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Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees

Beckers, Bram ; Op De Beeck, Michiel LU ; Weyens, Nele ; Boerjan, Wout and Vangronsveld, Jaco (2017) In Microbiome 5.
Abstract

BACKGROUND: 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.

METHODS: We sampled the rhizosphere soil,... (More)

BACKGROUND: 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.

METHODS: 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.

RESULTS: 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.

CONCLUSIONS: 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.

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author
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Bacteria/classification, Biodegradation, Environmental, High-Throughput Nucleotide Sequencing, Microbial Consortia, Microbiota/genetics, Plant Leaves/microbiology, Plant Roots/microbiology, Populus/microbiology, RNA, Ribosomal, 16S, Rhizosphere, Secondary Metabolism, Soil Microbiology
in
Microbiome
volume
5
article number
5:25
pages
17 pages
publisher
BioMed Central
external identifiers
  • pmid:28231859
  • scopus:85015845535
ISSN
2049-2618
DOI
10.1186/s40168-017-0241-2
language
English
LU publication?
no
id
e8294d48-8538-45ba-b530-7f82efdfa754
date added to LUP
2019-03-05 16:10:24
date last changed
2020-03-24 06:41:34
@article{e8294d48-8538-45ba-b530-7f82efdfa754,
  abstract     = {<p>BACKGROUND: 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.</p><p>METHODS: 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.</p><p>RESULTS: 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.</p><p>CONCLUSIONS: 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.</p>},
  author       = {Beckers, Bram and Op De Beeck, Michiel and Weyens, Nele and Boerjan, Wout and Vangronsveld, Jaco},
  issn         = {2049-2618},
  language     = {eng},
  month        = {02},
  publisher    = {BioMed Central},
  series       = {Microbiome},
  title        = {Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees},
  url          = {http://dx.doi.org/10.1186/s40168-017-0241-2},
  doi          = {10.1186/s40168-017-0241-2},
  volume       = {5},
  year         = {2017},
}