Exact meaning of “fewer than” concerning numbers

There are far fewer than previously thought. It's not stated, but read the next sentence:

The researchers say rather than tens of millions of species living on Earth, there could be between two and eight million.

This suggests that the previous estimates were too high. Since we've only found "more than a million species" and we previously thought there were "tens of millions", it can't be that we've discovered that many; the numbers simply don't add up. If the differences were due to mass extinctions or some other apocalyptic event, the article would probably mention that, too. Therefore, the only reasonable interpretation is that the estimates have been revised down.

Therefore, researchers previously thought there were more; now they think there are far fewer.

Prenote:

A lot of fewer is incorrect. Of comes before a noun, and doesn't exist in the adverbial form (which you want to use here, with an adjective), so it's a lot fewer.
Little and a little are different. I assume that you wanted to ask about a little.

Short answer

many fewer / a lot fewer / much fewer, and a little fewer

None of these adv+adj collocations are wrong. The first three of them mean almost the same thing: that the difference in number is big. The last one means the opposite: the difference in number is small.
But in terms of prevalence, there are better choices to make:

When there's big difference in number, the most common expression by far is far fewer:

There are far fewer people than usual in the street.

And when the difference is small, the most common expression appears to be slightly fewer:

There are slightly fewer people than usual in the street.

Long Answer

To cite an authority, this is what Longman Dictionary has to say about fewer:

fewer [quantifier]: a smaller number of people or things. Fewer is used with countable nouns:
Spending cuts will mean fewer social workers.

far fewer/a lot fewer:
There were far fewer women at the conference this year than last.

(Not a complete definition (fewer is not just a quantifier and has more common word partners than far and a lot), but was still worth mentioning.)

Now I'm going to search COCA for [be] . . . fewer than ^†, and present you with some statistics regarding what kinds of adverbs are how frequently used in that gap. This is to get a smaller sample to go through and get first clues; more relaxed searches will be done later on.

• [be] far fewer than: 22
• [be] considerably fewer than: 5
• [be] a lot fewer than: 2
• [be] substantially fewer than: 2
• [be] a few fewer than: 1
• [be] many fewer than: 1

I left less relevant results out of the list, like [be] probably fewer than: 7, [be] two fewer than: 2, [be] X percent fewer than: 2, etc.

As you see, far is by far the most prevalent one, and considerably comes second (, and both of them were offered in the comments/answer before). But are the other options wrong?

One thing that throws doubt on expressions like many fewer or a lot fewer is that they seem self-contradictory: How can there be a few of both Xs and Ys, and yet Xs be many fewer/more than Ys?! How can they both be a few and the difference between them be many?

The answer is simple: comparative and superlative adjectives don't go by that logic. You can say "The Earth is smaller than the Sun" without implying that any of them is small, and you can say of two newborn twins that "This one is older than that one" without suggesting that any of them is old.
Therefor, it's technically correct (but practically not best) to say "There are fewer people than ants", even though they're both many. (A more usual phrasing: "There are more ants than people".)

Another problem that some people seem to have with much/a little fewer is that much and a little are used before uncountable nouns, and few is used for/with countable nouns: you can't have *few water(s) or *much apples.

The answer to this one is that it's true for much and a little when they are determiners, and not necessarily when they are adverbs. You can safely say "There are much more thieves here than there are policemen" and "My pimples are a little more than yours".

Let's explore more of COCA:

• far fewer: 824
• many fewer: 127
• a lot fewer: 96
• considerably fewer: 40
• much fewer: 29
• substantially fewer: 27
• a few fewer: 5
• a little fewer: 2

Far fewer is still on top, but the order of the other expressions has changed dramatically. Most noticeably, many fewer has surpassed all the others by a good margin.

Many fewer comes second in Ngram viewer too:

And here's the Ngram comparison for when the difference is not big:

Note that even for a little fewer, which finished second to last in the previous Ngram, there are many legitimate instances in Google books.

_{† ...: I used it to represent a gap of up to two words;
[be]: In COCA it means any of the various forms of the verb be;
[be] and than added to reduce the number of the results and make it easier to go through them.}