Pythium ultimum is a devastating pathogen of seeds and seedlings. Germination of pathogen sporangia can be elicited by unsaturated long chain fatty acids that are released by germinating seeds. Sporangial activation and germination are critical for initiating Pythium disease development. Pythium infection can be prevented by applying the bacterium Enterobacter cloacae onto seeds and expression of bacterial fatty acid transport and degradation have been found to be important traits for this control. However, the bacterium is capable of protecting only certain seeds such as cotton and cucumber whereas other seeds, such as corn and pea succumb to Pythium infection. It has been postulated that differences in sugar released by seeds may explain this differential protection since sugars are able to repress fatty acid metabolism in E. cloacae. Corn and pea seeds are documented as seeds that release high amounts of simple sugars that can repress fatty acid uptake and catabolism. Experiments focused on the temporal release of corn and cucumber seed exudates and their induction of sporangial activation, germination, host colonization and the impact E. cloacae had on these pathogen responses while concomitant release of exudate sugars and fatty acids was also analyzed. E. cloacae is able to interrupt sporangial activation induced by cucumber seeds, but not in the corn spermosphere. This explains the differential control by the bacterium, since activation interference directly resulted in suppressed seed colonization. Both corn and cucumber seeds released unsaturated fatty acids as early as 15 min after sowing although quantities from corn exceeded that of cucumber. More importantly, corn seeds released much higher concentrations of simple sugars than cucumber already within 15 min. Quantities detected in corn seed exudate are large enough to completely shut down fatty acid degradation of E. cloacae. This provided the first evidence that interference with sporangial activation is the cause for plant protection by E. cloacae and seeds not protected by E. cloacae are incapable of interfering with sporangial activation. The bacterium does not interfere with sporangial activation because non protected seeds release sugars at such quantities that bacterial fatty acid degradation is repressed.