How do food jar factories put negative pressure into the jar to begin with?
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There are a few ways to achieve this; the main way is what everyone else has stated: heat the product before filling, and when it is sealed and cooled, the product will contract, vapors will condense, leaving more space for less gasses in the headspace, creating negative pressure. Hot filled products typically use this method.
For some seals, a blast of steam to the headspace of the product before sealing will create the negative pressure. It acts the exact same way as above to create negative pressure, but without the need to heat the product first. This could be done to seal a jar before the retort process. The retort process is essentially a large scale pressure cooker that can bring water to temperatures well above its typical boiling point (250F compared to 212F, respectively). It is important to note that the containers must be sealed before going into the retort.
The negative pressure helps in a few ways. First, it acts as a fail safe after processing. If the lid does not pop, then the seal is likely compromised and you should not eat that food. For canned products like this, the worry is that the bacteria clostridium botulinum could have some remaining cells alive in the food and can cause botulism. Second, during the thermal process in a retort, the sealed containers will see massive increases in pressure inside the container. Without creating an initial negative pressure, the rise in pressure could cause the seals to fail.
Whether using the heated product or by steam, the cooling after sealing is what creates that negative pressure.
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