In this case, the article suggests that there are "far fewer plants and animals left for [scientists/researchers] to find"
than there were in the past. The implication is that there were a huge number in the past, before we found them all, but as time passes and more and more species are discovered, that number continually wanes, to the point that it's been considered by some "to be an impossible task". (See edit at bottom of post.)
When a comparison is used like this, with no immediately obvious "than ..." clause (e.g. "far fewer than ..."), it can usually be assumed that the author means "than in the past", or some variation.
"Joseph Kony’s rebel group LRA killed far fewer civilians in 2012, group finds" - far fewer than in previous years
"Algerians Find Many More Dead at Hostage Site" - many more than they had previously
Counter example, since it isn't always this way:
- "Work is so much less stressful this way" - Less stressful than other ways. In this case, since the writer specified "this way", the implication is "than the alternative way".
Hopefully this makes sense. Ultimately, as with most things in English, it's based on context.
EDIT: In response to comments from @snailplane and @FumbleFingers, it is very likely that the article is implying "fewer than previously estimated", rather than "fewer than there were in the past, before we found them". The re-estimation work performed recently has changed the number of species thought to exist, as stated in the last sentence ("The researchers say rather than tens of millions of species living on Earth, there could be between two and eight million.").