Rotting apples, a common issue during storage, may soon have a new detective on the case: metabarcoding. This innovative technology could revolutionize the way we identify fungi that cause diseases in apples, both pre- and post-harvest.
But here's where it gets controversial: researchers are investigating whether fungal spores from rotten apples can spread through water during sorting, potentially infecting healthy apples.
At NIBIO, researchers are employing modern DNA-based methods to study this very question. Metabarcoding allows them to identify multiple microorganisms simultaneously, without the need for laboratory culturing.
"Many fungi cause diseases during storage. The apples look healthy at harvest, but after a few months, rot spots appear, leading to food waste," says NIBIO researcher Dalphy O. C. Harteveld.
These fungi often lie latent on the apples, existing on the surface without showing symptoms, only to break out later during storage. When apples are sorted, they're gently emptied into water, and researchers want to know if this water could be a vector for fungal spread.
Harteveld explains, "We're examining the water to see if we can find the same fungal species that cause rot. It's a crucial question for fruit storage facilities."
The metabarcoding method involves extracting DNA from water samples and amplifying specific genetic material as 'barcodes' for organisms. These sequences are then compared to databases to identify fungi and bacteria.
"Metabarcoding gives us a complete microbial community picture, not just culturable species," Harteveld emphasizes.
From the field to storage, researchers are following apples, recording diseases, and examining connections between fruit rot and fungi in the water. Some samples are cultured, while others are analyzed using PCR and sequencing.
The results are promising. Metabarcoding can detect fungal species in water that are challenging to culture, providing a more comprehensive understanding of microorganisms.
"It's an important starting point for investigating specific species," Harteveld says. "There are many bacterial and fungal species, and they influence each other. We're determining if we can detect multiple fruit rot-causing fungi simultaneously, and it seems possible."
Researchers are now exploring how the microbial community affects symptom development. They're comparing the apple peels of two varieties at harvest and after storage to understand microbial differences between healthy and rotting apples.
Another focus is bioinformatics, analyzing the vast DNA data from metabarcoding. An AI assistant is being developed to help interpret results, a valuable tool for making sense of the data.
"We're also using metabarcoding to assess cucumber health in hydroponic systems, studying how water quality and biostimulants impact plant health and microbial communities over time," Harteveld adds.
The goal is to refine metabarcoding into a precise tool for detecting multiple fungal infections in apples and studying their interactions with microbial communities, climate change, and plant protection practices.
"We're building the methodology for apple-relevant fungal species. Understanding and correctly using the technology is crucial to realizing its full potential," Harteveld concludes.
This research has the potential to significantly impact the apple industry, reducing food waste and improving fruit quality. But what do you think? Could metabarcoding be the key to unlocking the mysteries of apple rot? We'd love to hear your thoughts in the comments!
