Amplicon sequencing of Fusarium translation elongation factor 1α reveals that soil communities of Fusarium species are resilient to disturbances caused by crop and tillage practices

The fungal genus Fusarium contains plant pathogens, mutualists, and commensalists. As non-pathogenic Fusarium strains can contribute to disease-suppression in soil by competition or induced plant resistance, identifying factors that influence the abundance of non-pathogenic strains could lead to strategies that enhance plant-beneficial interactions and deter pathogen invasion. We developed a Fusarium-specific translation elongation factor 1α (EF-1α) high-throughput amplicon-sequencing method with sub-species resolution. Newly designed primers enabled reads to be joined for improved quality metrics after Illumina MiSeq sequencing. By including the ‘oligotyping’ program in our bioinformatic workflow, we reconstructed Fusarium EF-1α haplotypes with 100% accuracy. We conducted simulated crop rotation experiments in soil infested with the strawberry pathogen F. oxysporum f. sp. fragariae (Fof) and the following treatments: strawberry, blackberry, raspberry, lettuce, broccoli, and fallow. We profiled root Fusarium communities with EF-1α amplicons and observed that non-pathogenic strains of F. oxysporum did not colonize crops uniformly; some strains exhibited asymptomatic host preferences. In susceptible strawberry roots, >90% of sequences corresponded to Fof. Bulk soil communities of Fusarium were remarkably stable and had minimal treatment-dependent effects after one year. Similarly, in a long-term agricultural research experiment, 18 years of conservation tillage and cover cropping did not lead to bulk soil Fusarium communities that were significantly different than controls. While the roots of rotation crops can augment the abundance of non-pathogenic F. oxysporum strains, their abundance in bulk soil is unlikely to be altered after a single year. Climate and soil physicochemical properties may have a greater effect on Fusarium community structure.