Beneficial bacteria-plant interactions play an important role in plants, as bacterial endophytes do not cause apparent damage and contribute to host plant protection and survival. The first part of this study was aimed to characterise the bacterial communities present in soil, leaf surface (phyllosphere) and xylem sap (XS) of olive trees. The XS was extracted from olive shoots using Sholander pressure chambers. The experimental orchard has been divided in two plots that have been managed for 18 years with two different systems: a) ‘sustainable management’ (Smng), with no-tillage, fertigation and internal C-inputs (spontaneous weeds and pruning residues), and b) an adjacent rainfed ‘conventional management’ (Cmng), that included soil tillage and mineral fertilization. A metagenomic approach was used to detect microorganisms, in order to estimate bacterial diversity and abundance, and to identify the bacterial taxa of the three analysed compartments in plants subjected to the two systems. The abundance and diversity of bacterial taxa in soil was higher compared to those found in the phyllosphere and XS. Bacterial communities generally came from the soil and reached the aerial plant parts through the XS. The application of different agronomic practices strongly influenced the composition of soil, phyllosphere and XS bacterial communities. As an example, the Smng system caused an improvement in the abundance of soil N-cycling bacteria and the presence of plant protective bacterial species in the phyllosphere. In the second part of the study, in order to examine the chemical changes due to XS bacterial colonization under the two different management systems, XS metabolome was analyzed in two sampling times (ST1: May; ST2: October) by ultra-high performance liquid chromatography (UHPLC) coupled to a hybrid quadrupole-time-of-flight mass spectrometer (QTOF-MS). The discriminating compounds were 94 at ST1 and 119 at ST2, and 35 of them were in common between the two sampling times. The majority of the discriminating metabolites (73 on 94 at ST1, and 109 on 119 at ST2) were found at higher concentration in the XS of Smng plants, compared to that of Cmng ones. Most of the discriminating metabolites found in the XS (about 80%, both at ST1 and ST2) were involved in plant secondary metabolism, mainly for plant chemical defense, growth regulation and signal transduction. The most prevailing class of compounds included terpenoids, phytohormones, alkaloids, sterols/steroids, retinols/retinoids, tocopherols and carotenoids. The potential agronomic benefits of the specific bacterial taxa detected under the Smng system could improve plant growth protection and provide a higher crop quality in olive plants and similar fruit species. For the first time, we have demonstrated that the endophytes and the XS metabolome of a tree crop significantly respond to the agronomic practices adopted. On this basis, we can assert that the host plant and its microbiota can be considered as a halobiont, and that this ecological unit is not constant but depends on external conditions. From a practical point of view, the results of our study encourage the use of a set of sustainable agricultural practices in a productive orchard, in order to enhance plant physiological status, increase yield quantity/quality, safeguard the environment and ameliorate human health
