Occurrence, incidence, and severity of Alternaria leaf spot of cotton (Gossypium hirsutum L.) in major cotton-growing districts of the Lake Zone, Tanzania

Cotton is often called "white gold" because it is the fiber that clothes much of the world, and in Tanzania, it is a lifeline for hundreds of thousands of small farmers. For these growers, the crop is not just a commodity but a primary source of income and a pillar of the local economy. However, like many crops, cotton is vulnerable to nature's unseen enemies. One such enemy is a fungal disease known as Alternaria leaf spot. This disease does not attack the plant all at once; instead, it targets older leaves, causing them to develop brown, dead spots that often have concentric rings, like ripples in a pond. As these spots grow, they turn gray and dry out, causing the leaves to fall off prematurely. When a cotton plant loses its leaves too early, it cannot make enough food to support its cotton bolls, leading to smaller harvests and lower-quality fiber. While farmers in Tanzania's Lake Zone have long noticed this disease appearing more frequently, they have lacked a clear, systematic picture of just how widespread it is or how bad the damage truly is across their different regions.

To fill this gap, a team of researchers from Sokoine University of Agriculture and the Tanzania Agricultural Research Institute set out to map the disease across the four main cotton-growing districts of the Lake Zone: Bariadi, Bunda, Chato, and Magu. During the 2024 and 2025 growing season, the team visited twenty different cotton fields, selecting five fields in each district. They walked through these fields using a specific diagonal path to ensure they looked at a fair mix of plants from every corner and the center, examining a total of 1,000 individual cotton plants. Their goal was simple but critical: to count how many plants were sick, to measure how badly they were suffering, and to confirm that the fungus causing the trouble was indeed the one they suspected. They also collected samples of the fungus from the leaves to grow them in a lab, checking their physical features under a microscope to be certain of their identity.

The results of this survey revealed a stark reality: the disease is everywhere. In every single one of the twenty fields they visited, the researchers found signs of Alternaria leaf spot. This means the disease has a one hundred percent presence across the region, affecting every farm they checked. However, while the disease is everywhere, the amount of damage it causes varies significantly depending on where you are. On average, about sixty-four percent of the plants in any given field were infected. But this average hides a wide range of conditions. In the Bariadi district, the disease was most aggressive, with nearly eighty percent of the plants showing signs of infection. In contrast, the Magu district saw the lowest levels, with about fifty-two percent of plants affected. The researchers found that the disease was not just present but often severe, with the overall damage to the leaves reaching a level that indicates a moderate to serious threat to the crop's health.

When the team looked closer at the relationship between how many plants were sick and how sick those plants were, they found a surprising pattern. At first glance, it seemed that fields with more infected plants also had more severe damage. But when the researchers separated the healthy plants from the sick ones and looked only at the plants that were already infected, that strong connection disappeared. This suggests that the main driver of the problem in these fields is not that the disease is becoming more deadly to individual plants, but rather that more and more plants are catching the disease in the first place. The fungus is simply spreading to more hosts, rather than becoming more aggressive within the plants it has already infected.

To confirm the culprit, the researchers took samples from the infected leaves and grew the fungus in the lab. They examined the tiny spores produced by the fungus under a microscope, looking at their shape, size, and the number of internal walls they contained. Every single one of the forty samples they tested matched the physical description of the Alternaria genus. While the specific species of the fungus might vary, the team confirmed that the entire region is dealing with this specific type of fungal pathogen. The variation in the size and shape of the spores they found suggests that there may be a mix of different strains of the fungus circulating in the fields, but they all belong to the same family of troublemakers.

The study also looked at the weather patterns in the different districts to see if they could explain why some areas were hit harder than others. The districts with the highest disease levels, Bariadi and Bunda, tended to have more rainfall and higher humidity during the growing season compared to Chato and Magu. This aligns with what is known about how this fungus spreads, as it thrives in wet conditions where moisture helps the spores land on leaves and germinate. However, the researchers were careful to note that while the wet weather likely played a role, they did not prove a direct cause-and-effect link in this specific study. Other factors, such as how farmers manage their fields, whether they rotate crops, or if they use saved seeds from previous years, could also be helping the fungus survive and spread from one season to the next.

This work provides the first clear, systematic baseline for understanding Alternaria leaf spot in Tanzania's most important cotton region. It shows that the disease is no longer a rare occurrence but a constant presence that affects every farm. The findings suggest that managing this threat will require different strategies for different areas, as the pressure from the disease is not uniform across the Lake Zone. For farmers and agricultural officials, the message is clear: the disease is widespread, and while it varies in intensity, it poses a serious risk to the cotton harvest. The path forward involves keeping a close watch on the disease, understanding local conditions, and using a mix of farming practices to reduce the amount of fungus in the fields, ensuring that the "white gold" of Tanzania can continue to support the livelihoods of its people.