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

Authors: Henry, Peter; Koehler, Samuel; KAUR, SUKHWINDER - University Of California; EPSTEIN, LYNN - University Of California; MITCHELL, JEFFREY - University Of California; GORDON, THOMAS - University Of California; LEVEAU, JOHAN - University Of California

Submitted to: Phytobiomes Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/13/2022
Publication Date: 6/7/2022
Citation: Henry, P.M., Koehler, S., Kaur, S., Epstein, L., Mitchell, J.P., Gordon, T.R., Leveau, J.H. 2022. Amplicon sequencing of Fusarium translation elongation factor 1a reveals that soil communities of Fusarium species are resilient to disturbances caused by crop and tillage practices. Phytobiomes Journal. 6(3):261-274. https://doi.org/10.1094/PBIOMES-09-21-0053-R.
DOI: https://doi.org/10.1094/PBIOMES-09-21-0053-R

Interpretive Summary: Fungi can have many different impacts on plant growth and development. Some fungi improve plant growth and fitness, some have neutral effects, and others can reduce plant fitness. Strains of a single fungal species, called Fusarium oxysporum, can be either beneficial, neutral, or detrimental to plant health. The factors that enhance the abundance of beneficial strains of F. oxysporum in soil are not well known. If these factors were discovered, crop management strategies could be designed that improve the benefits of beneficial strains to plants. To identify these factors, we developed an efficient method to quantify all strains of F. oxysporum in soil based on high-throughput DNA sequencing. Using this method, we tested the impact of crop rotations, cover cropping, and tillage on the relative abundances of F. oxysporum strains. Disturbance caused by crop rotation, cover cropping, and tillage did not significantly alter soil communities of Fusarium. However, different crop species varied in their level of colonization by each strain. Other aspects of soil such as physical or chemical properties may have a greater impact on soil abundances of beneficial F. oxysporum strains and are a priority for future research on this topic.

Technical Abstract: 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 high-throughput translation elongation factor 1a (EF-1a) amplicon-sequencing method with sub-species resolution for Fusarium community analysis. Newly designed primer pairs 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-1a sequences 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-1a 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 and two consecutive crop rotations. Similarly, in a long-term agricultural research experiment, 18 years of conservation tillage and cover cropping did not significantly alter bulk soil Fusarium communities. While the roots of rotation crops can augment populations of non-pathogenic F. oxysporum strains, bulk soil populations are unlikely to be altered after a single year. Other factors may have a greater effect on the population structure of Fusarium communities.