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

Abstract

Up to date, the bacterial and fungal microbial communities from the olive (Olea europaea L.) root systems have not been simultaneously studied. In this work, we show 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 high proportion of so far unclassified fungal sequences at 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 suggests that there are still some fungi with important ecological and biotechnological implications that have yet to be discovered.

Verticillium Wilt of Olive and Its Control: What Did We Learn during the Last Decade?

“…Recently, the use of high-throughput sequencing allowed us to explore the composition and structure of microbial communities (fungi and bacteria) associated with olive cultivars from different geographical origins grown under the same climatic, agronomical, and pedological conditions [ 12 ]. Data revealed several interesting findings, making it possible to define a rather complete inventory of the rhizosphere and root endosphere microbiota (fungi and bacteria) associated with olive trees [ 12 ]. The results showed higher alfa diversity in the rhizosphere compared to that observed in the root endosphere.…”

“…While previous studies revealed the importance of the geographical origin in building up the endophytic prokaryotic communities found in olive leaf tissues [ 185 ], our study concluded that the genotype, rather than geographical origin, is the main factor in shaping the olive belowground microbial communities. Moreover, the genotype is more determinant in the rhizosphere than in the root endosphere, and more crucial for the bacteriota than for the mycota [ 12 ]. The study also revealed that Actinophytocola was the most abundant genus inhabiting olive roots, followed by the genera Streptomyces and Pseudonocardia .…”

“…The prevalent classes present in the olive root endosphere were Sordariomycetes and Eurotiomycetes , while Agaricomycetes , Eurotiomycetes, and Sordariomycetes were the predominant classes in the rhizosphere. Future research efforts should also be aimed at isolating and characterizing members of these relevant components of the olive belowground mycota [ 12 ].…”

“…For instance, the development of super high-density hedgerow orchards [ 11 ] ( Figure 1 ) and the use of drip irrigation systems are modifying the traditional olive landscape built over millennia in the Mediterranean countries. While these benefits are desirable, the increasing reduction in the number of cultivars or practices such as high inputs of fertilizers or fungicides may have detrimental consequences, namely the reduction in olive genetic diversity or harmful effects on the soil microbiota [ 12 , 13 ]. These alterations, coupled with the high vegetation densities usually present in high-density orchards, may pose problems related to increasing the incidence and severity of specific olive pests and soil-borne diseases, yet have been insufficiently evaluated [ 10 , 14 ].…”

Endophytic fungi of olive tree and their exploitation in the biological control of olive anthracnose = Hongos endofíticos del olivo y su aprovechamiento para el control biológico de la antracnosis del olivo

“…Overall, the fungal endophytes colonizing the vegetative organs of olive tree were highly diverse (total of 205 OTUs), being most of the isolates belonging to phylum Ascomycota and class Sordariomycetes. Similarly, previous studies using both culturaldependent and -independent approach (Abdelfattah et al, 2015;Fernández-González et al, 2019) Germplasm Collection (in Spain). Without excluding the potential biases related to culture-dependent method , this variation on the most abundant genera in roots could be related with differences on sampling sites and sampling time, which were recognized to influence endophytic fungal assemblage in olive tree .…”