Answer
Soybeans and wheat contain starch (a polymer of glucose). The microorganisms breakdown starch to glucose, and Glucose to pyruvate via glycolysis.
On the other hand fermentation is a process carried out in the absence of $O_{2}$ and convert Pyruvate to lactic acid and ethanol. If $O_{2}$ were present, Pyruvate would be oxidized to acetyl-CoA then $CO_{2}$ and $H_{2}$$O$.
Some of the Acetyl-CoA however, would also be Hydrolyzed to acetic acid (Vinegar) In the presence of oxygen.
Work Step by Step
Above is the reason to prevent the soy sauce from having a strong vinegar taste (vinegar is dilute acetic acid). Thus, oxygen must be kept out of the fermentation tank.
