Horses are non-kosher and its manure is also non-kosher. If you use the manure as fertilizer on, say, potatoes, isn't there some concern that the potatoes may absorb some part of the manure? If so, wouldn't that make the potatoes non-kosher?
The manure is completely broken down and absorbed by the soil. An analogy can be made using the difference between honey and milk. Manure is actually that which is rejected by the non-kosher animal. It is not created in the animal's body. As a result, it is considered as external chemical that have been separated from the food that the animal ate, broken down into chemical components (so it is no longer considered as having the status of that food) and then excreted without ever having been part of the animal.
The analogy of honey and milk is based on this fact. The honey is totally exterior to the bee and does not get the status of the bee as I explain at Was the honey that Samson ate from the lion kosher? and Is honey extracted from a dead bee kosher? Similarly, the manure is not "created" from the body of the animal and is kosher in the same way.
Additionally, you are not "eating" the manure. It is totally broken down, absorbed by the plants and used as food. An animal is allowed to eat non-kosher food and does not become non-kosher from doing so.
Another example would be the fact that fish eat worms and other non-Kosher things but that does not make them non-Kosher. Once the animal eats it, it loses its identity. Note that this means after it has been digested and absorbed into the animal. If it has not yet been digested, and is excreted unchanged, then it retains its original identity.
Note that the halachos of asur behana'ah do not apply with this matter.