MSc Romina Kalbermatten

05/2026

Supervision: Dr. Pascale Flury and Eva Burgunder

Abstract:

Climate change is projected to intensify soilborne disease pressure globally. In Switzerland, increasing post-harvest losses in table beet are suspected to reflect climate-driven shifts in soilborne pathogen dynamics. Yet how soil fungal communities and disease outcomes respond to multifactorial climate scenarios remains largely unknown. This study investigated whether simulated future climate scenarios alter disease dynamics in table beets and how this links to changes in root fungal community composition and diversity. Table beet seedlings were grown in native soils from six agricultural field sites and exposed to control and two future regionally projected climate scenarios based on moderate or extreme emission scenarios. The biotic basis of disease was assessed through a reinoculation experiment, soil and root fungal communities were assessed using long-read amplicon sequencing of the ITS region, and key pathogens were identified by culture-based isolation and used to establish artificial infection systems. 

Reinoculation partially restored disease levels, confirming that the disease-promoting capacity of native soils resides in the microbial community. Post-emergence disease incidence increased under future climate scenarios in four of six fields, while pre-emergence disease showed no consistent response, indicating stage-specific climate effects. Field-specific disease differences were more consistently predicted by baseline soil fungal alpha diversity than by root communities, with higher diversity consistently associated with lower disease across all climate treatments. Climate-driven changes in root fungal communities were detectable only at the level of individual taxa, among which ASV 25, mapping to the genus Fusarium, emerged as the key climate-responsive taxon positively associated with disease under RCP 8.5. ASV 25 matched with 100% sequence identity to an isolate recovered from symptomatic root tissue, which, together with a second isolate, was used to establish an artificial inoculation system. Both isolates induced disease at pre- and post-emergence stages under controlled conditions. 

This work advances understanding of climate-disease dynamics by revealing that warming effects operate through individual responsive taxa and that baseline soil diversity mediates disease outcomes, resulting in field-dependent outcomes that demonstrate spatial variability in climate-disease responses.