Post-doctoral fellowship position – Stellenbosch University

Department of Plant Pathology

Project title: The effect of long-term application of organic amendments on the microbiome of apple tree roots.

Scope: Apple replant disease (ARD) is a phenomenon where the growth of young apple trees is reduced when trees are replanted onto soil previously cultivated with apple or related crop species. The reduction in tree growth is a result of the long-term build-up of a complex of ARD causative agents (fungal, nematode and oomycete) in soil during the life-span of the previously planted orchard. The long-term use of compost and mulches may have the potential to reduce the build-up of ARD causative agents during the life span of an apple orchard, thus reducing disease severity in subsequently replanted orchards. The microbiome structure associated with the rhizosphere- and bulk soil in organically amended orchards may contribute significantly to the potential ARD suppressiveness of these soils.

Project aims:

  • Under glasshouse conditions investigate the rhizosphere microbiome associated with apple tree roots due to the long-term application (6-years) of (i) mulch, (ii) mulch + compost or (iii) no organic amendment treatments.
    • Amplicon sequencing
    • qPCR analyses of selected fungal and bacterial taxa
    • T-RFLPs
  • Under orchard conditions, investigate the bulk soil microbiome in orchard blocks that have received different organic amendment treatments for the past 6
    • Amplicon sequencing
    • qPCR analyses of selected fungal and bacterial taxa
    • T-RFLPs


  • PhD degree.
  • Plant pathology and or molecular biology post graduate training.
  • Experience in Next Generation Sequencing and bioinformatics.
  • Ability to provide research guidance to postgraduate students.
  • English proficiency including writing, reading, comprehension, listening and speech. The minimum English language proficiency requirements for acceptance are 6.15 IELTS band and 550 TOEFL. IELTS or TOEFL scores must be submitted where required.

Commencement and end-date: January 2020 to January 2023

Collaboration: The project will be conducted in collaboration with Prof. Mark Mazzola at the USDA.

Salary: R250,000.00 (two hundred and fifty thousand rand) annually, for a period of 3 years.

Application deadline: 30 September 2019

Enquiries: Send a letter of application, curriculum vitae and the contact information of two potential referees to Prof. Adéle McLeod at E-mail:

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