If you had read the article before responding, you'd have seen that they can tell the difference between the sound waves of different types of whales and marine animals and also the diff between animals and ships. Although this sounds like a "bubble" noise to us, the sound clip said it had been sped up to almost 16 times. (I suppose in order to make it short enough to download???)
In your minds, stretch that sound out, and imagine it. That would scare me!
They said it was more powerful of a noise than any of the largest whales known, and ruled out most likely, the possibility of a giant squid making the noise, since squids do not contain air/gas sacs capable of making that type of noise.
Maybe they'll find more info, if they return to this area and monitor it visually as well!