Diversity and Structure of the Endophytic Bacterial Communities Associated With Three Terrestrial Orchid Species as Revealed by 16S rRNA Gene Metabarcoding.

Pasquale Alibrandi,Sylvia Schnell,Silvia Perotto,Massimiliano Cardinale

doi:10.3389/fmicb.2020.604964

Pasquale Alibrandi, Sylvia Schnell + Show 2 more

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https://doi.org/10.3389/fmicb.2020.604964

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Abstract

The endophytic microbiota can establish mutualistic or commensalistic interactions within the host plant tissues. We investigated the bacterial endophytic microbiota in three species of Mediterranean orchids (Neottia ovata, Serapias vomeracea, and Spiranthes spiralis) by metabarcoding of the 16S rRNA gene. We examined whether the different orchid species and organs, both underground and aboveground, influenced the endophytic bacterial communities. A total of 1,930 operational taxonomic units (OTUs) were obtained, mainly Proteobacteria and Actinobacteria, whose distribution model indicated that the plant organ was the main determinant of the bacterial community structure. The co-occurrence network was not modular, suggesting a relative homogeneity of the microbiota between both plant species and organs. Moreover, the decrease in species richness and diversity in the aerial vegetative organs may indicate a filtering effect by the host plant. We identified four hub OTUs, three of them already reported as plant-associated taxa (Pseudoxanthomonas, Rhizobium, and Mitsuaria), whereas Thermus was an unusual member of the plant microbiota. Core microbiota analysis revealed a selective and systemic ascent of bacterial communities from the vegetative to the reproductive organs. The core microbiota was also maintained in the S. spiralis seeds, suggesting a potential vertical transfer of the microbiota. Surprisingly, some S. spiralis seed samples displayed a very rich endophytic microbiota, with a large number of OTUs shared with the roots, a situation that may lead to a putative restoring process of the root-associated microbiota in the progeny. Our results indicate that the bacterial community has adapted to colonize the orchid organs selectively and systemically, suggesting an active involvement in the orchid holobiont.

Highlights

Plants in natural and agricultural ecosystems interact with a multitude of microorganisms that colonize both the internal tissues and the outer surfaces of both underground and aboveground plant organs (Compant et al, 2019; EscuderoMartinez and Bulgarelli, 2019)
This study provides new insights into the distribution of bacteria across different organs of terrestrial orchid species, and sheds light on the fraction of the bacterial community potentially transferred to the plant generation by vertical transmission, pointing out a possible role of bacterial endophytes in orchid conservation
After length and quality filtering, 4,117,638 sequences remained, which were grouped into operational taxonomic units (OTUs) at 97% similarity level

Summary

Introduction

Plants in natural and agricultural ecosystems interact with a multitude of microorganisms that colonize both the internal tissues and the outer surfaces of both underground and aboveground plant organs (Compant et al, 2019; EscuderoMartinez and Bulgarelli, 2019) These plant-associated microbial communities are collectively known as the plant microbiota (Marchesi and Ravel, 2015) and can theoretically comprise mutualistic, commensal and latent pathogenic strains in apparently healthy plants (Brader et al, 2017). Endophytes can be defined as components of the plant microbiota that colonize internal healthy plant tissues and establish non-harmful relationships with their host (Hardoim et al, 2015) This definition includes mutualistic endophytes that form recognizable structures during plant colonization such as mycorrhizal fungi in the roots of land plants and rhizobia in legume root nodules - whose interactions with the host plant have been extensively investigated because of their beneficial influence on plant growth, productivity and health (Das et al, 2017; Masson-Boivin and Sachs, 2018; Genre et al, 2020). Bacterial endophytes can protect the host plant against pathogen invasion and disease through direct biocontrol activities or by inducing plant systemic resistance (Berg and Koskella, 2018; de Vrieze et al, 2018)

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