title: Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees.
abstract: The plant microbiome represents one of the key determinants of plant health and productivity by providing a plethora of functional capacities such as access to low-abundance nutrients, suppression of phytopathogens, and resistance to biotic and/or abiotic stressors. However, a robust understanding of the structural composition of the bacterial microbiome present in different plant microenvironments and especially the relationship between below-ground and above-ground communities has remained elusive. In this work, we addressed hypotheses regarding microbiome niche differentiation and structural stability of the bacterial communities within different ecological plant niches.
  
  
  
  We sampled the rhizosphere soil, root, stem, and leaf endosphere of field-grown poplar trees (Populus tremula × Populus alba) and applied 16S rRNA amplicon pyrosequencing to unravel the bacterial communities associated with the different plant habitats.
  
  
  
  We found that the structural variability of rhizosphere microbiomes in field-grown poplar trees (P. tremula × P. alba) is much lower than that of the endosphere microbiomes. Furthermore, our data not only confirm microbiome niche differentiation reports at the rhizosphere soil-root interface but also clearly show additional fine-tuning and adaptation of the endosphere microbiome in the stem and leaf compartment. Each plant compartment represents an unique ecological niche for the bacterial communities. Finally, we identified the core bacterial microbiome associated with the different ecological niches of Populus.
  
  
  
  Understanding the complex host-microbe interactions of Populus could provide the basis for the exploitation of the eukaryote-prokaryote associations in phytoremediation applications, sustainable crop production (bio-energy efficiency), and/or the production of secondary metabolites.
authors.affiliation: Centre for Environmental Sciences, Hasselt University, Agoralaan building D, B-3590, Diepenbeek, Belgium. bram.beckers@uhasselt.be.
authors.forename: Bram
authors.initials: B
authors.lastname: Beckers
authors.affiliation: Centre for Environmental Sciences, Hasselt University, Agoralaan building D, B-3590, Diepenbeek, Belgium.|Current address: Department of Biology, Lund University, Ecology Building, SE-22 362, Lund, Sweden.
authors.forename: Michiel
authors.initials: M
authors.lastname: Op De Beeck
authors.affiliation: Centre for Environmental Sciences, Hasselt University, Agoralaan building D, B-3590, Diepenbeek, Belgium.
authors.forename: Nele
authors.initials: N
authors.lastname: Weyens
authors.affiliation: Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Ghent, Belgium.|Department of Plant Biotechnology and Bioinformatics, UGent, Technologiepark 927, B-9052, Ghent, Belgium.
authors.forename: Wout
authors.initials: W
authors.lastname: Boerjan
authors.affiliation: Centre for Environmental Sciences, Hasselt University, Agoralaan building D, B-3590, Diepenbeek, Belgium.
authors.forename: Jaco
authors.initials: J
authors.lastname: Vangronsveld
mesh_terms: D001419:Bacteria / Q000145:classification / Q000302:isolation & purification* / Q000378:metabolism; D001673:Biodegradation, Environmental; D059014:High-Throughput Nucleotide Sequencing; D059013:Microbial Consortia; D064307:Microbiota / Q000235:genetics; D018515:Plant Leaves / Q000382:microbiology; D018517:Plant Roots / Q000382:microbiology; D032107:Populus / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S; D058441:Rhizosphere; D064210:Secondary Metabolism; D012988:Soil Microbiology
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: 16S rRNA amplicon pyrosequencing; Bacterial microbiome; Endosphere; Microbiome niche differentiation; Populus tremula × Populus alba; Rhizosphere