I wonder why "consequences of deforestation" is preceded by "the" […]?
*"One of consequences […]" would not be grammatical; we only use "one of" when there's another determiner ("one of the […]", "one of a few […]", "one of these […]", etc.) or a plural pronoun ("one of them", "one of whom", "one of which") or whatnot. Instead of *"one of consequences", we just say "one consequence" or "a consequence".
But then — why "one of the consequences of deforestation" rather than "one/a consequence of deforestation"? Honestly, I think either would be fine here. Unless the idea of consequences of deforestation has already been mentioned, the only difference I detect is that the version with of the presupposes that there are multiple consequences, and suggests that the author knows what they are (or at least what some of them are), whereas the version without of the leaves open the possibility that there's only one consequence. (We wouldn't say "one/a consequence" if we know that there's only one — in that case we'd say "the consequence" — but we can say it if we're not immediately certain whether there's only one.)
I wonder why […] "loss of biodiversity" is not [preceded by "the"]?
Unless a loss of biodiversity has previously been mentioned or can otherwise be assumed to be familiar to the reader, "the loss of biodiversity" would make it sound like biodiversity is now gone: in other words, like there was a complete loss of biodiversity. By contrast, "loss of biodiversity", with no article, just means that some biodiversity has been lost: that there are fewer species than before, but still some species.
That said, a phrase like "the loss of some biodiversity" — meaning that some biodiversity is now gone — would also be fine here, albeit a bit weaker-sounding.
I wonder why "consequences of deforestation" is preceded by "the" but "loss of biodiversity" is not?
Your phrasing seems to suggest that you would have expected that either both would have "the" or that neither would have "the"; but really, there's no reason to expect that. The two phrases are filling different roles in the sentence, and don't need any sort of parallel structure.