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ARS Home » Midwest Area » Madison, Wisconsin » Vegetable Crops Research » Research » Publications at this Location » Publication #377071

Research Project: Trait Discovery, Genetics, and Enhancement of Allium, Cucumis, and Daucus Germplasm

Location: Vegetable Crops Research

Title: Changes in the core endophytic mycobiome of carrot taproots in response to crop management and genotype

item ABDELRAZEK, SAHAR - Indiana University-Purdue University
item CHOUDHARI, SULBHA - Frederick National Laboratory For Cancer Research
item THIMMAPURAM, JYOTHI - Purdue University
item Simon, Philipp
item COLLEY, MICAELA - Organic Seed Alliance
item MENGISTE, TESFAYE - Purdue University
item HOAGLAND, LORI - Purdue University

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/30/2020
Publication Date: 8/13/2020
Citation: Abdelrazek, S., Choudhari, S., Thimmapuram, J., Simon, P.W., Colley, M., Mengiste, T., Hoagland, L. 2020. Changes in the core endophytic mycobiome of carrot taproots in response to crop management and genotype. Scientific Reports. 10. Article 13685.

Interpretive Summary: Microbes are familiar as pathogens or parasites causing diseases of living plants, and as saprophytes decomposing dead plants, but beyond these microbes, large numbers of diverse microbes called endophytes live in living tissues of plants causing no disease, and in some cases, benefitting the host organism. To better understand the role of endophytes in the growth of the carrot crop, three carrot breeding stocks were grown in fields under organic and conventional management and endophytes were evaluated. Crop management system had a larger effect on variation of endophyte composition than did genetic stocks, but carrots bred for nematode resistance had a distinctly different composition profile from carrots susceptible to nematodes. This research is of broad interest to plant pathologists, crop management specialists, vegetable growers and biologists.

Technical Abstract: Fungal endophytes have potential to help manage production and post-harvest challenges in carrot. However, the identity of fungal endophytes, as well as factors affecting their composition in carrot have not yet been determined, which prevents growers from leveraging these microbes to improve crop performance. To overcome this challenge, we characterized fungal endophytes in the taproots of three carrot genotypes that vary in resistance to root knot nematodes grown under organic and conventional management using Illumina sequencing of the ITS gene. 1,480 individual OTU’s were identified, demonstrating that carrots are colonized by a highly diverse set of fungal endophytes. Most were consistent across samples, indicating that they are part of a core microbiome in carrot. Members of the Ascomycota were most dominant, demonstrating that they are particularly well suited to survive in carrot taproots. Crop management altered soil health and had the greatest effect on the composition of fungal endophytes. Differences among individual OTU’s differed most between the resistant and susceptible genotypes, indicating that resistance to pathogenic nematodes could play a role in structuring fungal endophyte communities. Difficulties in isolating fungal endophytes must be overcome so that all fungal endophytes can be identified, and their functional roles in carrots determined.