Mycobiome Analysis of Tall Fescue Grass under Drought Stress Using the Illumina MiSeq and Oxford Nanopore Technology MinION

The effects mycobiomes have on physiological traits in turfgrasses are poorly understood. Drought tolerance, an economically and ecologically important trait, can be influenced by symbiotic fungi. In this two-year study, we evaluated the mycobiome associated with tall fescue exposed to prolonged periods of drought stress in a rainout shelter. Twelve plants, comprised of six sets of half-sibs (progenies having one parent in common), one exhibiting a drought tolerant phenotype and the other a susceptible phenotype were selected for analysis each year. The mycobiomes associated with the shoot, root, and rhizosphere soil was evaluated for each tall fescue half-sib pair using both short-read Illumina MiSeq and long-read Oxford Nanopore Technology (ONT) MinION sequencing pipelines. Both platforms sequenced portions of the fungal nuclear ribosomal RNA genes. The Illumina MiSeq sequenced the internal transcribed spacer region (ITS, 600 bp), while the ONT MinION covered the small subunit, ITS, and partial large subunit (4,600 bp). Both sequencing pipelines revealed that the mycobiomes associated with the roots, shoots, and soil were significantly different. The ONT MinION pipeline identified more diverse fungal lineages and had higher taxonomic resolution compared to the Illumina pipeline. Our results also indicated that root pathogens may play a more important role than the endophytic or mycorrhizal symbionts in tall fescue drought stress tolerance.