Petersen and Heckenberger, who is back in Brazil now, have since excavated four major sites and explored 30 others with the help of Eduardo Goes Neves, an archaeologist at the University of São Paulo, who brought along 20 of his students to help out in the digging.
Petersen, who specializes in ceramics, was blown away by the scale of the finding.
"There's literally hundreds of millions of ceramic shards at some of the larger settlements," he says.
It takes a lot of people to make that much pottery. So unlike the small villages found in the region today, Petersen thinks there were huge settlements, with possibly as many as 400,000 residents at a time when even major cities around the world were much smaller.
The shards contain carbon and thus can be carbon dated, and that's a blessing because most pottery does not have carbon. Petersen says they show that the Acutuba sites were occupied for about two millennia beginning around 450 B.C. Other evidence indicates that those early settlers were farming in the rich soils that they apparently helped create.
There is little doubt among scholars that the people somehow enriched the soil, but there is much debate over how they did it. An international team of experts met in Brazil recently to compare notes in an effort to figure that out.
The early settlers did not resort to the slash and burn tactics that have devastated much of Amazonia in recent decades. Burning enriches the soil for a few years, making agriculture possible for awhile, but it doesn't take long for nature to wash away the nutrients.
But researchers have found that returning some carbon to the soil is a critical part of the formula. It helps retain nutrients, like decomposing vegetation and even human wastes. So there was probably some burning going on, but whether it was deliberate or accidental is unknown.
In an effort to figure out the formula, Brazilian researchers added carbon to soil to see if it would stimulate growth, but they had no success. Then they tried just adding fertilizer, and still had no luck. But when they added carbon and fertilizer together, they saw an astonishing 880 percent increase in the growth of the rice and sorghum planted in the test plot.
So somehow, those early settlers must have added both carbon and fertilizer to their plots, in which they grew mostly maize, but did they really know what they were doing?
Probably not. The rich soils that have persisted to this day most likely came about by accident.
Petersen thinks those fertile plots are probably yesterday's garbage pits. Stir in a little charcoal, toss in the remains of fish harvested from the rivers, and over the years the dirt became better than gold.
While they may not have done all that on purpose, once the soil was there, it probably stimulated the growth of villages into cities, Petersen says. And that added more garbage, and more plots of enriched soil.
Those cities are long gone now. But the soil, and the legacy, remains.
Lee Dye’s column appears weekly on ABCNEWS.com. A former science writer for the Los Angeles Times, he now lives in Juneau, Alaska.