov. International Journal Of Systematic And Evolutionary Microbiology, 66(12), 5201–5210. doi:10.1099/ijsem.0.001496
    Résumé : The sole Frankia species with a validly published name, the type species F. alni, was described by Woronin (1886) as present in the root of alder. Until now no type strain has been designated for F. alni, even though the absence of a type strain has seriously inhibited the application of modern taxonomic methods to the genus Frankia. Thus, we propose that strain ACN14aT be recognized as the type strain of this species. We compare ACN14aT to two strains, CcI3T and BMG5.12T, isolated from Casuarina and Elaeagnus, respectively, based on chemotaxonomy, phenotype microarray data and molecular data retrieved from genome sequences. All three tested strains grow as branched hyphae, produce vesicles and multilocular sporangia containing non-motile spores, and metabolize short fatty acids, TCA-cycle intermediates and carbohydrates. Chemotaxonomically, the three strains are indistinguishable with respect to phospholipids and cell-sugar composition. The major fatty acids identified in all three strains were iso-C16:0, C17:1 ω8c, C15:0, C17:0, and C16:0. The major menaquinones identified in all three novel type strains were MK-9(H8), MK-9(H6) and MK-9(H4). Analysis of 16S rRNA gene sequences showed 98.1-98.9% identity between the three strains. Digital DNA:DNA hybridization similarities between the three type strains are well below 70%. These results confirm the separation of the strains into three distinct species, Frankia alni, Frankia casuarinae sp. nov. and Frankia elaeagni sp. nov. Thus we propose ACN14aT (= DSM 45986T = CECT 9034T), CcI3T (= DSM 45818T = CECT 9043T) and BMG5.12T (= DSM 46783T = CECT 9031T) as the respective type strains.
    Mots-clés : #1.


  • Persson, T., Van Nguyen, T., Alloisio, N., Pujic, P., Berry, A. M., Normand, P., & Pawlowski, K. (2016). The N-metabolites of roots and actinorhizal nodules from Alnus glutinosa and Datisca glomerata: can D. glomerata change N-transport forms when nodulated? Symbiosis, 70(1-3), 149–157. doi:10.1007/s13199-016-0407-x
    Résumé : To gain more insight in nitrogen metabolism in actinorhizal nodules, a comparison between the N metabolite profiles in roots vs. nodules was initiated for one host plant from the best-examined order of actinorhizal plants, Fagales, A. glutinosa (Betulaceae), a temperate tree, and one host plant from the Cucurbitales order, Datisca glomerata (Datiscaceae). For both symbioses, the symbiotic transcriptomes have been published and can be used to assess the expression of genes representing specific metabolic pathways in nodules. The amino acid profiles of roots in this study suggest that A. glutinosa transported aspartate, glutamate and citrulline in the xylem, a combination of nitrogenous solutes not published previously for this species. The amino acid profiles of D. glomerata roots depended on whether the plants were nodulated or grown on nitrate; roots of nodulated plants contained increased amounts of arginine. Although bacterial transcriptome data showed no symbiotic auxotrophy for branched chain amino acids (leucine, isoleucine, valine) in either symbiosis, D. glomerata nodules contained comparatively high levels of these amino acids. This might represent a response to osmotic stress.
    Mots-clés : #1, Actinorhiza, Arginine, Citrulline, developmental biology, ecology, evolutionary biology, Frankia, Gamma-aminobutyrate (GABA), Microbiology, Nitrogen-fixation, Plant Sciences.


  • Sarkar, I., Normand, P., Tisa, L. S., Gtari, M., Bothra, A., & Sen, A. (2016). Characterization of PAS domains in Frankia and selected Actinobacteria and their possible interaction with other co-domains for environmental adaptation. Symbiosis, 70(1-3), 69–78. doi:10.1007/s13199-016-0413-z
    Résumé : Functional domains are semi-autonomous parts of proteins. The Per-Arnt-Sim (PAS) domain functions as signal-sensor in two-component systems of several bacteria. This domain exhibits large sequence diversity and is linked to other co-domains to modulate their function. In the present study, we analyzed the PAS domains found in the proteomes of several actinobacteria representing a variety of niches. PAS-domain containing proteins were identified with the HMMER program and characterized via an in silico approach. In general, the PAS proteins were found to be in the COG T (signal transduction) category implying their role was indeed in signal transduction. Most of the PAS proteins were found to be structurally conserved and moderately expressed. However, they showed a strong bias towards the lagging strand which may be a result of their involvement in adaptive evolution. A structure based phylogenetic analysis showed that PAS domains with similar interacting co-domains grouped together in a cluster irrespective of the bacterial genus from which they were identified. Thus, we may say that the association of PAS with its co-domains is based upon the PAS domain structure and not on the sequence.
    Mots-clés : #1, Biological network, Co-domain, developmental biology, Domain-domain interaction, ecology, evolutionary biology, Microbiology, Plant Sciences, signal transduction, Structure-based phylogeny.

2015



  • Carro-Garcia, L., Pujic, P., Alloisio, N., Fournier, P., Boubakri, H., Hay, A. E., et al. (2015). Alnus peptides modify membrane porosity and induce the release of nitrogen-rich metabolites from nitrogen-fixing Frankia. The Isme Journal, 9(8), 1723–1733. doi:10.1038/ismej.2014.257
    Mots-clés : #1, #5, #cesn.


  • Granqvist, E., Sun, J., Op den Camp, R., Pujic, P., Hill, L., Normand, P., et al. (2015). Bacterial-induced calcium oscillations are common to nitrogen-fixing associations of nodulating legumes and nonlegumes. New Phytologist, n/a-n/a. doi:10.1111/nph.13464
    Résumé : * Plants that form root-nodule symbioses are within a monophyletic ‘nitrogen-fixing’ clade and associated signalling processes are shared with the arbuscular mycorrhizal symbiosis. Central to symbiotic signalling are nuclear-associated oscillations in calcium ions (Ca2+), occurring in the root hairs of several legume species in response to the rhizobial Nod factor signal. * In this study we expanded the species analysed for activation of Ca2+ oscillations, including nonleguminous species within the nitrogen-fixing clade. * We showed that Ca2+ oscillations are a common feature of legumes in their association with rhizobia, while Cercis, a non-nodulating legume, does not show Ca2+ oscillations in response to Nod factors from Sinorhizobium fredii NGR234. Parasponia andersonii, a nonlegume that can associate with rhizobia, showed Nod factor-induced calcium oscillations to S. fredii NGR234 Nod factors, but its non-nodulating sister species, Trema tomentosa, did not. Also within the nitrogen-fixing clade are actinorhizal species that associate with Frankia bacteria and we showed that Alnus glutinosa induces Ca2+ oscillations in root hairs in response to exudates from Frankia alni, but not to S. fredii NGR234 Nod factors. * We conclude that the ability to mount Ca2+ oscillations in response to symbiotic bacteria is a common feature of nodulating species within the nitrogen-fixing clade.
    Mots-clés : #1, actinorhizal, calcium oscillations, Frankia, legumes, nitrogen-fixing clade, nodulation, Parasponia, symbiotic signalling.


  • Gtari, M., Ghodhbane-Gtari, F., Nouioui, I., Ktari, A., Hezbri, K., Mimouni, W., et al. (2015). Cultivating the uncultured: growing the recalcitrant cluster-2 Frankia strains. Scientific Reports, 5, 13112. doi:10.1038/srep13112
    Mots-clés : #1.

  • Normand, P., Benson, D. R., & Tisa, L. S. (2015). Genome Characteristics of Frankia sp. Reflect Host Range and Host Plant Biogeography. Biological Nitrogen Fixation, 2 Volume Set, 245. Consulté de http://books.google.fr/books?hl=fr&lr=&id=TR3yCQAAQBAJ&oi=fnd&pg=PA245&ots=E7vL8QMfo0&sig=XPqUfEHoOQEIzXqSJW2HFiwK4I8
    Mots-clés : #1.


  • Persson, T., Battenberg, K., Demina, I. V., Vigil-Stenman, T., Vanden Heuvel, B., Pujic, P., et al. (2015). Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant. (F. Börnke, Éd.)Plos One, 10(5), e0127630. doi:10.1371/journal.pone.0127630
    Mots-clés : #1.


  • Sghaier, H., Hezbri, K., Ghodhbane-Gtari, F., Pujic, P., Sen, A., Daffonchio, D., et al. (2015). Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes. The Isme Journal, 10(1), 21–29. doi:10.1038/ismej.2015.108
    Résumé : The Geodermatophilaceae are unique model systems to study the ability to thrive on or within stones and their proteogenomes (referring to the whole protein arsenal encoded by the genome) could provide important insight into their adaptation mechanisms. Here we report the detailed comparative genome analysis of Blastococcus saxobsidens (Bs), Modestobacter marinus (Mm) and Geodermatophilus obscurus (Go) isolated respectively from the interior and the surface of calcarenite stones and from desert sandy soils. The genome-scale analysis of Bs, Mm and Go illustrates how adaptation to these niches can be achieved through various strategies including ‘molecular tinkering/opportunism’ as shown by the high proportion of lost, duplicated or horizontally transferred genes and ORFans. Using high-throughput discovery proteomics, the three proteomes under unstressed conditions were analyzed, highlighting the most abundant biomarkers and the main protein factors. Proteomic data corroborated previously demonstrated stone-related ecological distribution. For instance, these data showed starvation-inducible, biofilm-related and DNA-protection proteins as signatures of the microbes associated with the interior, surface and outside of stones, respectively.
    Mots-clés : #1.

2014



  • Nouioui, I., Ghodhbane-Gtari, F., Fernandez, M. P., Boudabous, A., Normand, P., & Gtari, M. (2014). Absence of Cospeciation between the Uncultured Frankia Microsymbionts and the Disjunct Actinorhizal Coriaria Species. Biomed Research International, 2014, 1-9. doi:10.1155/2014/924235
    Mots-clés : #1.


  • Sen, A., Daubin, V., Abrouk, D., Gifford, I., Berry, A. M., & Normand, P. (2014). The phylogeny of actinobacteria revisited in the light of complete genomes, the orders Frankiales and Micrococcales should be split into coherent entities. Proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov. International Journal Of Systematic And Evolutionary Microbiology, ijs.0.063966-0. doi:10.1099/ijs.0.063966-0
    Résumé : The phylogeny of Actinobacteria remains controversial, essentially because it is very sensitive to the choice of dataset and phylogenetic methods. We used a test proposed recently, based on complete genome data, which chooses among candidate species phylogenies based on the number of lateral gene transfers (LGT) needed to explain the diversity of histories among gene trees for a set of genomes. We used 100 completely sequenced genomes representing 35 families and 17 orders of Actinobacteria and evaluated eight different hypothesis for their phylogeny, including one based on a concatenate of 54 conserved proteins present in single copy in all these genomes, trees based on 16S rDNA and 23S rDNA or their concatenation, and a tree based on the concatenate of MLSA genes (AtpI, GyrA, FtsZ, SecA and DnaK). We used Prunier to infer the number of LGT in 579 proteins (different from those used to build the concatenate tree) present in at least 70 species, using the different hypothetical species trees as references. The best tree, with the lowest number of lateral transfers, was the one based on the concatenate of 54 proteins. In that tree, the orders Bifidobacteriales, Coriobacteriales, Corynebacteriales, Micromonosporales, Propionibacteriales, Pseudonocardiales, Streptomycetales and Streptosporangiales were recovered while the Frankiales and Micrococcales were not. It is thus proposed that the invalidly published order Frankiales be split into Frankiales (Frankiaceae), Geodermatophilales (Geodermatophilaceae), Acidothermales (Acidothermaceae) and Nakamurellales (Nakamurellaceae). The order Micrococcales should also be split into Micrococcales (Kocuria, Rothia, Micrococcus, Arthrobacter, Tropheryma, Microbacterium, Leifsonia and Clavibacter), Cellulomonales (Beutenbergia, Cellulomonas, Xylanimonas, Jonesia and Sanguibacter) and Brachybacteriales (Brachybacterium) but this will have to wait until more genomes become available for a significant proportion of strains in this order.
    Mots-clés : #1, #ibio, Acidothermales, Frankiales, Genomes, Geodermatophilales, Nakamurellales.

2013


  • Carro-Garcia, L., Pujic, P., Etrujillo, M., & Normand, P. (2013). Micromonospora is a normal occupant of actinorhizal nodules. J. Biosci, 38(4), 685–693. Consulté de http://www.ias.ac.in/jbiosci/nov2013/685.pdf
    Mots-clés : #1.


  • Normand, P. (2013). A brief history of Frankia and actinorhizal plants meetings. Journal Of Biosciences, 1-8. doi:10.1007/s12038-013-9373-0
    Résumé :
    Mots-clés : #1, Actinorhizal plants, Biomedicine general, Cell Biology, ecological role, Frankia, isolation, Life Sciences, general, meetings, Microbiology, Plant Sciences, Zoology.

  • Nouioui, I., Sbissi, I., Ghodhbane-Gtari, F., Benbrahim, K. F., Normand, P., & Gtari, M. (2013). First report on the occurrence of the uncultivated cluster 2 Frankia microsymbionts in soil outside the native actinorhizal host range area. J. Biosci, 38(4), 695–698. Consulté de http://www.ias.ac.in/jbiosci/nov2013/695.pdf
    Mots-clés : #1.

  • Thakur, S., Normand, P., Daubin, V., Tisa, L. S., & Sen, A. (2013). Contrasted evolutionary constraints on secreted and non-secreted proteomes of selected Actinobacteria. Bmc Genomics, 14(1), 474. Consulté de http://www.biomedcentral.com/1471-2164/14/474
    Mots-clés : #1.


  • Zoropogui, A., Pujic, P., Normand, P., Barbe, V., Belli, P., Graindorge, A., et al. (2013). The Nocardia cyriacigeorgica GUH-2 genome shows ongoing adaptation of an environmental Actinobacteria to a pathogen's lifestyle. Bmc Genomics, 14(1), 286. doi:10.1186/1471-2164-14-286
    Résumé : Nocardia cyriacigeorgica is recognized as one of the most prevalent etiological agents of human nocardiosis. Human exposure to these Actinobacteria stems from direct contact with contaminated environmental matrices. The full genome sequence of N. cyriacigeorgica strain GUH-2 was studied to infer major trends in its evolution, including the acquisition of novel genetic elements that could explain its ability to thrive in multiple habitats.

2012


  • Alonso-Vega, P., Normand, P., Bacigalupe, R., Pujic, P., Lajus, A., Vallenet, D., et al. (2012). Genome Sequence of <i>Micromonospora lupini</i> Lupac 08, Isolated from Root Nodules of <i>Lupinus angustifolius</i>. Journal Of Bacteriology, 194(15), 4135–4135. Consulté de http://jb.asm.org/content/194/15/4135.short
    Mots-clés : #1.


  • Chouaia, B., Crotti, E., Brusetti, L., Daffonchio, D., Essoussi, I., Nouioui, I., et al. (2012). Genome Sequence of <i>Blastococcus saxobsidens</i> DD2, a Stone-Inhabiting Bacterium. Journal Of Bacteriology, 194(10), 2752-2753. doi:10.1128/JB.00320-12
    Résumé : Members of the genus Blastococcus have been isolated from sandstone monuments, as well as from sea, soil, plant, and snow samples. We report here the genome sequence of a member of this genus, Blastococcus saxobsidens strain DD2, isolated from below the surface of a Sardinian wall calcarenite stone sample.
    Mots-clés : #1.


  • Gtari, M., Essoussi, I., Maaoui, R., Sghaier, H., Boujmil, R., Gury, J., et al. (2012). Contrasted resistance of stone-dwelling <i>Geodermatophilaceae</i> species to stresses known to give rise to reactive oxygen species. Fems Microbiology Ecology, 80(3), 566–577. doi:10.1111/j.1574-6941.2012.01320.x
    Résumé : Stones in arid environments are inhabited by actinobacteria of the family Geodermatophilaceae like the genera Blastococcus and Modestobacter frequently isolated from altered calcarenites. Their habitat requires adaptation to light-induced and other stresses that generate reactive oxygen species. Here, we show that representative members of the species Blastococcus saxobsidens,Geodermatophilus obscurus, and Modestobacter multiseptatus are differentially adapted to stresses associated with arid environments. Whereas B. saxobsidens was found to be sensitive to gamma radiation (D10 = 900 Gy; 10% survival at 900 Gy), M. multiseptatus was moderately (D10 = 6000 Gy) and G. obscurus was highly tolerant (D10 = 9000 Gy). A difference in resistance to high-frequency (λ value = 254 nm) UV was shown by B. saxobsidens,M. multiseptatus, and G. obscurus, being sensitive, tolerant, and highly tolerant (D10 of 6, 900, and > 3500 kJ m−2, respectively). Tolerance to desiccation, mitomycin C and hydrogen peroxide correlated with the ionizing radiation and UV resistance profiles of the three species and were correlated with the pigments synthesized. Resistance to heavy metals/metalloids did not follow the same pattern, with resistance to Ag2+ and Pb2+ being similar for B. saxobsidens,M. multiseptatus, and G. obscurus, whereas resistance to AsO43−, Cr2+, or Cu2+ was greater for B. saxobsidens than for the other two species. The stress resistance profiles of M. multiseptatus and B. saxobsidens were reflected in different calcarenite colonization patterns. While M. multiseptatus was predominantly isolated from the first two millimeters of stone surface, B. saxobsidens was predominantly isolated from the deeper part of the stone where it is better protected from sun irradiation, suggesting that the response to light- and desiccation-induced oxidative stress is an important driver for niche colonization in the stone biotope.
    Mots-clés : #1, gamma radiation, Geodermatophilaceae, heavy metals, ionizing radiation, reactive oxygen species-generating stresses, UV.


  • Normand, P., Gury, J., Pujic, P., Chouaia, B., Crotti, E., Brusetti, L., et al. (2012). Genome Sequence of Radiation-Resistant Modestobacter marinus Strain BC501, a Representative Actinobacterium That Thrives on Calcareous Stone Surfaces. Journal Of Bacteriology, 194(17), 4773-4774. doi:10.1128/JB.01029-12
    Résumé : Here we report the full genome sequence of Modestobacter marinus strain BC501, an actinobacterial isolate that thrives on stone surfaces. The generated chromosome is circular, with a length of 5.57 Mb and a G+C content of 74.13%, containing 5,445 protein-coding genes, 48 tRNAs, and 3 ribosomal operons.
    Mots-clés : #1.

  • Pujic, P., Fournier, P., Alloisio, N., Hay, A. E., Maréchal, J., Anchisi, S., & Normand, P. (2012). Lectin genes in the <i>Frankia alni</i> genome. Archives Of Microbiology, 194, 1–10. Consulté de http://www.springerlink.com/index/C25V4867648X1763.pdf
    Mots-clés : #1, #cesn.


  • Zoropogui, A., Pujic, P., Normand, P., Barbe, V., Beaman, B., Beaman, L., et al. (2012). Genome Sequence of the Human- and Animal-Pathogenic Strain <i>Nocardia cyriacigeorgica</i> GUH-2. Journal Of Bacteriology, 194(8), 2098-2099. doi:10.1128/JB.00161-12
    Résumé : The pathogenic strain Nocardia cyriacigeorgica GUH-2 was isolated from a fatal human nocardiosis case, and its genome was sequenced. The complete genomic sequence of this strain contains 6,194,645 bp, an average G+C content of 68.37%, and no plasmids. We also identified several protein-coding genes to which N. cyriacigeorgica's virulence can potentially be attributed.
    Mots-clés : #1, #6.

2011


  • Chuvochina, M. S., Marie, D., Chevaillier, S., Petit, J. R., Normand, P., Alekhina, I. A., & Bulat, S. A. (2011). Community variability of bacteria in alpine snow (Mont Blanc) containing Saharan dust deposition and their snow colonisation potential. Microbes And Environments, 26(3), 237–247. Consulté de http://japanlinkcenter.org/JST.JSTAGE/jsme2/ME11116?from=Google
    Mots-clés : #1.


  • Hocher, V., Alloisio, N., Auguy, F., Fournier, P., Doumas, P., Pujic, P., et al. (2011). Transcriptomics of Actinorhizal Symbioses Reveals Homologs of the Whole Common Symbiotic Signaling Cascade. Plant Physiology, 156(2), 700-711. doi:10.1104/pp.111.174151
    Résumé : Comparative transcriptomics of two actinorhizal symbiotic plants, Casuarina glauca and Alnus glutinosa, was used to gain insight into their symbiotic programs triggered following contact with the nitrogen-fixing actinobacterium Frankia. Approximately 14,000 unigenes were recovered in roots and 3-week-old nodules of each of the two species. A transcriptomic array was designed to monitor changes in expression levels between roots and nodules, enabling the identification of up- and down-regulated genes as well as root- and nodule-specific genes. The expression levels of several genes emblematic of symbiosis were confirmed by quantitative polymerase chain reaction. As expected, several genes related to carbon and nitrogen exchange, defense against pathogens, or stress resistance were strongly regulated. Furthermore, homolog genes of the common and nodule-specific signaling pathways known in legumes were identified in the two actinorhizal symbiotic plants. The conservation of the host plant signaling pathway is all the more surprising in light of the lack of canonical nod genes in the genomes of its bacterial symbiont, Frankia. The evolutionary pattern emerging from these studies reinforces the hypothesis of a common genetic ancestor of the Fabid (Eurosid I) nodulating clade with a genetic predisposition for nodulation.
    Mots-clés : #1, #5.

  • Hocher, V., Alloisio, N., Bogusz, D., & Normand, P. (2011). Early signaling in actinorhizal symbioses. Plant Signaling & Behavior, 6(9), 1377–1379. Consulté de http://www.landesbioscience.com/journals/10/article/16761/
    Mots-clés : #1.


  • Persson, T., Benson, D. R., Normand, P., Heuvel, B. V., Pujic, P., Chertkov, O., et al. (2011). Genome Sequence of “<i>Candidatus Frankia datiscae</i>” Dg1, the Uncultured Microsymbiont from Nitrogen-Fixing Root Nodules of the Dicot <i>Datisca glomerata</i>. Journal Of Bacteriology, 193(24), 7017-7018. doi:10.1128/JB.06208-11
    Résumé : Members of the noncultured clade of Frankia enter into root nodule symbioses with actinorhizal species from the orders Cucurbitales and Rosales. We report the genome sequence of a member of this clade originally from Pakistan but obtained from root nodules of the American plant Datisca glomerata without isolation in culture.
    Mots-clés : #1.

  • Vergnes, M., Ginevra, C., Kay, E., Normand, P., Thioulouse, J., Jarraud, S., et al. (2011). Insertion sequences as highly resolutive genomic markers for sequence type 1 <i>Legionella pneumophila</i> Paris. Journal Of Clinical Microbiology, 49(1), 315–324. Consulté de http://jcm.asm.org/content/49/1/315.short
    Mots-clés : #1.


  • Wisniewski-Dyé, F., Borziak, K., Khalsa-Moyers, G., Alexandre, G., Sukharnikov, L., Wuichet, K., et al. (2011). Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments. Plos Genet, 7(12), e1002430. doi:10.1371/journal.pgen.1002430
    Résumé : Genome sequencing and analysis of plant-associated beneficial soil bacteria Azospirillum spp. reveals that these organisms transitioned from aquatic to terrestrial environments significantly later than the suggested major Precambrian divergence of aquatic and terrestrial bacteria. Separation of Azospirillum from their close aquatic relatives coincided with the emergence of vascular plants on land. Nearly half of the Azospirillum genome has been acquired horizontally, from distantly related terrestrial bacteria. The majority of horizontally acquired genes encode functions that are critical for adaptation to the rhizosphere and interaction with host plants.
    Mots-clés : #1, #3, #7.

2010


  • Alloisio, N., Queiroux, C., Fournier, P., Pujic, P., Normand, P., Vallenet, D., et al. (2010). The <i>Frankia alni</i> symbiotic transcriptome. Molecular Plant-Microbe Interactions, 23(5), 593–607. Consulté de http://apsjournals.apsnet.org/doi/abs/10.1094/MPMI-23-5-0593
    Mots-clés : #1, #5, #ibio.
  • Kucho, K., Hay, A. E., & Normand, P. (2010). Actinorhizal symbiosis, a review. Microbes And Environments, 25, 241-252.
    Mots-clés : #1, #cesn, symbiosis.


  • Kucho, K. -ichi, Hay, A. E., & Normand, P. (2010). The Determinants of the Actinorhizal Symbiosis. Microbes And Environments, 25(4), 241-252. doi:10.1264/jsme2.ME10143
    Mots-clés : #1, #cesn, actinorhizal plant, Bacterial Proteins, Frankia, Gene Expression Regulation, Bacterial, nitrogen fixation, Plant Physiological Phenomena, Plants, Rhizobium, root nodule, symbiosis.

2009



  • Barabote, R. D., Xie, G., Leu, D. H., Normand, P., Necsulea, A., Daubin, V., et al. (2009). Complete genome of the cellulolytic thermophile <i>Acidothermus cellulolyticus</i> 11B provides insights into its ecophysiological and evolutionary adaptations. Genome Research, 19(6), 1033-1043. doi:10.1101/gr.084848.108
    Résumé : We present here the complete 2.4-Mb genome of the cellulolytic actinobacterial thermophile Acidothermus cellulolyticus 11B. New secreted glycoside hydrolases and carbohydrate esterases were identified in the genome, revealing a diverse biomass-degrading enzyme repertoire far greater than previously characterized and elevating the industrial value of this organism. A sizable fraction of these hydrolytic enzymes break down plant cell walls, and the remaining either degrade components in fungal cell walls or metabolize storage carbohydrates such as glycogen and trehalose, implicating the relative importance of these different carbon sources. Several of the A. cellulolyticus secreted cellulolytic and xylanolytic enzymes are fused to multiple tandemly arranged carbohydrate binding modules (CBM), from families 2 and 3. For the most part, thermophilic patterns in the genome and proteome of A. cellulolyticus were weak, which may be reflective of the recent evolutionary history of A. cellulolyticus since its divergence from its closest phylogenetic neighbor Frankia, a mesophilic plant endosymbiont and soil dweller. However, ribosomal proteins and noncoding RNAs (rRNA and tRNAs) in A. cellulolyticus showed thermophilic traits suggesting the importance of adaptation of cellular translational machinery to environmental temperature. Elevated occurrence of IVYWREL amino acids in A. cellulolyticus orthologs compared to mesophiles and inverse preferences for G and A at the first and third codon positions also point to its ongoing thermoadaptation. Additional interesting features in the genome of this cellulolytic, hot-springs-dwelling prokaryote include a low occurrence of pseudogenes or mobile genetic elements, an unexpected complement of flagellar genes, and the presence of three laterally acquired genomic islands of likely ecophysiological value.
    Mots-clés : #1, #4, #cesn.

  • Bickhart, D. M., Gogarten, J. P., Lapierre, P., Tisa, L. S., Normand, P., & Benson, D. R. (2009). Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium <i>Frankia</i>. Bmc Genomics, 10(1), 468. Consulté de http://www.biomedcentral.com/1471-2164/10/468/
    Mots-clés : #1.

  • Leul, M., Normand, P., & Sellstedt, A. (2009). The phylogeny of uptake hydrogenases in" <i>Frankia</i>". International Microbiology: Official Journal Of The Spanish Society For Microbiology, 12(1), 23–28. Consulté de http://dialnet.unirioja.es/servlet/articulo?codigo=2969117
    Mots-clés : #1.

  • Normand, P., & Fernandez, M. (2009). Evolution and diversity of <i>Frankia</i>. Prokaryotic Symbionts In Plants, 103–125. Consulté de http://www.springerlink.com/index/mr3273g447p05364.pdf
    Mots-clés : #1.

  • Santos, C. L., Tavares, F., Thioulouse, J., & Normand, P. (2009). A phylogenomic analysis of bacterial helix–turn–helix transcription factors. Fems Microbiology Reviews, 33(2), 411–429. Consulté de http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6976.2008.00154.x/full
    Mots-clés : #1.

  • Valiente Moro, C., Thioulouse, J., Chauve, C., Normand, P., & Zenner, L. (2009). Bacterial taxa associated with the hematophagous mite <i>Dermanyssus gallinae</i> detected by 16S rRNA PCR amplification and TTGE fingerprinting. Research In Microbiology, 160(1), 63–70. Consulté de http://www.sciencedirect.com/science/article/pii/S0923250808001769
    Mots-clés : #1, #7.

2008


  • Bertin, P. N., Médigue, C., & Normand, P. (2008). Advances in environmental genomics: towards an integrated view of micro-organisms and ecosystems. Microbiology, 154(2), 347–359. Consulté de http://mic.sgmjournals.org/content/154/2/347.short
    Mots-clés : #1.


  • Guinebretière, M. H., Thompson, F. L., Sorokin, A., Normand, P., Dawyndt, P., Ehling-Schulz, M., et al. (2008). Ecological diversification in the <i>Bacillus cereus</i> Group. Environmental Microbiology, 10(4), 851–865. doi:10.1111/j.1462-2920.2007.01495.x
    Résumé : The Bacillus cereus Group comprises organisms that are widely distributed in the environment and are of health and economic interest. We demonstrate an ‘ecotypic’ structure of populations in the B. cereus Group using (i) molecular data from Fluorescent Amplified Fragment Length Polymorphism patterns, ribosomal gene sequences, partial panC gene sequences, ‘psychrotolerant’ DNA sequence signatures and (ii) phenotypic and descriptive data from range of growth temperature, psychrotolerance and thermal niches. Seven major phylogenetic groups (I to VII) were thus identified, with ecological differences that provide evidence for a multiemergence of psychrotolerance in the B. cereus Group. A moderate thermotolerant group (VII) was basal to the mesophilic group I, from which in turn distinct thermal lineages have emerged, comprising two mesophilic groups (III, IV), an intermediate group (V) and two psychrotolerant groups (VI, II). This stepwise evolutionary transition toward psychrotolerance was particularly well illustrated by the relative abundance of the ‘psychrotolerant’rrs signature (as defined by Pruss et al.) copies accumulated in strains that varied according to the phylogenetic group. The ‘psychrotolerant’cspA signature (as defined by Francis et al.) was specific to group VI and provided a useful way to differentiate it from the psychrotolerant group II. This study illustrates how adaptation to novel environments by the modification of temperature tolerance limits has shaped historical patterns of global ecological diversification in the B. cereus Group. The implications for the taxonomy of this Group and for the human health risk are discussed.
    Mots-clés : #1.

  • Mastronunzio, J. E., Tisa, L. S., Normand, P., & Benson, D. R. (2008). Comparative secretome analysis suggests low plant cell wall degrading capacity in <i>Frankia</i> symbionts. Bmc Genomics, 9(1), 47. Consulté de http://www.biomedcentral.com/1471-2164/9/47/
    Mots-clés : #1.

  • Sen, A., Sur, S., Bothra, A. K., Benson, D. R., Normand, P., & Tisa, L. S. (2008). The implication of life style on codon usage patterns and predicted highly expressed genes for three <i>Frankia</i> genomes. Antonie Van Leeuwenhoek, 93(4), 335–346. Consulté de http://www.springerlink.com/index/ltwv5nl32j3rk5hl.pdf
    Mots-clés : #1.

  • Tisa, L. S., Benson, D. R., Smejkal, G. B., Lapierre, P., Gogarten, J. P., Normand, P., et al. (2008). Living Large: Elucidation of the <i>Frankia</i> EAN1pec Genome Sequence Shows Gene Expansion and Metabolic Versatility. Biological Nitrogen Fixation: Towards Poverty Alleviation Through Sustainable Agriculture, 255–255. Consulté de http://www.springerlink.com/index/m2486r47016v0672.pdf
    Mots-clés : #1.

2007


  • Alloisio, N., Félix, S., Maréchal, J., Pujic, P., Rouy, Z., Vallenet, D., et al. (2007). <i>Frankia alni</i> proteome under nitrogen-fixing and nitrogen-replete conditions. Physiologia Plantarum, 130(3), 440–453. Consulté de http://onlinelibrary.wiley.com/doi/10.1111/j.1399-3054.2007.00859.x/full
    Mots-clés : #1.

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Ouvrages

2014


  • Environmental microbiology: fundamentals and applications. (2014). Environmental microbiology: fundamentals and applications. (J. C. Bertrand, P. Caumette, P. Lebaron, R. Matheron, P. Normand, & T. Sime-Ngando, Éd.). New York, NY: Springer Berlin Heidelberg.

Année non précisée

  • Bertrand, J. C., Caumette, P., Lebaron, P., Matheron, R., & Normand, P. Ecologie microbienne: Microbiologie des milieux naturels et anthropisés (PUP , Pau.).
    Mots-clés : #1.

Chapitre d’ouvrages

2018



  • Bertrand, J. - C., Caumette, P., Normand, P., Ollivier, B., & Sime-Ngando, T. (2018). Prokaryote/Eukaryote Dichotomy and Bacteria/Archaea/Eukarya Domains: Two Inseparable Concepts. Dans J. - C. Bertrand, P. Normand, B. Ollivier, & T. Sime-Ngando (Éd.), Prokaryotes And Evolution (p. 1-21). Cham: Springer International Publishing. Consulté de https://doi.org/10.1007/978-3-319-99784-1_1
    Résumé : The various schemes proposed to classify microorganisms in the living world have long been subject of heated debates. The classical dichotomic distinction between Prokaryotae (cells without nucleus) and Eukaryotae (cells with nucleus) functional and phenotypic categories was deeply changed by rRNA gene-based analysis that divided the living world into three phylogenetic domains: the Bacteria, the Archaea (originally Archaebacteria), and the Eukarya. In this chapter, we review the terms of this debate between the prokaryotic/eukaryotic functional and phenotypic dichotomy and the 16S/18S phylogenetic dichotomy that separates prokaryotes into two distinct domains. The specific characteristics that emphasize the organizational and functional complexity of prokaryotes and justify maintaining this terminology are discussed. We conclude that the organizational and functional concept of a prokaryotes/eukaryotes dichotomy can be easily supplemented by the phylogenetic concept Bacteria/Archaea/Eukarya. The two concepts are not irreconcilable but complementary, resulting in a consensual proposal that integrates both phenotypic and genotypic criteria.
    Mots-clés : #1, Anammoxosome, Bacteria/Archaea/Eukarya domains, Horizontal gene transfers, Multicellularity and differentiation, Organelles in prokaryotes, Planctomycetes, Prokaryote/eukaryote dichotomy, Prokaryotic cytoskeleton, Prokaryotic membranes, Transcription-translation coupling.


  • Normand, P., & Caumette, P. (2018). Phylogeny and Biodiversity of Prokaryotes. Dans J. - C. Bertrand, P. Normand, B. Ollivier, & T. Sime-Ngando (Éd.), Prokaryotes And Evolution (p. 23-55). Cham: Springer International Publishing. Consulté de https://doi.org/10.1007/978-3-319-99784-1_2
    Résumé : Creating a hierarchical system for microbes began as soon as microbes were discovered and has been constantly evolving ever since. The larger categories, the techniques to define taxa, and the bibliographical conventions, all these are regularly changing. At the moment, there are 30 bacterial phyla and 6 archaeal phyla that are described. The impact of genomes on taxonomy and phylogeny is also discussed.
    Mots-clés : #1, Evolution, Family, Genome, Genus, Kingdom, Locus, Order, Phylogeny, Species, Taxonomy.


  • Wielgoss, S., Leblond, P., Masson-Boivin, C., & Normand, P. (2018). Evolution Underway in Prokaryotes. Dans J. - C. Bertrand, P. Normand, B. Ollivier, & T. Sime-Ngando (Éd.), Prokaryotes And Evolution (p. 339-391). Cham: Springer International Publishing. Consulté de https://doi.org/10.1007/978-3-319-99784-1_6
    Résumé : Evolution is a phenomenon that escapes immediate attention because changes occur at a very slow pace and are often considered at odds with a religious vision of the world. Using bacteria that replicate so much faster than eukaryotes has permitted to quantify and discern tendencies. Such laboratory evolution implies growth rate, ability to use this or that substrate, but also synthesis and resistance to antibiotics and the ability to interact with eukaryotic hosts.
    Mots-clés : #1, Antibiotic, Artificial selection, Cellular network, Deletion, Directed evolution, DNA repair, Endosymbiosis, Epistasis, Evolutionary constraint, Fitness, Fixation, Fixism, Historical contingency, Hitchhiking, Hypermutagenesis, Infection, Inhibitor, Mobile genetic element, Mutagenesis, Mutation, Mutator, Natural selection, Nitrogen fixation, Nodulation, Phenotype, Punctuated equilibrium, Regulator, Resistance, Saprophyte, Secondary metabolite, Selection, Soil, Stress, Virulence.

2015



  • Bertin, P. N., Michotey, V., & Normand, P. (2015). Contributions of Descriptive and Functional Genomics to Microbial Ecology. Dans J. - C. Bertrand, P. Caumette, P. Lebaron, R. Matheron, P. Normand, & T. Sime-Ngando (Éd.), Environmental Microbiology: Fundamentals And Applications (p. 831-846). Springer Netherlands. Consulté de http://link.springer.com/chapter/10.1007/978-94-017-9118-2_18
    Résumé : Originally, “genomics” was used only to describe a scientific discipline which consisted in mapping, sequencing, and analyzing genomes. Nowadays, this term is widely used by a growing number of people in a broader sense to describe global techniques for studying genomes including from a functional point of view. These include the analysis of messenger RNAs (transcriptomics), protein contents (proteomics), and metabolites (metabolomics). At a higher level of complexity, it also describes the so-called “meta” approaches that allow to investigate the ecology of microbial communities, including uncultured microorganisms. Based on the use of recent technological developments, the numerous examples provide an integrated view of how microorganisms adapt to particular ecological niches and participate in the dynamics of ecosystems.
    Mots-clés : #1, Bacterial artificial chromosome (BAC), Cloning, Cosmid, Cultured and uncultured strains, DNA chips, genomics, High-performance liquid chromatography or high-pressure liquid chromatography (HPLC), High-resolution liquid chromatography (HRLC), Isoelectric focusing (IEF), Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF), metabolomics, Metagenomics, microbial ecology, plasmid, proteomics, pyrosequencing, Sequencing, Shotgun, Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), Synteny, transcriptomics.


  • Bertrand, J. - C., Bonin, P., Caumette, P., Gattuso, J. - P., Grégori, G., Guyoneaud, R., et al. (2015). Biogeochemical Cycles. Dans J. - C. Bertrand, P. Caumette, P. Lebaron, R. Matheron, P. Normand, & T. Sime-Ngando (Éd.), Environmental Microbiology: Fundamentals And Applications (p. 511-617). Springer Netherlands. Consulté de http://link.springer.com/chapter/10.1007/978-94-017-9118-2_14
    Résumé : All living organisms contribute to the biogeochemical cycles, but microorganisms, due to their high abundance, their tremendous metabolic capacities and adaptation potential, play a key role in the functioning and the evolution of biogeochemical cycles. Consequently, they are keyplayers in adaptation, resistance and resilience of ecosystems. The role of microorganisms in the main biogeochemical cycles (carbon, nitrogen, sulfur, phosphorus, silicon, metals), in soils, freshwater and marine ecosystems is presented. Microbial processes involved in the turnover of biogeochemical cycles are discussed from gene to ecosystem (natural and anthropogenic ecosystems), at global, regional and local scales, as well as in targeted microenvironments (such as particles or microniches). The biodiversity of microorganisms is highlighted and their metabolic pathways on which are based exchanges and biotransformations of organic and mineral components within ecosystems are described in details. The impacts of human activities on the microbial actors and processes of biogeochemical cycles, and the cascading ecological effects (greenhouse gas emissions, acid rains, dystrophic crises, etc.), are also discussed.
    Mots-clés : #5, Anoxic zones, Biogeochemical cycles, Carbon cycle, Ecosystem functioning, Iron cycle, Lake ecosystems, Manganese cycle, Marine ecosystems, Mercury cycle, microbial ecology, Microbial functions, nitrogen cycle, Oxic zones, Phosphate cycle, Silicon cycle, Soils, Sulfur cycle.


  • Bertrand, J. - C., Caumette, P., Lebaron, P., & Normand, P. (2015). The Thematic Fields of Microbial Ecology. Dans J. - C. Bertrand, P. Caumette, P. Lebaron, R. Matheron, P. Normand, & T. Sime-Ngando (Éd.), Environmental Microbiology: Fundamentals And Applications (p. 3-7). Springer Netherlands. Consulté de http://link.springer.com/chapter/10.1007/978-94-017-9118-2_1
    Résumé : The microbial world, generally invisible to the naked eye, has largely shaped our environment and has been instrumental in the emergence and evolution of all other living organisms on Earth. These microscopic unicellular organisms were for 3 billion years the only forms of life on our planet. Their most spectacular action was the modification of the primitive atmosphere: the dioxygen certainly not present initially reached its present concentration (21 % of the gas content of the atmosphere) through the action of microorganisms that are able of oxygenic photosynthesis. For the evolution of life, it is now widely accepted that multicellular life forms extremely complex have emerged from eukaryote microorganisms classified in the kingdom Plantae and in the Stramenopiles and Opisthokonta (especially metazoans which includes humans). These life forms are still dependent on the activity of microorganisms. If a disaster, whether natural or caused by humans, should annihilate all nonmicrobial living species, it is likely that some microorganisms that have colonized all oceans (from the surface to the abyssal domain) and the earth’s crust (to a depth of hundreds of meters) would be spared and would allow the initiation of a new evolution process, whatever the new environmental conditions at the end of this disaster, except in the absence of liquid water.
    Mots-clés : #1, Biogeochemical cycle, Distribution, Diversity, Ecosystems, Evolution, Interactions, microbial ecology, Origin, Taxonomy, Xenobiotics.


  • Boudouresque, C. - F., Caumette, P., Bertrand, J. - C., Normand, P., & Sime-Ngando, T. (2015). Systematic and Evolution of Microorganisms: General Concepts. Dans J. - C. Bertrand, P. Caumette, P. Lebaron, R. Matheron, P. Normand, & T. Sime-Ngando (Éd.), Environmental Microbiology: Fundamentals And Applications (p. 107-144). Springer Netherlands. Consulté de http://link.springer.com/chapter/10.1007/978-94-017-9118-2_5
    Résumé : The diversity of metabolic activities is a characteristic of the microbial world. This enormous diversity needs to be structured in order to be understood, and as a result, taxonomy and systematics are constantly changing since the beginning of the history of microbiology and particularly today with the introduction in the last 20 years of phylogeny as the core of systematics. The history of concepts in systematics and classification is presented. Classification is the science of ordering microorganism groups (taxa) based on their interrelationships. Taxonomy is the discipline that defines the principles and laws of classification. Nomenclature is the science of defining and naming the taxonomic categories (species, genera, families, orders, classes, divisions, phyla, kingdoms, domains), according to their hierarchical rank. In this way, different schools of classification and bacterial systematics were developed in the twentieth century. Today, there is an international consensus based on the classification of the Bergey’s Manual revisited with the concepts of phylogeny. Through this classification, the concept of the prokaryotic world organization has evolved. From the idea of a kingdom of prokaryotes, the concept of three domains in the organization of life supported by phylogenetic trees is fully accepted today. Among these three domains, two are prokaryotic: Bacteria and Archaea. In this chapter, the role of horizontal gene transfers in the evolution of life is discussed. The origin of eukaryotes with the primary, secondary, and tertiary endosymbioses is also presented. This allows to improve or to transform the concept of the tree of life from phylogeny to full genome study.
    Mots-clés : #1, Endosymbiosis, Hierarchical classification, History of systematics, Life domains, Microbial classification, microbial ecology, Microbial systematics, Nomenclature codes, Phylogeny, Tree of life.


  • Caumette, P., Bertrand, J. - C., & Normand, P. (2015). Some Historical Elements of Microbial Ecology. Dans J. - C. Bertrand, P. Caumette, P. Lebaron, R. Matheron, P. Normand, & T. Sime-Ngando (Éd.), Environmental Microbiology: Fundamentals And Applications (p. 9-24). Springer Netherlands. Consulté de http://link.springer.com/chapter/10.1007/978-94-017-9118-2_2
    Résumé : We present briefly, first, the history of the discovery of microorganisms and particularly bacteria with the pioneering works of Antoni van Leeuwenhoek, Louis Pasteur, and Robert Koch, essentially. In a second and more detailed part, the history of microbial ecology is presented with particularly the very important work of Sergei Winogradsky and his discoveries of the main bacterial groups active in biogeochemical cycles. It is followed by a description of the major microbial ecologists who have been very active in promoting and developing microbial ecology throughout the world. Their role in the advances of microbial ecology is presented and discussed.
    Mots-clés : #1, Antoni van Leeuwenhoek, History of microbiology, Louis Pasteur, microbial ecology, Microorganisms discovery, Robert Koch, Sergei Winogradsky.


  • Caumette, P., Brochier-Armanet, C., & Normand, P. (2015). Taxonomy and Phylogeny of Prokaryotes. Dans J. - C. Bertrand, P. Caumette, P. Lebaron, R. Matheron, P. Normand, & T. Sime-Ngando (Éd.), Environmental Microbiology: Fundamentals And Applications (p. 145-190). Springer Netherlands. Consulté de http://link.springer.com/chapter/10.1007/978-94-017-9118-2_6
    Résumé : Classification of prokaryotes is hierarchically organized into seven levels: kingdoms, phyla, classes, orders, families, genera, and species. In prokaryotes, because they reproduce by clonal fission, the species, considered as the basic unit of the biological diversity, faces several problems such as the definition of an individual. A bacterial strain can be recognized as an individual belonging to a species. However, many inconsistencies exist between phenotypic similarity levels and evolutionary relationships deduced from molecular phylogenies. Most taxonomic groups have been reconsidered through phylogenetic analysis in the 1980s, and a consensus has been reached on the need for coherence between taxonomy and phylogeny. Thus, the multiple revisions of species, genera, or higher taxonomic levels pose many complex problems that are solved gradually. Prokaryotic microorganisms correspond to two of the three domains of life: Archaea and Bacteria. Their systematics is described in the “Bergey’s Manual for Systematic Bacteriology, second edition” published in five volumes. In the text, the Latin terms used are those accepted by the Nomenclature Committee, and the organization of the bacterial and archaeal domains is presented as they appear in the “Bergey’s Manual for Systematic Bacteriology.” They are discussed according to the recent data of the hierarchical classification of Prokaryotes.
    Mots-clés : #1, 16S RNA homology, Archaea, Bacteria, Bacterial taxonomy, Dendrogram, DNA/DNA hybridization, Domains, G + C%, Genotypic criteria, microbial ecology, Phenotypic criteria, Phyla, Phylogenetic tree, Systematics of prokaryotes.


  • Alloisio, N., Kucho, K., Pujic, P., & Normand, P. (2015). The <i>Frankia alni</i> Symbiotic Transcriptome. Dans F. J. de Bruijn (Éd.), Biological Nitrogen Fixation (p. 757-768). Hoboken, NJ, USA: John Wiley & Sons, Inc. Consulté de http://doi.wiley.com/10.1002/9781119053095.ch75
    Mots-clés : #1.


  • Lebaron, P., Cournoyer, B., Lemarchand, K., Nazaret, S., & Servais, P. (2015). Environmental and Human Pathogenic Microorganisms. Dans J. - C. Bertrand, P. Caumette, P. Lebaron, R. Matheron, P. Normand, & T. Sime-Ngando (Éd.), Environmental Microbiology: Fundamentals And Applications (p. 619-658). Springer Netherlands. Consulté de http://link.springer.com/chapter/10.1007/978-94-017-9118-2_15
    Résumé : As the study of interactions between pathogenic microorganisms and their environment is part of microbial ecology, this chapter reviews the different types of human pathogens found in the environment, the different types of fecal indicators used in water quality monitoring, the biotic and abiotic factors affecting the survival and the infectivity of pathogenic microorganisms during their transportation in the environment, and the methods presently available to detect rare microorganisms in environmental samples. This chapter exclusively focuses on human pathogens.
    Mots-clés : #6, Antibiotic resistance, Biological pollution, Dissemination, Environmental reservoirs, microbial ecology, Pathogens, Sanitary microbiology, Toxins, Wastewater treatment plant.


  • Normand, P., Caumette, P., Goulas, P., Pujic, P., & Wisniewski-Dyé, F. (2015). Adaptations of Prokaryotes to Their Biotopes and to Physicochemical Conditions in Natural or Anthropized Environments. Dans J. - C. Bertrand, P. Caumette, P. Lebaron, R. Matheron, P. Normand, & T. Sime-Ngando (Éd.), Environmental Microbiology: Fundamentals And Applications (p. 293-351). Springer Netherlands. Consulté de http://link.springer.com/chapter/10.1007/978-94-017-9118-2_9
    Résumé : Microorganisms to Physicochemical Conditions…?> live in a constantly changing environment and must modify their physiology and morphology to cope with these changes. The main systems for molecular adaptation to modifications of environmental conditions and the behavioral responses of prokaryotes in various habitats, excluding extreme habitats, are discussed. The main regulation systems that are described are transcription, signal transduction, and protein modifications. Three specialized systems are also presented in details: quorum sensing, phase variation, and antibiosis. Quorum sensing allows bacteria to trigger some responses when their density is high enough to permit the function to be successful. Phase variation is an adaptive process by which a bacterial subpopulation undergoes frequent, usually reversible phenotypic changes resulting from genetic or epigenetic alterations, allowing rapid modification of the cells physiology. Antibiosis is the ability to synthesize molecules that will impact other taxa and eventually provide a selective advantage to which some microbes respond by resisting to these molecules. Finally are described the physiological responses to various environmental parameters such as temperature, oxidants, salinity, acidity, pressure, desiccation, and how this translates in different biotopes such as soil, water bodies, sediments, biofilms, mats, air, and manmade biotopes.
    Mots-clés : #1, #3, Adaptability, adaptation, Antibiosis, Fitness, Glycosylation, Homeostasis, Metabolism, microbial ecology, Morphology, Phase variation, Physiology, Protein modification, Quorum sensing, signal transduction, Transcription.


  • Normand, P., Duran, R., Le Roux, X., Morris, C., & Poggiale, J. - C. (2015). Biodiversity and Microbial Ecosystems Functioning. Dans J. - C. Bertrand, P. Caumette, P. Lebaron, R. Matheron, P. Normand, & T. Sime-Ngando (Éd.), Environmental Microbiology: Fundamentals And Applications (p. 261-291). Springer Netherlands. Consulté de http://link.springer.com/chapter/10.1007/978-94-017-9118-2_8
    Résumé : All ecosystems are composed of multiple species performing numerous functions. This plurality identified as biodiversity has become a research topic of general importance for understanding how ecosystems function. The word “biodiversity” has subsequently received different interpretations we aim to describe. Microbial systems can be used to illustrate these definitions and to clarify paradigms that have emerged in general ecology. Microbial biodiversity can be characterized by the kind of biodiversity (taxa or functional groups present), the representativeness of samples, and the culturability of samples or taxa, in terms of genetic, functional, or physiological characteristics. Biodiversity is a major driver of ecosystem functioning, and this relation is described in the case of several biotopes. Several mathematical approaches have been used to quantify microbial diversity, and the various indices are described and discussed.
    Mots-clés : #1, #5, Alpha diversity, Beta diversity, Biodiversity, Canonical correspondence analysis, Chimeras, Cluster Analysis, Community structure, Cultural approach, Denaturing gradient gel electrophoresis (DGGE), Diversity indices, DNA arrays, DNA reassociation, Fingerprints, Functional groups, Identification, Linkage disequilibrium analysis, Lipids, Metabolic capacities of communities, Metabolites, microbial communities, microbial ecology, Multivariate analysis, Nei index, Nonparametric test, OTU (operational taxonomic unit), Parametric test, Phylotype, Pigment, Principal Component Analysis, Rarefaction curve, Ribosomal intergenic spacer analysis (RISA), Richness, Saturation analysis, Shannon alpha diversity index, Simpson index, Single-strand conformational polymorphism (SSCP), Spearman correlation tests, Species richness index, Temperature gradient gel electrophoresis (TGGE), Terminal-restriction fragment length polymorphism (T-RFLP), Variables.

2014



  • Berry, A. M., Barabote, R. D., & Normand, P. (2014). The Family Acidothermaceae. Dans E. Acosta-Cruz, E. F. DeLong, S. Lory, E. Stackebrandt, & F. Thompson (Éd.), The Prokaryotes (p. 13-19). Berlin, Heidelberg: Springer Berlin Heidelberg. Consulté de http://link.springer.com/10.1007/978-3-642-30138-4_199
    Mots-clés : #1.


  • Normand, P., Benson, D. R., Berry, A. M., & Tisa, L. S. (2014). The Family Frankiaceae. Dans E. Rosenberg, E. F. DeLong, S. Lory, E. Stackebrandt, & F. Thompson (Éd.), The Prokaryotes (p. 339-356). Berlin, Heidelberg: Springer Berlin Heidelberg. Consulté de http://link.springer.com/10.1007/978-3-642-30138-4_183
    Mots-clés : #1.


  • Normand, P., Daffonchio, D., & Gtari, M. (2014). The Family Geodermatophilaceae. Dans E. Rosenberg, E. F. DeLong, S. Lory, E. Stackebrandt, & F. Thompson (Éd.), The Prokaryotes (p. 361-379). Berlin, Heidelberg: Springer Berlin Heidelberg. Consulté de http://link.springer.com/10.1007/978-3-642-30138-4_180
    Mots-clés : #1.

2011


  • Bertrand, J. C., Bonin, P., Caumette, P., Gattuso, J. P., Grégori, G., Guyonneaud, R., et al. (2011). Les cycles biogéochimiques. Dans Ecologie Microbienne: Microbiologie Des Milieux Naturels Et Anthropisés (p. 545-657). Publications de l'Université de Pau et des Pays de l'Adour.
    Mots-clés : #1, #5.

  • Moënne-Loccoz, Y., Mavingui, P., Combes, C., Normand, P., & Steinberg, C. (2011). Micro-organismes et interactions biotiques. Dans Ecologie Microbienne: Microbiologie Des Milieux Naturels Et Anthropisés. Publications de l'Université de Pau et des Pays de l'Adour.
    Mots-clés : #1, #3, #7.

  • Normand, P., Duran, R., Le Roux, X., Morris, C. E., & Poggiale, J. C. (2011). Biodiversite et fonctionnement des ecosystemes microbiens. Dans Ecologie Microbienne: Microbiologie Des Milieux Naturels Et Anthropisés (p. 263-296). Publications de l'Université de Pau et des Pays de l'Adour.
    Mots-clés : #1, #5.

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