Knowing your onions: Using transparent soil and high throughput fluorescence microscopy to identify and characterize the infection of onion with the major phytopathogen Aspergillus niger

Aspergillus niger is a major fungal phytopathogen of agricultural crops, particularly onion ( Allium cepa L.) where it is the causative agent of post-harvest black mold contamination of mature onions. Post-harvest fungal pathogens in onion leads to reported losses in marketable crop of between 15 and 30%, but can be as high as 80% in warm climates. However, the relationship between A. niger and the A. cepa seedling is poorly understood as the disease is not commonly observed to manifest above the soil line during plant growth. Here, we present the first timelapse microscopy data of A. cepa seedlings being colonized by soil-dwelling A. niger using high throughput fluorescence microscopy and artificial transparent soil. Our model system mimics the natural environment in terms of soil structure, hydration, essential plant nutrients and light cycles. Using a specimen carousel to image up to ten specimens over time and hence increase the throughput of our study, we determined the anatomical location of initial infection along the hypocotyl-radical axis. We identified this point to be the junction between the hypocotyl and the radicle, i.e the 'shoot' and 'root'. Timelapse microscopy reveals that infection begins at this location before spreading locally along the plant. We characterized this point using colorimetric glucose sensors and determined that this location represents a local peak of glucose exudation in healthy A. cepa seedlings, which is then colonized readily upon the introduction of A. niger.