The main threat to the Amazon is loss of primary rain forest by deforestation. As the region's plants and animals are so poorly known, each time a piece of land is cleared undescribed species may be lost. The main causes of deforestation are settlement for agriculture and commercial logging. (See satellite images of deforestation for large-scale effects of deforestation on forest cover over time.)
A major cause of deforestation is settlers clearing land for crops or grazing. The rainforest soil is too poor to support intensive agriculture for more than two or three years, and the plot is soon abandoned.
When land is cleared, trees on the edge of the clearing die off because they are unable to tolerate the hotter temperatures and decreased humidity. If it recovers at all, such a patch will take over 500 years to attain the original diversity.