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

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

Internship 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’. 

Deliverables/Expectations

-​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. 

Faculty Name

Daniele Daffonchio

Field of Study

Plant-microbe interactions