A Nature News article Black is the new green (10 August 2006) explains research that aims to reinvent Terra Preta, anthropogenic highly productive charcoal rich soils, to improve soil for agriculture while sequestering carbon.
New ways of producing biofuels can to produce charcoal that can be used to enrich soil. This carbon is stored in the soil, and may be able to produce carbon negative fuels in a way that can boost agricultural productivity. From the Nature News article:

…[a group met at the] World Congress of Soil Science. Their agenda was to take terra preta from the annals of history and the backwaters of the Amazon into the twenty-first century world of carbon sequestration and biofuels.

They want to follow what the green revolution did for the developing world’s plants with a black revolution for the world’s soils. They are aware that this is a tough sell, not least because hardly anyone outside the room has heard of their product. But that does not dissuade them: more than one eye in the room had a distinctly evangelical gleam.

The soil scientists, archaeologists, geographers, agronomists, and anthropologists who study terra preta now agree that the Amazon’s dark earths, terra preta do índio, were made by the river basin’s original human residents, who were much more numerous than formerly supposed. The darkest patches correspond to the middens of settlements and are cluttered with crescents of broken pottery. The larger patches were once agricultural areas that the farmers enriched with charred trash of all sorts. Some soils are thought to be 7,000 years old. Compared with the surrounding soil, terra preta can contain three times as much phosphorus and nitrogen. And as its colour indicates, it contains far more carbon. In samples taken in Brazil by William Woods, an expert in abandoned settlements at the University of Kansas in Lawrence, the terra preta was up to 9% carbon, compared with 0.5% for plain soil from places nearby
…Take the work of Danny Day, the founder of Eprida. This “for-profit social-purpose enterprise” in Athens, Georgia, builds contraptions that farmers can use to turn farm waste into biofuel while making char. Farm waste (or a crop designed for biofuel use) is smouldered — pyrolysed, in the jargon — and this process gives off volatile organic molecules, which can be used as a basis for biodiesel or turned into hydrogen with the help of steam. After the pyrolysation, half of the starting material will be used up and half will be char. That can then be put back on the fields, where it will sequester carbon and help grow the next crop.

The remarkable thing about this process is that, even after the fuel has been burned, more carbon dioxide is removed from the atmosphere than is put back. Traditional biofuels claim to be ‘carbon neutral’, because the carbon dioxide assimilated by the growing biomass makes up for the carbon dioxide given off by the burning of the fuel. But as Lehmann points out, systems such as Day’s go one step further: “They are the only way to make a fuel that is actually carbon negative”.

Day’s pilot plant processes 10 to 25 kg of Georgia peanut hulls and pine pellets every hour. From 100 kg of biomass, the group gets 46 kg of carbon — half as char — and around 5 kg of hydrogen, enough to go 500 kilometres in a hydrogen-fuel-cell car (not that there are many around yet). Originally, Day was mostly interested in making biofuel; the char was just something he threw out, or used to make carbon filters. Then he discovered that his employees were reaping the culinary benefits of the enormous turnips that had sprung up on the piles of char lying around at the plant. Combining this char with ammonium bicarbonate, made using steam-recovered hydrogen, creates a soil additive that is now one of his process’s selling points; the ammonium bicarbonate is a nitrogen-based fertilizer.

update: WorldChanging has a bit more on the article