After botanist Ariel Novoplansky exposed plants to simulated drought, he discovered them and neighboring plants were communicating with each other through their roots.
them and neighboring plants were
them and neighboring plants as
them and neighboring plants as they were
they and neighboring plants to be
that neighboring plants and they were

Solution:
Correctly answering this question requires determining what makes sense in terms of what the botanist would have discovered and also understanding the correct use of the subject pronoun “they” and the object pronoun “them.” While some of the incorrect choices may seem possibly correct, the correct answer is so clearly correct that we can confidently choose it over any other.
(A) After botanist Ariel Novoplansky exposed plants to simulated drought, he discovered them and neighboring plants were communicating with each other through their roots.
This version incorrectly uses the object pronoun “them” as the subject of “were.”
While it may seem that “them” is correct since “them” seems to be the object of “he discovered,” what he discovered was not the plants themselves. He discovered the plants were communicating.
(B) After botanist Ariel Novoplansky exposed plants to simulated drought, he discovered them and neighboring plants as communicating with each other through their roots.
This version sounds incorrect and is incorrect, since in English there is no idiom “discovered … as” as in “discovered the plants as communicating.”
(C) After botanist Ariel Novoplansky exposed plants to simulated drought, he discovered them and neighboring plants as they were communicating with each other through their roots.
This version could be tempting, as it is grammatically correct, since “them” correctly functions as the object of “discovered.” However, the meaning conveyed is nonsensical, as the botanist would not have discovered the plants after the botanist exposed the plants to simulated drought.
(D) After botanist Ariel Novoplansky exposed plants to simulated drought, he discovered they and neighboring plants to be communicating with each other through their roots.
This version could be tempting if one perceives the subject pronoun “they” to be correctly serving as the subject of “to be communicating.” Let’s test the version though, by eliminating the non-pronoun part of the compound structure and seeing how the sentence reads.
botanist Ariel Novoplansky … discovered they to be communicating
Probably, even to someone who doesn’t know exactly how the idiom “discovered … to be” works, that version would sound incorrect, and it is in fact idiomatically incorrect.
CORRECT ANSWER(E) After botanist Ariel Novoplansky exposed plants to simulated drought, he discovered that neighboring plants and they were communicating with each other through their roots.
This version correctly uses the subject pronoun “they” as part of the compound subject of “were communicating” and conveys a meaning that makes sense.