Imagine biting into a crisp, juicy apple, only to discover it’s riddled with rot. It’s a frustrating reality for both consumers and farmers, and it’s a problem that doesn’t just disappear after harvest. But what if we could detect the hidden culprits behind this decay before it’s too late? Enter metabarcoding—a cutting-edge technique that’s poised to revolutionize how we identify rot-causing fungi in apples. And this is the part most people miss: it’s not just about saving apples; it’s about tackling food waste on a global scale.
Rot during fruit storage is a persistent challenge, but metabarcoding offers a promising solution by identifying fungi that cause diseases in apples, both pre- and post-harvest. Here’s the catch: while apples are often sorted in water at packing facilities, scientists are still unraveling whether fungal spores from rotten apples can spread through this water and infect healthy ones. Controversially, some experts argue that this water sorting process might inadvertently become a breeding ground for fungal transmission—a claim that sparks heated debates in the agricultural community.
At the Norwegian Institute of Bioeconomy Research (NIBIO), researchers are leveraging metabarcoding, a DNA-based method, to analyze sorting water. Unlike traditional lab cultures, metabarcoding can identify multiple microorganisms simultaneously, offering a faster and more comprehensive approach. But here’s where it gets controversial: while this method is groundbreaking, it’s not without limitations, and some critics question its ability to pinpoint specific fungal species accurately.
Dalphy O. C. Harteveld, a researcher at NIBIO, highlights the sneaky nature of these fungi. “Apples often look perfectly healthy at harvest, but after months in storage, rot suddenly appears,” she explains. This latent behavior leads to significant food waste, as affected apples must be discarded. The fungi, Harteveld notes, are frequently present on apples even before they leave the orchard, lying dormant until storage conditions trigger their growth.
During sorting, apples are gently emptied into water and transported through channels for size and color grading. Ideally, rotten apples are removed first, but the question remains: can fungal spores survive and spread in this water? Harteveld’s team examined the water to identify fungal species linked to rot, shedding light on this critical issue.
Metabarcoding works by extracting DNA from water, soil, or plant tissue samples and amplifying specific genetic sequences that act as unique identifiers for different organisms. These sequences are then compared to databases to determine which fungi and bacteria are present. “This method gives us a complete snapshot of the microbial community, not just the species we can culture,” Harteveld explains. But here’s the kicker: while metabarcoding is powerful, it’s not yet foolproof, and some argue that relying solely on DNA data might overlook complex ecological interactions.
The research team tracked apples from the orchard to storage, documenting diseases at harvest and post-storage. They also investigated whether fruit rot correlated with fungi found in the water. Some water samples were cultured in the lab, while others underwent DNA analysis using PCR and sequencing. This dual approach allowed researchers to compare cultured fungal species with those detected in the water.
The results are promising. Metabarcoding successfully identified fungal species in the water that are difficult to culture, providing a more complete microbial profile. However, Harteveld acknowledges that the method can’t yet identify all organisms to the species level, though it serves as a crucial starting point for further investigation. This raises a thought-provoking question: Is metabarcoding the ultimate solution, or just a stepping stone in our fight against fruit rot?
Looking ahead, researchers are exploring how microbial communities influence rot development. “We’re comparing apple peels of different varieties at harvest and after storage to see if microbial differences correlate with rot,” Harteveld explains. They’re also using bioinformatics and AI tools to analyze vast DNA datasets, a move that some critics argue might oversimplify complex biological systems.
Beyond apples, metabarcoding is being applied to assess cucumber health in hydroponic systems, studying how water quality and biostimulants impact plant and microbial health over time. The ultimate goal? To refine metabarcoding into a precise tool for detecting multiple fungi simultaneously and understanding how factors like climate change and plant protection practices influence their behavior.
As Harteveld concludes, “We’re still building the methodology for apple-relevant fungal species. Mastering this technology is key to unlocking its full potential.” But here’s the burning question for you: Do you think metabarcoding will revolutionize fruit storage, or are we placing too much hope in this emerging technology? Share your thoughts in the comments below!
