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

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.

Linking belowground microbial network changes to different tolerance level towards Verticillium wilt of olive

“…Olive (3-months old) plants of cultivars Picual and Frantoio, respectively qualified as VWO-susceptible and VWO-tolerant [10] and originating from a commercial nursery located in Córdoba province, were used in the greenhouse experiment. After reception from the nursery, plants were grown in pots (11 × 11 × 12 cm, one plant per pot), each containing a non-sterile, ad hoc prepared soil made of natural soil (70%, w/w) collected at the World Olive Germplasm Collection located at Córdoba municipality [18], sand (7.5%), and a commercial nursery potting substrate (7.5%). Prior to the inoculation with the pathogen, olive plants were acclimated during 3 months in the greenhouse under natural lighting and day/night temperature of 27/21°C.…”

“…All analyses were performed with scripts previously described by Fernández-González et al [18]. Briefly, alpha diversity indices (Observed and Chao1 richness; Shannon and InvSimpson) were compared with Kruskal-Wallis test and p values were FDR corrected by the Benjamini-Hochberg method using the R package agricolae.…”

“…While studies on specific beneficial components of the olive-associated microbiota have been conducted, some of them aiming to isolate and characterize biological control agents (BCA) against VWO [12][13][14], only very few examples are available on whole indigenous olive microbial communities [15,16] and their potential relationship with susceptibility to biotic constraints [17]. Recently, we described the belowground microbial communities of a range of olive cultivars from different geographical origin grown under the same climatic, agronomical and soil conditions, and in the absence of V. dahliae pressure [18].…”

“…Plant-associated microbial communities are one of the key determinants for plant health and productivity, aiding in nutrient availability and uptake, enhancing stress tolerance, providing disease resistance, and promoting biodiversity [19,20]. Interestingly, some plant species harbor similar communities when grown in different soils, while different genotypes or cultivars of the same species can host distinct root microbial communities, highlighting the fact that the plant genotype is crucial to shape the composition of its root-associated microbiome [18,[21][22][23]. Plants select and shape the belowground microbiome, stimulating or repressing certain members of the indigenous microbial communities which can act as the first defense line against soilborne pathogens through a range of mechanisms [2,20].…”

Soil Microbial Biomass and Community Composition Relates to Poplar Genotypes and Environmental Conditions

“…The role of plant genotypes in shaping soil microbial communities has less been studied, and most studies have focused on short-lived crop plants, e.g., barley, tomato, cucumber, sweet pepper and chickpea [10,13,14], or on trees at the early stage of growth [15]. Little is known about the extent to which different genotypes of trees affect different groups of soil microbiome after many years of tree growth under different soil conditions [16]. Schweizer et al [12] showed the significant influence of the genotype of Populus angustifolia and its F1 generation and backcross hybrids on the total microbial biomass in bulk soil but did not observe such effects for Populus fremontii.…”