CARROT ENDOPHYTES: DIVERSITY, ECOLOGY AND FUNCTION

Endophytes are a unique group of microorganisms that spend at least part of their life cycle within plant tissues. These microbes are increasingly being recognized for their potential to improve the health and productivity of their host plants. Recent studies indicate that endophytes could also influence human health by altering the composition of chemical compounds within plants, thereby affecting their nutritional quality and flavor. In addition, the presence of endophytes in edible plant tissues could directly affect human health by introducing microbes that can stimulate the immune system or act as opportunistic pathogens in people with compromised immune systems. However, despite their potential importance for plant and human health, these plant-associated microbes have been understudied due to a lack of visible symptoms associated with their presence and difficulty in isolating them from plant tissues. In the present studies, we hypothesized that endophytes play an important role in carrot, one of the most important vegetable crops in the world.

Carrot is well known as an important source of vitamins, antioxidants and other nutrients in the human diet, and carrot taproots are often consumed raw. Carrot crops are slow to establish and are subject to assault by a wide range of pests that negatively affect the health and productivity of this crop, as well as the storage potential of its taproots. Consequently, the aim of these studies was to examine endophyte dynamics in carrot. Studies were carried out in field, greenhouse and laboratory trials using a diverse set of carrot genotypes with broad genetic backgrounds and physiological characteristics. Endophyte communities were studied using traditional culture-based techniques, along with low and high throughput sequencing technologies.

Results of these studies demonstrate that carrot seeds and taproots are colonized by an abundant and diverse set of endophytic microbial taxa. Many of these endophytes could solubilize phosphorous, fix atmospheric nitrogen, produce siderophores and auxin and suppress infection by a key carrot pathogen, Alternaria dauci, demonstrating their potential importance for maintaining carrot health and productivity. Some of the endophytes identified in these trials were vertically transmitted to progeny inside carrot seeds, indicating that they could be part of a core microbiome that evolved alongside carrot plants, and are likely to be critical in early seedling establishment. We also determined that carrot endophytes could be acquired via horizontal transmission from soil with greater soil health in an organic relative to a conventionally managed system resulting in greater populations of endophytes with antagonistic activity against A. dauci. Finally, endophyte communities varied among the genotypes evaluated in this study, with some being more responsive to the presence of greater populations of beneficial endophytes in their environments. This indicates that it could someday be possible to begin selecting for these beneficial plant microbial relationships in breeding programs.

Based on the results of these studies, we conclude that endophytes do indeed play an important role in carrot. Additional research aimed at determining how these microbes functionally interact with carrot plants and identifying practical approaches to manipulate these communities to enhance the productivity and quality of carrot taproots, are recommended. A new isolation technique identified in these trials will aid in these efforts.