Seed ageing increases the influence of native microorganisms on germination

Improper seed storage conditions, such as elevated temperature and moisture, accelerate ageing and compromise seed quality. However, the impacts of ageing on the seed microbiome and the resulting consequences for germination performance remain poorly understood. Here, we characterised how ageing soybean (Glycine max) seeds at 45 °C and 75% RH affects seed fungal communities, metabolism relevant to microbial growth, and sensitivity of germination to fungal challenge. Additionally, we assessed a role for endophytic bacteria in controlling pathogenic fungi. Amplicon sequencing revealed that ageing decreased fungal richness and reshaped community structure and composition of dominant taxa in seeds. Fusarium and Rhizopus isolates inhibited germination of non-aged seeds, whereas Sarocladium, Plectosphaerella, and Cladosporium impaired germination of aged seeds only. During imbibition, ageing increased seed metabolite leakage, including pinitol, glucose, and fructose, which promoted fungal growth in vitro. Among 39 endophytic bacteria previously isolated from soybean seeds, Bacillus toyonensis C55 and B. pumilus AM26 antagonised fungal growth, consistent with genomic regions associated with antifungal activity. Ageing oxidised the seed cellular redox state, and fungi tolerated oxidative growth conditions better than bacteria. In two cultivars, seed inoculation with B. toyonensis C55 increased germination, supporting a role in regulating fungal infections, whereas B. pumilus AM26 impaired germination. Notably, neither Bacillus strain affected germination of high-vigour non-aged seeds. Fluorescence in situ hybridisation microscopy revealed that both strains recolonised the seed endosphere following ageing. We conclude that oxidation during seed ageing contributes to increased sensitivity to fungal pathogens, which can be modulated by certain bacteria.