Fruit might look perfect on the outside, but when peeled open it’s sometimes rotten at the core. University of Queensland PhD student Zali Mahony is working hard with others to find out more about black core rot. Symptoms of black core rot are expressed close to or at harvest when it is too late to apply control measure.

Black core rot is a fungal disease caused by Alternaria species and has emerged as an unpredictable and sporadic threat to our citrus industry’s fruit quality and yields. 

It was first reported in California in the 1900s and is reported to cause disease problems in Mediterranean climates like that of the Riverina, Sunraysia and Riverland growing regions in Australia.

Our understanding of this disease is limited so we don’t have an effective way to manage the disease. 

Suggested control practices recommend delaying harvest to let the infected fruit drop from the canopy. 

But this technique has its limitations for disease control. 

It also results in yield loss and is leading to missed market windows to sell fruit. 

It may also end up creating a reservoir of fungi in the orchard that could infect fruit the subsequent season.

What’s the answer?

Fungicide applications of copper or systemic products are sometimes applied but are not always effective for disease control in all situations. 

Symptoms of black core rot are expressed close to or at harvest when it is too late to apply control measures. 

Growers apply fungicides early in the growing season prior to knowing the level of disease in their orchard, to avoid having disease problems.

But the choice of agrichemicals and the timing of application is not based on an in-depth understanding of the disease cycle, which means key infection periods, such as flowering, may not be targeted, and sources of inoculum are not often taken into consideration.

How is this fungus different to emperor brown spot?

One of our aims is to characterise the fungal pathogen that causes black core rot. 

Our results and those from overseas indicate Alternaria alternata, which is a fungus causing leaf spots, rots, and blights, is the causal agent of black core rot. 

But this is also the reported causal agent of ‘Emperor’ brown spot. 

While these two diseases appear distinct in their symptoms and geographical distribution, the differences between the pathogen’s identities and disease cycles remains a gap in our knowledge.

We’re addressing this gap by comparing cultures obtained from field surveys using DNA (deoxyribonucleic acid) sequence information and conducting reciprocal inoculation experiments to see which cultures can cause which disease.

Where is the source of the infections?

We have been working closely with growers who have previous experience with black core rot to understand what conditions may contribute to its occurrence between seasons in orchards. 

An ongoing online survey has collected these experiences from several growing regions and confirms our in-field observations, which are this disease occurs sporadically in southern Australian citrus growing regions.

Samples of infected fruit have been obtained and analysed from regions including the NSW Riverina, Sunraysia, and northern NSW. 

Emperor brown spot samples have also been obtained from the Central Burnett region in Queensland. 

These samples have enabled those of us working on this project to look at the molecular (DNA) differences between the black core rot and Emperor brown spot pathogens.

The methodology did not entirely resolve the identities of these two pathogens, however, we are currently using controlled inoculation experiments with samples from both diseases to determine if we are dealing with one pathogen which can cause disease under different environmental conditions – or two different pathogen populations each causing a unique disease.

Additional collections of asymptomatic (or healthy) citrus material in orchards affected by black core rot were also sampled and tested to see if they were infected without showing symptoms. 

This provided a source of the pathogen to allow the persistence of the disease in an orchard.

Detached fruit evaluations are currently underway to determine whether the fungi sampled from these healthy tissue sources is able to cause black core rot.

How does the fungus infect the fruit?

To identify the timing of infection of the black core rot pathogen, we are using time-staggered fungicide applications to pinpoint the major infection periods. This trial is a large-scale operation set up on a grower’s property, and data is being collected from 144 trees. 

The trial is now in its third year.

To provide further evidence for the timing of infection, a second field trial is underway to test whether manual infection of Alternaria spores on citrus trees at different flower and fruit stages leads to fruit with black core rot symptoms at harvest.

An understanding of where the source of inoculum is and when the black core rot fungus infects the fruit may allow for targeted application and more effective disease management and reduce the disease’s impact on industry.