The story reports on science, which says that sperm whales in the Southern Ocean defecate in the upper ocean where phytoplankton use the iron from the feces to grow. This in turn, allows the phytoplankton to "absorb" more carbon. The idea is just like iron fertilization.
The point that they article makes is that the cycle actually reduces atmospheric CO2 because the amount of carbon used by the phytoplankton is twice as much as is breathed out by the whales. Thus, Michael Perry (the reporter) concludes, the whales offset their carbon and reduce their carbon footprint.
First off, whales don't have feet, so they have no footprint.
Second, though, whales also don't use fossil fuels, so whales have no carbon footprint.
The science sounds interesting enough, and it seems like they are showing that this aspect of the carbon cycle is a net sink of atmospheric carbon. One caveat that isn't dealt with is that the phytoplankton don't necessarily use the carbon immediately die and sink, there is also a lot of recycling in the upper ocean. So this "carbon sequestration" (which just means that the phytoplankton die and sink to the deep ocean) might not be as strong as this news article would lead us to believe.
A larger point is that in the absence of humans, this would just be one of many small carbon sinks that would balance a lot of carbon sources, closing the carbon cycle. Unperturbed ecosystems, much less individual species, are (over long time scales) in steady-state. Imagine that humans disappear, so all the anthropogenic CO2 stays around, but no more is added. These whales(+phytoplankton) might continue to act as a net carbon sink, but over the long run, they aren't going to suck all the carbon out of the atmosphere. Okay, I'll stop belaboring this point.
What makes this an even better example of lazy science reporting is that the really interesting point about the whales'(+phytoplankton's) role in the carbon cycle is buried in the last sentence:
Lavery said that without whaling there may have been 120,000 sperm whales in the Southern Ocean and, according to her calculations, some 2 million tonnes of carbon may have been removed from the atmosphere each year through this process.So what this says is that if the whale population was what it should be, the carbon source would be ten times larger (there are currently ~12,000 sperm whales in the Southern Ocean). So the interesting twist, in my opinion, isn't that the whales are "carbon negative," but really that whaling represents an increase in atmospheric CO2 by reducing a natural sink. This is just like (though much smaller than) land-use change, which removes carbon-absorbing ecosystems with cropland, removing a terrestrial sink. Does this raise the question of whether over-fishing represents such a decrease in a natural sink? So instead of going off half-cocked to do geoengineering through iron fertilization [e.g.], we should make a legitimate attempt to allow the natural ocean ecosystems to recover from the past couple of centuries of abuse.
An AP story also has most of this, but better covers the whaling angle: [LINK]