Microbial activity has been linked to volcanic rock weathering. It is thought that the process is generally driven by the nutrient requirement of the microbial community and occurs as a result of the sequestration of bioessential elements. Although we know that metabolising bacteria influence rock weathering, the molecular processes invloved are unknown. For the first time, we have used DNA microarray technology to investigate the genes involved in weathering, in particular the sequestering of iron using the heavy metal resistant bacterium, Cupriavidus metallidurans CH34. Extensive studies have characterized the heavy metal resistant and iron uptake mechanisms of this bacterium.Microarray analysis demonstrated that siderophore genes were not differentially expressed when grown in MM284 (iron-limited) with basalt. This was in concurrence with siderophore measurements using the CAS assay. Instead, a large number of porins and membrane transporters in concomitantly with genes associated with biofilm formation were up-regulated. Furthermore, genes linked to heavy metal resistance were upregulated. These results not only elucidate the mechanisms by which bacteria might have sequestered nutrients on the early Earth but also provide an explanation for the evolution of multiple heavy metal resistance genes long before the creation of contaminated industrial biotopes by human activity.