Carrot endophytes: role of crop management system and genotype on composition and antagonistic activity towards Alternaria dauci

Authors: ABDELRAZEK, SAHAR - Purdue University; Simon, Philipp; COLLEY, MICAELA - Organic Seed Alliance; AIME, CATHERINE - Purdue University; MENGISTE, TESFAYE - Purdue University; HOAGLAND, LORI - Purdue University

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/12/2020
Publication Date: 6/4/2020
Citation: Abdelrazek, S., Simon, P.W., Colley, M., Aime, C., Mengiste, T., Hoagland, L. 2020. Carrot endophytes: role of crop management system and genotype on composition and antagonistic activity towards Alternaria dauci. PLoS ONE. 15(6). Article e0233783. https://doi.org/10.1371/journal.pone.0233783.
DOI: https://doi.org/10.1371/journal.pone.0233783

Interpretive Summary: Managing pests in carrot production is challenging, especially when using low-input and organic practices. Endophytic microbes that live inside plants roots have been demonstrated to improve the health and productivity of many crops, but factors affecting the composition and potential functional role of endophytes in carrot is still not well understood. The goal of this study was to determine how crop management system and carrot genotype interact to affect the composition and potential of endophtyes to mitigate stress caused by Alternaria dauci, an important carrot pathogen. Twenty-eight unique endophytic isolates were collected from the taproots of nine diverse carrot genotypes grown in a long-term trial comparing organic and conventional management using selective media followed by sequencing. Antagonistic activity of the isolates was quantified using an in vitro assay, and potential for individual isolates to mitigate stress caused by A. dauci was determined in greenhouse trials using two common carrot varieties. Results confirm that like most crops, carrot taproots are colonized by an abundant and diverse assortment of bacteria and fungi representing at least distinct 13 genera. Soils in the organic farming system had greater soil organic matter, microbial biomass and activity than the conventional system, and composition of endophytes in taproots grown in this system were more abundant and diverse, and contained isolates with greater antagonistic activity against A. dauci. Carrot genotype also affected the abundance of endophytes in taproots, as well as potential for individual isolates to affect seed germination, early seedling growth and tolerance to A. dauci stress. The benefits of endophytes on carrot growth were greatest when plants were subject to A. dauci stress, highlighting the importance of environmental conditions in the potential functional role of endophytes. Results of this study provide evidence that endophytes can indeed play an important role in improving carrot performance and mediating stress caused by A. dauci, and it may someday be possible to select for these beneficial plant-microbial relationships in carrot breeding programs. Implementing soil-building practices commonly used in organic farming systems has potential to promote these beneficial plant-microbial relationships, and improve the health and productivity of carrot crops.

Technical Abstract: 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 discover the composition of carrot endophytes, in this study nine diverse carrots were grown under two different crop management systems – conventional and organic and the range of endophytic microbes was identified using molecular techniques to characterize DNA signatures that serve as “fingerprints” to their identity. A diverse range of bacteria and fungi were observed with many in common across the range of carrots and growing conditions, but also with significant differences in the composition of microbes observed that were associated with different carrots, and others associated with different crop management systems. Some of the endophytes observed have been associated with conferring benefits to plants were observed, and several microbes observed in this study had not been observed as endophytes in similar studies of other plants. In a separate study, two carrot varieties known to differ in their tolerance to a common pathogenic foliar pathogen called Alternaria leaf blight were found to differ in range of their endophytes and several found may play an antagonistic role in suppressing the attack of Alternaria. This research is of broad interest to plant pathologists, crop management specialists, vegetable growers and biologists.