Olive orchard microbiome: characterisation of bacterial communities in soil-plant compartments and their comparison between sustainable and conventional soil management systems

Abstract

Background: Beneficial bacteria-plant interactions play an important role in agriculture, positively affecting plant status and improving product quality. Bacterial endophytes contribute to host plant protection and survival. Aim: This study characterised the bacterial communities present in soil, leaf surface and xylem sap of olive trees, and investigated their response under a sustainable (Smng) or a conventional (Cmng) management system in an olive grove located in southern Italy. The aims are: (a) to understand if soil bacteria enter xylem and reach leaves and (b) to verify if the bacterial communities in the two management systems deeply differ due to the different agronomic practices applied in Smng and in Cmng. Methods: Therefore, a metagenomic approach was used to detect microorganisms, in order to estimate bacterial diversity and abundance, and to identify the bacterial taxa in the three analysed compartments in plants subjected to Smng and Cmng systems. Results: Bacterial communities came from the soil and reached aerial plant parts through xylem sap. The application of different agronomic practices influenced the composition of soil bacterial communities. Conclusions: The potential benefits of the specific bacterial taxa detected under the Smng system could improve plant growth protection and provide a higher crop quality in fruit plants.

Culture-Dependent and Culture-Independent Characterization of the Olive Xylem Microbiota: Effect of Sap Extraction Methods

“…However, while Actinobacteria and Proteobacteria bacteria were present in all three olive genotypes, only "Picual" contained Firmicutes and Bacteroidetes, and only "Acebuche" contained bacteria from the Deinococcus-Thermus phylum. These results are in accordance with those obtained previously following similar approaches from olive leaves and xylem sap (Müller et al, 2015;Fausto et al, 2018;Sofo et al, 2019) as well as from other woody plants, like grapes, oak, poplar, and Pinus (Uroz et al, 2010;Bonito et al, 2014;Cregger et al, 2018;Deyett and Rolshausen, 2019). Interestingly, our results were more in agreement with those obtained by Deyett and Rolshausen (2019) that found similar proportions for Proteobacteria and Actinobacteria on grapevine xylem sap than those on olives obtained by Fausto et al (2018), when using a similar xylem sap extraction method with a Scholander pressure chamber.…”

“…Some differences were also found among those studies at the genus level. Thus, Deyett and Rolshausen (2019) found bacteria in the Enterobacteriaceae family, and belonging to Streptococcus, Bacteroides, Bacillus, Acinetobacter, and Pseudomonas genera as the most abundant on grapewine sap, whereas Fausto et al (2018) identified some bacterial genera in the olive sap common to our study (e.g., Curtobacterium, Hymenobacter, Methylobacterium, and Sphingomonas), although they did not provide their relative abundance. Those differences may be due to the fact that different primers targeting different variable regions of the 16 rRNA were used for amplification in each study, or to the differences on environmental growing conditions and the plant genotypes evaluated.…”

“…Xylem vessels are considered ideal niches for microbial endophytes (bacteria or fungi; both beneficial or pathogenic) by providing an effective internal pathway for dispersion throughout the plant and a continuous source of nutrients (McCully, 2001). However, despite significant progress in research on plant microbiota over past years, only a few number of publications have revealed the nature and role of the xylem microbiome, and its relationship to plant health and crop productivity (e.g., Deyett et al, 2017;Fausto et al, 2018;Deyett and Rolshausen, 2019). This fact may be due to microbiome complexity, technical difficulties in the isolation of the xylem-inhabiting microorganisms, as well as to the myriad of biotic and abiotic factors that may affect and determine the microbial community composition and their interaction within the host plant (Vandenkoornhuyse et al, 2015).…”

“…With olive, most microbiome studies have focused on determining the microbial composition of the rhizosphere (Mercado-Blanco et al, 2004;Berg and Hallmann, 2006;Mendes et al, 2007;Aranda et al, 2011;Prieto et al, 2011;Montes-Borrego et al, 2013;Caliz et al, 2015;Gómez-Lama Cabanás et al, 2018), whereas only a few studies have focused on the endosphere or xylem microbiomes (Müller et al, 2015;Fausto et al, 2018;Sofo et al, 2019). Unraveling the microbiome of the olive xylem sap should provide a better understanding of the microbes that systemically move throughout the plant or are horizontally transmitted from plant to plant during vegetative propagation.…”

Metatranscriptomic dynamics after Verticillium dahliae infection and root damage in Olea europaea

“…Indeed, chitinolytic bacteria are well-known antagonists of plant pathogenic fungi [39]. It is well known that bacterial endophytes contribute to the survival and protection of both healthy and stressed fruit plants [40]. In fact, the rhizosphere of wild olive is a reservoir of bacterial antagonists of V. dahliae showing chitinolytic activity [41].…”