5. Two populations that were found on Limestone substrates have been trained to accept a cluttered closet as an excellent place for it to flourish.

Ans 5. Two populations that were found on limestone substrates have been trained to accept a cluttered closet as an excellent place for them to flourish.

1) the name of geological elements (e.g. mica, amethyst) are not capitalized. Therefore, limestone is not capitalized.

2) The pronoun here refers back to "two populations." That's plural. Therefore, you need to change it to the plural form of the pronoun.