This source identifies strategies for solving problems in Amazonia more than it presents threats, but I thought I would include it anyway.
Different habitats in the Amazon can be characterized by different periods of flooding duration, soil type, elevation, and distance from non- flooded forest. This paper describes a study in which floral composition was monitored in two different regions of three topographical levels each in which flooding occurs. The results indicated that there was significant change among the number of trees in relation to both site and level and species distribution was dependent on topographical level, but there was no significant variation in species richness across the different sites and levels (although the author noted that previous studies have shown that species richness increases for more highly elevated levels). The implications for conservation planning are that reserves are needed in a wide range of locations, topographic levels, and habitats to preserve biodiversity.