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The Lab

This is how the samples were dealt with once they were brought back to the lab:

  • Roots and shoots processed
  • Pure fungal cultures isolated
  • Identification of fungal cultures using traditional microscopy and molecular DNA extraction


Root processing

The roots were washed in tap water to remove excess soil then 10 root pieces per root were plated onto tap water agar:

root washingroot on PDA

This allowed any fungi in the roots to grow out. Individual hyphal tips of the fungi were removed and subcultured onto potato dextrose agar. This allowed my to create a collection of pure fungal cultures which could later be identified.

Leaf processing

The leaf samples were inspected for disease and a subset were then processed using two different techniques:

moist incubation 

Moist incubation


Surface sterilisation

Fungi were then isolated from these in the same way as the roots.

Pathogen Identification

The fungi were identified using two techniques: traditional microscopy and the sequencing of DNA from the ITS region.