Defining the root endosphere and rhizosphere microbiomes from the World Olive Germplasm Collection

Antonio J Fernández-González,Manuel Fernández-López,Jesús Mercado-Blanco,Antonio Valverde-Corredor,Angjelina Belaj,Pablo J Villadas,Carmen Gómez-Lama Cabanás

doi:10.1038/s41598-019-56977-9

Abstract

The bacterial and fungal communities from the olive (Olea europaea L.) root systems have not yet been simultaneously studied. We show in this work that microbial communities from the olive root endosphere are less diverse than those from the rhizosphere. But more relevant was to unveil that olive belowground communities are mainly shaped by the genotype of the cultivar when growing under the same environmental, pedological and agronomic conditions. Furthermore, Actinophytocola, Streptomyces and Pseudonocardia are the most abundant bacterial genera in the olive root endosphere, Actinophytocola being the most prevalent genus by far. In contrast, Gp6, Gp4, Rhizobium and Sphingomonas are the main genera in the olive rhizosphere. Canalisporium, Aspergillus, Minimelanolocus and Macrophomina are the main fungal genera present in the olive root system. Interestingly enough, a large number of as yet unclassified fungal sequences (class level) were detected in the rhizosphere. From the belowground microbial profiles here reported, it can be concluded that the genus Actinophytocola may play an important role in olive adaptation to environmental stresses. Moreover, the huge unknown fungal diversity here uncovered suggests that fungi with important ecological function and biotechnological potential are yet to be identified.

Highlights

The bacterial and fungal communities from the olive (Olea europaea L.) root systems have not yet been simultaneously studied
Recent literature provides solid evidence that olive roots are a good reservoir of beneficial microorganisms, including effective biocontrol agents (BCA)[15,16,17,18]
Bacterial communities associated with wild olive (Olea europaea L. subsp. europaea var. sylvestris) roots have been studied using fluorescent terminal restriction fragment length polymorphism (FT-RFLP) as well as by bacteria isolation in culturing media[15]

Summary

Introduction

The bacterial and fungal communities from the olive (Olea europaea L.) root systems have not yet been simultaneously studied. The reduction in the number of olive cultivars due to either commercial (for example improved yield, etc.) or phytopathological (as tolerance to www.nature.com/scientificreports diseases) reasons, a trend observed in many areas, will eventually lessen olive genetic diversity All these factors may have a profound, yet not evaluated impact on the composition, structure and functioning of belowground microbial communities[8]. Beneficial components of tree root-associated microbiota colonizing the rhizoplane and/or the rhizosphere soil can directly promote plant growth (as bio-fertilization, phyto-stimulation) or alleviate stress caused by either abiotic (for example environmental pollutants, drought, salinity resistance) or biotic (see above) constraints[8]. Microbial communities of the olive phyllosphere and carposphere have been analyzed using denaturing gradient gel electrophoresis (DGGE)[21], isolation of fungi in culturing media[22] and high-throughput sequencing of both fungal[23] and prokaryotic[24] communities

Methods

Results

Conclusion