Learn German: Er hilft den Pflanzen dadurch, dass er sie regelmäßig düngt. - He helps the plants by fertilizing them regularly.

In English, we express the method using "by" plus an "-ing" verb. German doesn't use an "-ing" form here. Instead, it uses dadurch, dass (literally: "through it, that") followed by a full subordinate clause with a subject (er) and the conjugated verb at the end (düngt). So literally, it says "He helps the plants through it, that he fertilizes them regularly."

Can I use indem instead of dadurch, dass in this sentence?

Yes! Both indem and dadurch, dass translate to "by doing something" and both send the conjugated verb to the end of the clause. dadurch, dass puts a slightly stronger emphasis on the cause-and-effect relationship, but saying Er hilft den Pflanzen, indem er sie regelmäßig düngt would be perfectly natural and mean the exact same thing.

Why is it den Pflanzen and not die Pflanzen?

The verb helfen is a dative verb, meaning the person or thing being helped must be in the dative case. Because Pflanzen is plural, the dative plural article is den. Normally you would also add an "-n" to the end of a dative plural noun, but Pflanzen already ends in "-n" in its regular plural form.

In the second half of the sentence, why are er and sie right next to each other?