A Rhizoctonia-like Ceratobasidium sp. AG-A causing damping-off of Arachis pintoi

In the hidden world beneath the soil, a constant negotiation takes place between plants and the microscopic fungi that surround them. Most of these fungi are harmless neighbors, or even helpful partners, living quietly on plant roots or decaying organic matter. However, under the right conditions, some of these fungi can shift their behavior, turning from passive residents into aggressive attackers that rot stems and kill young seedlings. One such group of fungi, often mistaken for a more famous cousin called Rhizoctonia, includes species that are difficult to identify by sight alone because they look so similar. Distinguishing between them requires looking at the number of nuclei inside their cells and analyzing their genetic code. This distinction matters deeply to farmers and gardeners, because different fungal groups attack different crops, and knowing exactly which one is causing trouble is the only way to stop it.

In early 2024, a certified nursery in the state of São Paulo, Brazil, faced a sudden and severe crisis with its pinto peanut crop. This specific peanut, known as Arachis pintoi, is a hardy tropical plant native to South America, prized for its ability to restore degraded pastures and improve soil health. The nursery was growing a popular variety called BRS Oquira, which is propagated by planting small stems rather than seeds. Suddenly, the seedling trays began to fail. The plants, which should have been thriving, started to develop dark, rotting stems and roots. Within weeks, the damage was catastrophic, with losses exceeding ninety percent of the young plants. The nursery operator watched as the once-vibrant trays turned into a mass of dead, withered seedlings, a phenomenon known as damping-off, where the stem base rots and the plant collapses.

A team of researchers from Embrapa, Brazil's agricultural research corporation, was called in to investigate the cause. They examined the dying plants under a microscope and found dark-brown fungal threads growing on the rotting tissue. These threads had a specific branching pattern, turning at sharp right angles, a feature typical of a group of fungi that includes both the well-known Rhizoctonia and a less familiar group called binucleate Rhizoctonia. To identify the exact culprit, the scientists took samples from the diseased plants and grew the fungus in a laboratory. They counted the nuclei, or the command centers inside the fungal cells, and found that each cell contained exactly two nuclei. This confirmed the fungus belonged to the binucleate group, which is now classified under the genus Ceratobasidium.

To be certain of the identity, the researchers extracted the DNA from the fungus and sequenced a specific genetic region. When they compared this genetic code to a massive database of known fungi, the results pointed clearly to a specific group known as AG-A. This genetic fingerprint placed the fungus in a family tree alongside other strains that cause root rot in peanuts in China, suggesting this pathogen is not unique to one location but may be widespread among peanut crops. The researchers then needed to prove that this specific fungus was indeed the one killing the pinto peanuts, and not just a bystander. They set up a controlled experiment, taking healthy pinto peanut stems and planting them in fresh soil. They inoculated one set of trays with the fungus they had isolated, while leaving another set untouched as a control.

The results were decisive. Within seven days, the plants exposed to the fungus began to show the same darkening and rot at the base of the stem that had been seen in the nursery. By the fifteenth day, eighty-nine percent of the inoculated plants had died, while only ten percent of the unexposed plants died, mostly due to natural rooting failures. The researchers then took the fungus from the newly dead plants and grew it again, confirming it was the same organism they started with. This cycle of isolation, infection, and re-isolation fulfilled the standard scientific requirements to prove the fungus was the true cause of the disease.

This discovery marks the first time this specific fungus, Ceratobasidium sp. AG-A, has been reported causing damping-off in pinto peanuts. While a similar fungus had been seen on other crops in Brazil, and a different species of Rhizoctonia had been loosely associated with pinto peanuts in the past, this is the first confirmed case of this particular genetic group attacking this specific plant. The findings suggest that this fungus may be more common in peanut production than previously realized, potentially jumping from other hosts or shifting its behavior due to changes in the environment. Following the diagnosis, the nursery implemented strict management changes, including treating the planting stems with fungicide, removing contaminated soil, and moving the seedling trays to areas with more direct sunlight and less continuous watering. These steps successfully stopped the outbreak, reducing losses to negligible levels. The case serves as a reminder that even hardy, native plants are vulnerable to microscopic shifts in the fungal world, and that precise identification is the first step toward protecting our food systems.