Manipulating atmospheric CO₂ concentration induces shifts in wheat leaf and spike microbiomes and in Fusarium pathogen communities

Changing atmospheric composition represents a source of uncertainty in our assessment of future disease risks, particularly in the context of mycotoxin producing fungal pathogens which are predicted to be more problematic with climate change. To address this uncertainty, we profiled microbiomes associated with wheat plants grown under ambient vs. elevated atmospheric carbon dioxide concentration [CO₂] in a field setting over 2 years. We also compared the dynamics of naturally infecting versus artificially introduced Fusarium spp. We found that the well-known temporal dynamics of plant-associated microbiomes were affected by [CO₂]. The abundances of many amplicon sequence variants significantly differed in response to [CO₂], often in an interactive manner with date of sample collection or with tissue type. In addition, we found evidence that two strains within Fusarium – an important group of mycotoxin producing fungal pathogens of plants – responded to changes in [CO₂]. The two sequence variants mapped to different phylogenetic subgroups within the genus Fusarium, and had differential [CO₂] responses. This work informs our understanding of how plant-associated microbiomes and pathogens may respond to changing atmospheric compositions.