It is always hard to document a roguelike properly, as one of the fun things is discovering the interaction between objects. But while some, like kicking out fires, might be left to chance, others need some guidance... Here are the relevant info snippets I hoped to guide people ...
Bottles:
An empty clay bottle, awaiting filling by some liquid or another.
Mushrooms:
Growing from trees, these mushrooms come in as many varieties as there are trees. You can tincture a bottle of water with them to form various magical potions. Unfortunately, the effect of each potion is one of those things that varies every incarnation. So consume with caution until the poisonous varieties are determined.
With the correct substrate, these can be grown underground.
Logs
The remains of a cut tree. Useful for building where sticks do not suffice, or for fueling forges or kilns. Mycologists pay careful attention to the type for growing fungi.
...
The command you need is "Apply", 'a' on the keyboard should include bottles in the list, and you can point to a source of water to get a water bottle. The water bottle itself can be applied again to tincture it, and it should prompt for any mushrooms in your inventory.
Happy mushroom farming!