T. Stappenbeck and H. Virgin, Accounting for reciprocal host???microbiome interactions in experimental science, Nature, vol.1, issue.7606, pp.191-200, 2016.
DOI : 10.4103/0976-500X.72351

N. Brereton, E. Gonzalez, J. Marleau, W. Nissim, M. Labrecque et al., sp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants, Plant Physiology, vol.171, issue.1, pp.3-24, 2016.
DOI : 10.1104/pp.16.00090

B. Haas, A. Papanicolaou, M. Yassour, M. Grabherr, P. Blood et al., De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis, Nature Protocols, vol.500, issue.8, pp.1494-512, 2013.
DOI : 10.1038/ng.2295
URL : http://europepmc.org/articles/pmc3875132?pdf=render

P. Henner, M. Schiavon, J. Morel, and E. Lichtfouse, Polycyclic aromatic hydrocarbon (PAH) occurrence and remediation methods, Analusis, vol.25, pp.56-65, 1997.
URL : https://hal.archives-ouvertes.fr/hal-00193277

D. Sousa and C. , Contaminated sites: The Canadian situation in an international context, Journal of Environmental Management, vol.62, issue.2, pp.131-54, 2001.
DOI : 10.1006/jema.2001.0431

E. Hamin, Turning brownfields into greenbacks, J Am Plan Assoc, vol.65, pp.236-243, 1999.

P. Panagos, M. Van-liedekerke, Y. Yigini, and L. Montanarella, Contaminated Sites in Europe: Review of the Current Situation Based on Data Collected through a European Network, Journal of Environmental and Public Health, vol.442, issue.2, p.158764, 2013.
DOI : 10.1016/j.scitotenv.2012.10.017

D. Glass, I. Raskin, and B. Ensley, Phytoremediation of toxic metals: using plants to clean up the environment. Phytoremediation toxic metals, p.304, 2000.

E. Pilon-smits and . Phytoremediation, PHYTOREMEDIATION, Annual Review of Plant Biology, vol.56, issue.1, pp.15-39, 2005.
DOI : 10.1146/annurev.arplant.56.032604.144214

I. Pulford and C. Watson, Phytoremediation of heavy metal-contaminated land by trees???a review, Environment International, vol.29, issue.4, pp.529-569, 2003.
DOI : 10.1016/S0160-4120(02)00152-6

T. Bell, S. Joly, F. Pitre, and E. Yergeau, Increasing phytoremediation efficiency and reliability using novel omics approaches, Trends in Biotechnology, vol.32, issue.5, pp.271-80, 2014.
DOI : 10.1016/j.tibtech.2014.02.008

T. Bell, S. El-din-hassan, A. Lauron-moreau, F. Otaibi, M. Hijri et al., Linkage between bacterial and fungal rhizosphere communities in hydrocarbon-contaminated soils is related to plant phylogeny, The ISME Journal, vol.38, issue.2, pp.331-374, 2014.
DOI : 10.1023/A:1021661621628
URL : http://europepmc.org/articles/pmc3906811?pdf=render

L. Bissonnette, M. St-arnaud, and M. Labrecque, Phytoextraction of heavy metals by two Salicaceae clones in symbiosis with arbuscular mycorrhizal fungi during the second year of a field trial, Plant and Soil, vol.298, issue.1-2, pp.55-67, 2010.
DOI : 10.2134/jeq2002.0109

, FCM: (The Federation of Canadian Municipalities) brownfields, sustainability snapshot, 2009.

M. Ray, N. Brereton, I. Shield, A. Karp, and R. Murphy, Variation in Cell Wall Composition and Accessibility in Relation to Biofuel Potential of Short Rotation Coppice Willows, BioEnergy Research, vol.3, issue.3, pp.1-14, 2012.
DOI : 10.1007/s12155-010-9077-3

M. Heller, G. Keoleian, M. Mann, and T. Volk, Life cycle energy and environmental benefits of generating electricity from willow biomass, Renewable Energy, vol.29, issue.7, pp.1023-1065, 2004.
DOI : 10.1016/j.renene.2003.11.018

E. Gnansounou and A. Dauriat, Techno-economic analysis of lignocellulosic ethanol: A review, Bioresource Technology, vol.101, issue.13, pp.4980-91, 2010.
DOI : 10.1016/j.biortech.2010.02.009
URL : https://infoscience.epfl.ch/record/147162/files/Techno-economic analysis of lignocellulosic ethanol- A review.pdf

M. Galbe, P. Sassner, A. Wingren, and G. Zacchi, Process Engineering Economics of Bioethanol Production, Biofuels, vol.108, pp.303-330, 2007.
DOI : 10.1007/10_2007_063

C. Hamelinck, G. Van-hooijdonk, and A. Faaij, Ethanol from lignocellulosic biomass: techno-economic performance in short-, middle- and long-term, Biomass and Bioenergy, vol.28, issue.4
DOI : 10.1016/j.biombioe.2004.09.002

, Biomass Bioenergy, vol.28, pp.384-410, 2005.

P. Bonfante and I. Anca, Plants, Mycorrhizal Fungi, and Bacteria: A Network of Interactions, Annual Review of Microbiology, vol.63, issue.1, pp.363-83, 2009.
DOI : 10.1146/annurev.micro.091208.073504

S. Hassan, T. Bell, F. Stefani, D. Denis, M. Hijri et al., Contrasting the Community Structure of Arbuscular Mycorrhizal Fungi from Hydrocarbon-Contaminated and Uncontaminated Soils following Willow (Salix spp. L.) Planting, PLoS ONE, vol.60, issue.7, p.102838, 2014.
DOI : 10.1371/journal.pone.0102838.s002

A. Almeida-rodríguez, M. Gómes, A. Loubert-hudon, S. Joly, and M. Labrecque, : modulation of plant responses under copper stress, Tree Physiology, vol.81, issue.4, pp.407-427, 2015.
DOI : 10.1007/s12033-008-9084-1

B. Wang and Y. Qiu, Phylogenetic distribution and evolution of mycorrhizas in land plants, Mycorrhiza, vol.10, issue.5, pp.299-363, 2006.
DOI : 10.1111/j.1095-8339.2000.tb01588.x

I. Grigoriev, R. Nikitin, S. Haridas, A. Kuo, R. Ohm et al., MycoCosm portal: gearing up for 1000 fungal genomes, Nucleic Acids Research, vol.33, issue.D1, pp.699-704, 2014.
DOI : 10.1093/nar/gkr1100

F. Abbasian, R. Lockington, T. Palanisami, K. Ramadass, M. Megharaj et al., Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by metagenomics analysis, Biotechnology Progress, vol.1, issue.2, pp.638-686, 2016.
DOI : 10.1002/cbdv.200490129

S. Bamforth and I. Singleton, Bioremediation of polycyclic aromatic hydrocarbons: current knowledge and future directions, Journal of Chemical Technology & Biotechnology, vol.91, issue.7, pp.723-759, 2005.
DOI : 10.1042/bj0910251

E. Yergeau, S. Sanschagrin, C. Maynard, M. St-arnaud, and C. Greer, Microbial expression profiles in the rhizosphere of willows depend on soil contamination, The ISME Journal, vol.11, issue.2, pp.344-58, 2014.
DOI : 10.1080/15226510802378483

S. Taktek, M. St-arnaud, Y. Piché, J. Fortin, and H. Antoun, Igneous phosphate rock solubilization by biofilm-forming mycorrhizobacteria and hyphobacteria associated with Rhizoglomus irregulare DAOM 197198, Mycorrhiza, vol.20, issue.1, pp.13-22, 2017.
DOI : 10.1007/s11356-012-1326-x

P. Frey-klett, J. Garbaye, and M. Tarkka, The mycorrhiza helper bacteria revisited, New Phytologist, vol.108, issue.1, pp.22-36, 2007.
DOI : 10.1104/pp.108.4.1519

J. Garbaye, Tansley Review No. 76 Helper bacteria: a new dimension to the mycorrhizal symbiosis, New Phytologist, vol.119, issue.2, pp.197-210, 1994.
DOI : 10.1007/BF00210586

S. Taghavi, D. Van-der-lelie, A. Hoffman, Y. Zhang, M. Walla et al., Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638, PLoS Genetics, vol.96, issue.5, p.1000943, 2010.
DOI : 10.1371/journal.pgen.1000943.s007

S. Chang, J. Puryear, and J. Cairney, A simple and efficient method for isolating RNA from pine trees, Plant Molecular Biology Reporter, vol.197, issue.3, pp.113-119, 1993.
DOI : 10.1007/BF02670468

G. Gambino, I. Perrone, and I. Gribaudo, A Rapid and effective method for RNA extraction from different tissues of grapevine and other woody plants, Phytochemical Analysis, vol.53, issue.6, pp.520-525, 2008.
DOI : 10.1104/pp.111.4.1059

F. Stewart, E. Ottesen, and E. Delong, Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics, The ISME Journal, vol.65, issue.7, pp.896-907, 2010.
DOI : 10.1073/pnas.0813403106
URL : http://www.nature.com/ismej/journal/v4/n7/pdf/ismej201018a.pdf

M. Meyer and M. Kircher, Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing, Cold Spring Harbor Protocols, vol.2010, issue.6, p.5448, 2010.
DOI : 10.1101/pdb.prot5448

M. Lohse, A. Bolger, A. Nagel, A. Fernie, J. Lunn et al., RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics, Nucleic Acids Research, vol.24, issue.18, pp.622-629, 2012.
DOI : 10.1093/bioinformatics/btn397
URL : https://academic.oup.com/nar/article-pdf/40/W1/W622/4932016/gks540.pdf

B. Langmead and S. Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-354, 2012.
DOI : 10.1093/bioinformatics/btp352
URL : http://europepmc.org/articles/pmc3322381?pdf=render

B. Langmead, Aligning Short Sequencing Reads with Bowtie, Curr Protoc Bioinformatics, vol.25, 2010.
DOI : 10.1093/bioinformatics/btp352
URL : http://europepmc.org/articles/pmc3010897?pdf=render

C. Villacorta-martin, N. De-cáceres-gonzález, F. De-haan, J. Huijben, K. Passarinho et al., Whole transcriptome profiling of the vernalization process in Lilium longiflorum (cultivar White Heaven) bulbs, BMC Genomics, vol.21, issue.4, p.550, 2015.
DOI : 10.1046/j.1365-313x.2000.00682.x

A. Roberts and L. Pachter, Streaming fragment assignment for real-time analysis of sequencing experiments, Nature Methods, vol.10, issue.1, pp.71-99, 2013.
DOI : 10.1093/nar/gkr1246
URL : http://europepmc.org/articles/pmc3880119?pdf=render

S. Anders and W. Huber, Differential expression analysis for sequence count data, Genome Biology, vol.11, issue.10, p.106, 2010.
DOI : 10.1186/gb-2010-11-10-r106
URL : http://precedings.nature.com/documents/4282/version/1/files/npre20104282-1.pdf

N. Leng, J. Dawson, J. Thomson, V. Ruotti, A. Rissman et al., EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments, Bioinformatics, vol.27, issue.8, pp.1035-1078, 2013.
DOI : 10.1093/bioinformatics/btr449
URL : https://academic.oup.com/bioinformatics/article-pdf/29/16/2073/525476/btt337.pdf

C. Soneson and M. Delorenzi, A comparison of methods for differential expression analysis of RNA-seq data, BMC Bioinformatics, vol.14, issue.1, p.91, 2013.
DOI : 10.1101/gr.101204.109

M. Robinson, D. Mccarthy, and G. Smyth, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, vol.9, issue.2, pp.139-179, 2010.
DOI : 10.1093/bib/bbm046
URL : https://academic.oup.com/bioinformatics/article-pdf/26/1/139/443156/btp616.pdf

M. Robinson and A. Oshlack, A scaling normalization method for differential expression analysis of RNA-seq data, Genome Biology, vol.11, issue.3, p.25, 2010.
DOI : 10.1186/gb-2010-11-3-r25
URL : https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2010-11-3-r25?site=genomebiology.biomedcentral.com

E. Gonzalez, N. Brereton, J. Marleau, G. Nissim, W. Labrecque et al., Meta-transcriptomics indicates biotic cross-tolerance in willow trees cultivated on petroleum hydrocarbon contaminated soil, BMC Plant Biology, vol.219, issue.3, p.246, 2015.
DOI : 10.1016/0022-2836(91)90193-A
URL : https://bmcplantbiol.biomedcentral.com/track/pdf/10.1186/s12870-015-0636-9?site=bmcplantbiol.biomedcentral.com

B. Ondov, N. Bergman, and A. Phillippy, Interactive metagenomic visualization in a Web browser, BMC Bioinformatics, vol.12, issue.1, p.385, 2011.
DOI : 10.1038/nature08821
URL : http://doi.org/10.1186/1471-2105-12-385

F. Mao, P. Dam, J. Chou, V. Olman, and Y. Xu, DOOR: a database for prokaryotic operons, Nucleic Acids Research, vol.1, issue.suppl_1, pp.459-63, 2009.
DOI : 10.1142/S0219720003000162
URL : https://academic.oup.com/nar/article-pdf/37/suppl_1/D459/16758078/gkn757.pdf

J. Hultman, M. Waldrop, R. Mackelprang, M. David, J. Mcfarland et al., Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes, Nature, vol.26, issue.7551, pp.208-220, 2015.
DOI : 10.1093/bioinformatics/btq041

A. Tveit, R. Schwacke, M. Svenning, and T. Urich, Organic carbon transformations in high-Arctic peat soils: key functions and microorganisms, The ISME Journal, vol.16, issue.2, pp.299-311, 2013.
DOI : 10.1890/0012-9658(2006)87[1659:MCCAFA]2.0.CO;2
URL : http://www.nature.com/ismej/journal/v7/n2/pdf/ismej201299a.pdf

S. Bent, J. Pierson, and L. Forney, Measuring Species Richness Based on Microbial Community Fingerprints: the Emperor Has No Clothes, Applied and Environmental Microbiology, vol.73, issue.7, pp.2399-401, 2007.
DOI : 10.1128/AEM.02383-06
URL : http://aem.asm.org/content/73/7/2399.full.pdf

E. Bellemain, T. Carlsen, C. Brochmann, E. Coissac, P. Taberlet et al., ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases, BMC Microbiology, vol.10, issue.1, p.189, 2010.
DOI : 10.1186/1471-2180-10-189
URL : https://hal.archives-ouvertes.fr/hal-00784435

D. Lindner and M. Banik, Mycologia, vol.103, issue.4, pp.731-771, 2011.
DOI : 10.1016/j.ympev.2004.07.005

T. Vetrovsky and P. Baldrian, The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses, PLoS ONE, vol.7, issue.2, p.57923, 2013.
DOI : 10.1371/journal.pone.0057923.s006

L. Guo, Z. Sui, S. Zhang, Y. Ren, and Y. Liu, Comparison of potential diatom ???barcode??? genes (the 18S rRNA gene and ITS, COI, rbcL) and their effectiveness in discriminating and determining species taxonomy in the Bacillariophyta, International Journal of Systematic and Evolutionary Microbiology, vol.53, issue.4, pp.1369-80, 2015.
DOI : 10.1029/2002GB002018

C. Maslunka, B. Gifford, J. Tucci, V. Gurtler, and R. Seviour, Insertions or Deletions (Indels) in the rrn 16S-23S rRNA Gene Internal Transcribed Spacer Region (ITS) Compromise the Typing and Identification of Strains within the Acinetobacter calcoaceticus-baumannii (Acb) Complex and Closely Related Members, PLoS ONE, vol.192, issue.8, p.105390, 2014.
DOI : 10.1371/journal.pone.0105390.s001

A. Porras-alfaro, K. Liu, C. Kuske, and G. Xie, ABSTRACT, Applied and Environmental Microbiology, vol.80, issue.3, pp.829-869, 2014.
DOI : 10.1128/AEM.02894-13

B. Iffis, M. St-arnaud, and M. Hijri, Petroleum hydrocarbon contamination, plant identity and arbuscular mycorrhizal fungal (AMF) community determine assemblages of the AMF spore-associated microbes, Environmental Microbiology, vol.186, issue.8, pp.2689-704, 2016.
DOI : 10.1016/j.jhazmat.2010.11.116

E. Yergeau, T. Bell, J. Champagne, C. Maynard, S. Tardif et al., Transplanting Soil Microbiomes Leads to Lasting Effects on Willow Growth, but not on the Rhizosphere Microbiome, Frontiers in Microbiology, vol.8, issue.771, p.1436, 2015.
DOI : 10.1038/ismej.2013.163

N. Brereton, F. Ahmed, D. Sykes, M. Ray, I. Shield et al., X-ray micro-computed tomography in willow reveals tissue patterning of reaction wood and delay in programmed cell death, BMC Plant Biology, vol.15, issue.1, p.83, 2015.
DOI : 10.1007/BF00203659

H. Sandermann, Plant metabolism of xenobiotics, Trends in Biochemical Sciences, vol.17, issue.2, pp.82-86, 1992.
DOI : 10.1016/0968-0004(92)90507-6

A. Noguchi, A. Saito, Y. Homma, M. Nakao, N. Sasaki et al., ) Seedlings, Journal of Biological Chemistry, vol.270, issue.32, pp.23581-90, 2007.
DOI : 10.1093/bioinformatics/12.4.357

R. Dixon, G. Wright, G. Behrns, R. Teskey, and T. Hinckley, Water deficits and root growth of ectomycorrhizal white oak seedlings, Canadian Journal of Forest Research, vol.10, issue.4, pp.545-553, 1980.
DOI : 10.1139/x80-089

R. Dixon, S. Pallardy, H. Garrett, G. Cox, and I. Sander, seedlings, Canadian Journal of Botany, vol.61, issue.6, pp.1559-65, 1983.
DOI : 10.1139/b83-168
URL : https://hal.archives-ouvertes.fr/hal-00882655

T. Lehto and J. Zwiazek, Ectomycorrhizas and water relations of trees: a review, Mycorrhiza, vol.97, issue.2, pp.71-90, 2011.
DOI : 10.1042/BC20040134

?. Marjanovi?, N. Uehlein, R. Kaldenhoff, J. Zwiazek, M. Weiß et al., Aquaporins in poplar: What a difference a symbiont makes!, Planta, vol.260, issue.2, pp.258-68, 2005.
DOI : 10.1111/j.1469-8137.1992.tb00094.x

W. Fischer, D. Loo, U. Ludewig, K. Boorer, M. Tegeder et al., -cotransporters for cellular import of neutral and charged amino acids, The Plant Journal, vol.29, issue.6, pp.717-748, 2002.
DOI : 10.1104/pp.76.4.865

K. Garcia, J. Doidy, S. Zimmermann, D. Wipf, and P. Courty, Take a Trip Through the Plant and Fungal Transportome of Mycorrhiza, Trends in Plant Science, vol.21, issue.11, pp.937-50, 2016.
DOI : 10.1016/j.tplants.2016.07.010
URL : https://hal.archives-ouvertes.fr/hal-01354681

A. Grennan, The Role of Trehalose Biosynthesis in Plants, PLANT PHYSIOLOGY, vol.144, issue.1, pp.3-5, 2007.
DOI : 10.1104/pp.104.900223

B. Bago, P. Pfeffer, D. Douds, J. Brouillette, G. Bécard et al., as Revealed by Nuclear Magnetic Resonance Spectroscopy, Plant Physiology, vol.121, issue.1, pp.263-72, 1999.
DOI : 10.1104/pp.121.1.263

A. Ferreira, M. Tótola, and A. Borges, Physiological implications of trehalose in the ectomycorrhizal fungus Pisolithus sp. under thermal stress, Journal of Thermal Biology, vol.32, issue.1, pp.34-41, 2007.
DOI : 10.1016/j.jtherbio.2006.08.009

L. Chen, B. Hou, S. Lalonde, H. Takanaga, M. Hartung et al., Sugar transporters for intercellular exchange and nutrition of pathogens, Nature, vol.22, issue.7323, pp.527-559, 2010.
DOI : 10.1155/2008/420747

J. Doidy, E. Grace, C. Kühn, F. Simon-plas, L. Casieri et al., Sugar transporters in plants and in their interactions with fungi, Trends in Plant Science, vol.17, issue.7, pp.413-435, 2012.
DOI : 10.1016/j.tplants.2012.03.009

J. Manck-götzenberger and N. Requena, Arbuscular mycorrhiza Symbiosis Induces a Major Transcriptional Reprogramming of the Potato SWEET Sugar Transporter Family, Frontiers in Plant Science, vol.25, issue.569, p.487, 2016.
DOI : 10.1016/j.cub.2015.06.075

H. Chen, J. Huh, Y. Yu, L. Ho, L. Chen et al., infection, The Plant Journal, vol.56, issue.6, pp.1046-58, 2015.
DOI : 10.1111/jipb.12173
URL : https://hal.archives-ouvertes.fr/hal-01796201

D. Floß, B. Hause, P. Lange, H. Kuester, D. Strack et al., inhibits formation of arbuscular mycorrhiza-induced apocarotenoids, and abolishes normal expression of mycorrhiza-specific plant marker genes, The Plant Journal, vol.16, issue.1, pp.86-100, 2008.
DOI : 10.1042/bj2950517

P. Salzer, B. Hubner, A. Sirrenberg, and A. Hager, Differential Effect of Purified Spruce Chitinases and [beta]-1,3-Glucanases on the Activity of Elicitors from Ectomycorrhizal Fungi, Plant Physiology, vol.114, issue.3, pp.957-68, 1997.
DOI : 10.1104/pp.114.3.957

C. Albrecht, T. Burgess, B. Dell, and F. Lapeyrie, Chitinase and peroxidase activities are induced in eucalyptus roots according to aggressiveness of Australian ectomycorrhizal strains of Pisolithus sp., New Phytologist, vol.94, issue.2, pp.217-239, 1994.
DOI : 10.1016/0885-5765(89)90059-3

F. Stefani, P. Tanguay, G. Pelletier, Y. Piché, and R. Hamelin, Impact of Endochitinase-Transformed White Spruce on Soil Fungal Biomass and Ectendomycorrhizal Symbiosis, Applied and Environmental Microbiology, vol.76, issue.8, pp.2607-2621, 2010.
DOI : 10.1128/AEM.02807-09
URL : http://aem.asm.org/content/76/8/2607.full.pdf

L. Quéré, A. Wright, D. Söderström, B. Tunlid, A. Johansson et al., (Batsch) Fr., Molecular Plant-Microbe Interactions, vol.18, issue.7, pp.659-73, 2005.
DOI : 10.1094/MPMI-18-0659

S. Chisholm, G. Coaker, B. Day, and B. Staskawicz, Host-Microbe Interactions: Shaping the Evolution of the Plant Immune Response, Cell, vol.124, issue.4, pp.803-817, 2006.
DOI : 10.1016/j.cell.2006.02.008

J. Plett, Y. Daguerre, S. Wittulsky, A. Vayssières, A. Deveau et al., Effector MiSSP7 of the mutualistic fungus Laccaria bicolor stabilizes the Populus JAZ6 protein and represses jasmonic acid (JA) responsive genes, Proceedings of the National Academy of Sciences, vol.24, issue.5, pp.8299-304, 2014.
DOI : 10.1105/tpc.112.097998
URL : https://hal.archives-ouvertes.fr/hal-01268578

G. Bonito, A. Gryganskyi, J. Trappe, and R. Vilgalys, A global meta-analysis of Tuber ITS rDNA sequences: species diversity, host associations and long-distance dispersal, Molecular Ecology, vol.7, issue.22, pp.4994-5008, 2010.
DOI : 10.1016/B978-0-12-372180-8.50042-1

M. Leonardi, M. Iotti, M. Oddis, G. Lalli, G. Pacioni et al., Assessment of ectomycorrhizal fungal communities in the natural habitats of Tuber magnatum (Ascomycota, Pezizales), Mycorrhiza, vol.71, issue.5, pp.349-58, 2013.
DOI : 10.1111/j.1574-6941.2009.00783.x

S. Sundaram, S. Kim, H. Suzuki, C. Mcquattie, S. Hiremath et al., Molecular Plant-Microbe Interactions, vol.14, issue.5, pp.618-646, 2001.
DOI : 10.1094/MPMI.2001.14.5.618

P. Matheny, J. Curtis, V. Hofstetter, M. Aime, J. Moncalvo et al., Major clades of Agaricales: a multilocus phylogenetic overview, Mycologia, vol.98, issue.6, pp.982-95, 2006.
DOI : 10.1080/15572536.2006.11832797

W. Hou, B. Lian, H. Dong, H. Jiang, and X. Wu, Distinguishing ectomycorrhizal and saprophytic fungi using carbon and nitrogen isotopic compositions, Geoscience Frontiers, vol.3, issue.3, pp.351-357, 2012.
DOI : 10.1016/j.gsf.2011.12.005

A. Pertsemlidis and J. Fondon, Having a BLAST with bioinformatics (and avoiding BLASTphemy), Genome Biol, vol.2, pp.2002-2001, 2001.

R. Koide, J. Sharda, J. Herr, and G. Malcolm, Ectomycorrhizal fungi and the biotrophy???saprotrophy continuum, New Phytologist, vol.23, issue.2, pp.230-233, 2008.
DOI : 10.1111/j.1469-8137.2007.02014.x

C. Pellegrin, E. Morin, F. Martin, and C. Veneault-fourrey, Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted Proteins, Frontiers in Microbiology, vol.15, issue.348, p.1278, 2015.
DOI : 10.1186/1471-2164-15-6
URL : https://hal.archives-ouvertes.fr/hal-01269483

A. Kohler, A. Kuo, L. Nagy, E. Morin, K. Barry et al., Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists, Nature Genetics, vol.30, issue.4, pp.410-415, 2015.
DOI : 10.1093/nar/30.7.1575
URL : https://hal.archives-ouvertes.fr/hal-01140842

F. Shah, C. Nicolás, J. Bentzer, M. Ellström, M. Smits et al., Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors, New Phytologist, vol.13, issue.4, pp.1705-1724, 2016.
DOI : 10.1111/j.1462-2920.2010.02417.x
URL : https://hal.archives-ouvertes.fr/hal-01439084

C. Navarre and A. Goffeau, Membrane hyperpolarization and salt sensitivity induced by deletion of PMP3, a highly conserved small protein of yeast plasma membrane, The EMBO Journal, vol.19, issue.11, pp.2515-2539, 2000.
DOI : 10.1093/emboj/19.11.2515

D. Block, J. Szopinska, A. Guerriat, B. Dodzian, J. Villers et al., Yeast Pmp3p has an important role in plasma membrane organization, Journal of Cell Science, vol.128, issue.19, pp.3646-59, 2015.
DOI : 10.1242/jcs.173211

R. Peng, A. Xiong, Y. Xue, X. Fu, F. Gao et al., Microbial biodegradation of polyaromatic hydrocarbons, FEMS Microbiology Reviews, vol.32, issue.6, pp.927-55, 2008.
DOI : 10.1007/978-1-4615-5925-2_14
URL : https://academic.oup.com/femsre/article-pdf/32/6/927/8426993/32-6-927.pdf

C. Chikere, G. Okpokwasili, and B. Chikere, Monitoring of microbial hydrocarbon remediation in the soil, 3 Biotech, vol.94, issue.3, pp.117-155, 2011.
DOI : 10.1046/j.1365-2672.2003.01826.x

T. Sipilä, A. Keskinen, M. Åkerman, C. Fortelius, K. Haahtela et al., High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I.E.3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil, The ISME Journal, vol.15, issue.9, pp.968-81, 2008.
DOI : 10.1080/16226510500214632

O. Carmel-harel and G. Storz, Responses to Oxidative Stress, Annual Review of Microbiology, vol.54, issue.1, pp.439-61, 2000.
DOI : 10.1146/annurev.micro.54.1.439

U. Nehls, N. Grunze, M. Willmann, M. Reich, and H. Kuester, Sugar for my honey: Carbohydrate partitioning in ectomycorrhizal symbiosis, Phytochemistry, vol.68, issue.1, pp.82-91, 2007.
DOI : 10.1016/j.phytochem.2006.09.024

U. Nehls, J. Wiese, M. Guttenberger, and R. Hampp, Carbon allocation in ectomycorrhizas, Physiological and Molecular Plant Pathology, vol.57, issue.3, pp.167-76, 1998.
DOI : 10.1006/pmpp.2000.0285

M. Fajardo-lópez, S. Dietz, N. Grunze, J. Bloschies, M. Weiß et al., : function in ectomycorrhizal symbiosis and soil-growing hyphae, New Phytologist, vol.23, issue.2, pp.365-78, 2008.
DOI : 10.1111/j.1438-8677.1991.tb00256.x

N. Hynson, M. Weiss, K. Preiss, G. Gebauer, and K. Treseder, Fungal host specificity is not a bottleneck for the germination of Pyroleae species (Ericaceae) in a Bavarian forest, Molecular Ecology, vol.178, issue.5, pp.1473-81, 2013.
DOI : 10.1111/j.1469-8137.2007.02362.x

S. Deshmukh, R. Hückelhoven, P. Schäfer, J. Imani, M. Sharma et al., The root endophytic fungus Piriformospora indica requires host cell death for proliferation during mutualistic symbiosis with barley, Proceedings of the National Academy of Sciences, vol.16, issue.4, pp.18450-18457, 2006.
DOI : 10.1094/MPMI.2003.16.4.306
URL : http://www.pnas.org/content/103/49/18450.full.pdf

A. Zuccaro, U. Lahrmann, U. Güldener, G. Langen, S. Pfiffi et al., Endophytic Life Strategies Decoded by Genome and Transcriptome Analyses of the Mutualistic Root Symbiont Piriformospora indica, PLoS Pathogens, vol.32, issue.10, p.1002290, 2011.
DOI : 10.1371/journal.ppat.1002290.s033
URL : https://doi.org/10.1371/journal.ppat.1002290

A. Roy, S. Hashmi, Z. Li, A. Dement, K. Cho et al., The glucose metabolite methylglyoxal inhibits expression of the glucose transporter genes by inactivating the cell surface glucose sensors Rgt2 and Snf3 in yeast, Molecular Biology of the Cell, vol.123, issue.5, pp.862-71, 2016.
DOI : 10.1126/science.123.3191.309

F. Martin, A. Aerts, D. Ahrén, A. Brun, E. Danchin et al., The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis, Nature, vol.14, issue.7183, pp.88-92, 2008.
DOI : 10.1038/nature06556
URL : https://hal.archives-ouvertes.fr/halsde-00261893

N. Nikolaidis, N. Doran, and D. Cosgrove, Plant Expansins in Bacteria and Fungi: Evolution by Horizontal Gene Transfer and Independent Domain Fusion, Molecular Biology and Evolution, vol.328, issue.2, pp.376-86, 2014.
DOI : 10.1126/science.1187145
URL : https://academic.oup.com/mbe/article-pdf/31/2/376/13170046/mst206.pdf

J. Rytioja, K. Hildén, J. Yuzon, A. Hatakka, R. De-vries et al., Plant-Polysaccharide-Degrading Enzymes from Basidiomycetes, Microbiology and Molecular Biology Reviews, vol.78, issue.4, pp.614-663, 2014.
DOI : 10.1271/bbb.100299
URL : http://mmbr.asm.org/content/78/4/614.full.pdf

F. Sillo, J. Fangel, B. Henrissat, A. Faccio, P. Bonfante et al., Understanding plant cell-wall remodelling during the symbiotic interaction between Tuber melanosporum and Corylus avellana using a carbohydrate microarray, Planta, vol.17, issue.2, pp.347-59, 2016.
DOI : 10.1016/j.tifs.2005.10.008
URL : https://hal.archives-ouvertes.fr/hal-01439118

C. Veneault-fourrey, A. Kohler, E. Morin, R. Balestrini, J. Plett et al., Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment, Fungal Genetics and Biology, vol.72, pp.168-81, 2014.
DOI : 10.1016/j.fgb.2014.08.007
URL : https://hal.archives-ouvertes.fr/hal-01123254

M. Peter, A. Kohler, R. Ohm, A. Kuo, J. Krützmann et al., Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum, Nature Communications, vol.18, p.12662, 2016.
DOI : 10.1093/bioinformatics/18.1.207
URL : https://hal.archives-ouvertes.fr/hal-01439098

G. Avigad, D. Amaral, C. Asensio, and B. Horecker, The D-galactose oxidase of Polyporus circinatus, J Biol Chem, vol.237, pp.2736-2779, 1962.

L. Donaldson and J. Knox, Localization of Cell Wall Polysaccharides in Normal and Compression Wood of Radiata Pine: Relationships with Lignification and Microfibril Orientation, PLANT PHYSIOLOGY, vol.158, issue.2, pp.642-53, 2012.
DOI : 10.1104/pp.111.184036

H. Massicotte, C. Ackerley, and R. Peterson, as demonstrated by lectin binding, Canadian Journal of Botany, vol.65, issue.6, pp.1127-1159, 1987.
DOI : 10.1139/b87-157

M. Giollant, J. Guillot, M. Damez, M. Dusser, P. Didier et al., Characterization of a Lectin from Lactarius deterrimus (Research on the Possible Involvement of the Fungal Lectin in Recognition between Mushroom and Spruce during the Early Stages of Mycorrhizae Formation), Plant Physiology, vol.101, issue.2, pp.513-535, 1993.
DOI : 10.1104/pp.101.2.513

F. Z. , Structure and function of carbohydrate-binding module families 13 and 42 of glycoside hydrolases, comprising a ?-trefoil fold, Biosci Biotechnol Biochem, vol.77, pp.1363-71, 2013.

F. Martin, M. Ramstedt, and K. Söderhäll, Carbon and nitrogen metabolism in ectomycorrhizal fungi and ectomycorrhizas, Biochimie, vol.69, issue.6-7, pp.569-81, 1987.
DOI : 10.1016/0300-9084(87)90176-3

A. Deveau, A. Kohler, P. Frey-klett, and F. Martin, S238N, New Phytologist, vol.2, issue.2, pp.379-90, 2008.
DOI : 10.1016/S0304-4165(98)00066-X
URL : https://hal.archives-ouvertes.fr/tel-01747014

P. Ceccaroli, M. Buffalini, R. Saltarelli, E. Barbieri, E. Polidori et al., Genomic profiling of carbohydrate metabolism in the ectomycorrhizal fungus Tuber melanosporum, New Phytologist, vol.332, issue.3, pp.751-64, 2011.
DOI : 10.1016/j.jmb.2003.08.009

F. Shah, F. Rineau, B. Canbäck, T. Johansson, and A. Tunlid, New Phytologist, vol.56, issue.3, pp.875-87, 2013.
DOI : 10.2307/3760641

E. Lucic, C. Fourrey, A. Kohler, F. Martin, M. Chalot et al., New Phytologist, vol.167, issue.Suppl. 1, pp.343-64, 2008.
DOI : 10.1016/j.bbaexp.2004.10.007

S. Sundaram, J. Brand, M. Hymes, S. Hiremath, and G. Podila, Isolation and analysis of a symbiosis-regulated and Ras-interacting vesicular assembly protein gene from the ectomycorrhizal fungus Laccaria bicolor, New Phytologist, vol.94, issue.2, pp.529-567, 2004.
DOI : 10.1083/jcb.141.1.71

B. Rajashekar, A. Kohler, T. Johansson, F. Martin, A. Tunlid et al., Expansion of signal pathways in the ectomycorrhizal fungus Laccaria bicolor- evolution of nucleotide sequences and expression patterns in families of protein kinases and RAS small GTPases, New Phytologist, vol.17, issue.2, pp.365-79, 2009.
DOI : 10.1093/bioinformatics/17.4.383

D. Camilli, P. Emr, S. Mcpherson, P. Novick, and P. , Phosphoinositides as Regulators in Membrane Traffic, Science, vol.271, issue.5255, p.1533, 1996.
DOI : 10.1126/science.271.5255.1533

S. Kim, S. Hiremath, and G. Podila, Cloning and identification of symbiosis-regulated genes from the ectomycorrhizal Laccaria bicolor, Mycological Research, vol.103, issue.2, pp.168-72, 1999.
DOI : 10.1017/S0953756298006881

P. De-freitas, B. Betancourth, J. Teixeira, M. Zubieta, M. De-queiroz et al., gene expression during ectomycorrhizal formation, Journal of Basic Microbiology, vol.183, issue.12, pp.1358-66, 2014.
DOI : 10.1111/j.1469-8137.2009.02860.x

N. Inada and T. Ueda, Membrane Trafficking Pathways and their Roles in Plant???Microbe Interactions, Plant and Cell Physiology, vol.8, issue.4, pp.672-86, 2014.
DOI : 10.1371/journal.pone.0070723

N. Sarkar, Polyadenylation of mRNA in bacteria. Microbiol-Uk, pp.3125-3158, 1996.

H. Nakazato, S. Venkatesan, and M. Edmonds, Polyadenylic acid sequences in E. coli messenger RNA, Nature, vol.253, issue.5513, pp.144-150, 1975.
DOI : 10.1038/256144a0

E. Hajnsdorf, F. Braun, J. Haugel-nielsen, and P. Regnier, Polyadenylylation destabilizes the rpsO mRNA of Escherichia coli., Proceedings of the National Academy of Sciences, vol.92, issue.9, pp.3973-3980, 1995.
DOI : 10.1073/pnas.92.9.3973

O. Hara, E. Chekanova, J. Ingle, C. Kushner, Z. Peters et al., Polyadenylylation helps regulate mRNA decay in Escherichia coli., Proceedings of the National Academy of Sciences, vol.92, issue.6, pp.1807-1818, 1995.
DOI : 10.1073/pnas.92.6.1807

Z. Li, S. Reimers, S. Pandit, and M. Deutscher, RNA quality control: degradation of defective transfer RNA, The EMBO Journal, vol.21, issue.5, pp.1132-1140, 2002.
DOI : 10.1093/emboj/21.5.1132

B. Mohanty and S. Kushner, Bacterial/archaeal/organellar polyadenylation, Wiley Interdisciplinary Reviews: RNA, vol.131, issue.2, pp.256-76, 2011.
DOI : 10.1016/j.cell.2007.10.041

S. Kushner, : a 20 year odyssey, RNA, vol.21, issue.4, pp.673-677, 2015.
DOI : 10.1261/rna.049700.115
URL : http://rnajournal.cshlp.org/content/21/4/673.full.pdf

P. Srinivasan, M. Ramanarayanan, and E. Rabbani, Presence of polyriboadenylate sequences in pulse-labeled RNA of Escherichia coli., Proceedings of the National Academy of Sciences, vol.72, issue.8, pp.2910-2914, 1975.
DOI : 10.1073/pnas.72.8.2910

N. Sarkar, D. Langley, and H. Paulus, Isolation and characterization of polyadenylate-containing RNA from Bacillus brevis, Biochemistry, vol.17, issue.17, pp.3468-74, 1978.
DOI : 10.1021/bi00610a007

B. Mohanty and S. Kushner, The majority of Escherichia coli mRNAs undergo post-transcriptional modification in exponentially growing cells, Nucleic Acids Research, vol.19, issue.19, pp.5695-704, 2006.
DOI : 10.1101/gad.1330405

J. Jasiecki and G. Wegrzyn, EMBO reports, vol.28, issue.2, pp.172-179, 2003.
DOI : 10.1093/nar/28.5.1139

A. Maes, C. Gracia, D. Brechemier, P. Hamman, E. Chatre et al., Role of polyadenylation in regulation of the flagella cascade and motility in Escherichia coli, Biochimie, vol.95, issue.2, pp.410-418, 2013.
DOI : 10.1016/j.biochi.2012.10.017

B. Mohanty and S. Kushner, Analysis of the function of Escherichia coli poly(A) polymerase I in RNA metabolism, Molecular Microbiology, vol.90, issue.5, pp.1094-108, 1999.
DOI : 10.1073/pnas.90.14.6756

R. Brouwer, O. Kuipers, and S. Van-hijum, The relative value of operon predictions, Briefings in Bioinformatics, vol.35, issue.suppl_1, pp.367-75, 2008.
DOI : 10.1093/nar/gkl1019

X. Mao, Q. Ma, B. Liu, X. Chen, H. Zhang et al., Revisiting operons: an analysis of the landscape of transcriptional units in E. coli, BMC Bioinformatics, vol.39, issue.22, p.356, 2015.
DOI : 10.1093/nar/gkr766

M. Heitkamp, J. Freeman, D. Miller, and C. Cerniglia, Pyrene degradation by a Mycobacterium sp.?identification of ring oxidation and ring fissionproducts, Appl Environ Microbiol, vol.54, pp.2556-65, 1988.

P. Yung, L. Grasso, L. Mohidin, A. Acerbi, E. Hinks et al., Global transcriptomic responses of Escherichia coli K-12 to volatile organic compounds. Sci Rep, 2016.

J. Malinverni and T. Silhavy, An ABC transport system that maintains lipid asymmetry in the Gram-negative outer membrane, Proceedings of the National Academy of Sciences, vol.280, issue.12, pp.8009-8023, 2009.
DOI : 10.1074/jbc.M414368200

J. Duan, W. Jiang, Z. Cheng, J. Heikkila, and B. Glick, The Complete Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas sp. UW4, PLoS ONE, vol.25, issue.7, p.58640, 2013.
DOI : 10.1371/journal.pone.0058640.s018

J. Van-der-ploeg, N. Cummings, T. Leisinger, and I. Connerton, Bacillus subtilis genes for the utilization of sulfur from aliphatic sulfonates. Microbiol-Uk, pp.2555-61, 1998.

S. Kane, A. Chakicherla, P. Chain, R. Schmidt, M. Shin et al., Whole-Genome Analysis of the Methyl tert-Butyl Ether-Degrading Beta-Proteobacterium Methylibium petroleiphilum PM1, Journal of Bacteriology, vol.189, issue.5, pp.1931-1976, 2007.
DOI : 10.1128/JB.01259-06

M. Pohnlein, R. Hausmann, S. Lang, and C. Syldatk, Enzymatic synthesis and modification of surface-active glycolipids, European Journal of Lipid Science and Technology, vol.50, issue.2, pp.145-55, 2015.
DOI : 10.1007/s002530051330

M. Müller, J. Kügler, M. Henkel, M. Gerlitzki, B. Hörmann et al., Rhamnolipids???Next generation surfactants?, Journal of Biotechnology, vol.162, issue.4, pp.366-80, 2012.
DOI : 10.1016/j.jbiotec.2012.05.022

R. Gutknecht, R. Beutler, L. Garcia-alles, U. Baumann, and B. Erni, The dihydroxyacetone kinase of Escherichia coli utilizes a phosphoprotein instead of ATP as phosphoryl donor, The EMBO Journal, vol.20, issue.10, pp.2480-2486, 2001.
DOI : 10.1093/emboj/20.10.2480

H. Li, H. Su, S. Kim, Y. Chang, S. Hong et al., Enhanced production of trehalose in Escherichia coli by homologous expression of otsBA in the presence of the trehalase inhibitor, validamycin A, at high osmolarity, Journal of Bioscience and Bioengineering, vol.113, issue.2, pp.224-256, 2012.
DOI : 10.1016/j.jbiosc.2011.09.018

N. Cabrera-valladares, A. Richardson, C. Olvera, L. Treviño, E. Déziel et al., Monorhamnolipids and 3-(3-hydroxyalkanoyloxy)alkanoic acids (HAAs) production using Escherichia coli as a heterologous host, Applied Microbiology and Biotechnology, vol.58, issue.1, pp.187-94, 2006.
DOI : 10.1099/00221287-146-11-2803

M. Henkel, M. Müller, J. Kügler, R. Lovaglio, J. Contiero et al., Rhamnolipids as biosurfactants from renewable resources: Concepts for next-generation rhamnolipid production, Process Biochemistry, vol.47, issue.8, pp.1207-1226, 2012.
DOI : 10.1016/j.procbio.2012.04.018

K. Zhu and C. Rock, RhlA Converts ??-Hydroxyacyl-Acyl Carrier Protein Intermediates in Fatty Acid Synthesis to the ??-Hydroxydecanoyl-??-Hydroxydecanoate Component of Rhamnolipids in Pseudomonas aeruginosa, Journal of Bacteriology, vol.190, issue.9, pp.3147-54, 2008.
DOI : 10.1128/JB.00080-08

A. Abdel-mawgoud, F. Lepine, and E. Deziel, A Stereospecific Pathway Diverts ??-Oxidation Intermediates to the Biosynthesis of Rhamnolipid Biosurfactants, Chemistry & Biology, vol.21, issue.1, pp.156-64, 2014.
DOI : 10.1016/j.chembiol.2013.11.010
URL : https://hal.archives-ouvertes.fr/pasteur-01134348

J. Campos-garcia, A. Caro, R. Najera, R. Miller-maier, R. Al-tahhan et al., The Pseudomonas aeruginosa rhlG gene encodes an NADPH-dependent beta-ketoacyl reductase which is specifically involved in rhamnolipid synthesis, J Bacteriol, vol.180, pp.4442-51, 1998.

R. Reis, A. Pereira, B. Neves, and D. Freire, Gene regulation of rhamnolipid production in Pseudomonas aeruginosa ??? A review, Bioresource Technology, vol.102, issue.11, pp.6377-84, 2011.
DOI : 10.1016/j.biortech.2011.03.074

J. Campbell, R. Morgan-kiss, and J. Cronan, A new Escherichia coli metabolic competency: growth on fatty acids by a novel anaerobic ??-oxidation pathway, Molecular Microbiology, vol.277, issue.3, pp.793-805, 2003.
DOI : 10.1074/jbc.M201399200
URL : http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2003.03341.x/pdf

C. Korea, R. Badouraly, M. Prevost, J. Ghigo, and C. Beloin, Escherichia coli K-12 possesses multiple cryptic but functional chaperone-usher fimbriae with distinct surface specificities, Environmental Microbiology, vol.93, issue.7, pp.1957-77, 2010.
DOI : 10.1128/jb.177.3.621-627.1995
URL : https://hal.archives-ouvertes.fr/pasteur-01393508

J. Warmink, R. Nazir, and J. Van-elsas, Universal and species-specific bacterial ???fungiphiles??? in the mycospheres of different basidiomycetous fungi, Environmental Microbiology, vol.2, issue.2, pp.300-312, 2009.
DOI : 10.1099/00221287-27-3-509

M. Dutton and C. Evans, Oxalate production by fungi: its role in pathogenicity and ecology in the soil environment, Canadian Journal of Microbiology, vol.97, issue.12, pp.881-95, 1996.
DOI : 10.1016/S0953-7562(09)80227-X

K. Nishino, Y. Inazumi, and A. Yamaguchi, Global Analysis of Genes Regulated by EvgA of the Two-Component Regulatory System in Escherichia coli, Journal of Bacteriology, vol.185, issue.8, pp.2667-72, 2003.
DOI : 10.1128/JB.185.8.2667-2672.2003

E. Fontenot, K. Ezelle, L. Gabreski, E. Giglio, J. Mcafee et al., YfdW and YfdU Are Required for Oxalate-Induced Acid Tolerance in Escherichia coli K-12, Journal of Bacteriology, vol.195, issue.7, pp.1446-55, 2013.
DOI : 10.1128/JB.01936-12
URL : http://jb.asm.org/content/195/7/1446.full.pdf

S. Takanao, S. Honma, T. Miura, C. Ogawa, H. Sugimoto et al., 2170, Bioscience, Biotechnology, and Biochemistry, vol.172, issue.3, pp.524-556, 2014.
DOI : 10.1371/journal.pone.0055126

N. Figueroa-bossi, M. Valentini, L. Malleret, and L. Bossi, Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target, Genes & Development, vol.23, issue.17, pp.2004-2019, 2009.
DOI : 10.1101/gad.541609
URL : http://genesdev.cshlp.org/content/23/17/2004.full.pdf

T. Toratani, T. Shoji, T. Ikehara, K. Suzuki, and T. Watanabe, The importance of chitobiase and N-acetylglucosamine (GlcNAc) uptake in N,N'-diacetylchitobiose [(GlcNAc)2] utilization by Serratia marcescens 2170, Microbiology, vol.281, issue.40, pp.1326-1358, 2008.
DOI : 10.1074/jbc.M605052200

J. Plumbridge and O. Pellegrini, Expression of the chitobiose operon of Escherichia coli is regulated by three transcription factors: NagC, ChbR and CAP, Molecular Microbiology, vol.97, issue.2, pp.437-486, 2004.
DOI : 10.1073/pnas.100127597

O. Francetic, D. Belin, C. Badaut, and A. Pugsley, Expression of the endogenous type II secretion pathway in Escherichia coli leads to chitinase secretion, The EMBO Journal, vol.19, issue.24, pp.6697-703, 2000.
DOI : 10.1093/emboj/19.24.6697

B. Citterio, M. Malatesta, S. Battistelli, F. Marcheggiani, W. Baffone et al., fruit bodies, Canadian Journal of Microbiology, vol.6, issue.3, pp.264-272, 2001.
DOI : 10.1007/s005720050104

D. Boer, W. Gunnewiek, P. Kowalchuk, G. Van-veen, and J. , Growth of Chitinolytic Dune Soil ??-Subclass Proteobacteria in Response to Invading Fungal Hyphae, Applied and Environmental Microbiology, vol.67, issue.8, pp.3358-62, 2001.
DOI : 10.1128/AEM.67.8.3358-3362.2001

G. Bending, E. Poole, J. Whipps, and D. Read, Characterisation of bacteria from Pinus sylvestris-Suillus luteus mycorrhizas and their effects on rootfungus interactions and plant growth, FEMS Microbiol Ecol, vol.39, pp.219-246, 2002.
DOI : 10.1016/s0168-6496(01)00215-x

S. Uroz, P. Courty, J. Pierrat, M. Peter, M. Buee et al., Functional Profiling and Distribution of the Forest Soil Bacterial Communities Along the Soil Mycorrhizosphere Continuum, Microbial Ecology, vol.4, issue.2, pp.404-419, 2013.
DOI : 10.1016/j.funeco.2011.04.002
URL : https://hal.archives-ouvertes.fr/hal-01001500

R. Van-houdt and C. Michiels, Role of bacterial cell surface structures in Escherichia coli biofilm formation, Research in Microbiology, vol.156, issue.5-6, pp.626-659, 2005.
DOI : 10.1016/j.resmic.2005.02.005

S. Kohlmeier, T. Smits, R. Ford, C. Keel, H. Harms et al., Taking the Fungal Highway:?? Mobilization of Pollutant-Degrading Bacteria by Fungi, Environmental Science & Technology, vol.39, issue.12, pp.4640-4646, 2005.
DOI : 10.1021/es047979z

I. Sarand, S. Timonen, E. Nurmiaho-lassila, T. Koivula, K. Haahtela et al., Microbial biofilms and catabolic plasmid harbouring degradative fluorescent pseudomonads in Scots pine mycorrhizospheres developed on petroleum contaminated soil, FEMS Microbiology Ecology, vol.138, issue.2, pp.115-141, 1998.
DOI : 10.1128/jb.176.8.2137-2142.1994

E. Tenorio, T. Saeki, K. Fujita, M. Kitakawa, T. Baba et al., genes/ORFs affecting biofilm formation, FEMS Microbiology Letters, vol.180, issue.1, pp.107-121, 2003.
DOI : 10.1046/j.1365-2958.2000.02008.x

M. Pion, R. Bshary, S. Bindschedler, S. Filippidou, L. Wick et al., ABSTRACT, Applied and Environmental Microbiology, vol.79, issue.22, pp.6862-6869, 2013.
DOI : 10.1128/AEM.01393-13

P. Samadder, J. Xicohtencatl-cortes, Z. Saldana, D. Jordan, P. Tarr et al., O157:H7, Environmental Microbiology, vol.191, issue.7, pp.1815-1841, 2009.
DOI : 10.1056/NEJM198303243081203

J. Overhage, S. Lewenza, A. Marr, and R. Hancock, Identification of Genes Involved in Swarming Motility Using a Pseudomonas aeruginosa PAO1 Mini-Tn5-lux Mutant Library, Journal of Bacteriology, vol.189, issue.5, pp.2164-2173, 2007.
DOI : 10.1128/JB.01623-06

T. Costa, C. Felisberto-rodrigues, A. Meir, M. Prevost, A. Redzej et al., Secretion systems in Gram-negative bacteria: structural and mechanistic insights, Nature Reviews Microbiology, vol.158, issue.6, pp.343-59, 2015.
DOI : 10.1038/158558a0

R. Gerlach and M. Hensel, Protein secretion systems and adhesins: The molecular armory of Gram-negative pathogens, International Journal of Medical Microbiology, vol.297, issue.6, pp.401-416, 2007.
DOI : 10.1016/j.ijmm.2007.03.017

J. Garnett, V. Martínez-santos, Z. Saldaña, T. Pape, W. Hawthorne et al., Structural insights into the biogenesis and biofilm formation by the Escherichia coli common pilus, Proceedings of the National Academy of Sciences, vol.50, issue.Pt 5, pp.3950-3955, 2012.
DOI : 10.1107/S0907444994003112

T. Lehti, P. Bauchart, J. Heikkinen, J. Hacker, T. Korhonen et al., Mat fimbriae promote biofilm formation by meningitis-associated Escherichia coli, Microbiology, vol.40, issue.11, pp.2408-2425, 2010.
DOI : 10.1128/JCM.40.11.3951-3955.2002

A. Otrelo-cardoso, M. Da-silva-correia, V. Schwuchow, D. Svergun, M. Romão et al., Structural Data on the Periplasmic Aldehyde Oxidoreductase PaoABC from Escherichia coli: SAXS and Preliminary X-ray Crystallography Analysis, International Journal of Molecular Sciences, vol.34, issue.2, pp.2223-2259, 2014.
DOI : 10.1107/S0021889800014126

P. Lee, D. Tullman-ercek, and G. Georgiou, The Bacterial Twin-Arginine Translocation Pathway, Annual Review of Microbiology, vol.60, issue.1, pp.373-95, 2006.
DOI : 10.1146/annurev.micro.60.080805.142212

K. Hatzixanthis, T. Palmer, and F. Sargent, A subset of bacterial inner membrane proteins integrated by the twin-arginine translocase, Molecular Microbiology, vol.20, issue.5, pp.1377-90, 2003.
DOI : 10.1093/emboj/20.10.2472

M. Barnhart and M. Chapman, Curli Biogenesis and Function, Annual Review of Microbiology, vol.60, issue.1, pp.131-178, 2006.
DOI : 10.1146/annurev.micro.60.080805.142106

H. Ogasawara, K. Yamamoto, and A. Ishihama, Role of the Biofilm Master Regulator CsgD in Cross-Regulation between Biofilm Formation and Flagellar Synthesis, Journal of Bacteriology, vol.193, issue.10, pp.2587-97, 2011.
DOI : 10.1128/JB.01468-10

K. Kjaergaard, M. Schembri, C. Ramos, S. Molin, and P. Klemm, Antigen 43 facilitates formation of multispecies biofilms, Environmental Microbiology, vol.136, issue.6, pp.695-702, 2000.
DOI : 10.1016/0378-1119(94)90237-2

T. Edgren and S. Nordlund, gene products, FEMS Microbiology Letters, vol.260, issue.1, pp.30-35, 2006.
DOI : 10.1111/j.1574-6968.2006.00297.x

H. Fischer, Genetic regulation of nitrogen fixation in rhizobia, Microbiol Rev, vol.58, pp.352-86, 1994.

K. Eichler, A. Buchet, F. Bourgis, H. Kleber, and M. Mandrand-berthelot, Thefix Escherichia coli region contains four genes related to carnitine metabolism, Journal of Basic Microbiology, vol.20, issue.4, pp.217-244, 1995.
DOI : 10.1094/MPMI-4-571

A. Walt and M. Kahn, The fixA and fixB Genes Are Necessary for Anaerobic Carnitine Reduction in Escherichia coli, Journal of Bacteriology, vol.184, issue.14, pp.4044-4051, 2002.
DOI : 10.1128/JB.184.14.4044-4047.2002
URL : http://jb.asm.org/content/184/14/4044.full.pdf

W. Jia and C. J. , Biochemical Society Transactions, vol.33, issue.1, pp.159-61, 2005.
DOI : 10.1042/BST0330159

C. Sparacino-watkins, J. Stolz, and P. Basu, Nitrate and periplasmic nitrate reductases, Chem. Soc. Rev., vol.693, issue.Pt 11, pp.676-706, 2014.
DOI : 10.1016/j.jelechem.2013.01.030

A. Gardner, R. Helmick, and P. Gardner, Journal of Biological Chemistry, vol.266, issue.10, pp.8172-8179, 2002.
DOI : 10.1093/dnares/8.1.11

N. Harborne, L. Griffiths, S. Busby, and J. Cole, Transcriptional control, translation and function of the products of the five open reading frames of the Escherichia coli nir operon, Molecular Microbiology, vol.2, issue.19, pp.2805-2818, 1992.
DOI : 10.1016/0014-5793(90)80640-5

F. Boogerd, H. Ma, F. Bruggeman, W. Van-heeswijk, R. García-contreras et al., transport in prokaryotes must be active and as a consequence regulation of transport by GlnK is mandatory to limit futile cycling of NH4+/NH3, FEBS Letters, vol.46, issue.1, pp.23-31, 2011.
DOI : 10.1046/j.1365-2958.2002.03153.x

M. Kobayashi and M. Ishimoto, Aerobic inhibition of nitrate assimilation in Escherichia coli. Zeitschrift für allgemeine Mikrobiologie, pp.405-418, 1973.

D. Degelmann, S. Kolb, M. Dumont, J. Murrell, and H. Drake, Enterobacteriaceae facilitate the anaerobic degradation of glucose by a forest soil, FEMS Microbiology Ecology, vol.57, issue.3, pp.312-321, 2009.
DOI : 10.1111/j.1574-6941.2002.tb00938.x

S. Schrey, M. Schellhammer, M. Ecke, R. Hampp, and M. Tarkka, Mycorrhiza helper bacterium Streptomyces AcH 505 induces differential gene expression in the ectomycorrhizal fungus Amanita muscaria, New Phytologist, vol.18, issue.1, pp.205-221, 2005.
DOI : 10.1093/jexbot/52.suppl_1.487

R. Sen, E. Nurmiaho-lassila, K. Haahtela, and K. Korhonen, Specificity and mode of primary attachment of Pseudomonas fluorescens strains to the cell walls of ectomycorrhizal fungi. Mycorrhizas in integrated systems: from genes to plant development ECSC-EC-EAEC, pp.661-665, 1996.

J. Leveau and G. Preston, Bacterial mycophagy: definition and diagnosis of a unique bacterial???fungal interaction, New Phytologist, vol.44, issue.4, pp.859-76, 2008.
DOI : 10.1094/PHYTO.2000.90.4.384

F. Lehembre, D. Doillon, E. David, S. Perrotto, J. Baude et al., Soil metatranscriptomics for mining eukaryotic heavy metal resistance genes, Environmental Microbiology, vol.16, pp.2829-2869, 2013.
DOI : 10.1091/mbc.E04-12-1130
URL : https://hal.archives-ouvertes.fr/hal-01115321

M. Brosche, B. Vinocur, E. Alatalo, A. Lamminmaki, T. Teichmann et al., Gene expression and metabolite profiling of Populus euphratica growing in the Negev desert, Genome Biology, vol.6, issue.12, p.101, 2005.
DOI : 10.1186/gb-2005-6-12-r101

T. Nanjo, T. Sakurai, Y. Totoki, A. Toyoda, M. Nishiguchi et al., Functional annotation of 19,841 Populus nigra full-length enriched cDNA clones, BMC Genomics, vol.8, issue.1, p.448, 2007.
DOI : 10.1186/1471-2164-8-448

F. Sterky, R. Bhalerao, P. Unneberg, B. Segerman, P. Nilsson et al., A Populus EST resource for plant functional genomics, Proceedings of the National Academy of Sciences, vol.300, issue.5625, pp.13951-13957, 2004.
DOI : 10.1126/science.1083264

A. Kohler, C. Delaruelle, D. Martin, N. Encelot, and F. Martin, The poplar root transcriptome: analysis of 7000 expressed sequence tags, FEBS Letters, vol.480, issue.1-3, pp.37-41, 2003.
DOI : 10.1016/S0014-5793(00)01772-5

S. Ralph, C. Oddy, D. Cooper, H. Yueh, S. Jancsik et al., Genomics of hybrid poplar (Populus trichocarpa?? deltoides) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full-length cDNA libraries, expressed sequence tags, and a cDNA microarray for the study of insect-induced defences, Molecular Ecology, vol.134, issue.5, pp.1275-97, 2006.
DOI : 10.1093/ee/27.6.1368

R. Varshney, P. Hiremath, P. Lekha, J. Kashiwagi, J. Balaji et al., A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.), BMC Genomics, vol.10, issue.1, p.523, 2009.
DOI : 10.1186/1471-2164-10-523

V. Gupta, S. Raghuvanshi, A. Gupta, N. Saini, A. Gaur et al., The water-deficit stress- and red-rot-related genes in sugarcane, Functional & Integrative Genomics, vol.271, issue.2, pp.207-221, 2010.
DOI : 10.1590/S1415-47572001000100002

H. Li, Y. Wang, J. Jiang, G. Liu, C. Gao et al., Identification of genes responsive to salt stress on Tamarix hispida roots, Gene, vol.433, issue.1-2, pp.65-71, 2009.
DOI : 10.1016/j.gene.2008.12.007

R. Lambilliotte, R. Cooke, D. Samson, C. Fizames, F. Gaymard et al., Large-scale identification of genes in the fungus Hebeloma cylindrosporum paves the way to molecular analyses of ectomycorrhizal symbiosis, New Phytologist, vol.528, issue.3, pp.505-518, 2004.
DOI : 10.1101/gr.8.3.175

D. Brown, F. Cheung, R. Proctor, R. Butchko, L. Zheng et al., Comparative analysis of 87,000 expressed sequence tags from the fumonisin-producing fungus Fusarium verticillioides, Fungal Genetics and Biology, vol.42, issue.10, pp.848-61, 2005.
DOI : 10.1016/j.fgb.2005.06.001

N. Karim, H. Shibuya, and T. Kikuchi, Analysis of expressed sequence tags from the wood-decaying fungus Fomitopsis palustris and identification of potential genes involved in the decay process, J Microbiol Biotechnol, vol.21, pp.347-58, 2011.

S. Geisler and J. Coller, RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts, Nature Reviews Molecular Cell Biology, vol.472, issue.11, pp.699-712, 2013.
DOI : 10.1038/nature09819
URL : http://europepmc.org/articles/pmc4852478?pdf=render

M. Ferracin, D. Gautheret, F. Hubé, S. Mani, J. Mattick et al., The Non-Coding RNA Journal Club: Highlights on Recent Papers, Non-Coding RNA, vol.1, issue.1, pp.87-93, 2015.
DOI : 10.15252/embj.201489499
URL : http://www.mdpi.com/2311-553X/1/1/87/pdf

C. Ponting and T. Belgard, Transcribed dark matter: meaning or myth?, Human Molecular Genetics, vol.38, issue.suppl_1, pp.162-170, 2010.
DOI : 10.1093/nar/gkp939
URL : https://academic.oup.com/hmg/article-pdf/19/R2/R162/1789807/ddq362.pdf

A. Palazzo and E. Lee, Non-coding RNA: what is functional and what is junk? Front Genet, 2015.
DOI : 10.3389/fgene.2015.00002
URL : http://journal.frontiersin.org/article/10.3389/fgene.2015.00002/pdf

C. Mora, D. Tittensor, S. Adl, A. Simpson, and B. Worm, How Many Species Are There on Earth and in the Ocean?, PLoS Biology, vol.93, issue.8, p.1001127, 2011.
DOI : 10.1371/journal.pbio.1001127.s004
URL : https://doi.org/10.1371/journal.pbio.1001127

H. Ellegren, Genome sequencing and population genomics in non-model organisms, Trends in Ecology & Evolution, vol.29, issue.1, pp.51-63, 2014.
DOI : 10.1016/j.tree.2013.09.008

J. Nesme, W. Achouak, S. Agathos, M. Bailey, P. Baldrian et al., Back to the Future of Soil Metagenomics, Frontiers in Microbiology, vol.7, issue.358, p.73, 2016.
DOI : 10.1038/nrmicro2119
URL : http://journal.frontiersin.org/article/10.3389/fmicb.2016.00073/pdf

T. Spribille, V. Tuovinen, P. Resl, D. Vanderpool, H. Wolinski et al., Basidiomycete yeasts in the cortex of ascomycete macrolichens, Science, vol.2, issue.6298, pp.488-92, 2016.
DOI : 10.1046/j.1469-8137.2001.00122.x