Diversity of carrot seed-borne endophytes and their applications for the promotion of plant growth and defence against fungal pathogens
(contact: Prof. Naceur DJEBALI, naceur.djebali@cbbc.rnrt.tn and Prof. C├ęcile BEN, C.Ben@skoltech.ru, PhD Thesis "En Co-tutelle" (doctorate in joint-supervision) between Skoltech Agro & Center of Biotechnology of Borj Cedria, Tunisia)

After decades of dependency on chemical pesticides, the modern agriculture system is moving increasingly towards more sustainable and eco-friendly practices to fight against plant diseases. The exploitation of natural resources that provide crop protection at lower ecological cost is a priority nowadays. Thus, the selection and formulation of biological agents that are able to promote growth and stimulate natural defences in plants is a promising approach for disease control. Plants are colonized by a large number of microorganisms that can inhabit either the surface or the internal plant tissues. Microbial endophytes are microorganisms occurring inside plant tissues without causing any apparent symptoms and have been detected in hundreds of plants, including many important agricultural crops such as carrot (Daucus carota). Correlations to growth promotion of plants were observed with inocula levels that promoted endophyte populations. In addition, endophytes may also induce plant defence mechanisms and produce volatile and soluble antibiotic substances. The efficient vertical transmission of seed-borne endophytes in a manner similar to maternally inherited genetic characters has allowed the production of infected seed at a commercial scale. So, this project aims to study the diversity of seed-borne bacteria endophytes of carrot and to select those that stimulate growth and defence of this plant to control soil-borne diseases. In addition, the nature of bioactive substances of the selected endophyte strains will be analyzed in order to identify new bioactive compounds that stimulate plant defences. Finally, carrot inoculated seeds will be developed using the most promising endophyte strains and tested in greenhouse and field conditions to study their effects on plant growth and defence mechanisms.

The objectives of this project include:

  1. To isolate and molecularly identify the endophytic bacteria from the hypocotyls and radicle growing from disinfected carrot seeds.
  2. To study the capacity of endophytic bacteria to increase carrot seed germination and seedling growth.
  3. To study the antifungal capacity of endophytic bacteria against soil born-diseases namely Rhizoctonia solani, Fusarium solani and Sclerotinia sclerotiorum.
  4. To study the capacity of endophytic bacteria to enhance carrot defence against the soil born-fungal pathogens by biochemical (dosage of enzymes involved in the antioxidant system and the phenylpropanoid pathway) and molecular (q-RT-PCR of defence related genes implicated in the main signalling pathways) approaches.
  5. To characterize of the volatile (by GC-MS) and soluble (by LC-MS) bioactive compounds with antifungal activities and validate the role of some molecules by CRISPR-Cas9 genome editing tool of target genes.
  6. To validate endophytic natures of the promising bacteria strains microscopically through GFP transformation of bacterial strains.
  7. To study the effect of carrot seeds bio-priming with promising endophytic bacteria on carrot growth and resistance against diseases infections in greenhouse and filed conditions.

Required skills: Microbiology (isolation and pure culture of microorganisms), Biostatistics (analyses of data with R), molecular biology (for molecular identification of microorganisms and gene expression), and knowledge of CRISPR-Cas9 genome editing tool.