The effect of rootstock-scion combination on microbiome selection by fruit plants

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Project Description

Grafting is a common agronomic practice performed on different fruit plants such as, among others, apple tree, other Rosaceae and grapevine. It is used for improving the fruit cultivar adaptation to specific soil and for controlling some plant parasites. The rootstock affects scion development by influencing the reproductive performance, vigor, biomass accumulation and distribution in the plant, phenology and fruit yield. Moreover, a recent publication highlighted that rootstock type influences the recruitment by plants of microorganisms from the soil, which can be defined as the ‘seed-bank’ for root microbiome assemblages (Marasco et al., 2018, Microbiome 6:3. Doi 10.1186/s40168-017-0391-2). An aspect that is still overlooked is if and how the rootstock-scion combination affect the recruitment of the microbiome and their migration and colonization of the tissues in different plant compartments and organs. A deeper knowledge on this aspect is pivotal to better understand the factors steering the recruitment and the flux of microorganisms from the soil through the roots and within the plant compartments. Moreover, it would be interesting to unravel which rootstock-scion combinations can primarily influence the fruit quality, by inferring the functional diversity of the selected microbiome starting from high-throughput Illumina 16S rRNA gene sequencing. To investigate the community structure of the endophytic microbiome in different plant compartments (e.g. root, shoot, leaf, fruit) comparing several combinations of rootstock-scion pairs. The research will be conducted on fruit trees, e.g. grapevine, and the bulk soil (i.e. the soil not affected by root exudates) will be used as the reference microbial ‘seed-bank’. ​​
Program - BioScience
Division - Biological and Environmental Sciences and Engineering
Field of Study - ​Plant-microbe interactions

About the
Researcher

Daniele Daffonchio

Professor, Bioscience

Daniele Daffonchio
Professor Daffonchio's research interests are in the microbial ecology of complex ecosystems in conventional and extreme aquatic and terrestrial habitats. His research is spanning from basic aspects of microbial ecology through the application of synthetic ecology approaches to applied aspects for the environmental protection and sustainability of agriculture.

Professor Daffonchio has developed research on the exploration and characterization of extreme marine and terrestrial environments, both pristine and polluted. He is actually dealing with the study and exploitation of extremophile microorganisms along the water stress continuity from the Arabian desert to the depth of the brine pools in the Red Sea. A particular focus is on the bacteria-host symbiosis with plants and animals in relation to the water and salinity stresses.

Desired Project Deliverables

-​Creation of 16S rRNA gene libraries from soil and plant metagenomes for the description of the structure and taxonomy of the bacterial community associated to different plant compartments and to the bulk soil - Quali/quantitative identification of the bacterial taxa present in 16S rRNA libraries - Study of the alpha- and beta-diversity of the microbiome in different plant compartments according to the rootstock-scion combinations.