Soil microbiome can improve carrot resistance to deadly fungus

On average, the endophytes in the organic system reduced growth of the Alternaria dauci pathogen by 44 percent, which was more than twice the protection conferred by endophytes in carrots grown in the conventional soil.

In the field trial, there was no difference in carrot root yield, but pathogen pressure can vary dramatically given environmental conditions, making it difficult to quantify disease suppression in the field. However, given the results of this trial, the scientists suspect that the carrots grown in the organic system would be better able to resist disease if environmental conditions were suitable for the disease to develop.

Results of these experiments also demonstrated that carrot genotype can play a role in supporting endophytes that can suppress this disease. In field trials, two of the nine experimental carrot genotypes had 34 percent and 93 percent lower disease severity in the organic system versus the conventional. Results of the greenhouse trials confirmed that differences in the ability of different carrot genotypes to resist the disease were related to their ability to host the beneficial endophytes.

“This demonstrates the potential effects of genotype, or variety, on a plant’s ability to harness the benefits of organic, healthy soils,” Hoagland said.

The research is part of the Carrot Improvement for Organic Agriculture (CIOA) program, a long-term breeding project aimed at addressing the needs of organic carrot farmers. Funded by the U.S. Department of Agriculture’s National Institute of Food and Agriculture, it brings together scientists from Purdue, the USDA’s Agriculture Research Service, the University of Wisconsin, the Organic Seed Alliance, the University of California Riverside, Washington State University and University of California Extension.

Hoagland said better understanding of the microbiomes of the soil — and the ways in which breeders and growers can affect them — can lead to invaluable methods of reducing disease, fighting weeds and addressing other needs of specialty crop growers.

“We’re still in the early stages of this work, but we see this as a tool that breeders can use when developing new carrot varieties,” Hoagland said. “Growers, too, may one day be able to impact the number and types of beneficial microbes to protect their plants. If growers focus on the health of their soils, they can see some benefits now.”