It makes more sense to me if it is written with a "with" - the crops are cultivated with (without) using natural fertilizers. -- No. 'With using' is wrong grammar in any register.
New words, one handy idiom, and a 2-minute quiz — delivered to your inbox to keep your streak alive.
Anonymouscrops are cultivated using natural fertilizers".....Using natural fertilizers" - The entire phrase modifies "the crops are cutivated" and "using" is a present participle used to construct the phrase. As you suggested "with" would in fact yield the similar meaning. However, "with natrural fertilizers" is a prep