OLIVE PHYTOMICROBIOME & QUALITY

Yuhan Wang's PhD

The soil surrounding the plant roots and all plant compartments (e.g., root, stem, leaf, flower, seeds) are hosts to a great diversity of microorganisms referred as the phytomicrobiome. The composition of microbial communities is determined by constantly changing environmental factors (soil type, temperature, precipiation, dirunal variations) and host factors (species, growth stage and compartment) (Vorholt, 2012, Bogino et al., 2013). The phytomicrobiome composition is also determined by the complex interactions between abiotic and biotic factors, including the complex matrix of plant-microbe and microbe-microbe communications (Peterson et al., 2006, Zgadzaj et al., 2019). The composition of plant bacterial communities and the abundance of specific taxa can usually be predicted by pH (Lauber et al., 2009), climate (Oliverio et al., 2017) and organic carbon utilization (Cederlund et al., 2014).  
Phytomicrobiome include both harmful and beneficial microorganisms, bacteria and fungi are the main microorganisms found in the soil, twice as much as the other main components of the soil microbiome (protozoa, archaea and viruses). These play an essential role in plant health, including defence against abiotic/biotic stresses and nutritional deficiencies (Backer et al., 2018). For example, critical microbial processes occurring in the soil can regulate the pH of the soil, modulate use of nitrogen, phosphorus and other nutrients, and the instability of the soil organic carbon pool (Fierer, 2017). The microbiome is involved in nutrient supply, antagonizing pathogens, and helping the host resist different types of environmental stress (Bakker et al., 2018). This may be related to more significant plant stress and rhizosphere phytomicrobiome communities (Fierer, 2017). Endophytic bacteria are microorganisms that live asymptomatic in plants. Endophytic phytomicrobiome are often functional because they bring nutrients from the soil to the plant, regulate plant development, increase stress tolerance, inhibit pathogen virulence, increase disease resistance, and inhibit the development of competing plants (White et al., 2019). This indicates that the microorganisms living inside plants can promote plant growth and health. 
The production of olives and their products sustains the economies of many EU countries (Duarte et al., 2008), being a critical crop to the food industry, it is critical to understand the link between olive phytomicrobiome and fruit quality. The cultivation of olives is subject to  biotic and abiotic constraints, and the interaction between plants and their phytomicrobiomes is highly complex and dynamic. At present, research has shown that olive tree rhizosphere microbes form a strong bond with the root system, allowing the plant to grow under limited conditions such as water scarcity, low salinity, and low soil fertility (Choudhary, 2012). Plant growth promotes increased tolerance of rhizosphere bacteria and arbuscular mycorrhizal fungi under abiotic stress. Fungi and actinomycetes also play a key role in maintaining soil health. They use root exudates as a carbon source to provide quickly absorbable nitrates to plants (Govaerts et al., 2008). Recent studies in olive orchards have shown that soil microorganisms can reach aerial plant parts through xylem sap(Fausto et al., 2018). The application of different agronomic methods affects the soil microbiome and fruit yield(Benitez et al., 2006).  In order to promote the growth of the host, endophytic fungi can produce plant hormones and compatible solutes under abiotic stress (Lata et al., 2018). Moreover, endophytes protect host plants from biological stress by producing bioactive compounds and stimulating defense responses (Yan et al., 2019). 
All the above indicate that the link between plant phytomicrobiome and crop quality is still elusive and not fully understood. Therefore, our hypothesis is that the plant phytomicrobiome directly or indirectly controls the quality of crops and final products in a complex but not yet fully understood way. Analysing suitable olive plantations will provide evidence to the link between phytomicrobiome and at least crop quality. Potentially, the quality of crops can be improved by cleverly controlling soil phytomicrobiome. 
The PhD project will focus on understanding the role of the plant phytomicrobiome in crop quality and thus, indirectly, its impact on food quality. The olive fruit will be used as the primary target. To obtain and analyse data from previous research studies for the correlation between phytomicrobiome in olives and olive quality or other chacteristics related to its cultivation.To identify variations in quality of olive fruits under different soil types/culitivation practises using chemical, physical and metabolomic analysis. Plant health markers (phytohormones) will also be measured to evaluate specific plant traits during the studied crop growth phases (budding, flowering and ripening)To characterise the phytomicrobiome of the olive using high-throughput sequencing of phylogenetic marker gene (e.g. 16S rRNA gene) in qualified samples.To establish the link between microbial community composition, olive fruit or olive oil quality and abiotic parameters using multivariate analysis.