, UMR Interactions Arbres/Microorganismes (IAM) 1136, INRA
, Instituto de Investigaciones Fisiol ogicas y Ecol ogicas Vinculadas a la Agricultura (IFEVA) and Consejo Nacional de Investigaciones Cient ?ficas y T ecnicas (CONICET), vol.4453, p.383393315
, email clemence.bonnot@inra.fr)
The powdery mildew-resistant Arabidopsis mlo2 mlo6 mlo12 triple mutant displays altered infection phenotypes with diverse types of phytopathogens, Scientific Reports, vol.7, pp.1-15, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01604162
Evolutionary genetics of plant adaptation, Trends in Genetics, vol.27, pp.258-266, 2011. ,
Photodegradation alleviates the lignin bottleneck for carbon turnover in terrestrial ecosystems, Proceedings of the National Academy of Sciences, vol.113, pp.1-6, 2016. ,
Plant litter decomposition in a semi-arid ecosystem controlled by photodegradation, Nature, vol.442, pp.555-558, 2006. ,
The rise of plants and their effect on weathering and atmospheric CO 2, Science, vol.276, pp.544-546, 1997. ,
Plant productivity and environment, Science, vol.218, pp.443-448, 1982. ,
Diversification of a transcription factor family led to the evolution of antagonistically acting genetic regulators of root hair growth report diversification of a transcription factor family led to the evolution of antagonistically acting genetic regulators of root hair growth, Current Biology, vol.26, pp.1622-1628, 2016. ,
Sustaining the future of plant breeding: the critical role of the USDA-ARS National Plant Germplasm System, Crop Science, vol.58, pp.1-18, 2018. ,
Multiple strategies for pathogen perception by plant immune receptors, New Phytologist, vol.219, pp.17-24, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-02622765
The POLARIS peptide of Arabidopsis regulates auxin transport and root growth via effects on ethylene signaling, Plant Cell, vol.18, pp.3058-3072, 2006. ,
Geology of mankind, Nature, vol.415, p.23, 2002. ,
On the various contrivances by which British and foreign orchids are fertilized by insects ,
Composition and method for modulating plant root hair development. US Patent Application no. 12/451,574. Ehrlich PR, Harte J, Proceedings of the National Academy of Sciences, vol.112, pp.1-2, 2011. ,
Cold damage and plant mortality in experimental provenance plantation with Scots Pine in Northern Sweden, Studia Forestalia Suecica, pp.39-3150, 1966. ,
Leaf starch turnover occurs in long days and in falling light at the end of the day, Plant Physiology, vol.174, pp.2199-2212, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-02622635
Food security: the challenge of feeding 9 billion people, Science, vol.327, pp.812-819, 2010. ,
Circadian control of carbohydrate availability for growth in Arabidopsis plants at night, Proceedings of the National Academy of Sciences, vol.107, pp.9458-9463, 2010. ,
Integrating pests and pathogens into the climate change/food security debate, Journal of Experimental Botany, vol.60, pp.2827-2838, 2009. ,
Global profiling of phytohormone dynamics during combined drought and pathogen stress in Arabidopsis thaliana reveals ABA and JA as major regulators, Scientific Report, vol.4, p.4017, 2017. ,
Temperature extremes: effect on plant growth and development, Weather and Climate Extremes, vol.10, pp.4-10, 2015. ,
Discovery, characterization and exploitation of Mlo powdery mildew resistance in barley, Euphytica, vol.63, pp.141-152, 1992. ,
Synergies between agricultural intensification and climate change could create surprising vulnerabilities for crops, AIBS Bulletin, vol.58, pp.847-854, 2008. ,
Climate change impacts, adaptive capacity and vulnerability of European forest ecosystems, Forest Ecology and Management, vol.259, pp.698-709, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-02669018
Global scale climate-crop yield relationships and the impacts of recent warming, Environmental Research Letters, vol.2, p.14002, 2007. ,
Assessing the impacts of global warming on forest pest dynamics, Frontiers in Ecology and the Environment, vol.1, pp.130-137, 2003. ,
Biodiversity and ecosystem functioning: current knowledge and future challenge, Science, vol.294, pp.804-808, 2001. ,
Advanced methods of plant disease detection, Agronomy for Sustainable Development, vol.35, pp.1-25, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01284270
Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways, Natural Product Reports, vol.33, pp.951-962, 2016. ,
The Aquilegia JAGGED homolog promotes proliferation of adaxial cell types in both leaves and stems, New Phytologist, vol.216, pp.536-548, 2017. ,
Plant communication in a widespread goldenrod: keeping herbivores on the move, British Ecological Society, vol.41, pp.1049-1061, 2017. ,
Anthropogenic ocean acidification over the twenty-first century and its impact on calcifying organisms, Nature, vol.437, pp.681-686, 2005. ,
URL : https://hal.archives-ouvertes.fr/hal-00124807
Harnessing plant metabolic diversity, Current Opinion in Chemical Biology, vol.40, pp.24-30, 2017. ,
A large and persistent carbon sink in the World's forest, Science, vol.333, pp.988-993, 2011. ,
The potential effects of climatic change on agricultural insect pests, Agricultural and Forest Meteorology, vol.57, pp.221-240, 1991. ,
RSL Class I genes controlled the development of epidermal structures in the common ancestor of land plants, Current Biology, vol.26, pp.93-99, 2016. ,
A translational synthetic biology platform for rapid access to gram-scale quantities of novel drug-like molecules, Metabolic Engineering, vol.42, pp.185-193, 2017. ,
Effect of the environment on the secondary metabolic profile of Tithonia diversifolia: a model for environmental metabolomics of plants, Scientific Report, vol.6, pp.1-11, 2016. ,
Nonlinear temperature effects indicate severe damages to U.S. crop yields under climate change, Proceedings of the National Academy of Sciences, vol.106, pp.15594-15598, 2009. ,
Arabidopsis plants perform arithmetic division to prevent starvation at night, vol.2, pp.1-24, 2013. ,
The Anthropocene: conceptual and historical perspectives, Philosophical Transactions. Series A: Mathematical, Physical, and Engineering Sciences, vol.369, pp.842-867, 2011. ,
Agricultural sustainability and intensive production practices, Nature, vol.418, pp.671-677, 2002. ,
, World population prospects: the 2015 revision, United Nations Department of Economic and Social Affairs, vol.33, pp.1-66, 2015.
Variation in drought resistance, drought acclimation and water conservation in four willow cultivars used for biomass production, Tree Physiology, vol.27, pp.1339-1346, 2007. ,
Plant responses to drought, acclimation and stress tolerance, Photosynthetica, vol.38, pp.171-186, 2000. ,
CBF-dependent signaling pathway: a key responder to low temperature stress in plants, Critical Reviews in Biotechnology, vol.31, pp.186-192, 2011. ,
Transcript profiling of a novel meristem, the monocot cambium, Journal of Integrative Plant Biology, vol.59, pp.436-449, 2017. ,
Environmental metabarcoding reveals contrasting belowground and aboveground fungal communities from Poplar at a Hg phytomanagement site, Microbiol. Ecol, vol.74, pp.795-809, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01518636
Structure, variation, and assembly of the root-associated microbiomes of rice, Proc. Natl. Acad. Sci, vol.112, issue.8, pp.911-920, 2015. ,
Phylogenetic analysis of community assembly and structure over space and time, Trends Ecol. Evol, vol.23, pp.619-630, 2008. ,
FROGS: Find, rapidly, OTUs with galaxy solution, Bioinformatics, vol.34, pp.1287-1294, 2018. ,
Understanding and engineering beneficial plant-microbe interactions: Plant growth promotion in energy crops, Plant Biotechnol. J, vol.12, pp.1193-1206, 2014. ,
Embracing the unknown: Disentangling the complexities of the soil microbiome, Nat. Rev. Microbiol, vol.15, pp.579-590, 2017. ,
Metacoder: An R package for visualization and manipulation of community taxonomic diversity data, PLOS Comput. Biol, vol.13, pp.1-15, 2017. ,
The mycorrhizal helper bacteria revisited, New Phytol, vol.176, pp.22-36, 2007. ,
Environmental and genetic effects on the formation of ectomycorrhizal and arbuscular mycorrhizal associations in cottonwoods, Oecologia, vol.149, pp.158-164, 2006. ,
Tree genetics defines fungal partner communities that may confer drought tolerance, Proc. Natl. Acad. Sci, vol.114, pp.11169-11174, 2017. ,
Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types, Appl. Environ. Microbiol, vol.77, pp.5934-5944, 2011. ,
Regulation of antibiotic production in rootcolonizing Pseudomonas spp. and relevance for biological control of plant disease, Annu. Rev. Phytopathol, vol.41, pp.117-153, 2003. ,
Microbial community response to growing season and plant nutrient optimisation in a boreal Norway spruce forest, Soil Biol. Biochem, vol.125, pp.197-209, 2018. ,
Towards a holistic understanding of the beneficial interactions across the Populus microbiome, New Phytol, vol.205, pp.1424-1430, 2015. ,
The water culture method for growing plant without soil. California Agric. Exp. Circ. 337. The College of Agriculture University of California, 1950. ,
The role of soil microorganisms in plant mineral nutrition-Current knowledge and future directions, Front. Plant Sci, vol.8, p.1617, 2017. ,
Plant root-microbe communication in shaping root microbiomes, Plant Mol. Biol, vol.90, pp.575-587, 2016. ,
Rapid responses of soil microorganisms improve plant fitness in novel environments, Proc. Natl. Acad. Sci, vol.109, pp.14058-14062, 2012. ,
Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa, Science, vol.349, pp.860-864, 2015. ,
Fungal endophytes of Populus trichocarpa alter host phenotype, gene expression and rhizobiome composition, Mol. Plant-Microbe Interact, vol.32, pp.853-864, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02627563
Forest soil bacteria: Diversity, involvement in ecosystem processes, and response to global change. Microbiol, Mol. Biol. Rev. (MMBR), vol.81, pp.63-79, 2017. ,
Practical innovations for high-throughput amplicon sequencing, Nat. Methods, vol.10, pp.999-1002, 2013. ,
Whole-genome draft assembly of Populus tremula × Populus alba clone INRA 717-1B4, Silvae Genet, vol.65, pp.74-79, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-02637979
Carbohydrate and amino acid metabolism in the Eucalyptus globulus-Pisolithus tinctorius ectomycorrhiza during glucose utilization, Plant Physiol, vol.118, pp.627-635, 1998. ,
URL : https://hal.archives-ouvertes.fr/hal-02692575
Impact of salicylic acid-and jasmonic acid-regulated defences on root colonization by Trichoderma harzianum T-78, Plant Signal. Behav, vol.12, p.1345404, 2017. ,
Analysis of single root tip microbiomes suggests that distinctive bacterial communities are selected by Pinus sylvestris roots colonized by different ectomycorrhizal fungi, Environ. Microbiol, vol.18, pp.1470-1483, 2016. ,
Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data, PLoS One, vol.8, p.61217, 2013. ,
Abiotic stress responses and microbe-mediated mitigation in plants: The omics strategies, Front. Plant Sci, vol.8, p.172, 2017. ,
Recent insights on biological and ecological aspects of ectomycorrhizal fungi and their interactions, Front. Microbiol, vol.9, p.216, 2018. ,
The rhizosphere microbiome: Significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms, FEMS Microbiol. Rev, vol.37, pp.634-663, 2013. ,
Belowground microbiota and the health of tree crops, Front. Microbiol, vol.9, p.1006, 2018. ,
Drought stress and root-associated bacterial communities, Front. Plant Sci, vol.8, p.2223, 2018. ,
Mastering ectomycorrhizal symbiosis: The impact of carbohydrates, J. Exp. Bot, vol.59, pp.1097-1108, 2008. ,
FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild, Fungal Ecol, vol.20, pp.241-248, 2016. ,
Multivariate Analysis of Ecological Communities in R: Vegan tutorial, 2015. ,
Attributing functions to ectomycorrhizal fungal identities in assemblages for nitrogen acquisition under stress, ISME J, vol.8, pp.321-330, 2014. ,
Functional outcomes of fungal community shifts driven by tree genotype and spatial-temporal factors in Mediterranean pine forests, Environ. Microbiol, vol.19, pp.1639-1652, 2017. ,
Impact of plant domestication on rhizosphere microbiome assembly and functions, Plant Mol. Biol, vol.90, pp.635-644, 2016. ,
Soil organisms and global climate change, Plant Pathol, vol.60, pp.82-99, 2011. ,
The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools, Nucleic Acids Res, vol.41, pp.590-596, 2013. ,
The rhizosphere: A playground and battlefield for soilborne pathogens and beneficial microorganisms, R: A language and environment for statistical computing. R Foundation for Statistical Computing, vol.321, pp.341-361, 2009. ,
mixOmics: An R package for 'omics feature selection and multiple data integration, PLOS Comput. Biol, vol.13, p.1005752, 2017. ,
A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees, PLoS One, vol.8, p.76382, 2013. ,
, Mycorrhizal Symbiosis, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01268065
Decoding the mannitol enigma in filamentous fungi, Trends Microbiol, vol.15, pp.257-262, 2007. ,
Abiotic stresses shift belowground Populus-associated bacteria toward a core stress microbiome, vol.3, pp.70-87, 2018. ,
,
Systematics and evolution of Populus, Biology of Populus. Stettler RF, pp.7-32, 1996. ,
The ethylene signal transduction pathway in plants, Science, vol.268, pp.667-675, 1995. ,
Structure, variation, and assembly of the root-associated microbiomes of rice, Proceedings of the National Academy of Sciences, vol.112, issue.8, pp.911-920, 2015. ,
Rhizospheric influence on soil respiration and decomposition in a temperate Norway spruce stand, Soil Biology & Biochemistry, vol.39, pp.2103-2110, 2007. ,
Agrobacterium tumefaciens as an agent of disease, Trends in Plant Science, vol.8, issue.8, pp.162-168, 2003. ,
New resources for genetic studies in Populus nigra: genome-wide SNP discovery and development of a 12k Infinium array, Mol Ecol Resour, vol.16, pp.1023-1036, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-02636258
Understanding and engineering beneficial plant-microbe interactions: Plant growth promotion in energy crops, Plant Biotechnology Journal, vol.12, issue.9, pp.1193-1206, 2014. ,
Molecular sensing of bacteria in plants. The highly conserved RNA-binding motif RNP-1 of bacterial cold shock proteins is recognized as an elicitor signal in tobacco, J. Biol. Chem, vol.278, pp.6201-6208, 2003. ,
Responses to Precipitation Reduction and Forest Management in Forest Ecosystems across Germany, PLoS ONE, vol.10, issue.4, pp.1-24, 2015. ,
The ectomycorrhizal fungus laccaria bicolor stimulates lateral root formation in poplar and arabidopsis through auxin transport and signaling, Plant Physiology, vol.151, issue.4, 1991. ,
URL : https://hal.archives-ouvertes.fr/hal-02667577
Burkholderia phytofirmans PsJN acclimates grapevine to cold by modulating carbohydrate metabolism, Mol. Plant-Microbe Interaction, vol.25, pp.496-504, 2012. ,
The diversity and biogeography of soil bacterial communities, Proceedings of the National Academy of Sciences of the United States of America, vol.103, pp.626-631, 2006. ,
Toward an ecological classification of soil bacteria, Ecology, vol.88, issue.6, pp.1354-1364, 2007. ,
, , 2012.
, Cross-biome metagenomic analyses of soil microbial communities and their functional attributes, Proceedings of the National Academy of Sciences, vol.109, issue.52, pp.21390-21395
, , 2013.
, Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States, Science, vol.342, issue.6158, pp.621-624
Embracing the unknown: Disentangling the complexities of the soil microbiome, Nature Reviews Microbiology, vol.15, issue.10, pp.579-590, 2017. ,
Agrobacterium mediated transformation and regeneration of Populus, Mol Gen Genet, vol.206, p.192, 1987. ,
, , 2018.
, Assembly and ecological function of the root microbiome across angiosperm plant species, Proceedings of the National Academy of Sciences, vol.115, issue.6
Experimental study of sequences of ectomycorrhizal fungi on 170 birch (Betula sp.) seedling root systems, Soil Biology & Biochemistry, vol.17, pp.591-600, 1985. ,
Impact of poplar-based phytomanagement on soil properties and microbial communities in a metal-contaminated site, FEMS Microbiology Ecology, vol.92, issue.10, pp.1-13, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01512324
, Transmission of Bacterial Endophytes. Microorganisms, vol.5, p.70, 2017.
The mycorrhiza helper bacteria revisited, New Phytologist, vol.176, pp.22-36, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-02667863
Bacterial-fungal interactions: hyphens between agricultural, clinical, environmental, and food microbiologists, Microbiology and Molecular Biology Reviews: MMBR, vol.75, issue.4, pp.583-609, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-02651157
Inside the root microbiome: Bacterial root endophytes and plant growth promotion, American Journal of Botany, vol.100, issue.9, pp.1738-1750, 2013. ,
Host Genotype and Nitrogen Form Shape the Root Microbiome of Pinus radiata, Microbial Ecology, vol.75, pp.419-433, 2018. ,
Helper bacteria: a new dimension to the mycorrhizal symbiosis (Tansley Review, 76), New Phytologist, vol.128, pp.197-210, 1994. ,
Environmental and genetic effects on the formation of ectomycorrhizal and arbuscular mycorrhizal associations in cottonwoods, Oecologia, vol.149, issue.1, pp.158-164, 2006. ,
Tree genetics defines fungal partner communities that may confer drought tolerance, Proceedings of the National Academy of Sciences of the United States of America, vol.114, pp.11169-11174, 2017. ,
Colonisation of poplar trees by gfp expressing bacterial endophytes, FEMS Microbiology Ecology, vol.48, issue.1, p.118, 2004. ,
Diversity of root-associated bacteria associated with field-grown canola (Brassica napus L.) and wheat (Triticum aestivum L.), FEMS Microb Ecol, vol.26, pp.43-50, 1998. ,
A novel baiting microcosm approach used to identify the bacterial community associated with Penicillium bilaii hyphae in soil, PLoS One, p.12, 2017. ,
Interplay between endophyte prevalence, effects and transmission: Insights from a natural grass population, PLoS ONE, vol.10, issue.10, pp.1-17, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-02631701
Nuclear jasmonate and salicylate signaling and crosstalk in defense against pathogens, Frontiers in Plant Science, vol.4, pp.1-11, 2013. ,
Identifying the active microbiome associated with roots and rhizosphere soil of oilseed rape, Applied and Environmental Microbiology, vol.83, issue.22, pp.1-14, 2017. ,
The Impact of Beneficial Plant-Associated Microbes on Plant Phenotypic Plasticity, J Chem Ecol, vol.39, pp.826-839, 2013. ,
, , 2016.
, Divergent habitat filtering of root and soil fungal communities in temperate beech forests, Scientific Report, pp.1-10
Forest management type influences diversity and community composition of soil fungi across temperate forest ecosystems, Frontiers in Microbiology, vol.6, pp.1-11, 2015. ,
Microscopic characterization of orchid mycorrhizal fungi: Scleroderma as a putative novel orchid mycorrhizal fungus of Vanilla in different crop systems, Phytobiomes Journal, vol.2, issue.3, pp.147-157, 2018. ,
Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types, Applied and Environmental Microbiology, vol.77, issue.17, pp.5934-5944, 2011. ,
Selective influence of plant species on microbial diversity in the rhizosphere, Soil Biol Biochem, vol.30, pp.369-378, 1998. ,
New North American truffles (Tuber spp.) and their ectomycorrhizal associations, Mycologia, vol.105, issue.1, pp.194-209, 2013. ,
Interactions with soil biota shift from negative to positive when a tree species is moved outside its native range, New Phytologist, vol.202, issue.2, pp.415-421, 2014. ,
Plant nutrient resource use strategies shape active rhizosphere microbiota through root exudation, Frontiers in Plant Science, vol.871, pp.1-13, 2018. ,
URL : https://hal.archives-ouvertes.fr/cea-01968948
Microbial community response to growing season and plant nutrient optimisation in a boreal Norway spruce forest, Soil Biology and Biochemistry, vol.125, pp.197-209, 2018. ,
Towards a holistic understanding of the beneficial interactions across the Populus microbiome, New Phytologist, vol.205, issue.4, pp.1424-1430, 2015. ,
The effects of host age and spatial location on bacterial community composition in the English Oak tree, Environmental Microbiology Reports, vol.8, issue.5, 2016. ,
Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies, Frontiers in Plant Science, vol.8, 2017. ,
Drought legacy effects on the composition of soil fungal and prokaryote communities, Frontiers in Microbiology, vol.9, issue.3, pp.1-12, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02626888
Comparative genomics of bacteria from the genus Collimonas: linking (dis)similarities in gene content to phenotypic variation and conservation, Environmental Microbiology Reports, vol.4, issue.4, pp.424-432, 2012. ,
The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms, FEMS Microbiology Reviews, vol.37, issue.5, pp.634-663, 2013. ,
Belowground Microbiota and the Health of Tree Crops, Front. Microbiol, vol.9, p.1006, 2018. ,
Colonization of Pinus radiata D. Don seedling roots by biocontrol bacteria Erwinia billingiae and Bacillus simplex, Forests, vol.10, issue.7, pp.1-13, 2019. ,
Yeast communities associated with the bulk-soil, rhizosphere and ectomycorrhizosphere of a Nothofagus pumilio forest in northwestern Patagonia, Argentina. FEMS Microbiology Ecology, vol.78, issue.3, pp.531-541, 2011. ,
, , 2013.
, Phytochemical analysis of mature tree root exudates in situ and their role in shaping soil microbial communities in relation to tree N-acquisition strategy, Plant Physiology and Biochemistry, vol.72, pp.169-177
Bacterial biofilm formation on the hyphae of ectomycorrhizal fungi: A widespread ability under controls?, FEMS Microbiology Ecology, vol.94, issue.7, pp.1-14, 2018. ,
Growing poplars for research with and without mycorrhizas, Frontiers in Plant Science, vol.4, pp.1-11, 2013. ,
Rhizosphere carbon deposition, oxidative stress and nutritional changes in two poplar species exposed to aluminum, Tree Physiology, vol.29, issue.3, pp.423-436, 2009. ,
Ethylene and 1-aminocyclopropane-1-carboxylate (ACC) in plant-bacterial interactions, Frontiers in Plant Science, vol.9, issue.2, pp.1-17, 2018. ,
Drought Stress and Root-Associated Bacterial Communities. Frontiers in Plant Science, vol.8, 2018. ,
Mastering ectomycorrhizal symbiosis: The impact of carbohydrates, Journal of Experimental Botany, vol.59, issue.5, pp.1097-1108, 2008. ,
Carbohydrates and nitrogen: nutrients and signals in ectomycorrhizas, Plant surface microbiology, pp.373-392, 2004. ,
The rhizosphere: carbon sources and microbial populations, Ecological Interactions in Soil, pp.107-121, 1985. ,
MAMP (microbe-associated molecular pattern) triggered immunity in plants, Frontiers in Plant Science, vol.4, pp.1-14, 2013. ,
A microcosm approach highlights the response of soil mineral weathering bacterial communities to an increase of K and Mg availability, Scientific Reports, vol.9, issue.1, pp.1-13, 2019. ,
Plant phenotypic plasticity in a changing climate, Trends in Plant Science, vol.15, issue.12, pp.684-692, 2010. ,
, , 2016.
, FUNGuild : An open annotation tool for parsing fungal community datasets by ecological guild, Fungal Ecology, vol.20, pp.241-248
Dynamics of aspen roots colonization by Pseudomonads reveals strain-specific and mycorrhizal-specific patterns of biofilm formation, Frontiers in Microbiology, vol.9, pp.1-16, 2018. ,
1-Aminocyclopropane-1-carboxylate deaminase enhances Agrobacterium tumefaciens-mediated gene transfer into plant cells, Applied and Environmental Microbiology, vol.74, issue.8, pp.2526-2528, 2008. ,
Verrucomicrobia subdivision 1 strains display a difference in the colonization of the leek (Allium porrum) rhizosphere, FEMS Microbiol Ecol, vol.78, pp.297-305, 2011. ,
Effects of ectomycorrhiza on host growth and carbon balance in a semihydroponic cultivation system, New Phytologist, vol.112, pp.389-398, 1989. ,
Sampling root exudates -mission impossible? Rhizosphere, vol.6, pp.116-133, 2018. ,
Multivariate Analysis of Ecological Communities in R : vegan tutorial, 2015. ,
Selection on soil microbiomes reveals reproducible impacts on plant function, ISME Journal, vol.9, issue.4, pp.980-989, 2015. ,
Macrofauna contributes to organic matter decomposition and soil quality in Himalayan agroecosystems, India. Appl. Soil Ecol, vol.120, pp.20-29, 2017. ,
Transformation of Poplar by Agrobacterium tumefaciens, Bio/Technology, vol.4, issue.6, pp.533-536, 1986. ,
The JAZ Proteins: A Crucial Interface in the Jasmonate Signaling Cascade, The Plant Cell, vol.23, issue.9, pp.3089-3100, 2011. ,
Attributing functions to ectomycorrhizal fungal identities in assemblages for nitrogen acquisition under stress, ISME Journal, vol.8, issue.2, pp.321-330, 2014. ,
Phyllosphere and carposhere bacterial communities in olive plants subjected to different cultural practices, International Journal of Plant Biology, pp.15-19, 2015. ,
Endophytes in plant system: Roles in growth promotion, mechanism and their potentiality in achieving agriculture sustainability, International Journal of Chemical Studies, vol.6, issue.1, pp.270-274, 2018. ,
Crosstalk between sugarcane and a plant-growth promoting Burkholderia species, Scientific Reports, 2016. ,
Laccaria bicolor MiSSP8 is a small-secreted protein decisive for the establishment of the ectomycorrhizal symbiosis, Environ Microbiol, vol.21, pp.3765-3779, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02627877
, , 2007.
, Concomitant Activation of Jasmonate and Ethylene Response Pathways Is Required for Induction of a Plant Defensin Gene in Arabidopsis, The Plant Cell, vol.10, issue.12, p.2103
Biodegradation and biological treatments of cellulose, hemicellulose and lignin: An overview, International Microbiology, vol.5, issue.2, pp.53-63, 2002. ,
Functional outcomes of fungal community shifts driven by tree genotype and spatial-temporal factors in Mediterranean pine forests, Environmental Microbiology, vol.19, issue.4, pp.1639-1652, 2017. ,
Genetic and functional diversity of ericoid mycorrhizal fungi, Symbiosis, vol.25, issue.1-3, pp.19-27, 1998. ,
Ecology, management, and use of aspen and balsam poplar in the prairie provinces, Forestry Canada, Special Report, vol.1, pp.1-252, 1992. ,
, , 2000.
, Arabidopsis map kinase 4 negatively regulates systemic acquired resistance, Cell, vol.103, issue.7, pp.1111-1131
Going back to the roots: the microbial ecology of the rhizosphere, Nature Reviews Microbiology, vol.11, p.789, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-02651785
NPR1: the spider in the web of induced resistance signaling pathways, Current Opinion in Plant Biology, vol.7, pp.456-464, 2004. ,
Microbial interactions in the rhizosphere: beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition process. A review, Biology and Fertility of Soils, vol.51, issue.4, pp.403-415, 2015. ,
Beneficial microbes in a changing environment : are they always helping plants to deal with insects ?, Functional Ecology, vol.27, pp.574-586, 2013. ,
Chapter 1 -Field trials with lignin-modi ed transgenic trees, Advances in Botanical Research, vol.61, pp.1-36, 2012. ,
Investigating potential of some poplar (Populus sp.) clones for phytoremediation of nitrates through biomass production. Environmental Applications of Poplar and Willow Working Party, pp.18-20, 2006. ,
Microbial products trigger amino acid exudation from plant roots, Plant Physiol, vol.136, pp.2887-2894, 2004. ,
, , 2014.
, 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.111, pp.8299-8304
A secreted effector protein of Laccaria bicolor is required for symbiosis development, Current Biology, vol.21, issue.14, pp.1197-1203, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-02651071
The AP2/ERF Domain Transcription Factor ORA59 Integrates Jasmonic Acid and Ethylene Signals in Plant Defense, Plant Physiology, vol.147, issue.3, pp.1347-1357, 2008. ,
Soil organisms and global climate change, Plant Pathology, vol.60, issue.1, pp.82-99, 2011. ,
The Microbiome of Endophytic, Wood Colonizing Bacteria from Pine Trees as Affected by Pine Wilt Disease, Scientific Reports, pp.1-9, 2017. ,
Secondary metabolites in fungus-plant interactions, Frontiers in Plant Science, vol.6, pp.1-23, 2015. ,
Exudation of organic acid anions from poplar roots after exposure to Al, Cu and Zn, Tree Physiology, vol.27, issue.2, pp.313-320, 2007. ,
The influences of four types of soil on the growth, physiological and biochemical characteristics of Lycoris aurea (L' Her, Herb. Scientific Reports, vol.7, pp.1-9, 2017. ,
The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools, Nucleic Acids Research, vol.41, pp.590-596, 2013. ,
The rhizosphere: A playground and battlefield for soilborne pathogens and beneficial microorganisms, Mycorrhizae: Sustainable Agriculture and Forestry, vol.321, pp.341-361, 2008. ,
,
Colonisation of Pinus halepensis roots by Pseudomonas fluorescens and interaction with the ectomycorrhizal fungus Suillus granulatus, FEMS Microbiology Ecology, vol.51, issue.3, pp.303-311, 2005. ,
Soil microbial communities under tillage systems in Australia, Plant, Soil and Microbes, vol.1, pp.93-102, 2015. ,
Collapse of riparian poplar forests downstream from dams in western prairies: Probable causes and prospects for mitigation, Environmental Management, vol.182, p.451, 1990. ,
Ve?etation alluviale et flux de nutriments : des liens interactifs, Les forets riveraines des cours d'eau. Écologie, fonctions et gestion / H. Piégay, G. Pautou, C. Ruffinoni, éditeurs, pp.134-154, 2003. ,
Editorial: Temperature and tree growth, Tree Physiology, vol.30, issue.6, pp.667-668, 2010. ,
Rhizosphere yeasts improve P uptake of a maize arbuscular mycorrhizal association, Applied Soil Ecology, vol.125, pp.18-25, 2018. ,
Feed your friends: do plant exudates shape the root microbiome?, Trends Plant Sci, vol.23, pp.25-41, 2018. ,
NIH Image to ImageJ: 25 years of image analysis, Nature methods, vol.9, issue.7, pp.671-675, 2012. ,
Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce, Frontiers in Microbiology, vol.5, pp.1-13, 2014. ,
, , 2010.
, Belowground carbon allocation by trees drives seasonal patterns of extracellular enzyme activities by altering microbial community composition in a beech forest soil, New Phytologist, vol.187, issue.3, pp.843-858
The land flora: a phototroph-fungus partnership?, Tree, issue.1, p.13, 1998. ,
URL : https://hal.archives-ouvertes.fr/hal-02699228
Effect of Laccaria bicolor strains inoculated on Douglas-fir (Pseudotsuga menziesii) several years after nursery inoculation, Canadian Journal of Forest Research, vol.30, issue.3, pp.360-371, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-02695964
Sebacinales form ectendomycorrhizas with Cavendishia nobilis, a member of the Andean clade of Ericaceae, in the mountain rain forest of southern Ecuador, New Phytologist, vol.169, issue.2, pp.355-365, 2006. ,
Salicylic acid signal transduction: the initiation of biosynthesis, perception and transcriptional reprogramming, Frontiers in Plant Science, vol.5, pp.1-10, 2014. ,
A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees, PLoS ONE, vol.8, issue.10, 2013. ,
Monitoring of root growth and redox conditions in paddy soil rhizotrons by redox electrodes and image analysis, Plant Soil, vol.341, pp.221-232, 2011. ,
Microbial community changes in the rhizospheres of white clover and perennial ryegrass exposed to free air carbon dioxide enrichment (FACE), Soil Biology and Biochemistry, vol.28, pp.1717-1724, 1996. ,
Fungus-associated bacteriome in charge of their host behavior, Fungal Genet Biol, 2016. ,
In situ sampling of low molecular weight organic anions from rhizosphere of radiata pine (Pinus radiata) grown in a rhizotron system, Environmental and Experimental Botany, vol.70, issue.2, pp.131-142, 2011. ,
,
Endophytic fungi in forest trees: are they mutualists?, Fungal Biology Review, vol.21, issue.2-3, pp.75-89, 2007. ,
In situ temperature response of photosynthesis of 42 tree and liana species in the canopy of two Panamanian lowland tropical forests with contrasting rainfall regimes, New Phytologist, vol.214, issue.3, pp.1103-1117, 2017. ,
Effects of high temperature on photosynthesis and related gene expression in poplar, BMC Plant Biology, vol.14, issue.111, pp.1-20, 2008. ,
The rhizosphere as a habitat for soil microorganisms, Modern soil microbiology, pp.21-45, 1997. ,
A study of the bacteria associated with the roots of subterranean clover and Wimmera ryegrass, Journal of Applied Bacteriology, vol.22, pp.85-95, 1995. ,
A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data, Frontiers in Microbiology, vol.6, pp.1-17, 2015. ,
Molecular mechanisms underlying the close association between soil Burkholderia and fungi, ISME J, vol.10, pp.253-64, 2016. ,
The origin and evolution of mycorrhizal symbioses: from palaeomycology to phylogenomics, New Phytologist, vol.220, issue.4, pp.1012-1030, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02018427
Soil Bacterial and Fungal Communities Show Distinct Recovery Patterns during Forest Ecosystem Restoration, Applied and Environmental Microbiology, vol.83, issue.14, pp.966-983, 2017. ,
What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs, MSphere, vol.3, issue.3, pp.1-14, 2018. ,
Genome Survey and Characterization of Endophytic Bacteria Exhibiting a Beneficial Effect on Growth and Development of Poplar Trees, Applied and Environmental Microbiology, vol.75, issue.3, pp.748-757, 2009. ,
The Arbuscular Mycorrhizal Status of Poplar Clones Selected for Phytoremediation of Soils Contaminated with Heavy Metals, Zeitschrift fur Naturforschung, vol.60, issue.3-4, pp.357-361, 2005. ,
Diversity of endophytic bacterial communities in poplar grown under field conditions, FEMS, vol.63, issue.2, pp.169-180, 2008. ,
Types, amounts and possible functions of com-pounds released into the rhizosphere by soilgrown plants, The Rhizosphere, Biochemistry and Organic Substances at the Soil-Plant Interface, pp.19-40, 2000. ,
Ecology of the forest microbiome: Highlights of temperate and boreal ecosystems, SBB, vol.103, pp.471-488, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01490075
Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities, Scientific Reports, vol.6, pp.1-11, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01579579
Efficient mineral weathering is a distinctive functional trait of the bacterial genus Collimonas, Soil Biology and Biochemistry, vol.41, issue.10, pp.2178-2186, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-02659896
Effect of the mycorrhizosphere on the genotypic and metabolic diversity of the bacterial communities involved in mineral weathering in a forest soil, Applied and Environmental Microbiology, vol.73, issue.9, pp.3019-3027, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-01195006
Effects of increased atmospheric CO2, temperature, and soil N availability on root exudation of dissolved organic carbon by a N-fixing tree (Robinia pseudoacacia L.), Plant and Soil, vol.222, p.191, 2000. ,
The unseen majority: Soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems, Ecology Letters, vol.11, issue.6, pp.1406-1423, 2008. ,
The importance of the microbiome of the plant holobiont, New Phytologist, vol.206, issue.4, pp.1196-1206, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01115639
Piriformospora indica, a Cultivable Plant-Growth-Promoting Root Endophyte, Applied and Environmental Microbiology, vol.65, issue.6, pp.2741-2744, 1999. ,
Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics, Front Cell Infect Microbiol, vol.4, p.29, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01153583
Development of the poplar-Laccaria bicolor ectomycorrhiza modifies root auxin metabolism, signaling, and response, Plant Physiology, vol.169, issue.1, pp.890-902, 2015. ,
Modification of plant cell wall chemistry impacts metabolome and microbiome composition in Populus PdKOR1 RNAi plants, Plant Soil, vol.429, pp.349-361, 2018. ,
Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but, it depends on soil origin, p.7, 2019. ,
Biosynthesis of Jasmonic Acid by Several Plant Species, Plant Physiology, vol.75, issue.2, pp.458-461, 1984. ,
An overview of methods for the detection and observation of arbuscular mycorrhizal fungi in roots, Physiologia Plantarum, vol.125, issue.4, pp.393-404, 2005. ,
Le Peuplier noir en France : pourquoi conserver ses ressources ge?etiques et comment les valoriser ? Revue forestiere francaise, vol.LXI, pp.457-466, 2009. ,
Survival of inoculated Laccaria bicolor in competition with native ectomycorrhizal fungi and effects on the growth of outplanted Douglas fir seedlings, Plant Soil, vol.135, p.95, 1991. ,
URL : https://hal.archives-ouvertes.fr/hal-02714298
16S rDNA profiling to reveal the influence of seed-applied biostimulants on the rhizosphere of young maize plants, Molecules, vol.23, issue.6, pp.1-18, 2018. ,
Realtime PCR quantification of arbuscular mycorrhizal fungi: does the use of nuclear or mitochondrial markers make a difference?, Mycorrhiza, vol.27, issue.6, pp.577-585, 2017. ,
Fungal community on decomposing leaf litter undergoes rapid successional changes, ISME J, vol.7, pp.477-486, 2013. ,
Host genotype and age shape the leaf and root microbiomes of a wild perennial plant, Nat. Commun, vol.7, p.12151, 2016. ,
A simple blue staining technique for arbuscular mycorrhizal and other root-inhabiting fungi, Inoculum, vol.56, pp.68-69, 2005. ,
A trait-based framework for predicting when and where microbial adaptation to climate change will affect ecosystem functioning, Biogeochemistry, vol.109, issue.1-3, pp.35-47, 2012. ,
The 20-year environmental safety record of GM trees, Nat Biotechnol, vol.28, issue.7, pp.656-658, 2010. ,
Role of Silicon on Plant-Pathogen Interactions, Frontiers in Plant Science, vol.8, pp.1-14, 2017. ,
Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Applied and Environmental Microbiology, vol.73, issue.16, pp.5261-5267, 2007. ,
Endophytic communities of transgenic poplar were determined by the environment and niche rather than by transgenic events, Frontiers in Microbiology, vol.10, pp.1-18, 2019. ,
Universal and species-specific bacterial "fungiphiles" in the mycospheres of different basidiomycetous fungi, Environ Microbiol, vol.11, pp.300-312, 2009. ,
The fungal-specific ?-glucan-binding lectin FGB1 alters cell-wall composition and suppresses glucan-triggered immunity in plants, Nature Communications, 2016. ,
Phyllosphere microbiology with special reference to diversity and plant genotype, Journal of Applied Microbiology, vol.105, issue.6, pp.1744-1755, 2008. ,
Differential responses of stomata and photosynthesis to elevated temperature in two co-occurring subtropical forest tree species, Frontiers in Plant Science, vol.9, pp.1-8, 2018. ,
Perspectives for genetic engineering of poplars for enhanced phytoremediation abilities, Ecotoxicology, vol.19, pp.1754-1588, 2010. ,
Rapid report Methanogenic Archaea dominate mature heartwood habitats of Eastern Cottonwood (Populus deltoides), New Phytologist, 2018. ,
Beneficial microbes going underground of root immunity, Plant Cell Environ, pp.1-11, 2019. ,
Ectendomycorrhizal associations -Characteristics and functions, Mycorrhiza, vol.11, issue.4, pp.167-177, 2001. ,
Yeasts of the soil -obscure but precious, Yeast, vol.35, issue.5, pp.369-378, 2018. ,
Modulation of Host Immunity by Beneficial Microbes, Molecular Plant-Microbe Interactions, vol.25, issue.2, pp.139-150, 2011. ,
Rhizosphere Microbes as Essential Partners for Plant Stress Tolerance, Molecular Plant Advance, pp.1-4, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-02651517
Salinity Is a Key Determinant for Soil Microbial Communities in a Desert Ecosystem, MSystems, vol.4, issue.1, pp.1-11, 2019. ,