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I appear to have mushrooms growing in my fortress, should I be worried about this and if so how should I deal with them?

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No, mushrooms are not dangerous but can be a nuisance.

Mushrooms are the underground equivalent of plants. Smaller mushrooms are collected with the Gather Plants designation and can be a source of alcohol, food and/or cloth, depending on the species. However, they're not that interesting- they're available when you embark and you've probably been cultivating them for a while.

Larger mushrooms are the equivalent of trees and can be cut down by woodcutters. They are a source of wood, sometimes in unusual colours. They're not dangerous but they might get in the way if they're growing in the middle of a corridor or a room.

Mushrooms will grow in any underground muddy area, i.e. any soil or areas of rock that have had water on them. To remove the mud, build a floor over the muddy area.

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    Requiring mud was only true in an earlier version -- once the caverns are breached, any underground soil, or muddied stone, is fair game. – Raven Dreamer Aug 11 '15 at 1:40
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    As Raven says, once you hit the caverns you might notice fungus sprouting up on your farm levels. The worst is when fungus-trees grow in your water ducts and block them up! – Samthere Aug 11 '15 at 8:18
  • @RavenDreamer Thanks, I edited that into the answer. – Studoku Aug 11 '15 at 17:19
  • @Samthere constructed floor all the things! – Raven Dreamer Aug 12 '15 at 1:16

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