Fungi and Bacteria Team Up with Carrots for Better Health

ARS researchers identify soil microbes that fight disease and promote growth in carrots.

The mysterious underground world of carrots may hold answers about powerful natural defenses against destructive plant diseases, according to Dr. Philipp Simon, plant geneticist and research leader of the ARS Vegetable Crops Research Unit in Madison, WI.  

Together with Dr. Lori Hoagland of Purdue University, Simon and his team have identified 13 specific genera of fungi and bacteria that live inside plants — collectively called endophytes — that can latch onto carrots and fight disease or even promote the carrots' growth.

The findings are significant, as carrots are the sixth most-consumed fresh vegetable in the United States and represent the largest market share of all crops in the organic sector. In 2020, U.S. domestic production totaled approximately 3.4 billion pounds. Simon and Hoagland's findings represent an important step in keeping that crop healthy.

"When properly 'paired' with these endophytic microbes, carrots were able to better tolerate stress induced by Alternaria leaf blight, a disease caused by the fungus Alternaria dauci," explained Simon. "Alternaria leaf blight is a destructive and costly carrot pathogen that can spread rapidly if not controlled, so any protection from it can have huge implications for growers. Traditionally, chemical fungicides, herbicides, and pesticides were used to address A. Dauci, but with endophytes, we are making use of allies that occur naturally."

Carrots freshly harvested from a farm garden.

The team found that certain bacterial families (Rhizobium, Bacililus, Stenotrophomonas and Pseudomonas) were able to move toward plant roots, enter and bypass plant immune systems, and successfully attach to carrots. They also identified two crucial factors that help foster partnerships between carrots and endophytes: carrot genes and soil building practices. 

After reviewing over 30 different commercial varieties and breeding lines, they observed that the genetic makeup of certain carrot varieties made them particularly receptive to bonding with endophytes. They also found that crop management tactics focused on building better soils — particularly by adding organic materials — improved the carrot-endophyte relationship.

Hoagland noted that several variables can influence soil health and the microbes that live in soil, including the soil's water retention capacity, available oxygen, and pH levels. Practices like tilling can also indirectly influence microbial activity, as tilling depletes the organic matter within soil that microbes 'feed' on. To help replenish organic matter and build a beneficial microbial community, Simon and Hoagland recommend growers reduce tillage, add compost, and cultivate cover crops.

"Although this research is still a work in progress, we see that utilizing these microbial allies to fight against carrot diseases like Alternaria leaf blight is entirely plausible," said Simon. "Studies of other crops have shown that plant-associated microbes can promote overall growth by helping to increase nutrient availability for plants."

Now, it appears, carrots can also benefit from that kind of healthy microbial alliance. By Georgia Jiang, ARS Office of Communications