Langues du site :

Partenaires

CNRS
UCBL
INRA
ENVL
FR41
IDEX




Rechercher

Sur ce site


Accueil > Pages Perso > Philippe Normand

Equipe de Recherche Symbiose actinorhizienne

Philippe Normand

Directeur de recherche CNRS

Activité

  • Thèmes de recherches :

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

2016



  • Carro L, et al. 2016. Organic acids metabolism in Frankia alni. Symbiosis. 1-12. 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 LS, Bogusz D. 2016. An update on research on Frankia. Symbiosis. 1-4. doi: 10.1007/s13199-016-0431-x.
    Mots-clés : #1.


  • Nouioui I, 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. 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, et al. 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. 1-9. 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, et al. 2016. Characterization of PAS domains in Frankia and selected Actinobacteria and their possible interaction with other co-domains for environmental adaptation. Symbiosis. 1-10. 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, et al. 2015. Alnus peptides modify membrane porosity and induce the release of nitrogen-rich metabolites from nitrogen-fixing Frankia. The ISME Journal. doi: 10.1038/ismej.2014.257.
    Mots-clés : #1, #5, #cesn.


  • Granqvist E, 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, 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 DR, Tisa LS. 2015. Genome Characteristics of Frankia sp. Reflect Host Range and Host Plant Biogeography. Biological Nitrogen Fixation, 2 Volume Set. 245. http://books.google.fr/books?hl=fr&lr=&id=TR3yCQAAQBAJ&oi=fnd&pg=PA245&ots=E7vL8QMfo0&sig=XPqUfEHoOQEIzXqSJW2HFiwK4I8.
    Mots-clés : #1.


  • Persson T, 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 Börnke, F. PLOS ONE. 10:e0127630. doi: 10.1371/journal.pone.0127630.
    Mots-clés : #1.


  • Sghaier H, et al. 2015. Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes. The ISME Journal. 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, et al. 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, et al. 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. 38:685–693. 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, et al. 2013. First report on the occurrence of the uncultivated cluster 2 Frankia microsymbionts in soil outside the native actinorhizal host range area. J. Biosci. 38:695–698. http://www.ias.ac.in/jbiosci/nov2013/695.pdf.
    Mots-clés : #1.

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


  • Zoropogui A, et al. 2013. The Nocardia cyriacigeorgica GUH-2 genome shows ongoing adaptation of an environmental Actinobacteria to a pathogen's lifestyle. BMC Genomics. 14:286. 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, et al. 2012. Genome Sequence of <i>Micromonospora lupini</i> Lupac 08, Isolated from Root Nodules of <i>Lupinus angustifolius</i>. Journal of bacteriology. 194:4135–4135. http://jb.asm.org/content/194/15/4135.short.
    Mots-clés : #1.


  • Chouaia B, et al. 2012. Genome Sequence of <i>Blastococcus saxobsidens</i> DD2, a Stone-Inhabiting Bacterium. Journal of Bacteriology. 194:2752-2753. 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, 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. 80:566–577. 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, et al. 2012. Genome Sequence of Radiation-Resistant Modestobacter marinus Strain BC501, a Representative Actinobacterium That Thrives on Calcareous Stone Surfaces. Journal of Bacteriology. 194:4773-4774. 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, et al. 2012. Lectin genes in the <i>Frankia alni</i> genome. Archives of microbiology. 194:1–10. http://www.springerlink.com/index/C25V4867648X1763.pdf.
    Mots-clés : #1, #cesn.


  • Zoropogui A, et al. 2012. Genome Sequence of the Human- and Animal-Pathogenic Strain <i>Nocardia cyriacigeorgica</i> GUH-2. Journal of Bacteriology. 194:2098-2099. 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 MS, et al. 2011. Community variability of bacteria in alpine snow (Mont Blanc) containing Saharan dust deposition and their snow colonisation potential. Microbes and environments. 26:237–247. http://japanlinkcenter.org/JST.JSTAGE/jsme2/ME11116?from=Google.
    Mots-clés : #1.


  • Hocher V, et al. 2011. Transcriptomics of Actinorhizal Symbioses Reveals Homologs of the Whole Common Symbiotic Signaling Cascade. Plant Physiology. 156:700-711. 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. 6:1377–1379. http://www.landesbioscience.com/journals/10/article/16761/.
    Mots-clés : #1.


  • Persson T, 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. 193:7017-7018. 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, et al. 2011. Insertion sequences as highly resolutive genomic markers for sequence type 1 <i>Legionella pneumophila</i> Paris. Journal of clinical microbiology. 49:315–324. http://jcm.asm.org/content/49/1/315.short.
    Mots-clés : #1.


  • Wisniewski-Dyé F, et al. 2011. Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments. PLoS Genet. 7: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, et al. 2010. The <i>Frankia alni</i> symbiotic transcriptome. Molecular plant-microbe interactions. 23:593–607. http://apsjournals.apsnet.org/doi/abs/10.1094/MPMI-23-5-0593.
    Mots-clés : #1, #5, #ibio.
  • Kucho K, Hay AE, Normand P. 2010. Actinorhizal symbiosis, a review. Microbes and Environments. 25:241-252.
    Mots-clés : #1, #cesn, symbiosis.


  • Kucho K-ichi, Hay AE, Normand P. 2010. The Determinants of the Actinorhizal Symbiosis. Microbes and Environments. 25:241-252. 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 RD, et al. 2009. Complete genome of the cellulolytic thermophile <i>Acidothermus cellulolyticus</i> 11B provides insights into its ecophysiological and evolutionary adaptations. Genome Research. 19:1033-1043. 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 DM, et al. 2009. Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium <i>Frankia</i>. BMC genomics. 10:468. 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. 12:23–28. 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. http://www.springerlink.com/index/mr3273g447p05364.pdf.
    Mots-clés : #1.

  • Santos CL, Tavares F, Thioulouse J, Normand P. 2009. A phylogenomic analysis of bacterial helix–turn–helix transcription factors. FEMS microbiology reviews. 33:411–429. 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. 160:63–70. http://www.sciencedirect.com/science/article/pii/S0923250808001769.
    Mots-clés : #1, #7.

2008


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


  • Guinebretière MH, et al. 2008. Ecological diversification in the <i>Bacillus cereus</i> Group. Environmental Microbiology. 10:851–865. 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 JE, Tisa LS, Normand P, Benson DR. 2008. Comparative secretome analysis suggests low plant cell wall degrading capacity in <i>Frankia</i> symbionts. BMC genomics. 9:47. http://www.biomedcentral.com/1471-2164/9/47/.
    Mots-clés : #1.

  • Sen A, et al. 2008. The implication of life style on codon usage patterns and predicted highly expressed genes for three <i>Frankia</i> genomes. Antonie Van Leeuwenhoek. 93:335–346. http://www.springerlink.com/index/ltwv5nl32j3rk5hl.pdf.
    Mots-clés : #1.

  • Tisa LS, 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. http://www.springerlink.com/index/m2486r47016v0672.pdf.
    Mots-clés : #1.

2007


  • Alloisio N, et al. 2007. <i>Frankia alni</i> proteome under nitrogen-fixing and nitrogen-replete conditions. Physiologia Plantarum. 130:440–453. http://onlinelibrary.wiley.com/doi/10.1111/j.1399-3054.2007.00859.x/full.
    Mots-clés : #1.

  • Bagnarol E, et al. 2007. Differential Frankia protein patterns induced by phenolic extracts from <i>Myricaceae</i> seeds. Physiologia Plantarum. 130:380–390. http://onlinelibrary.wiley.com/doi/10.1111/j.1399-3054.2007.00875.x/full.
    Mots-clés : #1.


  • Giraud E, et al. 2007. Legumes Symbioses: Absence of Nod Genes in Photosynthetic Bradyrhizobia. Science. 316:1307-1312. doi: 10.1126/science.1139548.
    Résumé : Leguminous plants (such as peas and soybeans) and rhizobial soil bacteria are symbiotic partners that communicate through molecular signaling pathways, resulting in the formation of nodules on legume roots and occasionally stems that house nitrogen-fixing bacteria. Nodule formation has been assumed to be exclusively initiated by the binding of bacterial, host-specific lipochito-oligosaccharidic Nod factors, encoded by the nodABC genes, to kinase-like receptors of the plant. Here we show by complete genome sequencing of two symbiotic, photosynthetic, Bradyrhizobium strains, BTAi1 and ORS278, that canonical nodABC genes and typical lipochito-oligosaccharidic Nod factors are not required for symbiosis in some legumes. Mutational analyses indicated that these unique rhizobia use an alternative pathway to initiate symbioses, where a purine derivative may play a key role in triggering nodule formation.
    Mots-clés : #1.

  • Herrera A, et al. 2007. Species richness and phylogenetic diversity comparisons of soil microbial communities affected by nickel-mining and revegetation efforts in New Caledonia. European journal of soil biology. 43:130–139. http://www.sciencedirect.com/science/article/pii/S1164556306001348.
    Mots-clés : #1.


  • Normand P, et al. 2007. Genome characteristics of facultatively symbiotic <i>Frankia</i> sp. strains reflect host range and host plant biogeography. Genome Research. 17:7-15. doi: 10.1101/gr.5798407.
    Résumé : Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N2-fixing root nodules on diverse and globally distributed angiosperms in the “actinorhizal” symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%–98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses.
    Mots-clés : #1, #4, #6, #cesn.

  • Normand P, et al. 2007. Exploring the genomes of <i>Frankia</i>. Physiologia Plantarum. 130:331–343. http://onlinelibrary.wiley.com/doi/10.1111/j.1399-3054.2007.00918.x/full.
    Mots-clés : #1, #5.

0 | 50 | 100

Ouvrages

2014


  • 2014. Environmental microbiology: fundamentals and applications. Springer Berlin Heidelberg: New York, NY.

Année non précisée

  • Bertrand JC, Caumette P, Lebaron P, Matheron R, Normand P. sans date. Ecologie microbienne: Microbiologie des milieux naturels et anthropisés. PUP , Pau.
    Mots-clés : #1.

Chapitre d’ouvrages

2015



  • Bertin PN, Michotey V, Normand P. 2015. Contributions of Descriptive and Functional Genomics to Microbial Ecology. In: Environmental Microbiology: Fundamentals and Applications. Bertrand, J-C, et al. Springer Netherlands p. 831-846. 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, et al. 2015. Biogeochemical Cycles. In: Environmental Microbiology: Fundamentals and Applications. Bertrand, J-C, et al. Springer Netherlands p. 511-617. 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. In: Environmental Microbiology: Fundamentals and Applications. Bertrand, J-C, et al. Springer Netherlands p. 3-7. 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. In: Environmental Microbiology: Fundamentals and Applications. Bertrand, J-C, et al. Springer Netherlands p. 107-144. 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. In: Environmental Microbiology: Fundamentals and Applications. Bertrand, J-C, et al. Springer Netherlands p. 9-24. 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. In: Environmental Microbiology: Fundamentals and Applications. Bertrand, J-C, et al. Springer Netherlands p. 145-190. 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. In: Biological Nitrogen Fixation. De Bruijn, FJ. John Wiley & Sons, Inc: Hoboken, NJ, USA p. 757-768. 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. In: Environmental Microbiology: Fundamentals and Applications. Bertrand, J-C, et al. Springer Netherlands p. 619-658. 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. In: Environmental Microbiology: Fundamentals and Applications. Bertrand, J-C, et al. Springer Netherlands p. 293-351. 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. In: Environmental Microbiology: Fundamentals and Applications. Bertrand, J-C, et al. Springer Netherlands p. 261-291. 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 AM, Barabote RD, Normand P. 2014. The Family Acidothermaceae. In: The Prokaryotes. Acosta-Cruz, E, DeLong, EF, Lory, S, Stackebrandt, E, & Thompson, F. Springer Berlin Heidelberg: Berlin, Heidelberg p. 13-19. http://link.springer.com/10.1007/978-3-642-30138-4_199.
    Mots-clés : #1.


  • Normand P, Benson DR, Berry AM, Tisa LS. 2014. The Family Frankiaceae. In: The Prokaryotes. Rosenberg, E, DeLong, EF, Lory, S, Stackebrandt, E, & Thompson, F. Springer Berlin Heidelberg: Berlin, Heidelberg p. 339-356. 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. In: The Prokaryotes. Rosenberg, E, DeLong, EF, Lory, S, Stackebrandt, E, & Thompson, F. Springer Berlin Heidelberg: Berlin, Heidelberg p. 361-379. http://link.springer.com/10.1007/978-3-642-30138-4_180.
    Mots-clés : #1.

2011


  • Bertrand JC, et al. 2011. Les cycles biogéochimiques. In: Ecologie microbienne: Microbiologie des milieux naturels et anthropisés. Publications de l'Université de Pau et des Pays de l'Adour p. 545-657.
    Mots-clés : #1, #5.

  • Moënne-Loccoz Y, Mavingui P, Combes C, Normand P, Steinberg C. 2011. Micro-organismes et interactions biotiques. In: Ecologie microbienne: Microbiologie des milieux naturels et anthropisés. Publications de l'Université de Pau et des Pays de l'Adour p. .
    Mots-clés : #1, #3, #7.

  • Normand P, Duran R, Le Roux X, Morris CE, Poggiale JC. 2011. Biodiversite et fonctionnement des ecosystemes microbiens. In: Ecologie microbienne: Microbiologie des milieux naturels et anthropisés. Publications de l'Université de Pau et des Pays de l'Adour p. 263-296.
    Mots-clés : #1, #5.

Vulgarisation

Communications Orales

Posters