Home22 November 2025
Apple scab fungus, the subject of Kara’s PhD. Image: Shutterstock.
Kara Pendavingh has just started her fourth year of her PhD at Massey University in Palmerston North. Looking back, the path has had plenty of obstacles and challenges that can plague the pursuit of new knowledge. Looking forward, Kara is excited to gain new technical expertise in her final year and, eventually, to return to Australia and virology with the broader perspective she has earned through her PhD.
For her PhD, Kara is investigating how the apple scab fungus (Venturia inaequalis) interacts with microorganisms (yeasts and bacteria) present on apple leaves. She has isolated and identified multiple “antagonistic” microorganisms –organisms with the ability to negatively impact the fungus – and has investigated the mechanisms of antagonism of these isolates. She is now analysing samples to understand how the pathogen influences the broader microbial community.
However, this was not always the plan for the project. Initially, the research was to be centred around effectors: small molecules released by microorganisms that can be used to promote virulence and may also mediate microbe-to-microbe interactions. To study effectors involved in these intermicrobial interactions, they often need to be expressed in a host, such as E. coli. This becomes problematic if the molecules are antimicrobial, as they can harm the expression host. After considerable difficulty with this system, and as other parts of the PhD began gaining traction, Kara shifted her focus toward these more promising research avenues.
Instead of effector expression, Kara investigated direct interactions between her isolated microorganisms and the apple scab pathogen, discovering many isolates that strongly inhibited fungal growth. She then used whole-genome sequencing and bioinformatics to characterise the microorganisms and identify potential genes involved in antagonism. This was paired with wet-lab testing of the enzymes these microorganisms produce.
To study the influence of V. inaequalis on the apple leaf microbiota, Kara conducted a field trial in Havelock North – not without its own challenges.
“I had some issues the first season,” says Kara. “There were a lot of aphids and some irrigation issues.”
She persevered and conducted the experiment the following season.
“I will be using amplicon-based metagenomics on 16S and ITS regions to study the microbiota, particularly the bacteria and yeasts,” says Kara. “This will allow me to characterise the microbial communities in the presence and absence of V. inaequalis.”
For her final data chapter, Kara is taking on a new technical challenge: a gene knockout of a potentially antagonistic gene family from a particularly inhibitory yeast isolate.
“I’m going to knock out an enzyme family and then see if the yeast is still antagonistic to V. inaequalis or if the gene knockout causes it to lose this ability.”
The value of the PhD challenge
Overcoming the uncertainty and constant troubleshooting inherent in research has taught Kara the value of backup plans.
“We built in a lot of safety nets so that if something didn’t work, it could be modified. And even some of the things that didn’t work can still be put to good use, either for a kind of micro-study or as a foundation for future students.”
For Kara, her PhD has provided her transferable technical skills, project management experience, and a clearer pathway back to the type of work she enjoys most.
“I used to be in government procurement, but then I did my Master’s at the University of Queensland, where I fell in love with molecular biology, particularly plant pathology.”
After a stint in Brisbane as a plant pathology research assistant focusing on viruses, she joined BA to pursue her PhD. While the PhD has deepened her research skills and independence, she has realised that of all the microbes, she enjoys working with viruses the most.
“I’d love to go back to virology – maybe biosecurity virology in Australia or Europe.”
With her future plans clarified, she is energetically embarking on her final PhD year.
“I can see the light at the end of the tunnel and I’m genuinely excited to learn new technical skills as I tackle my last data chapter.”
More Information
- Research | Understanding the antagonistic fungus–microbe interactions of apple scab
Learn more about Kara’s research with Bioprotection Aotearoa, understanding apple scab fungus interactions with leaf phyllosphere microbiota, and the role of Venturia inaequalis secreted effector proteins in these interactions.