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

Bram Beckers,Jaco Vangronsveld,Wout Boerjan,Nele Weyens,Michiel Op De Beeck

doi:10.1186/s40168-017-0241-2

Bram Beckers, Jaco Vangronsveld + Show 3 more

Open Access

https://doi.org/10.1186/s40168-017-0241-2

Copy DOI

Abstract

BackgroundThe 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.MethodsWe 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.ResultsWe 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.ConclusionsUnderstanding 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.

Highlights

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
We determined the co-amplification of non-target 16S ribosomal RNA (rRNA) and the number of singletons identified within each plant compartment (%), as well as the number of reads that could not be unambiguously classified at the phylum level (Table 1)
Notwithstanding these elements, our results indicate that the high discrepancy in the number of singletons between the plant compartments could be attributable to more genuine rare operational taxonomic unit (OTU) in the rhizosphere soil (Table 1)

Summary

Introduction

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. Bacterial microbiota may improve nutrient bioavailability and transport from the soil as well as increase host tolerance to biotic (and abiotic stresses), promote stress resistance, and influence crop yield and quality. We can distinguish the bacterial colonization of the anthosphere (flower) [32], the spermosphere (seeds) [33, 34], and the carposphere (fruit) [35] All these microenvironments provide specific biotic and abiotic conditions for the residing bacterial communities

Methods

Results

Discussion

Conclusion