Temperature is one of the defining parameters of an ecological niche, and ambient temperature change is a physiological challenge faced by all living cells. Most organisms are adapted to growing within a temperature range that rarely exceeds ~ 30°C, but the deep subsurface bacterium Kosmotoga olearia is capable of growing over an extremely wide temperature range (20°C - 79°C). To pinpoint genomic determinants of this flexible phenotype, we compared transcriptomes of K. olearia cultures grown at its optimal 65°C to those at 30°C, 40°C, and 77°C. We found that changes in temperature significantly affect expression of 573 of 2,224 K. olearia genes. Notably, this transcriptional response elicits re-modeling of the cellular membrane and changes in metabolism, with increased expression of genes involved in energy and carbohydrate metabolism at high temperatures versus up-regulation of amino acid metabolism at lower temperatures. Such massive effects on the transcriptome indicate that temperature response is a complex polygenic trait. Moreover, at 77°C one third of the up-regulated genes are of hypothetical function, indicating that many features of high temperature growth are unknown. Via comparative genomic analysis of additional Thermotogae, we inferred that one of K. olearia's strategies for low temperature adaptation is to increase gene copy number through both duplication and lateral acquisition. Our finding of coordinated temperature-specific gene expression patterns, and by extension temperature specific metabolism, suggests that Kosmotoga populations encounter variable environments, probably through migration. Therefore, we conjecture that deep subsurface microbial communities are more dynamic than currently perceived.