Metagenomic Comparison of How Three Genotypes and Two Management Regimes Influence Carrot Endophyte Fungal Communities.

Endophytic microbial communities are present in almost all plant species, however knowledge of their response to different production practices in important storage root crops like carrot are still poorly understood. In this study, we compared management regime and carrot genotype influence on fungal endophyte community composition. Three carrot genotypes (Exp PY191, Exp B0252, and Exp Nb3999) with diverse genetic backgrounds were grown under organic or conventional management and endophyte community composition was determined using high throughput Illumina sequencing of the fungal ITS region and the QIIME (Quantitative Insights Into Microbial Ecology). Results provide evidence that carrot roots are colonized with a total of 55 fungal genera, with most belonging to Ascomycota, Basidiomycota and Chytridiomycota fungal phyla. The most abundant genera in all samples were characterized as Rhizoctonia followed by Fusarium. Changing the management regime altered the composition and abundance of these fungal communities while genotype only affected the abundance of certain genera. Carrots grown under organic management had a greater diversity of fungal endophytes, and genera representing Olpidium, Ossicaulis, Microdochium, Glomerella, Myrothecium, Claviceps and Cercospora were only represented under organic management, whereas Nomuraea, Schizophyllum, and Phoma fungal genera were only represented under conventional management. Carrot genotype Exp PY191 had the greatest abundance of total fungal endophytes among the tested genotypes. Results from this study suggest that management regime has a greater influence on carrot fungal endophyte microbial community structure than genotype and organic management permits a wider diversity of fungal endophytes to colonize carrot roots. These findings confirm earlier studies suggesting that organic practices promote biodiversity, providing potential benefits for plant health and productivity. While not as dramatic, differences in the abundance of individual genera among genotypes could also play a role in carrot fitness and should be further explored within the context of varietal development and selection.