Linking land management, the soil microbiome and suppression of Fusarium wilt disease

Abstract

Plant pathogens cause great loss of food production across the world. This problem is even more important given the need to produce more food for a growing human population. Given the negative effects of current pesticide-based management strategies, there is an urgent need to develop more sustainable alternatives. In this thesis, I addressed different strategies (especially the bio-organic fertilizer amendment) of disease suppression to control Fusarium wilt disease. The main goal of this research is to provide insights into the mechanisms of Fusarium wilt disease suppression, thereby yielding the necessary information to advise farmers on how to best improve soil health with suitable agricultural management measures. I first highlight that microbial communities play an important role in the suppression of soil-borne plant diseases. Most notably, the dominant fungal Mortierella populations and highly connected fungal networks in the naturally Fusarium wilt disease suppressive soil were important biological components of disease suppression. Then, I addressed different strategies of disease suppression to control Fusarium wilt disease including crop rotation and bio-organic fertilizers inoculated with beneficial microbes, with both approaches proving to be efficient and environmentally friendly agriculture managements. I found that the reconstructed microbial communities affected by these soil managements are directly responsible for the disease suppression. I also found bio-fertilizers can serve as one of the most efficient soil managements used to control Fusarium wilt disease, thereby also reducing the need for chemical fertilizers and hazardous pesticides. In addition to seeking antagonistic microbes based on their direct inhibitory activity, disease suppression may also be achieved by promoting beneficial microbes already resident in the soil. In addition, I highlight that protists, an often overlooked component of the soil microbiome encompassing most eukaryotic lineages, also play central roles in soil functioning and disease suppression. Results in this thesis demonstrate that protist communities show long-lasting responses to soil management. Treatment with chemical fertilizer promoted plant and animal parasites among the protists, whereas organic fertilizers stimulated bacterivorous and omnivorous groups, suggesting improvements of the detritivorous food web. Network analysis also placed protists as a central hub in the soil microbiome, linking diverse bacterial and fungal communities. Given the complexity of the soil food-web, the work in this thesis suggests that manipulation of higher trophic levels of organisms, such as protists, will offer new avenues to promote soil health and plant performance. In sum, this research will improve the insights in the mechanisms of soil-borne disease suppression, thereby yielding valuable advice for farmers to improve soil health with suitable agricultural management measures.