Canning jars are typically filled as high as possible with liquid and heated. The liquid expands when it gets warmer so it pushes all the air out and the lid is put on while it’s hot. When the liquid cools down it wants to shrink, that’s where the negative pressure comes from. Home canning uses the same basic principle as the cans in the grocery store, if you want to learn more about it there are tons of resources for that.
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